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Plant Molecular Biology

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (31 December 2016) | Viewed by 491169

Special Issue Editors

Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, LE, Italy
Interests: endomembrane trafficking; unconventional routes; metabolites and xenobiotics compartmentalization; biostimulation
Special Issues, Collections and Topics in MDPI journals
Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
Interests: canola and wheat pathology; epidemiology of plant pathogens; evolution/genetic variation of fungal pathogens; biological control of plant diseases; breeding for disease resistance microbial; ecology and microbial interactions
Special Issues, Collections and Topics in MDPI journals
Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, 20133 Milan, Italy
Interests: essential oils; bioactive phytochemicals; ethnopharmacology; antimicrobial resistance; one health; food security
Special Issues, Collections and Topics in MDPI journals
Biochimie et Physiologie Moleculaire des Plantes Research Unit, Montpellier SupAgro, 2, Place Pierre Viala 34060 Montpellier CEDEX 2, France
Interests: plants; mineral nutrition; ions homeostasis, transport; membrane transporters, signalling; heavy metal; phytoremediation
Special Issues, Collections and Topics in MDPI journals
Institute for Genomics of Crop Abiotic Stress Tolerance (IGCAST), Texas Tech University, Lubbock, TX 79409, USA
Interests: plants; environmental stress; signaling molecules; transcription factors; gene identification and analysis; gene regulatory network; signal transduction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Plant molecular biology is a complex issue. In living organisms, the molecular level includes essential macromolecules, consisting of carbohydrates, lipids, proteins and nucleic acids, as well as low-molecular weight compounds, commonly named secondary metabolites and mainly involved in ecological relationships. Integrations between molecular and cell levels are pivotal in the comprehension of biological phenomena: communication with neighboring cells, perception of external stimuli by receptors, signal transduction pathways, transcriptional regulation by transcription factors, protein biosynthesis and post-transductional modifications, epigenetic mechanisms involved in gene expression, and programmed cell death are only some processes in the complex scenario of molecular and cell biology. These levels, in turn, are tightly connected to the higher levels of tissue, organ, organism and ecosystem, and, therefore, molecular biology is a basic science which deserves particular attention due to its unique role of integrating different issues of plant biology.

We invite investigators to submit both original research and review articles that explore all the aspects of plant molecular biology, at gene, protein and metabolite levels.

Potential topics include, but are not limited to:

  • Plant primary metabolism
  • Plant secondary metabolism
  • Plant-environment interaction
  • Plant-microbe interaction
  • Plant-insect interaction
  • Chemical ecology
  • Plant innate immunity
  • Climate change biology
  • Water, air and soil pollution
  • Fitness costs
  • Bioactive phytochemicals

Since the new Section "Molecular Botany" (https://www.mdpi.com/journal/ijms/sections/botany) has been set up, all submissions after 1 March 2016 in this Topical Collection will be moved to the section.

Prof. Dr. Marcello Iriti
Dr. Jianhua Zhu
Prof. Dr. Gian-Pietro Di Sansebastiano
Dr. Lam-Son Phan Tran
Dr. Hatem Rouached
Prof. Dr. Dilantha Fernando
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant stress physiology and biology
  • plant physiopathology
  • biotic/abiotic/environmental stresses
  • plant secondary metabolites
  • plant immune system

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Published Papers (302 papers)

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Editorial

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145 KiB  
Editorial
Regulation of Plant Mineral Nutrition: Transport, Sensing and Signaling
by Hatem Rouached and Lam-Son Phan Tran
Int. J. Mol. Sci. 2015, 16(12), 29717-29719; https://doi.org/10.3390/ijms161226198 - 11 Dec 2015
Cited by 7 | Viewed by 5038
Abstract
Limitation in crop yield productivity significantly contributes to the pressing problem of food security and malnutrition worldwide. [...] Full article
626 KiB  
Editorial
Symbiotic Nitrogen Fixation in Legume Nodules: Metabolism and Regulatory Mechanisms
by Saad Sulieman and Lam-Son Phan Tran
Int. J. Mol. Sci. 2014, 15(11), 19389-19393; https://doi.org/10.3390/ijms151119389 - 24 Oct 2014
Cited by 23 | Viewed by 6836
Abstract
The special issue “Symbiotic Nitrogen Fixation in Legume Nodules: Metabolism and Regulatory Mechanisms” aims to investigate the physiological and biochemical advances in the symbiotic process with an emphasis on nodule establishment, development and functioning. The original research articles included in this issue provide [...] Read more.
The special issue “Symbiotic Nitrogen Fixation in Legume Nodules: Metabolism and Regulatory Mechanisms” aims to investigate the physiological and biochemical advances in the symbiotic process with an emphasis on nodule establishment, development and functioning. The original research articles included in this issue provide important information regarding novel aspects of nodule metabolism and various regulatory pathways, which could have important future implications. This issue also included one review article that highlights the importance of using legume trees in the production of renewable biofuels. Full article
169 KiB  
Editorial
Plant Neurobiology, a Fascinating Perspective in the Field of Research on Plant Secondary Metabolites
by Marcello Iriti
Int. J. Mol. Sci. 2013, 14(6), 10819-10821; https://doi.org/10.3390/ijms140610819 - 23 May 2013
Cited by 20 | Viewed by 7745
Abstract
In this Editorial, I comment on the exciting and original topic of plant neurobiology, focusing on natural products whose biosynthesis is shared by animal and plant organisms, i.e., indoleamines (melatonin and serotonin) and catecholamines (dopamine, norepinephrine and epinephrine). Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Research

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1850 KiB  
Article
Comparative Metabolite Profiling of Triterpenoid Saponins and Flavonoids in Flower Color Mutations of Primula veris L.
by Lysanne Apel, Dietmar R. Kammerer, Florian C. Stintzing and Otmar Spring
Int. J. Mol. Sci. 2017, 18(1), 153; https://doi.org/10.3390/ijms18010153 - 13 Jan 2017
Cited by 33 | Viewed by 9672
Abstract
Primula veris L. is an important medicinal plant with documented use for the treatment of gout, headache and migraine reaching back to the Middle Ages. Triterpenoid saponins from roots and flowers are used in up-to-date phytotherapeutic treatment of bronchitis and colds due to [...] Read more.
Primula veris L. is an important medicinal plant with documented use for the treatment of gout, headache and migraine reaching back to the Middle Ages. Triterpenoid saponins from roots and flowers are used in up-to-date phytotherapeutic treatment of bronchitis and colds due to their expectorant and secretolytic effects. In addition to the wild type plants with yellow petals, a red variant and an intermediate orange form of Primula veris L. have recently been found in a natural habitat. The secondary metabolite profiles of roots, leaves and flowers of these rare variants were investigated and compared with the wild type metabolome. Two flavonoids, six flavonoid glycosides, four novel methylated flavonoid glycosides, five anthocyanins and three triterpenoid saponins were identified in alcoholic extracts from the petals, leaves and roots of the three variants by high performance liquid chromatography (HPLC)-diode array detection (DAD)/mass spectrometry (MSn) analyses. Anthocyanins were detected in the petals of the red and orange variety, but not in the wild type. No other effects on the metabolite profiles of the three varieties have been observed. The possibility is discussed that a regulatory step of the anthocyanin biosynthetic pathway may have been affected by mutation thus triggering color polymorphism in the petals. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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1531 KiB  
Communication
Plant-to-Plant Variability in Root Metabolite Profiles of 19 Arabidopsis thaliana Accessions Is Substance-Class-Dependent
by Susann Mönchgesang, Nadine Strehmel, Diana Trutschel, Lore Westphal, Steffen Neumann and Dierk Scheel
Int. J. Mol. Sci. 2016, 17(9), 1565; https://doi.org/10.3390/ijms17091565 - 16 Sep 2016
Cited by 19 | Viewed by 6099
Abstract
Natural variation of secondary metabolism between different accessions of Arabidopsis thaliana (A. thaliana) has been studied extensively. In this study, we extended the natural variation approach by including biological variability (plant-to-plant variability) and analysed root metabolic patterns as well as their [...] Read more.
Natural variation of secondary metabolism between different accessions of Arabidopsis thaliana (A. thaliana) has been studied extensively. In this study, we extended the natural variation approach by including biological variability (plant-to-plant variability) and analysed root metabolic patterns as well as their variability between plants and naturally occurring accessions. To screen 19 accessions of A. thaliana, comprehensive non-targeted metabolite profiling of single plant root extracts was performed using ultra performance liquid chromatography/electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC/ESI-QTOF-MS) and gas chromatography/electron ionization quadrupole mass spectrometry (GC/EI-QMS). Linear mixed models were applied to dissect the total observed variance. All metabolic profiles pointed towards a larger plant-to-plant variability than natural variation between accessions and variance of experimental batches. Ratios of plant-to-plant to total variability were high and distinct for certain secondary metabolites. None of the investigated accessions displayed a specifically high or low biological variability for these substance classes. This study provides recommendations for future natural variation analyses of glucosinolates, flavonoids, and phenylpropanoids and also reference data for additional substance classes. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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2245 KiB  
Article
Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae—A 2D NMR Metabolomics Study
by Fredd Vergara, Amiu Shino and Jun Kikuchi
Int. J. Mol. Sci. 2016, 17(9), 1470; https://doi.org/10.3390/ijms17091470 - 02 Sep 2016
Cited by 8 | Viewed by 5425
Abstract
Cannibalism is known in many insect species, yet its impact on insect metabolism has not been investigated in detail. This study assessed the effects of cannibalism on the metabolism of fourth-instar larvae of the non-predatory insect Helicoverpa armigera (Lepidotera: Noctuidea). Two groups of [...] Read more.
Cannibalism is known in many insect species, yet its impact on insect metabolism has not been investigated in detail. This study assessed the effects of cannibalism on the metabolism of fourth-instar larvae of the non-predatory insect Helicoverpa armigera (Lepidotera: Noctuidea). Two groups of larvae were analyzed: one group fed with fourth-instar larvae of H. armigera (cannibal), the other group fed with an artificial plant diet. Water-soluble small organic compounds present in the larvae were analyzed using two-dimensional nuclear magnetic resonance (NMR) and principal component analysis (PCA). Cannibalism negatively affected larval growth. PCA of NMR spectra showed that the metabolic profiles of cannibal and herbivore larvae were statistically different with monomeric sugars, fatty acid- and amino acid-related metabolites as the most variable compounds. Quantitation of 1H-13C HSQC (Heteronuclear Single Quantum Coherence) signals revealed that the concentrations of glucose, glucono-1,5-lactone, glycerol phosphate, glutamine, glycine, leucine, isoleucine, lysine, ornithine, proline, threonine and valine were higher in the herbivore larvae. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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4558 KiB  
Article
Piriformospora indica Stimulates Root Metabolism of Arabidopsis thaliana
by Nadine Strehmel, Susann Mönchgesang, Siska Herklotz, Sylvia Krüger, Jörg Ziegler and Dierk Scheel
Int. J. Mol. Sci. 2016, 17(7), 1091; https://doi.org/10.3390/ijms17071091 - 08 Jul 2016
Cited by 33 | Viewed by 10776
Abstract
Piriformospora indica is a root-colonizing fungus, which interacts with a variety of plants including Arabidopsis thaliana. This interaction has been considered as mutualistic leading to growth promotion of the host. So far, only indolic glucosinolates and phytohormones have been identified as key [...] Read more.
Piriformospora indica is a root-colonizing fungus, which interacts with a variety of plants including Arabidopsis thaliana. This interaction has been considered as mutualistic leading to growth promotion of the host. So far, only indolic glucosinolates and phytohormones have been identified as key players. In a comprehensive non-targeted metabolite profiling study, we analyzed Arabidopsis thaliana’s roots, root exudates, and leaves of inoculated and non-inoculated plants by ultra performance liquid chromatography/electrospray ionization quadrupole-time-of-flight mass spectrometry (UPLC/(ESI)-QTOFMS) and gas chromatography/electron ionization quadrupole mass spectrometry (GC/EI-QMS), and identified further biomarkers. Among them, the concentration of nucleosides, dipeptides, oligolignols, and glucosinolate degradation products was affected in the exudates. In the root profiles, nearly all metabolite levels increased upon co-cultivation, like carbohydrates, organic acids, amino acids, glucosinolates, oligolignols, and flavonoids. In the leaf profiles, we detected by far less significant changes. We only observed an increased concentration of organic acids, carbohydrates, ascorbate, glucosinolates and hydroxycinnamic acids, and a decreased concentration of nitrogen-rich amino acids in inoculated plants. These findings contribute to the understanding of symbiotic interactions between plant roots and fungi of the order of Sebacinales and are a valid source for follow-up mechanistic studies, because these symbioses are particular and clearly different from interactions of roots with mycorrhizal fungi or dark septate endophytes Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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2462 KiB  
Article
Stable Isotope-Assisted Evaluation of Different Extraction Solvents for Untargeted Metabolomics of Plants
by Maria Doppler, Bernhard Kluger, Christoph Bueschl, Christina Schneider, Rudolf Krska, Sylvie Delcambre, Karsten Hiller, Marc Lemmens and Rainer Schuhmacher
Int. J. Mol. Sci. 2016, 17(7), 1017; https://doi.org/10.3390/ijms17071017 - 28 Jun 2016
Cited by 56 | Viewed by 7783
Abstract
The evaluation of extraction protocols for untargeted metabolomics approaches is still difficult. We have applied a novel stable isotope-assisted workflow for untargeted LC-HRMS-based plant metabolomics , which allows for the first time every detected feature to be considered for method evaluation. The efficiency [...] Read more.
The evaluation of extraction protocols for untargeted metabolomics approaches is still difficult. We have applied a novel stable isotope-assisted workflow for untargeted LC-HRMS-based plant metabolomics , which allows for the first time every detected feature to be considered for method evaluation. The efficiency and complementarity of commonly used extraction solvents, namely 1 + 3 (v/v) mixtures of water and selected organic solvents (methanol, acetonitrile or methanol/acetonitrile 1 + 1 (v/v)), with and without the addition of 0.1% (v/v) formic acid were compared. Four different wheat organs were sampled, extracted and analysed by LC-HRMS. Data evaluation was performed with the in-house-developed MetExtract II software and R. With all tested solvents a total of 871 metabolites were extracted in ear, 785 in stem, 733 in leaf and 517 in root samples, respectively. Between 48% (stem) and 57% (ear) of the metabolites detected in a particular organ were found with all extraction mixtures, and 127 of 996 metabolites were consistently shared between all extraction agent/organ combinations. In aqueous methanol, acidification with formic acid led to pronounced pH dependency regarding the precision of metabolite abundance and the number of detectable metabolites, whereas extracts of acetonitrile-containing mixtures were less affected. Moreover, methanol and acetonitrile have been found to be complementary with respect to extraction efficiency. Interestingly, the beneficial properties of both solvents can be combined by the use of a water-methanol-acetonitrile mixture for global metabolite extraction instead of aqueous methanol or aqueous acetonitrile alone. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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3236 KiB  
Article
Metabolic Responses of Poplar to Apripona germari (Hope) as Revealed by Metabolite Profiling
by Lijuan Wang, Liangjian Qu, Liwei Zhang, Jianjun Hu, Fang Tang and Mengzhu Lu
Int. J. Mol. Sci. 2016, 17(6), 923; https://doi.org/10.3390/ijms17060923 - 20 Jun 2016
Cited by 14 | Viewed by 6078
Abstract
Plants have developed biochemical responses to adapt to biotic stress. To characterize the resistance mechanisms in poplar tree against Apripona germari, comprehensive metabolomic changes of poplar bark and xylem in response to A. germari infection were examined by gas chromatography time-of-flight mass [...] Read more.
Plants have developed biochemical responses to adapt to biotic stress. To characterize the resistance mechanisms in poplar tree against Apripona germari, comprehensive metabolomic changes of poplar bark and xylem in response to A. germari infection were examined by gas chromatography time-of-flight mass spectrometry (GC–TOF/MS). It was found that, four days after feeding (stage I), A. germari infection brought about changes in various metabolites, such as phenolics, amino acids and sugars in both bark and xylem. Quinic acid, epicatechin, epigallocatechin and salicin might play a role in resistance response in bark, while coniferyl alcohol, ferulic acid and salicin contribute resistance in xylem. At feeding stages II when the larvae fed for more than one month, fewer defensive metabolites were induced, but levels of many intermediates of glycolysis and the tricarboxylic acid (TCA) cycle were reduced, especially in xylem. These results suggested that the defense strategies against A. germari might depend mainly on the early defense responses in poplar. In addition, it was found that bark and xylem in infected trees accumulated higher levels of salicylic acid and 4-aminobutyric acid, respectively, these tissues displaying a direct and systemic reaction against A. germari. However, the actual role of the two metabolites in A. germari-induced defense in poplar requires further investigation. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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3894 KiB  
Article
Metabolic Fingerprinting to Assess the Impact of Salinity on Carotenoid Content in Developing Tomato Fruits
by Lieven Van Meulebroek, Jochen Hanssens, Kathy Steppe and Lynn Vanhaecke
Int. J. Mol. Sci. 2016, 17(6), 821; https://doi.org/10.3390/ijms17060821 - 26 May 2016
Cited by 10 | Viewed by 7310
Abstract
As the presence of health-promoting substances has become a significant aspect of tomato fruit appreciation, this study investigated nutrient solution salinity as a tool to enhance carotenoid accumulation in cherry tomato fruit (Solanum lycopersicum L. cv. Juanita). Hereby, a key objective was [...] Read more.
As the presence of health-promoting substances has become a significant aspect of tomato fruit appreciation, this study investigated nutrient solution salinity as a tool to enhance carotenoid accumulation in cherry tomato fruit (Solanum lycopersicum L. cv. Juanita). Hereby, a key objective was to uncover the underlying mechanisms of carotenoid metabolism, moving away from typical black box research strategies. To this end, a greenhouse experiment with five salinity treatments (ranging from 2.0 to 5.0 decisiemens (dS) m−1) was carried out and a metabolomic fingerprinting approach was applied to obtain valuable insights on the complicated interactions between salinity treatments, environmental conditions, and the plant’s genetic background. Hereby, several hundreds of metabolites were attributed a role in the plant’s salinity response (at the fruit level), whereby the overall impact turned out to be highly depending on the developmental stage. In addition, 46 of these metabolites embraced a dual significance as they were ascribed a prominent role in carotenoid metabolism as well. Based on the specific mediating actions of the retained metabolites, it could be determined that altered salinity had only marginal potential to enhance carotenoid accumulation in the concerned tomato fruit cultivar. This study invigorates the usefulness of metabolomics in modern agriculture, for instance in modeling tomato fruit quality. Moreover, the metabolome changes that were caused by the different salinity levels may enclose valuable information towards other salinity-related plant processes as well. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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1439 KiB  
Article
Analysis of 2-(2-Phenylethyl)chromones by UPLC-ESI-QTOF-MS and Multivariate Statistical Methods in Wild and Cultivated Agarwood
by Yuanbin Li, Nan Sheng, Lingli Wang, Shijie Li, Jiannan Chen and Xiaoping Lai
Int. J. Mol. Sci. 2016, 17(5), 771; https://doi.org/10.3390/ijms17050771 - 23 May 2016
Cited by 28 | Viewed by 6422
Abstract
Agarwood is the fragrant resinous material mainly formed from species of Aquilaria. 2-(2-phenylethyl)chromones, especially the highly oxidized 5,6,7,8-tetrahydro-2-(2-phenylethyl)chromones, are the main representative compounds from agarwood. It is important to determine whether agarwood in trade is from cultivated trees or natural trees in [...] Read more.
Agarwood is the fragrant resinous material mainly formed from species of Aquilaria. 2-(2-phenylethyl)chromones, especially the highly oxidized 5,6,7,8-tetrahydro-2-(2-phenylethyl)chromones, are the main representative compounds from agarwood. It is important to determine whether agarwood in trade is from cultivated trees or natural trees in the Convention on the International Trade in Endangered Species (CITES). We characterized the 2-(2-phenylethyl)chromones in agarwood by ultra-performance liquid chromatography coupled with electrospray ionization mass spectrometry (UPLC–ESI-QTOF-MS) and differentiated wild from cultivated agarwood by metabolomic analysis. A total of 141 chromones including 50 potentially new compounds were evaluated as belonging to four structural classes (unoxidized 2-(2-phenylethyl)chromones, 5,6,7,8-tetrahydro-2-(2-phenylethyl)-chromones, bi-2-(2-phenylethyl)chromones, and tri-2-(2-phenylethyl)chromones). The metabolic difference between wild and cultivated agarwood was analyzed by component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA). Fourteen markers of metabolisms in wild and cultivated agarwood were constructed (e.g., 6,7-dimethoxy-2-(2-phenylethyl)chromone, 6,8-dihydroxy-2-(2-phenylethyl)chromone, 6-methoxy-2-(2-phenylethyl)chromone, etc.). These results indicated that UPLC–ESI-QTOF-MS-based metabonomics analysis in agarwood may be useful for distinguishing wild agarwood from cultivated agarwood. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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11186 KiB  
Article
Overexpression of the Transcription Factors GmSHN1 and GmSHN9 Differentially Regulates Wax and Cutin Biosynthesis, Alters Cuticle Properties, and Changes Leaf Phenotypes in Arabidopsis
by Yangyang Xu, Hanying Wu, Mingming Zhao, Wang Wu, Yinong Xu and Dan Gu
Int. J. Mol. Sci. 2016, 17(4), 587; https://doi.org/10.3390/ijms17040587 - 21 Apr 2016
Cited by 23 | Viewed by 7290
Abstract
SHINE (SHN/WIN) clade proteins, transcription factors of the plant-specific APETALA 2/ethylene-responsive element binding factor (AP2/ERF) family, have been proven to be involved in wax and cutin biosynthesis. Glycine max is an important economic crop, but its molecular mechanism of wax biosynthesis is rarely [...] Read more.
SHINE (SHN/WIN) clade proteins, transcription factors of the plant-specific APETALA 2/ethylene-responsive element binding factor (AP2/ERF) family, have been proven to be involved in wax and cutin biosynthesis. Glycine max is an important economic crop, but its molecular mechanism of wax biosynthesis is rarely characterized. In this study, 10 homologs of Arabidopsis SHN genes were identified from soybean. These homologs were different in gene structures and organ expression patterns. Constitutive expression of each of the soybean SHN genes in Arabidopsis led to different leaf phenotypes, as well as different levels of glossiness on leaf surfaces. Overexpression of GmSHN1 and GmSHN9 in Arabidopsis exhibited 7.8-fold and 9.9-fold up-regulation of leaf cuticle wax productions, respectively. C31 and C29 alkanes contributed most to the increased wax contents. Total cutin contents of leaves were increased 11.4-fold in GmSHN1 overexpressors and 5.7-fold in GmSHN9 overexpressors, mainly through increasing C16:0 di-OH and dioic acids. GmSHN1 and GmSHN9 also altered leaf cuticle membrane ultrastructure and increased water loss rate in transgenic Arabidopsis plants. Transcript levels of many wax and cutin biosynthesis and leaf development related genes were altered in GmSHN1 and GmSHN9 overexpressors. Overall, these results suggest that GmSHN1 and GmSHN9 may differentially regulate the leaf development process as well as wax and cutin biosynthesis. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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2529 KiB  
Article
Environmental Conditions Influence Induction of Key ABC-Transporter Genes Affecting Glyphosate Resistance Mechanism in Conyza canadensis
by Eleni Tani, Demosthenis Chachalis, Ilias S. Travlos and Dimitrios Bilalis
Int. J. Mol. Sci. 2016, 17(4), 342; https://doi.org/10.3390/ijms17040342 - 20 Apr 2016
Cited by 22 | Viewed by 5684
Abstract
Conyza canadensis has been reported to be the most frequent weed species that evolved resistance to glyphosate in various parts of the world. The objective of the present study was to investigate the effect of environmental conditions (temperature and light) on the expression [...] Read more.
Conyza canadensis has been reported to be the most frequent weed species that evolved resistance to glyphosate in various parts of the world. The objective of the present study was to investigate the effect of environmental conditions (temperature and light) on the expression levels of the EPSPS gene and two major ABC-transporter genes (M10 and M11) on glyphosate susceptible (GS) and glyphosate resistant (GR) horseweed populations, collected from several regions across Greece. Real-time PCR was conducted to determine the expression level of the aforementioned genes when glyphosate was applied at normal (1×; 533 g·a.e.·ha−1) and high rates (4×, 8×), measured at an early one day after treatment (DAT) and a later stage (four DAT) of expression. Plants were exposed to light or dark conditions, at three temperature regimes (8, 25, 35 °C). GR plants were made sensitive when exposed to 8 °C with light; those sensitized plants behaved biochemically (shikimate accumulation) and molecularly (expression of EPSPS and ABC-genes) like the GS plants. Results from the current study show the direct link between the environmental conditions and the induction level of the above key genes that likely affect the efficiency of the proposed mechanism of glyphosate resistance. Full article
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Article
Physical Characteristics of the Leaves and Latex of Papaya Plants Infected with the Papaya meleira Virus
by Anuar Magaña-Álvarez, Jean Carlos Vencioneck Dutra, Tarcio Carneiro, Daisy Pérez-Brito, Raúl Tapia-Tussell, Jose Aires Ventura, Inocencio Higuera-Ciapara, Patricia Machado Bueno Fernandes and Antonio Alberto Ribeiro Fernandes
Int. J. Mol. Sci. 2016, 17(4), 574; https://doi.org/10.3390/ijms17040574 - 15 Apr 2016
Cited by 4 | Viewed by 6027
Abstract
Sticky disease, which is caused by Papaya meleira virus (PMeV), is a significant papaya disease in Brazil and Mexico, where it has caused severe economic losses, and it seems to have spread to Central and South America. Studies assessing the pathogen-host interaction at [...] Read more.
Sticky disease, which is caused by Papaya meleira virus (PMeV), is a significant papaya disease in Brazil and Mexico, where it has caused severe economic losses, and it seems to have spread to Central and South America. Studies assessing the pathogen-host interaction at the nano-histological level are needed to better understand the mechanisms that underlie natural resistance. In this study, the topography and mechanical properties of the leaf midribs and latex of healthy and PMeV-infected papaya plants were observed by atomic force microscopy and scanning electron microscopy. Healthy plants displayed a smooth surface with practically no roughness of the leaf midribs and the latex and a higher adhesion force than infected plants. PMeV promotes changes in the leaf midribs and latex, making them more fragile and susceptible to breakage. These changes, which are associated with increased water uptake and internal pressure in laticifers, causes cell disruption that leads to spontaneous exudation of the latex and facilitates the spread of PMeV to other laticifers. These results provide new insights into the papaya-PMeV interaction that could be helpful for controlling papaya sticky disease. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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4923 KiB  
Article
Comparative Small RNA Analysis of Pollen Development in Autotetraploid and Diploid Rice
by Xiang Li, Muhammad Qasim Shahid, Jinwen Wu, Lan Wang, Xiangdong Liu and Yonggen Lu
Int. J. Mol. Sci. 2016, 17(4), 499; https://doi.org/10.3390/ijms17040499 - 12 Apr 2016
Cited by 87 | Viewed by 9228
Abstract
MicroRNAs (miRNAs) play key roles in plant reproduction. However, knowledge on microRNAome analysis in autotetraploid rice is rather limited. Here, high-throughput sequencing technology was employed to analyze miRNAomes during pollen development in diploid and polyploid rice. A total of 172 differentially expressed miRNAs [...] Read more.
MicroRNAs (miRNAs) play key roles in plant reproduction. However, knowledge on microRNAome analysis in autotetraploid rice is rather limited. Here, high-throughput sequencing technology was employed to analyze miRNAomes during pollen development in diploid and polyploid rice. A total of 172 differentially expressed miRNAs (DEM) were detected in autotetraploid rice compared to its diploid counterpart, and 57 miRNAs were specifically expressed in autotetraploid rice. Of the 172 DEM, 115 and 61 miRNAs exhibited up- and down-regulation, respectively. Gene Ontology analysis on the targets of up-regulated DEM showed that they were enriched in transport and membrane in pre-meiotic interphase, reproduction in meiosis, and nucleotide binding in single microspore stage. osa-miR5788 and osa-miR1432-5p_R+1 were up-regulated in meiosis and their targets revealed interaction with the meiosis-related genes, suggesting that they may involve in the genes regulation associated with the chromosome behavior. Abundant 24 nt siRNAs associated with transposable elements were found in autotetraploid rice during pollen development; however, they significantly declined in diploid rice, suggesting that 24 nt siRNAs may play a role in pollen development. These findings provide a foundation for understanding the effect of polyploidy on small RNA expression patterns during pollen development that cause pollen sterility in autotetraploid rice. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Expression of Castor LPAT2 Enhances Ricinoleic Acid Content at the sn-2 Position of Triacylglycerols in Lesquerella Seed
by Grace Q. Chen, Harrie Van Erp, Jose Martin-Moreno, Kumiko Johnson, Eva Morales, John Browse, Peter J. Eastmond and Jiann-Tsyh Lin
Int. J. Mol. Sci. 2016, 17(4), 507; https://doi.org/10.3390/ijms17040507 - 06 Apr 2016
Cited by 39 | Viewed by 7007
Abstract
Lesquerella is a potential industrial oilseed crop that makes hydroxy fatty acid (HFA). Unlike castor its seeds are not poisonous but accumulate lesquerolic acid mostly at the sn-1 and sn-3 positions of triacylglycerol (TAG), whereas castor contains ricinoleic acid (18:1OH) at [...] Read more.
Lesquerella is a potential industrial oilseed crop that makes hydroxy fatty acid (HFA). Unlike castor its seeds are not poisonous but accumulate lesquerolic acid mostly at the sn-1 and sn-3 positions of triacylglycerol (TAG), whereas castor contains ricinoleic acid (18:1OH) at all three positions. To investigate whether lesquerella can be engineered to accumulate HFAs in the sn-2 position, multiple transgenic lines were made that express castor lysophosphatidic acid acyltransferase 2 (RcLPAT2) in the seed. RcLPAT2 increased 18:1OH at the sn-2 position of TAGs from 2% to 14%–17%, which resulted in an increase of tri-HFA-TAGs from 5% to 13%–14%. Our result is the first example of using a LPAT to increase ricinoleic acid at the sn-2 position of seed TAG. This work provides insights to the mechanism of HFA-containing TAG assembly in lesquerella and directs future research to optimize this plant for HFA production. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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Development and Characterization of Novel Microsatellite Markers for the Peach Fruit Moth Carposina sasakii (Lepidoptera: Carposinidae) Using Next-Generation Sequencing
by You-Zhu Wang, Li-Jun Cao, Jia-Ying Zhu and Shu-Jun Wei
Int. J. Mol. Sci. 2016, 17(3), 362; https://doi.org/10.3390/ijms17030362 - 15 Mar 2016
Cited by 20 | Viewed by 4808
Abstract
The peach fruit moth Carposina sasakii is an economically important pest on dozens of fruits from Rosaceae and Rhamnaceae in Northeast Asia. We developed novel microsatellite markers for C. sasakii from randomly sequenced regions of the genome using next-generation sequencing. In total, 95,153 [...] Read more.
The peach fruit moth Carposina sasakii is an economically important pest on dozens of fruits from Rosaceae and Rhamnaceae in Northeast Asia. We developed novel microsatellite markers for C. sasakii from randomly sequenced regions of the genome using next-generation sequencing. In total, 95,153 microsatellite markers were isolated from 4.70 GB genomic sequences. Thirty-five polymorphic markers were developed by assessing in 63 individuals from two geographical populations. The allele numbers ranged from 2 to 9 with an average value of 4.60 per locus, while the polymorphism information content ranged from 0.075 to 0.696 with an average value of 0.407. Furthermore, the observed and expected heterozygosity varied from 0.000 to 0.677 and 0.062 to 0.771, respectively. The microsatellites developed provide abundant molecular markers for investigating genetic structure, genetic diversity, and existence of host-plant associated biotypes of C. sasakii. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Genetic Diversity and Population Structure of Broomcorn Millet (Panicum miliaceum L.) Cultivars and Landraces in China Based on Microsatellite Markers
by Minxuan Liu, Yue Xu, Jihong He, Shuang Zhang, Yinyue Wang and Ping Lu
Int. J. Mol. Sci. 2016, 17(3), 370; https://doi.org/10.3390/ijms17030370 - 14 Mar 2016
Cited by 52 | Viewed by 6516
Abstract
Broomcorn millet (Panicum miliaceum L.), one of the first domesticated crops, has been grown in Northern China for at least 10,000 years. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, [...] Read more.
Broomcorn millet (Panicum miliaceum L.), one of the first domesticated crops, has been grown in Northern China for at least 10,000 years. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, we analyzed the genetic diversity of 88 accessions of broomcorn millet collected from various provinces of China. Amplification with 67 simple sequence repeat (SSR) primers revealed moderate levels of diversity in the investigated accessions. A total of 179 alleles were detected, with an average of 2.7 alleles per locus. Polymorphism information content and expected heterozygosity ranged from 0.043 to 0.729 (mean = 0.376) and 0.045 to 0.771 (mean = 0.445), respectively. Cluster analysis based on the unweighted pair group method of mathematical averages separated the 88 accessions into four groups at a genetic similarity level of 0.633. A genetic structure assay indicated a close correlation between geographical regions and genetic diversity. The uncovered information will be valuable for defining gene pools and developing breeding programs for broomcorn millet. Furthermore, the millet-specific SSR markers developed in this study should serve as useful tools for assessment of genetic diversity and elucidation of population structure in broomcorn millet. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Identification, Functional Study, and Promoter Analysis of HbMFT1, a Homolog of MFT from Rubber Tree (Hevea brasiliensis)
by Zhenghong Bi, Xiang Li, Huasun Huang and Yuwei Hua
Int. J. Mol. Sci. 2016, 17(3), 247; https://doi.org/10.3390/ijms17030247 - 02 Mar 2016
Cited by 22 | Viewed by 6329
Abstract
A homolog of MOTHER OF FT AND TFL1 (MFT) was isolated from Hevea brasiliensis and its biological function was investigated. Protein multiple sequence alignment and phylogenetic analysis revealed that HbMFT1 conserved critical amino acid residues to distinguish MFT, FLOWERING LOCUS T [...] Read more.
A homolog of MOTHER OF FT AND TFL1 (MFT) was isolated from Hevea brasiliensis and its biological function was investigated. Protein multiple sequence alignment and phylogenetic analysis revealed that HbMFT1 conserved critical amino acid residues to distinguish MFT, FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1)-like proteins and showed a closer genetic relationship to the MFT-like group. The accumulation of HbMFT1 was generally detected in various tissues except pericarps, with the highest expression in embryos and relatively higher expression in roots and stems of seedlings, flowering inflorescences, and male and female flowers. HbMFT1 putative promoter analysis showed that tissue-specific, environmental change responsive and hormone-signaling responsive elements were generally present. HbMFT1 was strongly induced under a short-day condition at 28 °C, with the highest expression after the onset of a day. Overexpression of HbMFT1 inhibited seed germination, seedling growth, and flowering in transgenic Arabidopsis. The qRT-PCR further confirmed that APETALA1 (AP1) and FRUITFULL (FUL) were drastically down-regulated in 35S::HbMFT1 plants. A histochemical β-glucuronidase (GUS) assay showed that HbMFT1::GUS activity was mainly detected in stamens and mature seeds coinciding with its original expression and notably induced in rosette leaves and seedlings of transgenic Arabidopsis by exogenous abscisic acid (ABA) due to the presence of ABA cis-elements in HbMFT1 promoter. These results suggested that HbMFT1 was mainly involved in maintenance of seed maturation and stamen development, but negatively controlled germination, growth and development of seedlings and flowering. In addition, the HbMFT1 promoter can be utilized in controlling transgene expression in stamens and seeds of rubber tree or other plant species. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
AfAP2-1, An Age-Dependent Gene of Aechmea fasciata, Responds to Exogenous Ethylene Treatment
by Ming Lei, Zhi-Ying Li, Jia-Bin Wang, Yun-Liu Fu, Meng-Fei Ao and Li Xu
Int. J. Mol. Sci. 2016, 17(3), 303; https://doi.org/10.3390/ijms17030303 - 27 Feb 2016
Cited by 6 | Viewed by 5380
Abstract
The Bromeliaceae family is one of the most morphologically diverse families with a pantropical distribution. To schedule an appropriate flowering time for bromeliads, ethylene is commonly used to initiate flower development in adult plants. However, the mechanism by which ethylene induces flowering in [...] Read more.
The Bromeliaceae family is one of the most morphologically diverse families with a pantropical distribution. To schedule an appropriate flowering time for bromeliads, ethylene is commonly used to initiate flower development in adult plants. However, the mechanism by which ethylene induces flowering in adult bromeliads remains unknown. Here, we identified an APETALA2 (AP2)-like gene, AfAP2-1, in Aechmea fasciata. AfAP2-1 contains two AP2 domains and is a nuclear-localized protein. It functions as a transcriptional activator, and the activation domain is located in the C-terminal region. The expression level of AfAP2-1 is higher in juvenile plants than in adult plants, and the AfAP2-1 transcript level was rapidly and transiently reduced in plants treated with exogenous ethylene. Overexpression of AfAP2-1 in Arabidopsis thaliana results in an extremely delayed flowering phenotype. These results suggested that AfAP2-1 responds to ethylene and is a putative age-dependent flowering regulator in A. fasciata. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
The Indeterminate Domain Protein ROC1 Regulates Chilling Tolerance via Activation of DREB1B/CBF1 in Rice
by Mingzhu Dou, Shuai Cheng, Baotian Zhao, Yuanhu Xuan and Minglong Shao
Int. J. Mol. Sci. 2016, 17(3), 233; https://doi.org/10.3390/ijms17030233 - 25 Feb 2016
Cited by 26 | Viewed by 6198
Abstract
Abiotic stress, including salinity, drought and cold, severely affect diverse aspects of plant development and production. Rice is an important crop that does not acclimate to cold; therefore, it is relatively sensitive to low temperature stress. Dehydration-responsive element-binding protein 1s (DREB1s)/C-repeat binding factors [...] Read more.
Abiotic stress, including salinity, drought and cold, severely affect diverse aspects of plant development and production. Rice is an important crop that does not acclimate to cold; therefore, it is relatively sensitive to low temperature stress. Dehydration-responsive element-binding protein 1s (DREB1s)/C-repeat binding factors (CBFs) are well known for their function in cold tolerance, but the transcriptional regulation of CBFs remains elusive, especially in rice. Here, we performed a yeast one-hybrid assay using the promoter of CBF1, a cold-induced gene, to isolate transcriptional regulators of CBF1. Among the seven candidates identified, an indeterminate domain (IDD) protein named ROC1 (a regulator of CBF1) was further analyzed. The ROC1 transcript was induced by exogenously-treated auxin, while it was not altered by cold or ABA stimuli. ROC1-GFP was localized at the nucleus, and ROC1 showed trans-activation activity in yeast. The electrophoretic mobility shift assay (EMSA) and ChIP analyses revealed that ROC1 directly bound to the promoter of CBF1. Furthermore, ROC1 mutants exhibited chilling-sensitive symptoms and inhibited cold-mediated induction of CBF1 and CBF3, indicating that ROC1 is a positive regulator of cold stress responses. Taken together, this study identified the CBF1 regulator, and the results are important for rice plant adaptation to chilling stress. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Cloning and Characterization of a Flavonoid 3′-Hydroxylase Gene from Tea Plant (Camellia sinensis)
by Tian-Shan Zhou, Rui Zhou, You-Ben Yu, Yao Xiao, Dong-Hua Li, Bin Xiao, Oliver Yu and Ya-Jun Yang
Int. J. Mol. Sci. 2016, 17(2), 261; https://doi.org/10.3390/ijms17020261 - 22 Feb 2016
Cited by 34 | Viewed by 7659
Abstract
Tea leaves contain abundant flavan-3-ols, which include dihydroxylated and trihydroxylated catechins. Flavonoid 3′-hydroxylase (F3′H: EC 1.14.13.21) is one of the enzymes in the establishment of the hydroxylation pattern. A gene encoding F3′H, designated as CsF3H, was isolated from Camellia sinensis [...] Read more.
Tea leaves contain abundant flavan-3-ols, which include dihydroxylated and trihydroxylated catechins. Flavonoid 3′-hydroxylase (F3′H: EC 1.14.13.21) is one of the enzymes in the establishment of the hydroxylation pattern. A gene encoding F3′H, designated as CsF3H, was isolated from Camellia sinensis with a homology-based cloning technique and deposited in the GenBank (GenBank ID: KT180309). Bioinformatic analysis revealed that CsF3H was highly homologous with the characterized F3Hs from other plant species. Four conserved cytochrome P450-featured motifs and three F3′H-specific conserved motifs were discovered in the protein sequence of CsF3H. Enzymatic analysis of the heterologously expressed CsF3H in yeast demonstrated that tea F3′H catalyzed the 3′-hydroxylation of naringenin, dihydrokaempferol and kaempferol. Apparent Km values for these substrates were 17.08, 143.64 and 68.06 μM, and their apparent Vmax values were 0.98, 0.19 and 0.44 pM·min−1, respectively. Transcription level of CsF3H in the new shoots, during tea seed germination was measured, along with that of other key genes for flavonoid biosynthesis using real-time PCR technique. The changes in 3′,4′-flavan-3-ols, 3′,4′,5′-flavan-3-ols and flavan-3-ols, were consistent with the expression level of CsF3H and other related genes in the leaves. In the study of nitrogen supply for the tea plant growth, our results showed the expression level of CsF3H and all other tested genes increased in response to nitrogen depletion after 12 days of treatment, in agreement with a corresponding increase in 3′,4′-catechins, 3′,4′,5′-catechins and flavan 3-ols content in the leaves. All these results suggest the importance of CsF3H in the biosynthesis of 3′,4′-catechins, 3′,4′,5′-catechins and flavan 3-ols in tea leaves. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
Investigation of the Antiproliferative Properties of Natural Sesquiterpenes from Artemisia asiatica and Onopordum acanthium on HL-60 Cells in Vitro
by Judit Molnár, Gábor J. Szebeni, Boglárka Csupor-Löffler, Zsuzsanna Hajdú, Thomas Szekeres, Philipp Saiko, Imre Ocsovszki, László G. Puskás, Judit Hohmann and István Zupkó
Int. J. Mol. Sci. 2016, 17(2), 83; https://doi.org/10.3390/ijms17020083 - 17 Feb 2016
Cited by 16 | Viewed by 6135
Abstract
Plants and plant extracts play a crucial role in the research into novel antineoplastic agents. Four sesquiterpene lactones, artecanin (1), 3β-chloro-4α,10α-dihydroxy-1α,2α-epoxy-5α,7αH-guaia-11(13)-en-12,6α-olide (2), iso-seco-tanapartholide 3-O-methyl ether (3) and 4β,15-dihydro-3-dehydrozaluzanin C (4), were isolated from two [...] Read more.
Plants and plant extracts play a crucial role in the research into novel antineoplastic agents. Four sesquiterpene lactones, artecanin (1), 3β-chloro-4α,10α-dihydroxy-1α,2α-epoxy-5α,7αH-guaia-11(13)-en-12,6α-olide (2), iso-seco-tanapartholide 3-O-methyl ether (3) and 4β,15-dihydro-3-dehydrozaluzanin C (4), were isolated from two traditionally used Asteraceae species (Onopordum acanthium and Artemisia asiatica). When tested for antiproliferative action on HL-60 leukemia cells, these compounds exhibited reasonable IC50 values in the range 3.6–13.5 μM. Treatment with the tested compounds resulted in a cell cycle disturbance characterized by increases in the G1 and G2/M populations, while there was a decrease in the S phase. Additionally, 1–3 elicited increases in the hypodiploid (subG1) population. The compounds elicited concentration-dependent chromatin condensation and disruption of the membrane integrity, as revealed by Hoechst 33258–propidium staining. Treatment for 24 h resulted in significant increases in activity of caspases-3 and -9, indicating that the tested sesquiterpenes induced the mitochondrial pathway of apoptosis. The proapoptotic properties of the sesquiterpene lactones were additionally demonstrated withannexin V staining. Compounds 1 and 2 increased the Bax/Bcl-2 expression and decreased the expressions of CDK1 and cyclin B2, as determined at the mRNA level by means of RT-PCR. These experimental results indicate that sesquiterpene lactones may be regarded as potential starting structures for the development of novel anticancer agents. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal
by Diana Tomás, Joana Rodrigues, Ana Varela, Maria Manuela Veloso, Wanda Viegas and Manuela Silva
Int. J. Mol. Sci. 2016, 17(2), 203; https://doi.org/10.3390/ijms17020203 - 04 Feb 2016
Cited by 13 | Viewed by 5336
Abstract
Genomic diversity of Portuguese accessions of Avena species—diploid A. strigosa and hexaploids A. sativa and A. sterilis—was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species—rye subtelomeric sequence (pSc200) and cereal centromeric sequence [...] Read more.
Genomic diversity of Portuguese accessions of Avena species—diploid A. strigosa and hexaploids A. sativa and A. sterilis—was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species—rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies—IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)—were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Identification of Powdery Mildew Responsive Genes in Hevea brasiliensis through mRNA Differential Display
by Xiang Li, Zhenghong Bi, Rong Di, Peng Liang, Qiguang He, Wenbo Liu, Weiguo Miao and Fucong Zheng
Int. J. Mol. Sci. 2016, 17(2), 181; https://doi.org/10.3390/ijms17020181 - 29 Jan 2016
Cited by 20 | Viewed by 6000
Abstract
Powdery mildew is an important disease of rubber trees caused by Oidium heveae B. A. Steinmann. As far as we know, none of the resistance genes related to powdery mildew have been isolated from the rubber tree. There is little information available at [...] Read more.
Powdery mildew is an important disease of rubber trees caused by Oidium heveae B. A. Steinmann. As far as we know, none of the resistance genes related to powdery mildew have been isolated from the rubber tree. There is little information available at the molecular level regarding how a rubber tree develops defense mechanisms against this pathogen. We have studied rubber tree mRNA transcripts from the resistant RRIC52 cultivar by differential display analysis. Leaves inoculated with the spores of O. heveae were collected from 0 to 120 hpi in order to identify pathogen-regulated genes at different infection stages. We identified 78 rubber tree genes that were differentially expressed during the plant–pathogen interaction. BLAST analysis for these 78 ESTs classified them into seven functional groups: cell wall and membrane pathways, transcription factor and regulatory proteins, transporters, signal transduction, phytoalexin biosynthesis, other metabolism functions, and unknown functions. The gene expression for eight of these genes was validated by qRT-PCR in both RRIC52 and the partially susceptible Reyan 7-33-97 cultivars, revealing the similar or differential changes of gene expressions between these two cultivars. This study has improved our overall understanding of the molecular mechanisms of rubber tree resistance to powdery mildew. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Genome-Wide Identification, Characterization and Expression Analysis of the Chalcone Synthase Family in Maize
by Yahui Han, Ting Ding, Bo Su and Haiyang Jiang
Int. J. Mol. Sci. 2016, 17(2), 161; https://doi.org/10.3390/ijms17020161 - 27 Jan 2016
Cited by 75 | Viewed by 7809
Abstract
Members of the chalcone synthase (CHS) family participate in the synthesis of a series of secondary metabolites in plants, fungi and bacteria. The metabolites play important roles in protecting land plants against various environmental stresses during the evolutionary process. Our research was conducted [...] Read more.
Members of the chalcone synthase (CHS) family participate in the synthesis of a series of secondary metabolites in plants, fungi and bacteria. The metabolites play important roles in protecting land plants against various environmental stresses during the evolutionary process. Our research was conducted on comprehensive investigation of CHS genes in maize (Zea mays L.), including their phylogenetic relationships, gene structures, chromosomal locations and expression analysis. Fourteen CHS genes (ZmCHS01–14) were identified in the genome of maize, representing one of the largest numbers of CHS family members identified in one organism to date. The gene family was classified into four major classes (classes I–IV) based on their phylogenetic relationships. Most of them contained two exons and one intron. The 14 genes were unevenly located on six chromosomes. Two segmental duplication events were identified, which might contribute to the expansion of the maize CHS gene family to some extent. In addition, quantitative real-time PCR and microarray data analyses suggested that ZmCHS genes exhibited various expression patterns, indicating functional diversification of the ZmCHS genes. Our results will contribute to future studies of the complexity of the CHS gene family in maize and provide valuable information for the systematic analysis of the functions of the CHS gene family. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
Comparative Transcriptome Profile of the Cytoplasmic Male Sterile and Fertile Floral Buds of Radish (Raphanus sativus L.)
by Shiyong Mei, Touming Liu and Zhiwei Wang
Int. J. Mol. Sci. 2016, 17(1), 42; https://doi.org/10.3390/ijms17010042 - 06 Jan 2016
Cited by 31 | Viewed by 8237
Abstract
Radish cytoplasmic male sterility (CMS) has been widely used for breeding in Raphanus and Brassica genera. However, the detailed regulation network of the male sterility remains to be determined. Our previous work has shown that the abnormalities in a CMS radish appeared shortly [...] Read more.
Radish cytoplasmic male sterility (CMS) has been widely used for breeding in Raphanus and Brassica genera. However, the detailed regulation network of the male sterility remains to be determined. Our previous work has shown that the abnormalities in a CMS radish appeared shortly after the tetrad stage when microspores were malformed and the tapetal cells grew abnormally large. In this work, histological analysis shows that anthers are at the tetrad stage when the radish buds are about 1.5 mm in length. Furthermore, a high throughput RNA sequencing technology was employed to characterize the transcriptome of radish buds with length about 1.5 mm from two CMS lines possessing the CMS-inducing orf138 gene and corresponding near-isogenic maintainer lines. A total of 67,140 unigenes were functionally annotated. Functional terms for these genes are significantly enriched in 55 Gene Ontology (GO) groups and 323 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The transcriptome detected transcripts for 72 out of a total of 79 protein genes encoded in the chloroplast genome from radish. In contrast, the radish mitochondrial genome contains 34 protein genes, but only 16 protein transcripts were detected from the transcriptome. The transcriptome comparison between CMS and near-isogenic maintainer lines revealed 539 differentially expressed genes (DEGs), indicating that the false positive rate for comparative transcriptome profiling was clearly decreased using two groups of CMS/maintainer lines with different nuclear background. The level of 127 transcripts was increased and 412 transcripts were decreased in the CMS lines. No change in levels of transcripts except CMS-inducing orf138 was identified from the mitochondrial and chloroplast genomes. Some DEGs which would be associated with the CMS, encoding MYB and bHLH transcription factors, pentatricopeptide repeat (PPR) proteins, heat shock transcription factors (HSFs) and heat shock proteins (HSPs), are discussed. The transcriptome dataset and comparative analysis will provide an important resource for further understanding anther development, the CMS mechanism and to improve molecular breeding in radish. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Anion Channel Inhibitor NPPB-Inhibited Fluoride Accumulation in Tea Plant (Camellia sinensis) Is Related to the Regulation of Ca2+, CaM and Depolarization of Plasma Membrane Potential
by Xian-Chen Zhang, Hong-Jian Gao, Tian-Yuan Yang, Hong-Hong Wu, Yu-Mei Wang, Zheng-Zhu Zhang and Xiao-Chun Wan
Int. J. Mol. Sci. 2016, 17(1), 57; https://doi.org/10.3390/ijms17010057 - 05 Jan 2016
Cited by 147 | Viewed by 6011
Abstract
Tea plant is known to be a hyper-accumulator of fluoride (F). Over-intake of F has been shown to have adverse effects on human health, e.g., dental fluorosis. Thus, understanding the mechanisms fluoride accumulation and developing potential approaches to decrease F uptake in tea [...] Read more.
Tea plant is known to be a hyper-accumulator of fluoride (F). Over-intake of F has been shown to have adverse effects on human health, e.g., dental fluorosis. Thus, understanding the mechanisms fluoride accumulation and developing potential approaches to decrease F uptake in tea plants might be beneficial for human health. In the present study, we found that pretreatment with the anion channel inhibitor NPPB reduced F accumulation in tea plants. Simultaneously, we observed that NPPB triggered Ca2+ efflux from mature zone of tea root and significantly increased relative CaM in tea roots. Besides, pretreatment with the Ca2+ chelator (EGTA) and CaM antagonists (CPZ and TFP) suppressed NPPB-elevated cytosolic Ca2+ fluorescence intensity and CaM concentration in tea roots, respectively. Interestingly, NPPB-inhibited F accumulation was found to be significantly alleviated in tea plants pretreated with either Ca2+ chelator (EGTA) or CaM antagonists (CPZ and TFP). In addition, NPPB significantly depolarized membrane potential transiently and we argue that the net Ca2+ and H+ efflux across the plasma membrane contributed to the restoration of membrane potential. Overall, our results suggest that regulation of Ca2+-CaM and plasma membrane potential depolarization are involved in NPPB-inhibited F accumulation in tea plants. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Cloning, Characterization and Expression Pattern Analysis of a Cytosolic Copper/Zinc Superoxide Dismutase (SaCSD1) in a Highly Salt Tolerant Mangrove (Sonneratia alba)
by Enze Yang, Shanze Yi, Fang Bai, Dewei Niu, Junjie Zhong, Qiuhong Wu, Shufang Chen, Renchao Zhou and Feng Wang
Int. J. Mol. Sci. 2016, 17(1), 4; https://doi.org/10.3390/ijms17010004 - 22 Dec 2015
Cited by 10 | Viewed by 5585
Abstract
Mangroves are critical marine resources for their remarkable ability to tolerate seawater. Antioxidant enzymes play an especially significant role in eliminating reactive oxygen species and conferring abiotic stress tolerance. In this study, a cytosolic copper/zinc superoxide dismutase (SaCSD1) cDNA of Sonneratia [...] Read more.
Mangroves are critical marine resources for their remarkable ability to tolerate seawater. Antioxidant enzymes play an especially significant role in eliminating reactive oxygen species and conferring abiotic stress tolerance. In this study, a cytosolic copper/zinc superoxide dismutase (SaCSD1) cDNA of Sonneratia alba, a mangrove species with high salt tolerance, was successfully cloned and then expressed in Escherichia coli Rosetta-gami (designated as SaCSD1). SaCSD1 comprised a complete open reading frame (ORF) of 459 bp which encoded a protein of 152 amino acids. Its mature protein is predicted to be 15.32 kDa and the deduced isoelectric point is 5.78. SaCSD1 has high sequence similarity (85%–90%) with the superoxide dismutase (CSD) of some other plant species. SaCSD1 was expressed with 30.6% yield regarding total protein content after being introduced into the pET-15b (Sma I) vector for expression in Rosetta-gami and being induced with IPTG. After affinity chromatography on Ni-NTA, recombinant SaCSD1 was obtained with 3.2-fold purification and a specific activity of 2200 U/mg. SaCSD1 showed good activity as well as stability in the ranges of pH between 3 and 7 and temperature between 25 and 55 °C. The activity of recombinant SaCSD1 was stable in 0.25 M NaCl, Dimethyl Sulphoxide (DMSO), glycerol, and chloroform, and was reduced to a great extent in β-mercaptoethanol, sodium dodecyl sulfate (SDS), H2O2, and phenol. Moreover, the SaCSD1 protein was very susceptive to pepsin digestion. Real-time Quantitative Polymerase Chain Reaction (PCR) assay demonstrated that SaCSD1 was expressed in leaf, stem, flower, and fruit organs, with the highest expression in fruits. Under 0.25 M and 0.5 M salt stress, the expression of SaCSD1 was down-regulated in roots, but up-regulated in leaves. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Cloning of the Lycopene β-cyclase Gene in Nicotiana tabacum and Its Overexpression Confers Salt and Drought Tolerance
by Yanmei Shi, Jinggong Guo, Wei Zhang, Lifeng Jin, Pingping Liu, Xia Chen, Feng Li, Pan Wei, Zefeng Li, Wenzheng Li, Chunyang Wei, Qingxia Zheng, Qiansi Chen, Jianfeng Zhang, Fucheng Lin, Lingbo Qu, John Hugh Snyder and Ran Wang
Int. J. Mol. Sci. 2015, 16(12), 30438-30457; https://doi.org/10.3390/ijms161226243 - 21 Dec 2015
Cited by 34 | Viewed by 6742
Abstract
Carotenoids are important pigments in plants that play crucial roles in plant growth and in plant responses to environmental stress. Lycopene β cyclase (β-LCY) functions at the branch point of the carotenoid biosynthesis pathway, catalyzing the cyclization of lycopene. Here, a β-LCY gene [...] Read more.
Carotenoids are important pigments in plants that play crucial roles in plant growth and in plant responses to environmental stress. Lycopene β cyclase (β-LCY) functions at the branch point of the carotenoid biosynthesis pathway, catalyzing the cyclization of lycopene. Here, a β-LCY gene from Nicotiana tabacum, designated as Ntβ-LCY1, was cloned and functionally characterized. Robust expression of Ntβ-LCY1 was found in leaves, and Ntβ-LCY1 expression was obviously induced by salt, drought, and exogenous abscisic acid treatments. Strong accumulation of carotenoids and expression of carotenoid biosynthesis genes resulted from Ntβ-LCY1 overexpression. Additionally, compared to wild-type plants, transgenic plants with overexpression showed enhanced tolerance to salt and drought stress with higher abscisic acid levels and lower levels of malondialdehyde and reactive oxygen species. Conversely, transgenic RNA interference plants had a clear albino phenotype in leaves, and some plants did not survive beyond the early developmental stages. The suppression of Ntβ-LCY1 expression led to lower expression levels of genes in the carotenoid biosynthesis pathway and to reduced accumulation of carotenoids, chlorophyll, and abscisic acid. These results indicate that Ntβ-LCY1 is not only a likely cyclization enzyme involved in carotenoid accumulation but also confers salt and drought stress tolerance in Nicotiana tabacum. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Effects of Heat Stress on Metabolite Accumulation and Composition, and Nutritional Properties of Durum Wheat Grain
by Anna Maria De Leonardis, Mariagiovanna Fragasso, Romina Beleggia, Donatella Bianca Maria Ficco, Pasquale De Vita and Anna Maria Mastrangelo
Int. J. Mol. Sci. 2015, 16(12), 30382-30404; https://doi.org/10.3390/ijms161226241 - 19 Dec 2015
Cited by 47 | Viewed by 7282
Abstract
Durum wheat (Triticum turgidum (L.) subsp. turgidum (L.) convar. durum (Desf.)) is momentous for human nutrition, and environmental stresses can strongly limit the expression of yield potential and affect the qualitative characteristics of the grain. The aim of this study was to [...] Read more.
Durum wheat (Triticum turgidum (L.) subsp. turgidum (L.) convar. durum (Desf.)) is momentous for human nutrition, and environmental stresses can strongly limit the expression of yield potential and affect the qualitative characteristics of the grain. The aim of this study was to determine how heat stress (five days at 37 °C) applied five days after flowering affects the nutritional composition, antioxidant capacity and metabolic profile of the grain of two durum wheat genotypes: “Primadur”, an elite cultivar with high yellow index, and “T1303”, an anthocyanin-rich purple cultivar. Qualitative traits and metabolite evaluation (by gas chromatography linked to mass spectrometry) were carried out on immature (14 days after flowering) and mature seeds. The effects of heat stress were genotype-dependent. Although some metabolites (e.g., sucrose, glycerol) increased in response to heat stress in both genotypes, clear differences were observed. Following the heat stress, there was a general increase in most of the analyzed metabolites in “Primadur”, with a general decrease in “T1303”. Heat shock applied early during seed development produced changes that were observed in immature seeds and also long-term effects that changed the qualitative and quantitative parameters of the mature grain. Therefore, short heat-stress treatments can affect the nutritional value of grain of different genotypes of durum wheat in different ways. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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Article
Comparative Transcriptome Analysis of Genes Involved in GA-GID1-DELLA Regulatory Module in Symbiotic and Asymbiotic Seed Germination of Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae)
by Si-Si Liu, Juan Chen, Shu-Chao Li, Xu Zeng, Zhi-Xia Meng and Shun-Xing Guo
Int. J. Mol. Sci. 2015, 16(12), 30190-30203; https://doi.org/10.3390/ijms161226224 - 18 Dec 2015
Cited by 48 | Viewed by 9480
Abstract
Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae) is an endangered medicinal plant in China, also called “King Medicine”. Due to lacking of sufficient nutrients in dust-like seeds, orchid species depend on mycorrhizal fungi for seed germination in the wild. As part of a conservation plan [...] Read more.
Anoectochilus roxburghii (Wall.) Lindl. (Orchidaceae) is an endangered medicinal plant in China, also called “King Medicine”. Due to lacking of sufficient nutrients in dust-like seeds, orchid species depend on mycorrhizal fungi for seed germination in the wild. As part of a conservation plan for the species, research on seed germination is necessary. However, the molecular mechanism of seed germination and underlying orchid-fungus interactions during symbiotic germination are poorly understood. In this study, Illumina HiSeq 4000 transcriptome sequencing was performed to generate a substantial sequence dataset of germinating A. roxburghii seed. A mean of 44,214,845 clean reads were obtained from each sample. 173,781 unigenes with a mean length of 653 nt were obtained. A total of 51,514 (29.64%) sequences were annotated, among these, 49 unigenes encoding proteins involved in GA-GID1-DELLA regulatory module, including 31 unigenes involved in GA metabolism pathway, 5 unigenes encoding GID1, 11 unigenes for DELLA and 2 unigenes for GID2. A total of 11,881 genes showed significant differential expression in the symbiotic germinating seed sample compared with the asymbiotic germinating seed sample, of which six were involved in the GA-GID1-DELLA regulatory module, and suggested that they might be induced or suppressed by fungi. These results will help us understand better the molecular mechanism of orchid seed germination and orchid-fungus symbiosis. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Exogenous Spermidine Alleviates Low Temperature Injury in Mung Bean (Vigna radiata L.) Seedlings by Modulating Ascorbate-Glutathione and Glyoxalase Pathway
by Kamrun Nahar, Mirza Hasanuzzaman, Md. Mahabub Alam and Masayuki Fujita
Int. J. Mol. Sci. 2015, 16(12), 30117-30132; https://doi.org/10.3390/ijms161226220 - 17 Dec 2015
Cited by 74 | Viewed by 7305
Abstract
The role of exogenous spermidine (Spd) in alleviating low temperature (LT) stress in mung bean (Vigna radiata L. cv. BARI Mung-3) seedlings has been investigated. Low temperature stress modulated the non-enzymatic and enzymatic components of ascorbate-glutathione (AsA-GSH) cycle, increased H2O [...] Read more.
The role of exogenous spermidine (Spd) in alleviating low temperature (LT) stress in mung bean (Vigna radiata L. cv. BARI Mung-3) seedlings has been investigated. Low temperature stress modulated the non-enzymatic and enzymatic components of ascorbate-glutathione (AsA-GSH) cycle, increased H2O2 content and lipid peroxidation, which indicate oxidative damage of seedlings. Low temperature reduced the leaf relative water content (RWC) and destroyed leaf chlorophyll, which inhibited seedlings growth. Exogenous pretreatment of Spd in LT-affected seedlings significantly increased the contents of non-enzymatic antioxidants of AsA-GSH cycle, which include AsA and GSH. Exogenous Spd decreased dehydroascorbate (DHA), increased AsA/DHA ratio, decreased glutathione disulfide (GSSG) and increased GSH/GSSG ratio under LT stress. Activities of AsA-GSH cycle enzymes such as ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR) and glutathione reductase (GR) increased after Spd pretreatment in LT affected seedlings. Thus, the oxidative stress was reduced. Protective effects of Spd are also reflected from reduction of methylglyoxal (MG) toxicity by improving glyoxalase cycle components, and by maintaining osmoregulation, water status and improved seedlings growth. The present study reveals the vital roles of AsA-GSH and glyoxalase cycle in alleviating LT injury. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Biosynthesis of Essential Polyunsaturated Fatty Acids in Wheat Triggered by Expression of Artificial Gene
by Daniel Mihálik, Lenka Klčová, Katarína Ondreičková, Martina Hudcovicová, Marcela Gubišová, Tatiana Klempová, Milan Čertík, János Pauk and Ján Kraic
Int. J. Mol. Sci. 2015, 16(12), 30046-30060; https://doi.org/10.3390/ijms161226137 - 16 Dec 2015
Cited by 10 | Viewed by 6335
Abstract
The artificial gene D6D encoding the enzyme ∆6desaturase was designed and synthesized using the sequence of the same gene from the fungus Thamnidium elegans. The original start codon was replaced by the signal sequence derived from the wheat gene for [...] Read more.
The artificial gene D6D encoding the enzyme ∆6desaturase was designed and synthesized using the sequence of the same gene from the fungus Thamnidium elegans. The original start codon was replaced by the signal sequence derived from the wheat gene for high-molecular-weight glutenin subunit and the codon usage was completely changed for optimal expression in wheat. Synthesized artificial D6D gene was delivered into plants of the spring wheat line CY-45 and the gene itself, as well as transcribed D6D mRNA were confirmed in plants of T0 and T1 generations. The desired product of the wheat genetic modification by artificial D6D gene was the γ-linolenic acid. Its presence was confirmed in mature grains of transgenic wheat plants in the amount 0.04%–0.32% (v/v) of the total amount of fatty acids. Both newly synthesized γ-linolenic acid and stearidonic acid have been detected also in leaves, stems, roots, awns, paleas, rachillas, and immature grains of the T1 generation as well as in immature and mature grains of the T2 generation. Contents of γ-linolenic acid and stearidonic acid varied in range 0%–1.40% (v/v) and 0%–1.53% (v/v) from the total amount of fatty acids, respectively. This approach has opened the pathway of desaturation of fatty acids and production of essential polyunsaturated fatty acids in wheat. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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Article
Elicitation of Diosgenin Production in Trigonella foenum-graecum (Fenugreek) Seedlings by Methyl Jasmonate
by Spandan Chaudhary, Surendra K. Chikara, Mahesh C. Sharma, Abhinav Chaudhary, Bakhtiyar Alam Syed, Pooja S. Chaudhary, Aditya Mehta, Maulik Patel, Arpita Ghosh and Marcello Iriti
Int. J. Mol. Sci. 2015, 16(12), 29889-29899; https://doi.org/10.3390/ijms161226208 - 15 Dec 2015
Cited by 43 | Viewed by 8232
Abstract
The effects of methyl jasmonate (MeJA), an elicitor of plant defense mechanisms, on the biosynthesis of diosgenin, a steroidal saponin, were investigated in six fenugreek (Trigonella foenum-graecum) varieties (Gujarat Methi-2, Kasuri-1, Kasuri-2, Pusa Early Branching, Rajasthan Methi and Maharashtra Methi-5). Treatment [...] Read more.
The effects of methyl jasmonate (MeJA), an elicitor of plant defense mechanisms, on the biosynthesis of diosgenin, a steroidal saponin, were investigated in six fenugreek (Trigonella foenum-graecum) varieties (Gujarat Methi-2, Kasuri-1, Kasuri-2, Pusa Early Branching, Rajasthan Methi and Maharashtra Methi-5). Treatment with 0.01% MeJA increased diosgenin levels, in 12 days old seedlings, from 0.5%–0.9% to 1.1%–1.8%. In addition, MeJA upregulated the expression of two pivotal genes of the mevalonate pathway, the metabolic route leading to diosgenin: 3-hydroxy-3-methylglutaryl-CoA reductase (HMG) and sterol-3-β-glucosyl transferase (STRL). In particular, MeJA increased the expression of HMG and STRL genes by 3.2- and 22.2-fold, respectively, in the Gujarat Methi-2 variety, and by 25.4- and 28.4-fold, respectively, in the Kasuri-2 variety. Therefore, MeJA may be considered a promising elicitor for diosgenin production by fenugreek plants. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
De Novo Transcriptome Sequencing of Oryza officinalis Wall ex Watt to Identify Disease-Resistance Genes
by Bin He, Yinghong Gu, Xiang Tao, Xiaojie Cheng, Changhe Wei, Jian Fu, Zaiquan Cheng and Yizheng Zhang
Int. J. Mol. Sci. 2015, 16(12), 29482-29495; https://doi.org/10.3390/ijms161226178 - 10 Dec 2015
Cited by 14 | Viewed by 5583
Abstract
Oryza officinalis Wall ex Watt is one of the most important wild relatives of cultivated rice and exhibits high resistance to many diseases. It has been used as a source of genes for introgression into cultivated rice. However, there are limited genomic resources [...] Read more.
Oryza officinalis Wall ex Watt is one of the most important wild relatives of cultivated rice and exhibits high resistance to many diseases. It has been used as a source of genes for introgression into cultivated rice. However, there are limited genomic resources and little genetic information publicly reported for this species. To better understand the pathways and factors involved in disease resistance and accelerating the process of rice breeding, we carried out a de novo transcriptome sequencing of O. officinalis. In this research, 137,229 contigs were obtained ranging from 200 to 19,214 bp with an N50 of 2331 bp through de novo assembly of leaves, stems and roots in O. officinalis using an Illumina HiSeq 2000 platform. Based on sequence similarity searches against a non-redundant protein database, a total of 88,249 contigs were annotated with gene descriptions and 75,589 transcripts were further assigned to GO terms. Candidate genes for plant–pathogen interaction and plant hormones regulation pathways involved in disease-resistance were identified. Further analyses of gene expression profiles showed that the majority of genes related to disease resistance were all expressed in the three tissues. In addition, there are two kinds of rice bacterial blight-resistant genes in O. officinalis, including two Xa1 genes and three Xa26 genes. All 2 Xa1 genes showed the highest expression level in stem, whereas one of Xa26 was expressed dominantly in leaf and other 2 Xa26 genes displayed low expression level in all three tissues. This transcriptomic database provides an opportunity for identifying the genes involved in disease-resistance and will provide a basis for studying functional genomics of O. officinalis and genetic improvement of cultivated rice in the future. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Allyl Isothiocyanate Inhibits Actin-Dependent Intracellular Transport in Arabidopsis thaliana
by Bjørnar Sporsheim, Anders Øverby and Atle Magnar Bones
Int. J. Mol. Sci. 2015, 16(12), 29134-29147; https://doi.org/10.3390/ijms161226154 - 07 Dec 2015
Cited by 11 | Viewed by 6107
Abstract
Volatile allyl isothiocyanate (AITC) derives from the biodegradation of the glucosinolate sinigrin and has been associated with growth inhibition in several plants, including the model plant Arabidopsis thaliana. However, the underlying cellular mechanisms of this feature remain scarcely investigated in plants. In [...] Read more.
Volatile allyl isothiocyanate (AITC) derives from the biodegradation of the glucosinolate sinigrin and has been associated with growth inhibition in several plants, including the model plant Arabidopsis thaliana. However, the underlying cellular mechanisms of this feature remain scarcely investigated in plants. In this study, we present evidence of an AITC-induced inhibition of actin-dependent intracellular transport in A. thaliana. A transgenic line of A. thaliana expressing yellow fluorescent protein (YFP)-tagged actin filaments was used to show attenuation of actin filament movement by AITC. This appeared gradually in a time- and dose-dependent manner and resulted in actin filaments appearing close to static. Further, we employed four transgenic lines with YFP-fusion proteins labeling the Golgi apparatus, endoplasmic reticulum (ER), vacuoles and peroxisomes to demonstrate an AITC-induced inhibition of actin-dependent intracellular transport of or, in these structures, consistent with the decline in actin filament movement. Furthermore, the morphologies of actin filaments, ER and vacuoles appeared aberrant following AITC-exposure. However, AITC-treated seedlings of all transgenic lines tested displayed morphologies and intracellular movements similar to that of the corresponding untreated and control-treated plants, following overnight incubation in an AITC-absent environment, indicating that AITC-induced decline in actin-related movements is a reversible process. These findings provide novel insights into the cellular events in plant cells following exposure to AITC, which may further expose clues to the physiological significance of the glucosinolate-myrosinase system. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora)
by Le Liu, Shijie Zhang and Chunlan Lian
Int. J. Mol. Sci. 2015, 16(12), 29047-29059; https://doi.org/10.3390/ijms161226139 - 04 Dec 2015
Cited by 14 | Viewed by 5746
Abstract
Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 [...] Read more.
Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 million sequencing clean reads from P. densiflora mRNA were produced using Illumina paired-end sequencing technology. It yielded 83,913 unigenes with a mean length of 751 bp, of which 54,530 (64.98%) unigenes showed similarity to sequences in the NCBI database. Among which the best matches in the NCBI Nr database were Picea sitchensis (41.60%), Amborella trichopoda (9.83%), and Pinus taeda (4.15%). A total of 1953 putative microsatellites were identified in 1784 unigenes using MISA (MicroSAtellite) software, of which the tri-nucleotide repeats were most abundant (50.18%) and 629 EST-SSR (expressed sequence tag- simple sequence repeats) primer pairs were successfully designed. Among 20 EST-SSR primer pairs randomly chosen, 17 markers yielded amplification products of the expected size in P. densiflora. Our results will provide a valuable resource for gene-function analysis, germplasm identification, molecular marker-assisted breeding and resistance-related gene(s) mapping for pine for P. densiflora. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Diversity and Inheritance of Intergenic Spacer Sequences of 45S Ribosomal DNA among Accessions of Brassica oleracea L. var. capitata
by Kiwoung Yang, Arif Hasan Khan Robin, Go-Eun Yi, Jonghoon Lee, Mi-Young Chung, Tae-Jin Yang and Ill-Sup Nou
Int. J. Mol. Sci. 2015, 16(12), 28783-28799; https://doi.org/10.3390/ijms161226125 - 03 Dec 2015
Cited by 12 | Viewed by 10058
Abstract
Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed [...] Read more.
Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were quite similar in length. The 45S IGSs were found to follow Mendelian inheritance in a population of 15 F1s and their 30 inbred parental lines, which suggests that these sequences could be useful for development of new breeding tools. In addition, this study represents the first report of intra-specific (within subspecies) variation of the 45S IGS in B. oleracea. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Omics-Based Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes during Early Infestation by Small Brown Planthopper
by Weilin Zhang, Ling Yang, Mei Li, Bojun Ma, Chengqi Yan and Jianping Chen
Int. J. Mol. Sci. 2015, 16(12), 28746-28764; https://doi.org/10.3390/ijms161226128 - 03 Dec 2015
Cited by 11 | Viewed by 5952
Abstract
The small brown planthopper (SBPH) is one of the destructive pests of rice. Although different biochemical pathways that are involved in rice responding to planthopper infestation have been documented, it is unclear which individual metabolic pathways are responsive to planthopper infestation. In this [...] Read more.
The small brown planthopper (SBPH) is one of the destructive pests of rice. Although different biochemical pathways that are involved in rice responding to planthopper infestation have been documented, it is unclear which individual metabolic pathways are responsive to planthopper infestation. In this study, an omics-based comparative transcriptional profiling of two contrasting rice genotypes, an SBPH-resistant and an SBPH-susceptible rice line, was assessed for rice individual metabolic pathways responsive to SBPH infestation. When exposed to SBPH, 166 metabolic pathways were differentially regulated; of these, more than one-third of metabolic pathways displayed similar change patterns between these two contrasting rice genotypes; the difference of change pattern between these two contrasting rice genotypes mostly lies in biosynthetic pathways and the obvious difference of change pattern lies in energy metabolism pathways. Combining the Pathway Tools Omics Viewer with the web tool Venn, 21 and 6 metabolic pathways which potentially associated with SBPH resistance and susceptibility, respectively were identified. This study presents an omics-based comparative transcriptional profiling of SBPH-resistant and SBPH-susceptible rice plants during early infestation by SBPH, which will be very informative in studying rice-insect interaction. The results will provide insight into how rice plants respond to early infestation by SBPH from the biochemical pathways perspective. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
Transcriptome Profiling of Louisiana iris Root and Identification of Genes Involved in Lead-Stress Response
by Songqing Tian, Chunsun Gu, Liangqin Liu, Xudong Zhu, Yanhai Zhao and Suzhen Huang
Int. J. Mol. Sci. 2015, 16(12), 28087-28097; https://doi.org/10.3390/ijms161226084 - 25 Nov 2015
Cited by 23 | Viewed by 6603
Abstract
Louisiana iris is tolerant to and accumulates the heavy metal lead (Pb). However, there is limited knowledge of the molecular mechanisms behind this feature. We describe the transcriptome of Louisiana iris using Illumina sequencing technology. The root transcriptome of Louisiana iris under control [...] Read more.
Louisiana iris is tolerant to and accumulates the heavy metal lead (Pb). However, there is limited knowledge of the molecular mechanisms behind this feature. We describe the transcriptome of Louisiana iris using Illumina sequencing technology. The root transcriptome of Louisiana iris under control and Pb-stress conditions was sequenced. Overall, 525,498 transcripts representing 313,958 unigenes were assembled using the clean raw reads. Among them, 43,015 unigenes were annotated and their functions classified using the euKaryotic Orthologous Groups (KOG) database. They were divided into 25 molecular families. In the Gene Ontology (GO) database, 50,174 unigenes were categorized into three GO trees (molecular function, cellular component and biological process). After analysis of differentially expressed genes, some Pb-stress-related genes were selected, including biosynthesis genes of chelating compounds, metal transporters, transcription factors and antioxidant-related genes. This study not only lays a foundation for further studies on differential genes under Pb stress, but also facilitates the molecular breeding of Louisiana iris. Full article
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Article
Genotypic Variation under Fe Deficiency Results in Rapid Changes in Protein Expressions and Genes Involved in Fe Metabolism and Antioxidant Mechanisms in Tomato Seedlings (Solanum lycopersicum L.)
by Sowbiya Muneer and Byoung Ryong Jeong
Int. J. Mol. Sci. 2015, 16(12), 28022-28037; https://doi.org/10.3390/ijms161226086 - 25 Nov 2015
Cited by 1 | Viewed by 6116
Abstract
To investigate Fe deficiency tolerance in tomato cultivars, quantification of proteins and genes involved in Fe metabolism and antioxidant mechanisms were performed in “Roggusanmaru” and “Super Doterang”. Fe deficiency (Moderate, low and –Fe) significantly decreased the biomass, total, and apoplastic Fe concentration of [...] Read more.
To investigate Fe deficiency tolerance in tomato cultivars, quantification of proteins and genes involved in Fe metabolism and antioxidant mechanisms were performed in “Roggusanmaru” and “Super Doterang”. Fe deficiency (Moderate, low and –Fe) significantly decreased the biomass, total, and apoplastic Fe concentration of “Roggusanmaru”, while a slight variation was observed in “Super Doterang” cultivar. The quantity of important photosynthetic pigments such as total chlorophyll and carotenoid contents significantly decreased in “Roggusanmaru” than “Super Doterang” cultivar. The total protein profile in leaves and roots determines that “Super Doterang” exhibited an optimal tolerance to Fe deficiency compared to “Roggusanmaru” cultivar. A reduction in expression of PSI (photosystem I), PSII (photosystem II) super-complexes and related thylakoid protein contents were detected in “Roggusanmaru” than “Super Doterang” cultivar. Moreover, the relative gene expression of SlPSI and SlPSII were well maintained in “Super Doterang” than “Roggusanmaru” cultivar. The relative expression of genes involved in Fe-transport (SlIRT1 and SlIRT2) and Fe(III) chelates reductase oxidase (SlFRO1) were relatively reduced in “Roggusanmaru”, while increased in “Super Doterang” cultivar under Fe deficient conditions. The H+-ATPase relative gene expression (SlAHA1) in roots were maintained in “Super Doterang” compared to “Roggusanmaru”. Furthermore, the gene expressions involved in antioxidant defense mechanisms (SlSOD, SlAPX and SlCAT) in leaves and roots showed that these genes were highly increased in “Super Doterang”, whereas decreased in “Roggusanmaru” cultivar under Fe deficiency. The present study suggested that “Super Doterang” is better tomato cultivar than “Roggusanmaru” for calcareous soils. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
A PPO Promoter from Betalain-Producing Red Swiss Chard, Directs Petiole- and Root-Preferential Expression of Foreign Gene in Anthocyanins-Producing Plants
by Zhi-Hai Yu, Ya-Nan Han and Xing-Guo Xiao
Int. J. Mol. Sci. 2015, 16(11), 27032-27043; https://doi.org/10.3390/ijms161126011 - 12 Nov 2015
Cited by 15 | Viewed by 6273
Abstract
A 1670 bp 5′-flanking region of the polyphenol oxidase (PPO) gene was isolated from red Swiss chard, a betalain-producing plant. This region, named promoter BvcPPOP, and its 5′-truncated versions were fused with the GUS gene and introduced into Arabidopsis, an anthocyanins-producing plant. [...] Read more.
A 1670 bp 5′-flanking region of the polyphenol oxidase (PPO) gene was isolated from red Swiss chard, a betalain-producing plant. This region, named promoter BvcPPOP, and its 5′-truncated versions were fused with the GUS gene and introduced into Arabidopsis, an anthocyanins-producing plant. GUS histochemical staining and quantitative analysis of transgenic plants at the vegetative and reproductive stages showed that BvcPPOP could direct GUS gene expression in vegetative organs with root- and petiole-preference, but not in reproductive organs including inflorescences shoot, inflorescences leaf, flower, pod and seed. This promoter was regulated by developmental stages in its driving strength, but not in expression pattern. It was also regulated by the abiotic stressors tested, positively by salicylic acid (SA) and methyl jasmonate (MeJA) but negatively by abscisic acid (ABA), gibberellin (GA), NaCl and OH. Its four 5′-truncated versions varied in the driving strength, but not obviously in expression pattern, and even the shortest version (−225 to +22) retained the root- and petiole- preference. This promoter is, to our knowledge, the first PPO promoter cloned and functionally elucidated from the betalain-producing plant, and thus provides not only a useful tool for expressing gene(s) of agricultural interest in vegetative organs, but also a clue to clarify the function of metabolism-specific PPO in betalain biosynthesis. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Metabolic Profiling of Pyrrolizidine Alkaloids in Foliage of Two Echium spp. Invaders in Australia—A Case of Novel Weapons?
by Dominik Skoneczny, Paul A. Weston, Xiaocheng Zhu, Geoff M. Gurr, Ragan M. Callaway and Leslie A. Weston
Int. J. Mol. Sci. 2015, 16(11), 26721-26737; https://doi.org/10.3390/ijms161125979 - 06 Nov 2015
Cited by 31 | Viewed by 7220
Abstract
Metabolic profiling allows for simultaneous and rapid annotation of biochemically similar organismal metabolites. An effective platform for profiling of toxic pyrrolizidine alkaloids (PAs) and their N-oxides (PANOs) was developed using ultra high pressure liquid chromatography quadrupole time-of-flight (UHPLC-QTOF) mass spectrometry. Field-collected populations of [...] Read more.
Metabolic profiling allows for simultaneous and rapid annotation of biochemically similar organismal metabolites. An effective platform for profiling of toxic pyrrolizidine alkaloids (PAs) and their N-oxides (PANOs) was developed using ultra high pressure liquid chromatography quadrupole time-of-flight (UHPLC-QTOF) mass spectrometry. Field-collected populations of invasive Australian weeds, Echium plantagineum and E. vulgare were raised under controlled glasshouse conditions and surveyed for the presence of related PAs and PANOs in leaf tissues at various growth stages. Echium plantagineum possessed numerous related and abundant PANOs (>17) by seven days following seed germination, and these were also observed in rosette and flowering growth stages. In contrast, the less invasive E. vulgare accumulated significantly lower levels of most PANOs under identical glasshouse conditions. Several previously unreported PAs were also found at trace levels. Field-grown populations of both species were also evaluated for PA production and highly toxic echimidine N-oxide was amongst the most abundant PANOs in foliage of both species. PAs in field and glasshouse plants were more abundant in the more widely invasive species, E. plantagineum, and may provide competitive advantage by increasing the plant’s capacity to deter natural enemies in its invaded range through production of novel weapons. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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Article
CONSTITUTIVE PHOTOMORPHOGENIC 10 (COP10) Contributes to Floral Repression under Non-Inductive Short Days in Arabidopsis
by Min-Young Kang, Hye-Young Kwon, Na-Yun Kim, Yasuhito Sakuraba and Nam-Chon Paek
Int. J. Mol. Sci. 2015, 16(11), 26493-26505; https://doi.org/10.3390/ijms161125969 - 05 Nov 2015
Cited by 3 | Viewed by 7803
Abstract
In Arabidopsis, CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETIOLATED/FUSCA (COP/DET/FUS) genes act in repression of photomorphogenesis in darkness, and recent reports revealed that some of these genes, such as COP1 and DET1, also have important roles in controlling flowering time and circadian rhythm. The [...] Read more.
In Arabidopsis, CONSTITUTIVE PHOTOMORPHOGENIC/DE-ETIOLATED/FUSCA (COP/DET/FUS) genes act in repression of photomorphogenesis in darkness, and recent reports revealed that some of these genes, such as COP1 and DET1, also have important roles in controlling flowering time and circadian rhythm. The COP/DET/FUS protein COP10 interacts with DET1 and DNA DAMAGE-BINDING PROTEIN 1 (DDB1) to form a CDD complex and represses photomorphogenesis in darkness. The cop10-4 mutants flower normally in inductive long days (LD) but early in non-inductive short days (SD) compared with wild type (WT); however, the role of COP10 remains unknown. Here, we investigate the role of COP10 in SD-dependent floral repression. Reverse transcription-quantitative PCR revealed that in SD, expression of the LD-dependent floral inducers GI, FKF1, and FT significantly increased in cop10-4 mutants, compared with WT. This suggests that COP10 mainly regulates FT expression in a CO-independent manner. We also show that COP10 interacts with GI in vitro and in vivo, suggesting that COP10 could also affect GI function at the posttranslational level. Moreover, FLC expression was repressed drastically in cop10-4 mutants and COP10 interacts with MULTICOPY SUPPRESSOR OF IRA1 4 (MSI4)/FVE (MSI4/FVE), which epigenetically inhibits FLC expression. These data suggest that COP10 contributes to delaying flowering in the photoperiod and autonomous pathways by downregulating FT expression under SD. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
ClRTL1 Encodes a Chinese Fir RNase III–Like Protein Involved in Regulating Shoot Branching
by Xia Li, Qian Su, Renhua Zheng, Guangxin Liu, Ye Lu, Liming Bian, Jinhui Chen and Jisen Shi
Int. J. Mol. Sci. 2015, 16(10), 25691-25710; https://doi.org/10.3390/ijms161025691 - 26 Oct 2015
Cited by 4 | Viewed by 6205
Abstract
Identification of genes controlling shoot branching is crucial for improving plant architecture and increasing crop yield or biomass. A branching mutant of Chinese fir named “Dugansha” (Cunninghamia lanceolata var. dugan.) has been isolated in our laboratory. We chose the cDNA-AFLP technique [...] Read more.
Identification of genes controlling shoot branching is crucial for improving plant architecture and increasing crop yield or biomass. A branching mutant of Chinese fir named “Dugansha” (Cunninghamia lanceolata var. dugan.) has been isolated in our laboratory. We chose the cDNA-AFLP technique and an effective strategy to screen genes that potentially regulate shoot branching in Chinese fir using this mutant. An RNase III-like1 cDNA fragment named ClRTL1 was identified as a potential positive regulator. To investigate the function of ClRTL1 in regulating shoot branching, we cloned the full-length cDNA sequence from C. lanceolata (Lamb.) Hook, deduced its secondary structure and function, and overexpressed the coding sequence in Arabidopsis. The ClRTL1 cDNA is 1045 bp and comprises an open reading frame of 705 bp. It encodes a protein of 235 amino acids. The deduced secondary structure of the ClRTL1 indicates that it is a mini-RNase III-like protein. The expression analysis and phenotypes of 35S: ClRTL1 in A. thaliana implies that ClRTL1 plays a role in promoting shoot branching in Chinese fir. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
De Novo Sequencing and Analysis of the Safflower Transcriptome to Discover Putative Genes Associated with Safflor Yellow in Carthamus tinctorius L.
by Xiuming Liu, Yuanyuan Dong, Na Yao, Yu Zhang, Nan Wang, Xiyan Cui, Xiaowei Li, Yanfang Wang, Fawei Wang, Jing Yang, Lili Guan, Linna Du, Haiyan Li and Xiaokun Li
Int. J. Mol. Sci. 2015, 16(10), 25657-25677; https://doi.org/10.3390/ijms161025657 - 26 Oct 2015
Cited by 25 | Viewed by 7533
Abstract
Safflower (Carthamus tinctorius L.), an important traditional Chinese medicine, is cultured widely for its pharmacological effects, but little is known regarding the genes related to the metabolic regulation of the safflower’s yellow pigment. To investigate genes related to safflor yellow biosynthesis, 454 [...] Read more.
Safflower (Carthamus tinctorius L.), an important traditional Chinese medicine, is cultured widely for its pharmacological effects, but little is known regarding the genes related to the metabolic regulation of the safflower’s yellow pigment. To investigate genes related to safflor yellow biosynthesis, 454 pyrosequencing of flower RNA at different developmental stages was performed, generating large databases.In this study, we analyzed 454 sequencing data from different flowering stages in safflower. In total, 1,151,324 raw reads and 1,140,594 clean reads were produced, which were assembled into 51,591 unigenes with an average length of 679 bp and a maximum length of 5109 bp. Among the unigenes, 40,139 were in the early group, 39,768 were obtained from the full group and 28,316 were detected in both samples. With the threshold of “log2 ratio ≥ 1”, there were 34,464 differentially expressed genes, of which 18,043 were up-regulated and 16,421 were down-regulated in the early flower library. Based on the annotations of the unigenes, 281 pathways were predicted. We selected 12 putative genes and analyzed their expression levels using quantitative real time-PCR. The results were consistent with the 454 sequencing results. In addition, the expression of chalcone synthase, chalcone isomerase and anthocyanidin synthase, which are involved in safflor yellow biosynthesis and safflower yellow pigment (SYP) content, were analyzed in different flowering periods, indicating that their expression levels were related to SYP synthesis. Moreover, to further confirm the results of the 454 pyrosequencing, full-length cDNA of chalcone isomerase (CHI) and anthocyanidin synthase (ANS) were cloned from safflower petal by RACE (Rapid-amplification of cDNA ends) method according to fragment of the transcriptome. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Molecular Cloning and Characterization of DXS and DXR Genes in the Terpenoid Biosynthetic Pathway of Tripterygium wilfordii
by Yuru Tong, Ping Su, Yujun Zhao, Meng Zhang, Xiujuan Wang, Yujia Liu, Xianan Zhang, Wei Gao and Luqi Huang
Int. J. Mol. Sci. 2015, 16(10), 25516-25535; https://doi.org/10.3390/ijms161025516 - 23 Oct 2015
Cited by 57 | Viewed by 7815
Abstract
1-Deoxy-d-xylulose-5-phosphate synthase (DXS) and 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) genes are the key enzyme genes of terpenoid biosynthesis but still unknown in Tripterygium wilfordii Hook. f. Here, three full-length cDNA encoding DXS1, DXS2 and DXR were cloned from suspension cells of T. wilfordii with ORF [...] Read more.
1-Deoxy-d-xylulose-5-phosphate synthase (DXS) and 1-deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) genes are the key enzyme genes of terpenoid biosynthesis but still unknown in Tripterygium wilfordii Hook. f. Here, three full-length cDNA encoding DXS1, DXS2 and DXR were cloned from suspension cells of T. wilfordii with ORF sizes of 2154 bp (TwDXS1, GenBank accession no.KM879187), 2148 bp (TwDXS2, GenBank accession no.KM879186), 1410 bp (TwDXR, GenBank accession no.KM879185). And, the TwDXS1, TwDXS2 and TwDXR were characterized by color complementation in lycopene accumulating strains of Escherichia coli, which indicated that they encoded functional proteins and promoted lycopene pathway flux. TwDXS1 and TwDXS2 are constitutively expressed in the roots, stems and leaves and the expression level showed an order of roots > stems > leaves. After the suspension cells were induced by methyl jasmonate, the mRNA expression level of TwDXS1, TwDXS2, and TwDXR increased, and triptophenolide was rapidly accumulated to 149.52 µg·g−1, a 5.88-fold increase compared with the control. So the TwDXS1, TwDXS2, and TwDXR could be important genes involved in terpenoid biosynthesis in Tripterygium wilfordii Hook. f. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
Increased Uptake of Chelated Copper Ions by Lolium perenne Attributed to Amplified Membrane and Endodermal Damage
by Anthea Johnson and Naresh Singhal
Int. J. Mol. Sci. 2015, 16(10), 25264-25284; https://doi.org/10.3390/ijms161025264 - 23 Oct 2015
Cited by 6 | Viewed by 6318
Abstract
The contributions of mechanisms by which chelators influence metal translocation to plant shoot tissues are analyzed using a combination of numerical modelling and physical experiments. The model distinguishes between apoplastic and symplastic pathways of water and solute movement. It also includes the barrier [...] Read more.
The contributions of mechanisms by which chelators influence metal translocation to plant shoot tissues are analyzed using a combination of numerical modelling and physical experiments. The model distinguishes between apoplastic and symplastic pathways of water and solute movement. It also includes the barrier effects of the endodermis and plasma membrane. Simulations are used to assess transport pathways for free and chelated metals, identifying mechanisms involved in chelate-enhanced phytoextraction. Hypothesized transport mechanisms and parameters specific to amendment treatments are estimated, with simulated results compared to experimental data. Parameter values for each amendment treatment are estimated based on literature and experimental values, and used for model calibration and simulation of amendment influences on solute transport pathways and mechanisms. Modeling indicates that chelation alters the pathways for Cu transport. For free ions, Cu transport to leaf tissue can be described using purely apoplastic or transcellular pathways. For strong chelators (ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA)), transport by the purely apoplastic pathway is insufficient to represent measured Cu transport to leaf tissue. Consistent with experimental observations, increased membrane permeability is required for simulating translocation in EDTA and DTPA treatments. Increasing the membrane permeability is key to enhancing phytoextraction efficiency. Full article
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Article
Stress Sensitivity Is Associated with Differential Accumulation of Reactive Oxygen and Nitrogen Species in Maize Genotypes with Contrasting Levels of Drought Tolerance
by Liming Yang, Jake C. Fountain, Hui Wang, Xinzhi Ni, Pingsheng Ji, Robert D. Lee, Robert C. Kemerait, Brian T. Scully and Baozhu Guo
Int. J. Mol. Sci. 2015, 16(10), 24791-24819; https://doi.org/10.3390/ijms161024791 - 19 Oct 2015
Cited by 38 | Viewed by 7413
Abstract
Drought stress decreases crop growth, yield, and can further exacerbate pre-harvest aflatoxin contamination. Tolerance and adaptation to drought stress is an important trait of agricultural crops like maize. However, maize genotypes with contrasting drought tolerances have been shown to possess both common and [...] Read more.
Drought stress decreases crop growth, yield, and can further exacerbate pre-harvest aflatoxin contamination. Tolerance and adaptation to drought stress is an important trait of agricultural crops like maize. However, maize genotypes with contrasting drought tolerances have been shown to possess both common and genotype-specific adaptations to cope with drought stress. In this research, the physiological and metabolic response patterns in the leaves of maize seedlings subjected to drought stress were investigated using six maize genotypes including: A638, B73, Grace-E5, Lo964, Lo1016, and Va35. During drought treatments, drought-sensitive maize seedlings displayed more severe symptoms such as chlorosis and wilting, exhibited significant decreases in photosynthetic parameters, and accumulated significantly more reactive oxygen species (ROS) and reactive nitrogen species (RNS) than tolerant genotypes. Sensitive genotypes also showed rapid increases in enzyme activities involved in ROS and RNS metabolism. However, the measured antioxidant enzyme activities were higher in the tolerant genotypes than in the sensitive genotypes in which increased rapidly following drought stress. The results suggest that drought stress causes differential responses to oxidative and nitrosative stress in maize genotypes with tolerant genotypes with slower reaction and less ROS and RNS production than sensitive ones. These differential patterns may be utilized as potential biological markers for use in marker assisted breeding. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
Metabolic and Physiological Responses of Shiraz and Cabernet Sauvignon (Vitis vinifera L.) to Near Optimal Temperatures of 25 and 35 °C
by Uri Hochberg, Albert Batushansky, Asfaw Degu, Shimon Rachmilevitch and Aaron Fait
Int. J. Mol. Sci. 2015, 16(10), 24276-24294; https://doi.org/10.3390/ijms161024276 - 14 Oct 2015
Cited by 50 | Viewed by 6055
Abstract
Shiraz and Cabernet Sauvignon (Cs) grapevines were grown at near optimal temperatures (25 or 35 °C). Gas exchange, fluorescence, metabolic profiling and correlation based network analysis were used to characterize leaf physiology. When grown at 25 °C, the growth rate and photosynthesis of [...] Read more.
Shiraz and Cabernet Sauvignon (Cs) grapevines were grown at near optimal temperatures (25 or 35 °C). Gas exchange, fluorescence, metabolic profiling and correlation based network analysis were used to characterize leaf physiology. When grown at 25 °C, the growth rate and photosynthesis of both cultivars were similar. At 35 °C Shiraz showed increased respiration, non-photochemical quenching and reductions of photosynthesis and growth. In contrast, Cs maintained relatively stable photosynthetic activity and growth regardless of the condition. In both cultivars, growth at 35 °C resulted in accumulations of secondary sugars (raffinose, fucose and ribulose) and reduction of primary sugars concentration (glucose, fructose and sucrose), more noticeably in Shiraz than Cs. In spite of similar patterns of metabolic changes in response to growth at 35 °C, significant differences in important leaf antioxidants and antioxidant precursors (DHA/ascorbate, quinates, cathechins) characterized the cultivar response. Correlation analysis reinforced Shiraz sensitivity to the 35 °C, showing higher number of newly formed edges at 35 °C and higher modularity in Shiraz as compared to Cs. The results suggest that the optimal growth temperatures of grapevines are cultivar dependent, and allow a first insight into the variability of the metabolic responses of grapevines under varied temperatures. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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Article
Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response
by Qianqian Wang, Jinyang Liu, Yu Wang, Yang Zhao, Haiyang Jiang and Beijiu Cheng
Int. J. Mol. Sci. 2015, 16(10), 23517-23544; https://doi.org/10.3390/ijms161023517 - 30 Sep 2015
Cited by 34 | Viewed by 7049
Abstract
Plant homeodomain (PHD)-finger proteins were found universally in eukaryotes and known as key players in regulating transcription and chromatin structure. Many PHD-finger proteins have been well studied on structure and function in animals. Whereas, only a few of plant PHD-finger factors had been [...] Read more.
Plant homeodomain (PHD)-finger proteins were found universally in eukaryotes and known as key players in regulating transcription and chromatin structure. Many PHD-finger proteins have been well studied on structure and function in animals. Whereas, only a few of plant PHD-finger factors had been characterized, and majority of PHD-finger proteins were functionally unclear. In this study, a complete comprehensive analysis of maize PHD family is presented. Sixty-seven PHD-finger genes in maize were identified and further divided into ten groups according to phylogenetic analysis that was supported by motif and intron/exon analysis. These genes were unevenly distributed on ten chromosomes and contained 12 segmental duplication events, suggesting that segmental duplications were the major contributors in expansion of the maize PHD family. The paralogous genes mainly experienced purifying selection with restrictive functional divergence after the duplication events on the basis of the Ka/Ks ratio. Gene digital expression analysis showed that the PHD family had a wide expression profile in maize development. In addition, 15 potential stress response genes were detected by promoter cis-element and expression analysis. Two proteins ZmPHD14 and ZmPHD19 were located in the nucleus. These results provided a solid base for future functional genome study of the PHD-finger family in maize and afforded important clues for characterizing and cloning potentially important candidates in response to abiotic stresses. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Exogenous GA3 Application Enhances Xylem Development and Induces the Expression of Secondary Wall Biosynthesis Related Genes in Betula platyphylla
by Huiyan Guo, Yucheng Wang, Huizi Liu, Ping Hu, Yuanyuan Jia, Chunrui Zhang, Yanmin Wang, Shan Gu, Chuanping Yang and Chao Wang
Int. J. Mol. Sci. 2015, 16(9), 22960-22975; https://doi.org/10.3390/ijms160922960 - 23 Sep 2015
Cited by 35 | Viewed by 6612
Abstract
Gibberellin (GA) is a key signal molecule inducing differentiation of tracheary elements, fibers, and xylogenesis. However the molecular mechanisms underlying the effect of GA on xylem elongation and secondary wall development in tree species remain to be determined. In this study, Betula platyphylla [...] Read more.
Gibberellin (GA) is a key signal molecule inducing differentiation of tracheary elements, fibers, and xylogenesis. However the molecular mechanisms underlying the effect of GA on xylem elongation and secondary wall development in tree species remain to be determined. In this study, Betula platyphylla (birch) seeds were treated with 300 ppm GA3 and/or 300 ppm paclobutrazol (PAC), seed germination was recorded, and transverse sections of hypocotyls were stained with toluidine blue; the two-month-old seedlings were treated with 50 μM GA3 and/or 50 μM PAC, transverse sections of seedling stems were stained using phloroglucinol–HCl, and secondary wall biosynthesis related genes expression was analyzed by real-time quantitative PCR. Results indicated that germination percentage, energy and time of seeds, hypocotyl height and seedling fresh weight were enhanced by GA3, and reduced by PAC; the xylem development was wider in GA3-treated plants than in the control; the expression of NAC and MYB transcription factors, CESA, PAL, and GA oxidase was up-regulated during GA3 treatment, suggesting their role in GA3-induced xylem development in the birch. Our results suggest that GA3 induces the expression of secondary wall biosynthesis related genes to trigger xylogenesis in the birch plants. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
Phenotypic and Transcriptomic Analyses of Autotetraploid and Diploid Mulberry (Morus alba L.)
by Fanwei Dai, Zhenjiang Wang, Guoqing Luo and Cuiming Tang
Int. J. Mol. Sci. 2015, 16(9), 22938-22956; https://doi.org/10.3390/ijms160922938 - 22 Sep 2015
Cited by 49 | Viewed by 7188
Abstract
Autopolyploid plants and their organs are often larger than their diploid counterparts, which makes them attractive to plant breeders. Mulberry (Morus alba L.) is an important commercial woody plant in many tropical and subtropical areas. In this study, we obtained a series [...] Read more.
Autopolyploid plants and their organs are often larger than their diploid counterparts, which makes them attractive to plant breeders. Mulberry (Morus alba L.) is an important commercial woody plant in many tropical and subtropical areas. In this study, we obtained a series of autotetraploid mulberry plants resulting from a colchicine treatment. To evaluate the effects of genome duplications in mulberry, we compared the phenotypes and transcriptomes of autotetraploid and diploid mulberry trees. In the autotetraploids, the height, breast-height diameter, leaf size, and fruit size were larger than those of diploids. Transcriptome data revealed that of 21,229 expressed genes only 609 (2.87%) were differentially expressed between diploids and autotetraploids. Among them, 30 genes were associated with the biosynthesis and signal transduction of plant hormones, including cytokinin, gibberellins, ethylene, and auxin. In addition, 41 differentially expressed genes were involved in photosynthesis. These results enhance our understanding of the variations that occur in mulberry autotetraploids and will benefit future breeding work. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Structure Conservation and Differential Expression of Farnesyl Diphosphate Synthase Genes in Euphorbiaceous Plants
by Dong Guo, Hui-Liang Li and Shi-Qing Peng
Int. J. Mol. Sci. 2015, 16(9), 22402-22414; https://doi.org/10.3390/ijms160922402 - 15 Sep 2015
Cited by 10 | Viewed by 4847
Abstract
Farnesyl diphosphate synthase (FPS) is a key enzyme of isoprenoids biosynthesis. However, knowledge of the FPSs of euphorbiaceous species is limited. In this study, ten FPSs were identified in four euphorbiaceous plants. These FPSs exhibited similar exon/intron structure. The deduced FPS proteins [...] Read more.
Farnesyl diphosphate synthase (FPS) is a key enzyme of isoprenoids biosynthesis. However, knowledge of the FPSs of euphorbiaceous species is limited. In this study, ten FPSs were identified in four euphorbiaceous plants. These FPSs exhibited similar exon/intron structure. The deduced FPS proteins showed close identities and exhibited the typical structure of plant FPS. The members of the FPS family exhibit tissue expression patterns that vary among several euphorbiaceous plant species under normal growth conditions. The expression profiles reveal spatial and temporal variations in the expression of FPSs of different tissues from Euphorbiaceous plants. Our results revealed wide conservation of FPSs and diverse expression in euphorbiaceous plants during growth and development. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae
by Monika Szczecińska and Jakub Sawicki
Int. J. Mol. Sci. 2015, 16(9), 22258-22279; https://doi.org/10.3390/ijms160922258 - 15 Sep 2015
Cited by 26 | Viewed by 6822
Abstract
Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the [...] Read more.
Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. Conclusions/significance: The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Molecular Identification of Dendrobium Species (Orchidaceae) Based on the DNA Barcode ITS2 Region and Its Application for Phylogenetic Study
by Shangguo Feng, Yan Jiang, Shang Wang, Mengying Jiang, Zhe Chen, Qicai Ying and Huizhong Wang
Int. J. Mol. Sci. 2015, 16(9), 21975-21988; https://doi.org/10.3390/ijms160921975 - 11 Sep 2015
Cited by 52 | Viewed by 7740
Abstract
The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In [...] Read more.
The over-collection and habitat destruction of natural Dendrobium populations for their commercial medicinal value has led to these plants being under severe threat of extinction. In addition, many Dendrobium plants are similarly shaped and easily confused during the absence of flowering stages. In the present study, we examined the application of the ITS2 region in barcoding and phylogenetic analyses of Dendrobium species (Orchidaceae). For barcoding, ITS2 regions of 43 samples in Dendrobium were amplified. In combination with sequences from GenBank, the sequences were aligned using Clustal W and genetic distances were computed using MEGA V5.1. The success rate of PCR amplification and sequencing was 100%. There was a significant divergence between the inter- and intra-specific genetic distances of ITS2 regions, while the presence of a barcoding gap was obvious. Based on the BLAST1, nearest distance and TaxonGAP methods, our results showed that the ITS2 regions could successfully identify the species of most Dendrobium samples examined; Second, we used ITS2 as a DNA marker to infer phylogenetic relationships of 64 Dendrobium species. The results showed that cluster analysis using the ITS2 region mainly supported the relationship between the species of Dendrobium established by traditional morphological methods and many previous molecular analyses. To sum up, the ITS2 region can not only be used as an efficient barcode to identify Dendrobium species, but also has the potential to contribute to the phylogenetic analysis of the genus Dendrobium. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Metabolite Profiling of Diverse Rice Germplasm and Identification of Conserved Metabolic Markers of Rice Roots in Response to Long-Term Mild Salinity Stress
by Myung Hee Nam, Eunjung Bang, Taek Yun Kwon, Yuran Kim, Eun Hee Kim, Kyungwon Cho, Woong June Park, Beom-Gi Kim and In Sun Yoon
Int. J. Mol. Sci. 2015, 16(9), 21959-21974; https://doi.org/10.3390/ijms160921959 - 11 Sep 2015
Cited by 71 | Viewed by 6628
Abstract
The sensitivity of rice to salt stress greatly depends on growth stages, organ types and cultivars. Especially, the roots of young rice seedlings are highly salt-sensitive organs that limit plant growth, even under mild soil salinity conditions. In an attempt to identify metabolic [...] Read more.
The sensitivity of rice to salt stress greatly depends on growth stages, organ types and cultivars. Especially, the roots of young rice seedlings are highly salt-sensitive organs that limit plant growth, even under mild soil salinity conditions. In an attempt to identify metabolic markers of rice roots responding to salt stress, metabolite profiling was performed by 1H-NMR spectroscopy in 38 rice genotypes that varied in biomass accumulation under long-term mild salinity condition. Multivariate statistical analysis showed separation of the control and salt-treated rice roots and rice genotypes with differential growth potential. By quantitative analyses of 1H-NMR data, five conserved salt-responsive metabolic markers of rice roots were identified. Sucrose, allantoin and glutamate accumulated by salt stress, whereas the levels of glutamine and alanine decreased. A positive correlation of metabolite changes with growth potential and salt tolerance of rice genotypes was observed for allantoin and glutamine. Adjustment of nitrogen metabolism in rice roots is likely to be closely related to maintain the growth potential and increase the stress tolerance of rice. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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Article
Can Clethra barbinervis Distinguish Nickel and Cobalt in Uptake and Translocation?
by Tsuyoshi Yamaguchi, Rie Tomioka and Chisato Takenaka
Int. J. Mol. Sci. 2015, 16(9), 21378-21391; https://doi.org/10.3390/ijms160921378 - 07 Sep 2015
Cited by 6 | Viewed by 7857
Abstract
Clethra barbinervis Sieb. et Zucc. accumulates Nickel (Ni) and Cobalt (Co) at high concentrations., We hypothesized that C. barbinervis cannot distinguish between Ni and Co because of the similar chemical properties of these two elements. To confirm this hypothesis and understand the [...] Read more.
Clethra barbinervis Sieb. et Zucc. accumulates Nickel (Ni) and Cobalt (Co) at high concentrations., We hypothesized that C. barbinervis cannot distinguish between Ni and Co because of the similar chemical properties of these two elements. To confirm this hypothesis and understand the role of these elements in C. barbinervis, we conducted a hydroponic split-root experiment using Ni and Co solutions. We found that the bioconcentration factor (BCF; metal concentration of each tissue/metal concentrations of each treatment solution) of Ni and Co did not significantly differ in the roots, but the BCF for Co was higher than that for Ni in the leaves. The leaves of C. barbinervis accumulated Ni or Co at high concentrations. We also found the simultaneous accumulation of Ni and Co by the multiple heavy metal treatments (Ni and Co) at high concentrations similar to those for the single treatments (Ni or Co). Elevated sulfur concentrations occurred in the roots and leaves of Co-treated seedlings but not in Ni. This result indicates that S was related to Co accumulation in the leaves. These results suggest that C. barbinervis distinguishes between Ni and Co during transport and accumulation in the leaves but not during root uptake. Full article
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Article
A Novel Sucrose-Regulatory MADS-Box Transcription Factor GmNMHC5 Promotes Root Development and Nodulation in Soybean (Glycine max [L.] Merr.)
by Wei Liu, Xiangdong Han, Ge Zhan, Zhenfang Zhao, Yongjun Feng and Cunxiang Wu
Int. J. Mol. Sci. 2015, 16(9), 20657-20673; https://doi.org/10.3390/ijms160920657 - 31 Aug 2015
Cited by 27 | Viewed by 6029
Abstract
The MADS-box protein family includes many transcription factors that have a conserved DNA-binding MADS-box domain. The proteins in this family were originally recognized to play prominent roles in floral development. Recent findings, especially with regard to the regulatory roles of the AGL17 subfamily [...] Read more.
The MADS-box protein family includes many transcription factors that have a conserved DNA-binding MADS-box domain. The proteins in this family were originally recognized to play prominent roles in floral development. Recent findings, especially with regard to the regulatory roles of the AGL17 subfamily in root development, have greatly broadened their known functions. In this study, a gene from soybean (Glycine max [L.] Merr.), GmNMHC5, was cloned from the Zigongdongdou cultivar and identified as a member of the AGL17 subfamily. Real-time fluorescence quantitative PCR analysis showed that GmNMHC5 was expressed at much higher levels in roots and nodules than in other organs. The activation of expression was first examined in leaves and roots, followed by shoot apexes. GmNMHC5 expression levels rose sharply when the plants were treated under short-day conditions (SD) and started to pod, whereas low levels were maintained in non-podding plants under long-day conditions (LD). Furthermore, overexpression of GmNMHC5 in transgenic soybean significantly promoted lateral root development and nodule building. Moreover, GmNMHC5 is upregulated by exogenous sucrose. These results indicate that GmNMHC5 can sense the sucrose signal and plays significant roles in lateral root development and nodule building. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Evaluation of Appropriate Reference Genes for Reverse Transcription-Quantitative PCR Studies in Different Tissues of a Desert Poplar via Comparision of Different Algorithms
by Hou-Ling Wang, Lan Li, Sha Tang, Chao Yuan, Qianqian Tian, Yanyan Su, Hui-Guang Li, Lin Zhao, Weilun Yin, Rui Zhao and Xinli Xia
Int. J. Mol. Sci. 2015, 16(9), 20468-20491; https://doi.org/10.3390/ijms160920468 - 28 Aug 2015
Cited by 30 | Viewed by 6452
Abstract
Despite the unshakable status of reverse transcription-quantitative PCR in gene expression analysis, it has certain disadvantages, including that the results are highly dependent on the reference genes selected for data normalization. Since inappropriate endogenous control genes will lead to inaccurate target gene expression [...] Read more.
Despite the unshakable status of reverse transcription-quantitative PCR in gene expression analysis, it has certain disadvantages, including that the results are highly dependent on the reference genes selected for data normalization. Since inappropriate endogenous control genes will lead to inaccurate target gene expression profiles, the validation of suitable internal reference genes is essential. Given the increasing interest in functional genes and genomics of Populus euphratica, a desert poplar showing extraordinary adaptation to salt stress, we evaluated the expression stability of ten candidate reference genes in P. euphratica roots, stems, and leaves under salt stress conditions. We used five algorithms, namely, ΔCt, NormFinder, geNorm, GrayNorm, and a rank aggregation method (RankAggreg) to identify suitable normalizers. To support the suitability of the identified reference genes and to compare the relative merits of these different algorithms, we analyzed and compared the relative expression levels of nine P. euphratica functional genes in different tissues. Our results indicate that a combination of multiple reference genes recommended by GrayNorm algorithm (e.g., a combination of Actin, EF1α, GAPDH, RP, UBQ in root) should be used instead of a single reference gene. These results are valuable for research of gene identification in different P. euphratica tissues. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Rapid Bioassay-Guided Isolation of Antibacterial Clerodane Type Diterpenoid from Dodonaea viscosa (L.) Jaeq.
by Muhammad Khurram, Linda A. Lawton, Christine Edwards, Marcello Iriti, Abdul Hameed, Murad A. Khan, Farman A. Khan and Shafiq Ur Rahman
Int. J. Mol. Sci. 2015, 16(9), 20290-20307; https://doi.org/10.3390/ijms160920290 - 27 Aug 2015
Cited by 10 | Viewed by 7084
Abstract
Plant extracts are complex matrices and, although crude extracts are widely in use, purified compounds are pivotal in drug discovery. This study describes the application of automated preparative-HPLC combined with a rapid off-line bacterial bioassay, using reduction of a tetrazolium salt as an [...] Read more.
Plant extracts are complex matrices and, although crude extracts are widely in use, purified compounds are pivotal in drug discovery. This study describes the application of automated preparative-HPLC combined with a rapid off-line bacterial bioassay, using reduction of a tetrazolium salt as an indicator of bacterial metabolism. This approach enabled the identification of fractions from Dodonaea viscosa that were active against Staphylococcus aureus and Escherichia coli, which, ultimately, resulted in the identification of a clerodane type diterpenoid, 6β-hydroxy-15,16-epoxy-5β, 8β, 9β, 10α-cleroda-3, 13(16), 14-trien-18-oic acid, showing bacteriostatic activity (minimum inhibitory concentration (MIC) = 64–128 µg/mL) against test bacteria. To the best of our knowledge, this is the first report on antibacterial activity of this metabolite from D. viscosa. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
Genome-Wide Identification and Expression Analyses of Aquaporin Gene Family during Development and Abiotic Stress in Banana
by Wei Hu, Xiaowan Hou, Chao Huang, Yan Yan, Weiwei Tie, Zehong Ding, Yunxie Wei, Juhua Liu, Hongxia Miao, Zhiwei Lu, Meiying Li, Biyu Xu and Zhiqiang Jin
Int. J. Mol. Sci. 2015, 16(8), 19728-19751; https://doi.org/10.3390/ijms160819728 - 20 Aug 2015
Cited by 58 | Viewed by 8585
Abstract
Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana [...] Read more.
Aquaporins (AQPs) function to selectively control the flow of water and other small molecules through biological membranes, playing crucial roles in various biological processes. However, little information is available on the AQP gene family in bananas. In this study, we identified 47 banana AQP genes based on the banana genome sequence. Evolutionary analysis of AQPs from banana, Arabidopsis, poplar, and rice indicated that banana AQPs (MaAQPs) were clustered into four subfamilies. Conserved motif analysis showed that all banana AQPs contained the typical AQP-like or major intrinsic protein (MIP) domain. Gene structure analysis suggested the majority of MaAQPs had two to four introns with a highly specific number and length for each subfamily. Expression analysis of MaAQP genes during fruit development and postharvest ripening showed that some MaAQP genes exhibited high expression levels during these stages, indicating the involvement of MaAQP genes in banana fruit development and ripening. Additionally, some MaAQP genes showed strong induction after stress treatment and therefore, may represent potential candidates for improving banana resistance to abiotic stress. Taken together, this study identified some excellent tissue-specific, fruit development- and ripening-dependent, and abiotic stress-responsive candidate MaAQP genes, which could lay a solid foundation for genetic improvement of banana cultivars. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Overexpressing Ferredoxins in Chlamydomonas reinhardtii Increase Starch and Oil Yields and Enhance Electric Power Production in a Photo Microbial Fuel Cell
by Li-Fen Huang, Ji-Yu Lin, Kui-You Pan, Chun-Kai Huang and Ying-Kai Chu
Int. J. Mol. Sci. 2015, 16(8), 19308-19325; https://doi.org/10.3390/ijms160819308 - 14 Aug 2015
Cited by 25 | Viewed by 6869
Abstract
Ferredoxins (FDX) are final electron carrier proteins in the plant photosynthetic pathway, and function as major electron donors in diverse redox-driven metabolic pathways. We previously showed that overexpression of a major constitutively expressed ferredoxin gene PETF in Chlamydomonas decreased the reactive oxygen species [...] Read more.
Ferredoxins (FDX) are final electron carrier proteins in the plant photosynthetic pathway, and function as major electron donors in diverse redox-driven metabolic pathways. We previously showed that overexpression of a major constitutively expressed ferredoxin gene PETF in Chlamydomonas decreased the reactive oxygen species (ROS) level and enhanced tolerance to heat stress. In addition to PETF, an endogenous anaerobic induced FDX5 was overexpressed in transgenic Chlamydomonas lines here to address the possible functions of FDX5. All the independent FDX transgenic lines showed decreased cellular ROS levels and enhanced tolerance to heat and salt stresses. The transgenic Chlamydomonas lines accumulated more starch than the wild-type line and this effect increased almost three-fold in conditions of nitrogen depletion. Furthermore, the lipid content was higher in the transgenic lines than in the wild-type line, both with and without nitrogen depletion. Two FDX-overexpressing Chlamydomonas lines were assessed in a photo microbial fuel cell (PMFC); power density production by the transgenic lines was higher than that of the wild-type cells. These findings suggest that overexpression of either PETF or FDX5 can confer tolerance against heat and salt stresses, increase starch and oil production, and raise electric power density in a PMFC. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Comparative Analysis of the Brassica napus Root and Leaf Transcript Profiling in Response to Drought Stress
by Chunqing Liu, Xuekun Zhang, Ka Zhang, Hong An, Kaining Hu, Jing Wen, Jinxiong Shen, Chaozhi Ma, Bin Yi, Jinxing Tu and Tingdong Fu
Int. J. Mol. Sci. 2015, 16(8), 18752-18777; https://doi.org/10.3390/ijms160818752 - 11 Aug 2015
Cited by 40 | Viewed by 10128
Abstract
Drought stress is one of the major abiotic factors affecting Brassica napus (B. napus) productivity. In order to identify genes of potential importance to drought stress and obtain a deeper understanding of the molecular mechanisms regarding the responses of B. napus [...] Read more.
Drought stress is one of the major abiotic factors affecting Brassica napus (B. napus) productivity. In order to identify genes of potential importance to drought stress and obtain a deeper understanding of the molecular mechanisms regarding the responses of B. napus to dehydration stress, we performed large-scale transcriptome sequencing of B. napus plants under dehydration stress using the Illumina sequencing technology. In this work, a relatively drought tolerant B. napus line, Q2, identified in our previous study, was used. Four cDNA libraries constructed from mRNAs of control and dehydration-treated root and leaf were sequenced by Illumina technology. A total of 6018 and 5377 differentially expressed genes (DEGs) were identified in root and leaf. In addition, 1745 genes exhibited a coordinated expression profile between the two tissues under drought stress, 1289 (approximately 74%) of which showed an inverse relationship, demonstrating different regulation patterns between the root and leaf. The gene ontology (GO) enrichment test indicated that up-regulated genes in root were mostly involved in “stimulus” “stress” biological process, and activated genes in leaf mainly functioned in “cell” “cell part” components. Furthermore, a comparative network related to plant hormone signal transduction and AREB/ABF, AP2/EREBP, NAC, WRKY and MYC/MYB transcription factors (TFs) provided a view of different stress tolerance mechanisms between root and leaf. Some of the DEGs identified may be candidates for future research aimed at detecting drought-responsive genes and will be useful for understanding the molecular mechanisms of drought tolerance in root and leaf of B. napus. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Comparison of Soybean Transformation Efficiency and Plant Factors Affecting Transformation during the Agrobacterium Infection Process
by Yuying Jia, Xingdong Yao, Mingzhe Zhao, Qiang Zhao, Yanli Du, Cuimei Yu and Futi Xie
Int. J. Mol. Sci. 2015, 16(8), 18522-18543; https://doi.org/10.3390/ijms160818522 - 07 Aug 2015
Cited by 23 | Viewed by 8656
Abstract
The susceptibility of soybean genotype to Agrobacterium infection is a key factor for the high level of genetic transformation efficiency. The objective of this study is to evaluate the plant factors related to transformation in cotyledonary nodes during the Agrobacterium infection process. This [...] Read more.
The susceptibility of soybean genotype to Agrobacterium infection is a key factor for the high level of genetic transformation efficiency. The objective of this study is to evaluate the plant factors related to transformation in cotyledonary nodes during the Agrobacterium infection process. This study selected three genotypes (Williams 82, Shennong 9 and Bert) with high transformation efficiency, which presented better susceptibility to Agrobacterium infection, and three low transformation efficiency genotypes (General, Liaodou 16 and Kottman), which showed a relatively weak susceptibility. Gibberellin (GA) levels and soybean GA20ox2 and CYP707A2 transcripts of high-efficiency genotypes increased and were higher than those of low-efficiency genotypes; however, the opposite performance was shown in abscisic acid (ABA). Higher zeatin riboside (ZR) content and DNA quantity, and relatively higher expression of soybean IPT5, CYCD3 and CYCA3 were obtained in high-efficiency genotypes. High-efficiency genotypes had low methyl jasmonate (MeJA) content, polyphenol oxidase (PPO) and peroxidase (POD) activity, and relatively lower expression of soybean OPR3, PPO1 and PRX71. GA and ZR were positive plant factors for Agrobacterium-mediated soybean transformation by facilitating germination and growth, and increasing the number of cells in DNA synthesis cycle, respectively; MeJA, PPO, POD and ABA were negative plant factors by inducing defence reactions and repressing germination and growth, respectively. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Involvement of Ethylene in the Latex Metabolism and Tapping Panel Dryness of Hevea brasiliensis
by Riza-Arief Putranto, Eva Herlinawati, Maryannick Rio, Julie Leclercq, Piyanuch Piyatrakul, Eric Gohet, Christine Sanier, Fetrina Oktavia, Julien Pirrello, Kuswanhadi and Pascal Montoro
Int. J. Mol. Sci. 2015, 16(8), 17885-17908; https://doi.org/10.3390/ijms160817885 - 04 Aug 2015
Cited by 43 | Viewed by 10110
Abstract
Ethephon, an ethylene releaser, is used to stimulate latex production in Hevea brasiliensis. Ethylene induces many functions in latex cells including the production of reactive oxygen species (ROS). The accumulation of ROS is responsible for the coagulation of rubber particles in latex [...] Read more.
Ethephon, an ethylene releaser, is used to stimulate latex production in Hevea brasiliensis. Ethylene induces many functions in latex cells including the production of reactive oxygen species (ROS). The accumulation of ROS is responsible for the coagulation of rubber particles in latex cells, resulting in the partial or complete stoppage of latex flow. This study set out to assess biochemical and histological changes as well as changes in gene expression in latex and phloem tissues from trees grown under various harvesting systems. The Tapping Panel Dryness (TPD) susceptibility of Hevea clones was found to be related to some biochemical parameters, such as low sucrose and high inorganic phosphorus contents. A high tapping frequency and ethephon stimulation induced early TPD occurrence in a high latex metabolism clone and late occurrence in a low latex metabolism clone. TPD-affected trees had smaller number of laticifer vessels compared to healthy trees, suggesting a modification of cambial activity. The differential transcript abundance was observed for twenty-seven candidate genes related to TPD occurrence in latex and phloem tissues for ROS-scavenging, ethylene biosynthesis and signalling genes. The predicted function for some Ethylene Response Factor genes suggested that these candidate genes should play an important role in regulating susceptibility to TPD. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Composition, Cytotoxic and Antimicrobial Activities of Satureja intermedia C.A.Mey Essential Oil
by Javad Sharifi-Rad, Mehdi Sharifi-Rad, Seyedeh Mahsan Hoseini-Alfatemi, Marcello Iriti, Majid Sharifi-Rad and Marzieh Sharifi-Rad
Int. J. Mol. Sci. 2015, 16(8), 17812-17825; https://doi.org/10.3390/ijms160817812 - 03 Aug 2015
Cited by 54 | Viewed by 6583
Abstract
In this study, the essential oil (EO) constituents from the aerial parts of Satureja intermedia C.A.Mey were detected by GC and GC/MS. The antimicrobial activity of EO on oral pathogens and its cytotoxicity to human cancer cells were determined by the microbroth dilution [...] Read more.
In this study, the essential oil (EO) constituents from the aerial parts of Satureja intermedia C.A.Mey were detected by GC and GC/MS. The antimicrobial activity of EO on oral pathogens and its cytotoxicity to human cancer cells were determined by the microbroth dilution method and the crystal violet staining method, respectively. Thirty-nine compounds were identified and the main EO constituents were γ-terpinene (37.1%), thymol (30.2%), p-cymene (16.2%), limonene (3.9%), α-terpinene (3.3%), myrcene (2.5%), germacrene B (1.4%), elemicine (1.1%) and carvacrol (0.5%). The S. intermedia EO showed a concentration-dependent decrease in viability of Hep-G2 (hepatocellular carcinoma) and MCF-7 (breast adenocarcinoma) human cancer cell lines (p < 0.05). Antimicrobial screening of S. intermedia EO demonstrated slight antibacterial and antifungal activities against Streptococcus mutants, S. salivarius, Enterococcus faecalis, Staphylococcus aureus, Candida albicans and C. glabrata. Further preclinical studies are needed to assess the efficacy and safety of S. intermedia EO as a new promising anticancer agent. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line
by Liyuan Hou, Xiaojun Zhang, Xin Li, Juqing Jia, Huizhen Yang, Haixian Zhan, Linyi Qiao, Huijuan Guo and Zhijian Chang
Int. J. Mol. Sci. 2015, 16(8), 17231-17244; https://doi.org/10.3390/ijms160817231 - 28 Jul 2015
Cited by 7 | Viewed by 5917
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible [...] Read more.
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68–0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Characterization of a Type 1 Metallothionein Gene from the Stresses-Tolerant Plant Ziziphus jujuba
by Mingxia Yang, Fan Zhang, Fan Wang, Zhigang Dong, Qiufen Cao and Mingchang Chen
Int. J. Mol. Sci. 2015, 16(8), 16750-16762; https://doi.org/10.3390/ijms160816750 - 23 Jul 2015
Cited by 40 | Viewed by 6239
Abstract
Plant metallothioneins (MTs) are a family of low molecular weight, cysteine-rich, and metal-binding proteins, which play an important role in the detoxification of heavy metal ions, osmotic stresses, and hormone treatment. Sequence analysis revealed that the open-reading frame (ORF) of ZjMT was 225 [...] Read more.
Plant metallothioneins (MTs) are a family of low molecular weight, cysteine-rich, and metal-binding proteins, which play an important role in the detoxification of heavy metal ions, osmotic stresses, and hormone treatment. Sequence analysis revealed that the open-reading frame (ORF) of ZjMT was 225 bp, which encodes a protein composed of 75 amino acid residues with a calculated molecular mass of 7.376 kDa and a predicated isoelectric point (pI) of 4.83. ZjMT belongs to the type I MT, which consists of two highly conserved cysteine-rich terminal domains linked by a cysteine free region. Our studies showed that ZjMT was primarily localized in the cytoplasm and the nucleus of cells and ZjMT expression was up-regulated by NaCl, CdCl2 and polyethylene glycol (PEG) treatments. Constitutive expression of ZjMT in wild type Arabidopsis plants enhanced their tolerance to NaCl stress during the germination stage. Compared with the wild type, transgenic plants accumulate more Cd2+ in root, but less in leaf, suggesting that ZjMT may have a function in Cd2+ retension in roots and, therefore, decrease the toxicity of Cd2+. Full article
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Article
Differential Antioxidant Responses and Perturbed Porphyrin Biosynthesis after Exposure to Oxyfluorfen and Methyl Viologen in Oryza sativa
by Nhi-Thi Pham, Jin-Gil Kim and Sunyo Jung
Int. J. Mol. Sci. 2015, 16(7), 16529-16544; https://doi.org/10.3390/ijms160716529 - 21 Jul 2015
Cited by 13 | Viewed by 5847
Abstract
We compared antioxidant responses and regulation of porphyrin metabolism in rice plants treated with oxyfluorfen (OF) or methyl viologen (MV). Plants treated with MV exhibited not only greater increases in conductivity and malondialdehyde but also a greater decline in Fv/Fm [...] Read more.
We compared antioxidant responses and regulation of porphyrin metabolism in rice plants treated with oxyfluorfen (OF) or methyl viologen (MV). Plants treated with MV exhibited not only greater increases in conductivity and malondialdehyde but also a greater decline in Fv/Fm, compared to plants treated with OF. MV-treated plants had greater increases in activities of superoxide dismutase (SOD) and catalase (CAT) as well as transcript levels of SODA and CATA than OF-treated plants after 28 h of the treatments, whereas increases in ascorbate peroxidase (APX) activity and transcript levels of APXA and APXB were greater in OF-treated plants. Both OF- and MV-treated plants resulted in not only down-regulation of most genes involved in porphyrin biosynthesis but also disappearance of Mg-porphyrins during the late stage of photooxidative stress. By contrast, up-regulation of heme oxygenase 2 (HO2) is possibly part of an efficient antioxidant response to compensate photooxidative damage in both treatments. Our data show that down-regulated biosynthesis and degradation dynamics of porphyrin intermediates have important roles in photoprotection of plants from perturbed porphyrin biosynthesis and photosynthetic electron transport. This study suggests that porphyrin scavenging as well as strong antioxidative activities are required for mitigating reactive oxygen species (ROS) production under photooxidative stress caused by OF and MV. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Morphogenesis, Flowering, and Gene Expression of Dendranthema grandiflorum in Response to Shift in Light Quality of Night Interruption
by Yoo Gyeong Park, Sowbiya Muneer and Byoung Ryong Jeong
Int. J. Mol. Sci. 2015, 16(7), 16497-16513; https://doi.org/10.3390/ijms160716497 - 21 Jul 2015
Cited by 35 | Viewed by 6893
Abstract
The impact of shifts in the spectral quality of light on morphogenesis, flowering, and photoperiodic gene expression during exposure to light quality of night interruption (NI) was investigated in Dendranthema grandiflorum. The circadian rhythms of plants grown in a closed walk-in growth [...] Read more.
The impact of shifts in the spectral quality of light on morphogenesis, flowering, and photoperiodic gene expression during exposure to light quality of night interruption (NI) was investigated in Dendranthema grandiflorum. The circadian rhythms of plants grown in a closed walk-in growth chamber were interrupted at night for a total of 4 h, using light-emitting diodes with an intensity of 10 μmol·m2·s1 PPF. The light quality of the NI was shifted from one wavelength to another after the first 2 h. Light treatments consisting of all possible pairings of blue (B), red (R), far-red (Fr), and white (W) light were tested. Plants in the NI treatment groups exposed to Fr light grew larger than plants in other treatment groups. Of plants in NI treatment groups, those in the NI-WB treatment grew the least. In addition, the impact of shifts in the light quality of NI on leaf expansion was greater in treatment groups exposed to a combination of either B and R or R and W light, regardless of their order of supply. Flowering was observed in the NI-RB, NI-FrR, NI-BFr, NI-FrB, NI-WB, NI-FrW, NI-WFr, NI-WR, and SD (short-day) treatments, and was especially promoted in the NI-BFr and NI-FrB treatments. In a combined shift treatment of B and R or B and W light, the NI concluded with B light (NI-RB and NI-WB) treatment induced flowering. The transcriptional factors phyA, cry1 and FTL (FLOWERING LOCUS T) were positively affected, while phyB and AFT were negatively affected. In conclusion, morphogenesis, flowering, and transcriptional factors were all significantly affected either positively or negatively by shifts in the light quality of NI. The light quality of the first 2 h of NI affected neither morphogenesis nor flowering, while the light quality of the last 2 h of NI significantly affected both morphogenesis and flowering. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Stress-Responsive Expression, Subcellular Localization and Protein–Protein Interactions of the Rice Metacaspase Family
by Lei Huang, Huijuan Zhang, Yongbo Hong, Shixia Liu, Dayong Li and Fengming Song
Int. J. Mol. Sci. 2015, 16(7), 16216-16241; https://doi.org/10.3390/ijms160716216 - 17 Jul 2015
Cited by 38 | Viewed by 7856
Abstract
Metacaspases, a class of cysteine-dependent proteases like caspases in animals, are important regulators of programmed cell death (PCD) during development and stress responses in plants. The present study was focused on comprehensive analyses of expression patterns of the rice metacaspase (OsMC) [...] Read more.
Metacaspases, a class of cysteine-dependent proteases like caspases in animals, are important regulators of programmed cell death (PCD) during development and stress responses in plants. The present study was focused on comprehensive analyses of expression patterns of the rice metacaspase (OsMC) genes in response to abiotic and biotic stresses and stress-related hormones. Results indicate that members of the OsMC family displayed differential expression patterns in response to abiotic (e.g., drought, salt, cold, and heat) and biotic (e.g., infection by Magnaporthe oryzae, Xanthomonas oryzae pv. oryzae and Rhizoctonia solani) stresses and stress-related hormones such as abscisic acid, salicylic acid, jasmonic acid, and 1-amino cyclopropane-1-carboxylic acid (a precursor of ethylene), although the responsiveness to these stresses or hormones varies to some extent. Subcellular localization analyses revealed that OsMC1 was solely localized and OsMC2 was mainly localized in the nucleus. Whereas OsMC3, OsMC4, and OsMC7 were evenly distributed in the cells, OsMC5, OsMC6, and OsMC8 were localized in cytoplasm. OsMC1 interacted with OsLSD1 and OsLSD3 while OsMC3 only interacted with OsLSD1 and that the zinc finger domain in OsMC1 is responsible for the interaction activity. The systematic expression and biochemical analyses of the OsMC family provide valuable information for further functional studies on the biological roles of OsMCs in PCD that is related to abiotic and biotic stress responses. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Analysis of Cell Wall-Related Genes in Organs of Medicago sativa L. under Different Abiotic Stresses
by Marc Behr, Sylvain Legay, Jean-Francois Hausman and Gea Guerriero
Int. J. Mol. Sci. 2015, 16(7), 16104-16124; https://doi.org/10.3390/ijms160716104 - 16 Jul 2015
Cited by 45 | Viewed by 6513
Abstract
Abiotic constraints are a source of concern in agriculture, because they can have a strong impact on plant growth and development, thereby affecting crop yield. The response of plants to abiotic constraints varies depending on the type of stress, on the species and [...] Read more.
Abiotic constraints are a source of concern in agriculture, because they can have a strong impact on plant growth and development, thereby affecting crop yield. The response of plants to abiotic constraints varies depending on the type of stress, on the species and on the organs. Although many studies have addressed different aspects of the plant response to abiotic stresses, only a handful has focused on the role of the cell wall. A targeted approach has been used here to study the expression of cell wall-related genes in different organs of alfalfa plants subjected for four days to three different abiotic stress treatments, namely salt, cold and heat stress. Genes involved in different steps of cell wall formation (cellulose biosynthesis, monolignol biosynthesis and polymerization) have been analyzed in different organs of Medicago sativa L. Prior to this analysis, an in silico classification of dirigent/dirigent-like proteins and class III peroxidases has been performed in Medicago truncatula and M. sativa. The final goal of this study is to infer and compare the expression patterns of cell wall-related genes in response to different abiotic stressors in the organs of an important legume crop. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Chromium-Induced Ultrastructural Changes and Oxidative Stress in Roots of Arabidopsis thaliana
by Eleftherios P. Eleftheriou, Ioannis-Dimosthenis S. Adamakis, Emmanuel Panteris and Maria Fatsiou
Int. J. Mol. Sci. 2015, 16(7), 15852-15871; https://doi.org/10.3390/ijms160715852 - 13 Jul 2015
Cited by 94 | Viewed by 15026
Abstract
Chromium (Cr) is an abundant heavy metal in nature, toxic to living organisms. As it is widely used in industry and leather tanning, it may accumulate locally at high concentrations, raising concerns for human health hazards. Though Cr effects have extensively been investigated [...] Read more.
Chromium (Cr) is an abundant heavy metal in nature, toxic to living organisms. As it is widely used in industry and leather tanning, it may accumulate locally at high concentrations, raising concerns for human health hazards. Though Cr effects have extensively been investigated in animals and mammals, in plants they are poorly understood. The present study was then undertaken to determine the ultrastructural malformations induced by hexavalent chromium [Cr(VI)], the most toxic form provided as 100 μM potassium dichromate (K2Cr2O7), in the root tip cells of the model plant Arabidopsis thaliana. A concentration-dependent decrease of root growth and a time-dependent increase of dead cells, callose deposition, hydrogen peroxide (H2O2) production and peroxidase activity were found in Cr(VI)-treated seedlings, mostly at the transition root zone. In the same zone, nuclei remained ultrastructurally unaffected, but in the meristematic zone some nuclei displayed bulbous outgrowths or contained tubular structures. Endoplasmic reticulum (ER) was less affected under Cr(VI) stress, but Golgi bodies appeared severely disintegrated. Moreover, mitochondria and plastids became spherical and displayed translucent stroma with diminished internal membranes, but noteworthy is that their double-membrane envelopes remained structurally intact. Starch grains and electron dense deposits occurred in the plastids. Amorphous material was also deposited in the cell walls, the middle lamella and the vacuoles. Some vacuoles were collapsed, but the tonoplast appeared integral. The plasma membrane was structurally unaffected and the cytoplasm contained opaque lipid droplets and dense electron deposits. All electron dense deposits presumably consisted of Cr that is sequestered from sensitive sites, thus contributing to metal tolerance. It is concluded that the ultrastructural changes are reactive oxygen species (ROS)-correlated and the malformations observed are organelle specific. Full article
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Article
Purification and Structural Identification of Polysaccharides from Bamboo Shoots (Dendrocalamus latiflorus)
by Jinsong Wu, Jiong Zheng, Xuejuan Xia and Jianquan Kan
Int. J. Mol. Sci. 2015, 16(7), 15560-15577; https://doi.org/10.3390/ijms160715560 - 09 Jul 2015
Cited by 32 | Viewed by 6329
Abstract
Three kinds of polysaccharides, namely, BSP1A, BSP2A, and BSP3B, were isolated from raw bamboo shoot (Dendrocalamus latiflorus) after purification and classification by DEAE cellulose-52 (ion-exchange chromatography) and Sephadex G-50. The molecular weights of BSP1A, BSP2A, and BSP3B were 10.2, 17.0 and [...] Read more.
Three kinds of polysaccharides, namely, BSP1A, BSP2A, and BSP3B, were isolated from raw bamboo shoot (Dendrocalamus latiflorus) after purification and classification by DEAE cellulose-52 (ion-exchange chromatography) and Sephadex G-50. The molecular weights of BSP1A, BSP2A, and BSP3B were 10.2, 17.0 and 20.0 kDa, respectively, which were measured through GPC (gel performance chromtatography) methods. BSP1A contained arabinose, glucose, and galactose in a molar ratio of 1.0:40.6:8.7. BSP2A and BSP3B contained arabinose, xylose, glucose, and galactose in molar ratios of 6.6:1.0:5.2:10.4 and 8.5:1.0:5.1:11.1, respectively. The existence of the O-glycopeptide bond in BSP1A, BSP2A, and BSP3B was demonstrated by β-elimination reaction. FTIR spectra of the three polysaccharides showed that both BSP2A and BSP3B contained β-d-pyranose sugar rings. However, BSP1A exhibited both β-d-pyranose and α-d-pyranose sugar rings. Congo red test indicated that BSP1A and BSP2A displayed triple helix structures, but BSP3B did not. NMR spectroscopy revealed that BSP1A may exhibit a β-1,6-Glucan pyran type as the main link, and few 1,6-glycosidic galactose pyranose and arabinose bonds were connected; BSP2A mainly demonstrated →5)β-Ara(1→and→3)β-Gal(1→connection. Furthermore, BSP3B mainly presented →3)β-Glu(1→and→3)β-Gal(1→connection and may also contain few other glycosidic bonds. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
β-Radiation Stress Responses on Growth and Antioxidative Defense System in Plants: A Study with Strontium-90 in Lemna minor
by Arne Van Hoeck, Nele Horemans, May Van Hees, Robin Nauts, Dries Knapen, Hildegarde Vandenhove and Ronny Blust
Int. J. Mol. Sci. 2015, 16(7), 15309-15327; https://doi.org/10.3390/ijms160715309 - 07 Jul 2015
Cited by 22 | Viewed by 5997
Abstract
In the following study, dose dependent effects on growth and oxidative stress induced by β-radiation were examined to gain better insights in the mode of action of β-radiation induced stress in plant species. Radiostrontium (90Sr) was used to test for β-radiation [...] Read more.
In the following study, dose dependent effects on growth and oxidative stress induced by β-radiation were examined to gain better insights in the mode of action of β-radiation induced stress in plant species. Radiostrontium (90Sr) was used to test for β-radiation induced responses in the freshwater macrophyte Lemna minor. The accumulation pattern of 90Sr was examined for L. minor root and fronds separately over a seven-day time period and was subsequently used in a dynamic dosimetric model to calculate β-radiation dose rates. Exposing L. minor plants for seven days to a 90Sr activity concentration of 25 up to 25,000 kBq·L−1 resulted in a dose rate between 0.084 ± 0.004 and 97 ± 8 mGy·h−1. After seven days of exposure, root fresh weight showed a dose dependent decrease starting from a dose rate of 9.4 ± 0.5 mGy·h−1. Based on these data, an EDR10 value of 1.5 ± 0.4 mGy·h−1 was estimated for root fresh weight and 52 ± 17 mGy·h1 for frond fresh weight. Different antioxidative enzymes and metabolites were further examined to analyze if β-radiation induces oxidative stress in L. minor. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Global Reprogramming of Transcription in Chinese Fir (Cunninghamia lanceolata) during Progressive Drought Stress and after Rewatering
by Ruiyang Hu, Bo Wu, Huiquan Zheng, Dehuo Hu, Xinjie Wang, Hongjing Duan, Yuhan Sun, Jinxing Wang, Yue Zhang and Yun Li
Int. J. Mol. Sci. 2015, 16(7), 15194-15219; https://doi.org/10.3390/ijms160715194 - 06 Jul 2015
Cited by 11 | Viewed by 6125
Abstract
Chinese fir (Cunninghamia lanceolata), an evergreen conifer, is the most commonly grown afforestation species in southeast China due to its rapid growth and good wood qualities. To gain a better understanding of the drought-signalling pathway and the molecular metabolic reactions involved [...] Read more.
Chinese fir (Cunninghamia lanceolata), an evergreen conifer, is the most commonly grown afforestation species in southeast China due to its rapid growth and good wood qualities. To gain a better understanding of the drought-signalling pathway and the molecular metabolic reactions involved in the drought response, we performed a genome-wide transcription analysis using RNA sequence data. In this study, Chinese fir plantlets were subjected to progressively prolonged drought stress, up to 15 d, followed by rewatering under controlled environmental conditions. Based on observed morphological changes, plantlets experienced mild, moderate, or severe water stress before rehydration. Transcriptome analysis of plantlets, representing control and mild, moderate, and severe drought-stress treatments, and the rewatered plantlets, identified several thousand genes whose expression was altered in response to drought stress. Many genes whose expression was tightly coupled to the levels of drought stress were identified, suggesting involvement in Chinese fir drought adaptation responses. These genes were associated with transcription factors, signal transport, stress kinases, phytohormone signalling, and defence/stress response. The present study provides the most comprehensive transcriptome resource and the first dynamic transcriptome profiles of Chinese fir under drought stress. The drought-responsive genes identified in this study could provide further information for understanding the mechanisms of drought tolerance in Chinese fir. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Transcriptome Sequencing of Lima Bean (Phaseolus lunatus) to Identify Putative Positive Selection in Phaseolus and Legumes
by Fengqi Li, Depan Cao, Yang Liu, Ting Yang and Guirong Wang
Int. J. Mol. Sci. 2015, 16(7), 15172-15187; https://doi.org/10.3390/ijms160715172 - 03 Jul 2015
Cited by 12 | Viewed by 5569
Abstract
The identification of genes under positive selection is a central goal of evolutionary biology. Many legume species, including Phaseolus vulgaris (common bean) and Phaseolus lunatus (lima bean), have important ecological and economic value. In this study, we sequenced and assembled the transcriptome of [...] Read more.
The identification of genes under positive selection is a central goal of evolutionary biology. Many legume species, including Phaseolus vulgaris (common bean) and Phaseolus lunatus (lima bean), have important ecological and economic value. In this study, we sequenced and assembled the transcriptome of one Phaseolus species, lima bean. A comparison with the genomes of six other legume species, including the common bean, Medicago, lotus, soybean, chickpea, and pigeonpea, revealed 15 and 4 orthologous groups with signatures of positive selection among the two Phaseolus species and among the seven legume species, respectively. Characterization of these positively selected genes using Non redundant (nr) annotation, gene ontology (GO) classification, GO term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that these genes are mostly involved in thylakoids, photosynthesis and metabolism. This study identified genes that may be related to the divergence of the Phaseolus and legume species. These detected genes are particularly good candidates for subsequent functional studies. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Identification of miRNAs and Their Targets in Cotton Inoculated with Verticillium dahliae by High-Throughput Sequencing and Degradome Analysis
by Yujuan Zhang, Wei Wang, Jie Chen, Jubo Liu, Minxuan Xia and Fafu Shen
Int. J. Mol. Sci. 2015, 16(7), 14749-14768; https://doi.org/10.3390/ijms160714749 - 30 Jun 2015
Cited by 45 | Viewed by 6373
Abstract
MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs that play important roles in plant growth, development, and stress response processes. Verticillium wilt is a vascular disease in plants mainly caused by Verticillium dahliae Kleb., the soil-borne fungal pathogen. However, the role [...] Read more.
MicroRNAs (miRNAs) are a group of endogenous small non-coding RNAs that play important roles in plant growth, development, and stress response processes. Verticillium wilt is a vascular disease in plants mainly caused by Verticillium dahliae Kleb., the soil-borne fungal pathogen. However, the role of miRNAs in the regulation of Verticillium defense responses is mostly unknown. This study aimed to identify new miRNAs and their potential targets that are involved in the regulation of Verticillium defense responses. Four small RNA libraries and two degradome libraries from mock-infected and infected roots of cotton (both Gossypium hirsutum L. and Gossypium barbadense L.) were constructed for deep sequencing. A total of 140 known miRNAs and 58 novel miRNAs were identified. Among the identified miRNAs, many were differentially expressed between libraries. Degradome analysis showed that a total of 83 and 24 genes were the targets of 31 known and 14 novel miRNA families, respectively. Gene Ontology analysis indicated that many of the identified miRNA targets may function in controlling root development and the regulation of Verticillium defense responses in cotton. Our findings provide an overview of potential miRNAs involved in the regulation of Verticillium defense responses in cotton and the interactions between miRNAs and their corresponding targets. The profiling of these miRNAs lays the foundation for further understanding of the function of small RNAs in regulating plant response to fungal infection and Verticillium wilt in particular. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Lack of Globulin Synthesis during Seed Development Alters Accumulation of Seed Storage Proteins in Rice
by Hye-Jung Lee, Yeong-Min Jo, Jong-Yeol Lee, Sun-Hyung Lim and Young-Mi Kim
Int. J. Mol. Sci. 2015, 16(7), 14717-14736; https://doi.org/10.3390/ijms160714717 - 30 Jun 2015
Cited by 25 | Viewed by 7619
Abstract
The major seed storage proteins (SSPs) in rice seeds have been classified into three types, glutelins, prolamins, and globulin, and the proportion of each SSP varies. It has been shown in rice mutants that when either glutelins or prolamins are defective, the expression [...] Read more.
The major seed storage proteins (SSPs) in rice seeds have been classified into three types, glutelins, prolamins, and globulin, and the proportion of each SSP varies. It has been shown in rice mutants that when either glutelins or prolamins are defective, the expression of another type of SSP is promoted to counterbalance the deficit. However, we observed reduced abundances of glutelins and prolamins in dry seeds of a globulin-deficient rice mutant (Glb-RNAi), which was generated with RNA interference (RNAi)-induced suppression of globulin expression. The expression of the prolamin and glutelin subfamily genes was reduced in the immature seeds of Glb-RNAi lines compared with those in wild type. A proteomic analysis of Glb-RNAi seeds showed that the reductions in glutelin and prolamin were conserved at the protein level. The decreased pattern in glutelin was also significant in the presence of a reductant, suggesting that the polymerization of the glutelin proteins via intramolecular disulfide bonds could be interrupted in Glb-RNAi seeds. We also observed aberrant and loosely packed structures in the storage organelles of Glb-RNAi seeds, which may be attributable to the reductions in SSPs. In this study, we evaluated the role of rice globulin in seed development, showing that a deficiency in globulin could comprehensively reduce the expression of other SSPs. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Analysis of Phenolic Compounds and Antioxidant Activity in Wild Blackberry Fruits
by Jan Oszmiański, Paulina Nowicka, Mirosława Teleszko, Aneta Wojdyło, Tomasz Cebulak and Krzysztof Oklejewicz
Int. J. Mol. Sci. 2015, 16(7), 14540-14553; https://doi.org/10.3390/ijms160714540 - 26 Jun 2015
Cited by 63 | Viewed by 7453
Abstract
Twenty three different wild blackberry fruit samples were assessed regarding their phenolic profiles and contents (by LC/MS quadrupole time-of-flight (QTOF) and antioxidant activity (ferric reducing ability of plasma (FRAP) and 2,2-azinobis (3-ethyl-benzothiazoline-6-sulfonic acid) (ABTS)) by two different extraction methods. Thirty four phenolic compounds [...] Read more.
Twenty three different wild blackberry fruit samples were assessed regarding their phenolic profiles and contents (by LC/MS quadrupole time-of-flight (QTOF) and antioxidant activity (ferric reducing ability of plasma (FRAP) and 2,2-azinobis (3-ethyl-benzothiazoline-6-sulfonic acid) (ABTS)) by two different extraction methods. Thirty four phenolic compounds were detected (8 anthocyanins, 15 flavonols, 3 hydroxycinnamic acids, 6 ellagic acid derivatives and 2 flavones). In samples, where pressurized liquid extraction (PLE) was used for extraction, a greater increase in yields of phenolic compounds was observed, especially in ellagic acid derivatives (max. 59%), flavonols (max. 44%) and anthocyanins (max. 29%), than after extraction by the ultrasonic technique extraction (UAE) method. The content of phenolic compounds was significantly correlated with the antioxidant activity of the analyzed samples. Principal component analysis (PCA) revealed that the PLE method was more suitable for the quantitative extraction of flavonols, while the UAE method was for hydroxycinnamic acids. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Molecular Mechanisms Underlying Hull-Caryopsis Adhesion/Separation Revealed by Comparative Transcriptomic Analysis of Covered/Naked Barley (Hordeum vulgare L.)
by Ruijun Duan, Huiyan Xiong, Aidong Wang and Guoxiong Chen
Int. J. Mol. Sci. 2015, 16(6), 14181-14193; https://doi.org/10.3390/ijms160614181 - 23 Jun 2015
Cited by 18 | Viewed by 5605
Abstract
The covered/naked caryopsis trait of barley is an important agronomic trait because it is directly linked to dietary use. The formation of covered/naked caryopsis is controlled by an NUD transcription factor, which is involved in pericarp cuticle development. However, the molecular mechanism underlying [...] Read more.
The covered/naked caryopsis trait of barley is an important agronomic trait because it is directly linked to dietary use. The formation of covered/naked caryopsis is controlled by an NUD transcription factor, which is involved in pericarp cuticle development. However, the molecular mechanism underlying this trait remains so far largely unknown. In this study, comparative transcriptomes of grains three weeks after anthesis of Tibetan Hulless barley landrace Dulihuang and covered barley Morex were analyzed using RNA-seq technique. A total of 4031 differentially expressed genes (DEGs) were identified. The Nud gene was overexpressed in Morex, with trace expression in Dulihuang. Among seventeen cuticle related DEGs, sixteen were down regulated and one up regulated in Morex. These results suggest that the Nud gene in covered caryopsis might down regulate cuticle related genes, which may cause a permeable cuticle over pericarp, leading to a hull-caryopsis organ fusion. A functional cuticle covering the pericarp of naked caryopsis might be the result of deletion or low expression level of the Nud gene. The functional cuticle defines a perfect boundary to separate the caryopsis from the hull in naked barley. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Leaf Age-Dependent Photoprotective and Antioxidative Response Mechanisms to Paraquat-Induced Oxidative Stress in Arabidopsis thaliana
by Julietta Moustaka, Georgia Tanou, Ioannis-Dimosthenis Adamakis, Eleftherios P. Eleftheriou and Michael Moustakas
Int. J. Mol. Sci. 2015, 16(6), 13989-14006; https://doi.org/10.3390/ijms160613989 - 18 Jun 2015
Cited by 77 | Viewed by 8929
Abstract
Exposure of Arabidopsis thaliana young and mature leaves to the herbicide paraquat (Pq) resulted in a localized increase of hydrogen peroxide (H2O2) in the leaf veins and the neighboring mesophyll cells, but this increase was not similar in the [...] Read more.
Exposure of Arabidopsis thaliana young and mature leaves to the herbicide paraquat (Pq) resulted in a localized increase of hydrogen peroxide (H2O2) in the leaf veins and the neighboring mesophyll cells, but this increase was not similar in the two leaf types. Increased H2O2 production was concomitant with closed reaction centers (qP). Thirty min after Pq exposure despite the induction of the photoprotective mechanism of non-photochemical quenching (NPQ) in mature leaves, H2O2 production was lower in young leaves mainly due to the higher increase activity of ascorbate peroxidase (APX). Later, 60 min after Pq exposure, the total antioxidant capacity of young leaves was not sufficient to scavenge the excess reactive oxygen species (ROS) that were formed, and thus, a higher H2O2 accumulation in young leaves occurred. The energy allocation of absorbed light in photosystem II (PSII) suggests the existence of a differential photoprotective regulatory mechanism in the two leaf types to the time-course Pq exposure accompanied by differential antioxidant protection mechanisms. It is concluded that tolerance to Pq-induced oxidative stress is related to the redox state of quinone A (QA). Full article
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Article
Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing
by Min Chen, Hai Bao, Qiuming Wu and Yanwei Wang
Int. J. Mol. Sci. 2015, 16(6), 13937-13958; https://doi.org/10.3390/ijms160613937 - 18 Jun 2015
Cited by 23 | Viewed by 6116
Abstract
miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, [...] Read more.
miRNAs are endogenous non-coding small RNAs with important regulatory roles in stress responses. Nitrogen (N) is an indispensable macronutrient required for plant growth and development. Previous studies have identified a variety of known and novel miRNAs responsive to low N stress in plants, including Populus. However, miRNAs involved in the cleavage of target genes and the corresponding regulatory networks in response to N stress in Populus remain largely unknown. Consequently, degradome sequencing was employed for global detection and validation of N-responsive miRNAs and their targets. A total of 60 unique miRNAs (39 conserved, 13 non-conserved, and eight novel) were experimentally identified to target 64 mRNA transcripts and 21 precursors. Among them, we further verified the cleavage of 11 N-responsive miRNAs identified previously and provided empirical evidence for the cleavage mode of these miRNAs on their target mRNAs. Furthermore, five miRNA stars (miRNA*s) were shown to have cleavage function. The specificity and diversity of cleavage sites on the targets and miRNA precursors in P. tomentosa were further detected. Identification and annotation of miRNA-mediated cleavage of target genes in Populus can increase our understanding of miRNA-mediated molecular mechanisms of woody plants adapted to low N environments. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Genome-Wide Analysis of Sorbitol Dehydrogenase (SDH) Genes and Their Differential Expression in Two Sand Pear (Pyrus pyrifolia) Fruits
by Meisong Dai, Zebin Shi and Changjie Xu
Int. J. Mol. Sci. 2015, 16(6), 13065-13083; https://doi.org/10.3390/ijms160613065 - 09 Jun 2015
Cited by 16 | Viewed by 6678
Abstract
Through RNA-seq of a mixed fruit sample, fourteen expressed sorbitol dehydrogenase (SDH) genes have been identified from sand pear (Pyrus pyrifolia Nakai). Comparative phylogenetic analysis of these PpySDHs with those from other plants supported the closest relationship of sand pear [...] Read more.
Through RNA-seq of a mixed fruit sample, fourteen expressed sorbitol dehydrogenase (SDH) genes have been identified from sand pear (Pyrus pyrifolia Nakai). Comparative phylogenetic analysis of these PpySDHs with those from other plants supported the closest relationship of sand pear with Chinese white pear (P. bretschneideri). The expression levels varied greatly among members, and the strongest six (PpySDH2, PpySDH4, PpySDH8, PpySDH12, PpySDH13 and PpySDH14) accounted for 96% of total transcript abundance of PpySDHs. Tissue-specific expression of these six members was observed in nine tissues or organs of sand pear, with the greatest abundance found in functional leaf petioles, followed by the flesh of young fruit. Expression patterns of these six PpySDH genes during fruit development were analyzed in two sand pear cultivars, “Cuiguan” and “Cuiyu”. Overall, expression of PpySDHs peaked twice, first at the fruitlet stage and again at or near harvest. The transcript abundance of PpySDHs was higher in “Cuiguan” than in “Cuiyu”, accompanied by a higher content of sugars and higher ratio of fructose to sorbitol maintained in the former cultivar at harvest. In conclusion, it was suggested that multiple members of the SDH gene family are possibly involved in sand pear fruit development and sugar accumulation and may affect both the sugar amount and sugar composition. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
De Novo Characterization of Flower Bud Transcriptomes and the Development of EST-SSR Markers for the Endangered Tree Tapiscia sinensis
by Xiao-Jun Zhou, Yue-Yue Wang, Ya-Nan Xu, Rong-Shan Yan, Peng Zhao and Wen-Zhe Liu
Int. J. Mol. Sci. 2015, 16(6), 12855-12870; https://doi.org/10.3390/ijms160612855 - 05 Jun 2015
Cited by 28 | Viewed by 6272
Abstract
Tapiscia sinensis Oliv (Tapisciaceae) is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex [...] Read more.
Tapiscia sinensis Oliv (Tapisciaceae) is an endangered species native to China famous for its androdioecious breeding system. However, there is a lack of genomic and transcriptome data on this species. In this study, the Tapiscia sinensis transcriptomes from two types of sex flower buds were sequenced. A total of 97,431,176 clean reads were assembled into 52,169 unigenes with an average length of 1116 bp. Through similarity comparison with known protein databases, 36,662 unigenes (70.27%) were annotated. A total of 10,002 (19.17%) unigenes were assigned to 124 pathways using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database. Additionally, 10,371 simple sequence repeats (SSRs) were identified in 8608 unigenes, with 16,317 pairs of primers designed for applications. 150 pairs of primers were chosen for further validation, and the 68 pairs (45.5%) were able to produce clear polymorphic bands. Six polymorphic SSR markers were used to Bayesian clustering analysis of 51 T. sinensis individuals. This is the first report to provide transcriptome information and to develop large-scale SSR molecular markers for T. sinensis. This study provides a valuable resource for conservation genetics and functional genomics research on T. sinensis for future work. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
The Stable Level of Glutamine synthetase 2 Plays an Important Role in Rice Growth and in Carbon-Nitrogen Metabolic Balance
by Aili Bao, Zhuqing Zhao, Guangda Ding, Lei Shi, Fangsen Xu and Hongmei Cai
Int. J. Mol. Sci. 2015, 16(6), 12713-12736; https://doi.org/10.3390/ijms160612713 - 04 Jun 2015
Cited by 52 | Viewed by 7356
Abstract
Glutamine synthetase 2 (GS2) is a key enzyme involved in the ammonium metabolism in plant leaves. In our previous study, we obtained GS2-cosuppressed plants, which displayed a normal growth phenotype at the seedling stage, while at the tillering stage they showed a [...] Read more.
Glutamine synthetase 2 (GS2) is a key enzyme involved in the ammonium metabolism in plant leaves. In our previous study, we obtained GS2-cosuppressed plants, which displayed a normal growth phenotype at the seedling stage, while at the tillering stage they showed a chlorosis phenotype. In this study, to investigate the chlorosis mechanism, we systematically analyzed the plant growth, carbon-nitrogen metabolism and gene expressions between the GS2-cosuppressed rice and wild-type plants. The results revealed that the GS2-cosuppressed plants exhibited a poor plant growth phenotype and a poor nitrogen transport ability, which led to nitrogen accumulation and a decline in the carbon/nitrogen ratio in the stems. Interestingly, there was a higher concentration of soluble proteins and a lower concentration of carbohydrates in the GS2-cosuppressed plants at the seedling stage, while a contrasting result was displayed at the tillering stage. The analysis of the metabolic profile showed a significant increase of sugars and organic acids. Additionally, gene expression patterns were different in root and leaf of GS2-cosuppressed plants between the seedling and tillering stage. These results indicated the important role of a stable level of GS2 transcription during normal rice development and the importance of the carbon-nitrogen metabolic balance in rice growth. Full article
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Article
Selection of Reliable Reference Genes for Gene Expression Studies of a Promising Oilseed Crop, Plukenetia volubilis, by Real-Time Quantitative PCR
by Longjian Niu, Yan-Bin Tao, Mao-Sheng Chen, Qiantang Fu, Chaoqiong Li, Yuling Dong, Xiulan Wang, Huiying He and Zeng-Fu Xu
Int. J. Mol. Sci. 2015, 16(6), 12513-12530; https://doi.org/10.3390/ijms160612513 - 03 Jun 2015
Cited by 39 | Viewed by 9135
Abstract
Real-time quantitative PCR (RT-qPCR) is a reliable and widely used method for gene expression analysis. The accuracy of the determination of a target gene expression level by RT-qPCR demands the use of appropriate reference genes to normalize the mRNA levels among different samples. [...] Read more.
Real-time quantitative PCR (RT-qPCR) is a reliable and widely used method for gene expression analysis. The accuracy of the determination of a target gene expression level by RT-qPCR demands the use of appropriate reference genes to normalize the mRNA levels among different samples. However, suitable reference genes for RT-qPCR have not been identified in Sacha inchi (Plukenetia volubilis), a promising oilseed crop known for its polyunsaturated fatty acid (PUFA)-rich seeds. In this study, using RT-qPCR, twelve candidate reference genes were examined in seedlings and adult plants, during flower and seed development and for the entire growth cycle of Sacha inchi. Four statistical algorithms (delta cycle threshold (ΔCt), BestKeeper, geNorm, and NormFinder) were used to assess the expression stabilities of the candidate genes. The results showed that ubiquitin-conjugating enzyme (UCE), actin (ACT) and phospholipase A22 (PLA) were the most stable genes in Sacha inchi seedlings. For roots, stems, leaves, flowers, and seeds from adult plants, 30S ribosomal protein S13 (RPS13), cyclophilin (CYC) and elongation factor-1alpha (EF1α) were recommended as reference genes for RT-qPCR. During the development of reproductive organs, PLA, ACT and UCE were the optimal reference genes for flower development, whereas UCE, RPS13 and RNA polymerase II subunit (RPII) were optimal for seed development. Considering the entire growth cycle of Sacha inchi, UCE, ACT and EF1α were sufficient for the purpose of normalization. Our results provide useful guidelines for the selection of reliable reference genes for the normalization of RT-qPCR data for seedlings and adult plants, for reproductive organs, and for the entire growth cycle of Sacha inchi. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Induction of Oxidative Stress and Antioxidative Mechanisms in Arabidopsis thaliana after Uranium Exposure at pH 7.5
by Eline Saenen, Nele Horemans, Nathalie Vanhoudt, Hildegarde Vandenhove, Geert Biermans, May Van Hees, Jean Wannijn, Jaco Vangronsveld and Ann Cuypers
Int. J. Mol. Sci. 2015, 16(6), 12405-12423; https://doi.org/10.3390/ijms160612405 - 02 Jun 2015
Cited by 17 | Viewed by 5887
Abstract
To evaluate the environmental impact of uranium (U) contamination, it is important to investigate the effects of U at ecologically relevant conditions. Since U speciation, and hence its toxicity, strongly depends on environmental pH, the present study aimed to investigate dose-dependent effects of [...] Read more.
To evaluate the environmental impact of uranium (U) contamination, it is important to investigate the effects of U at ecologically relevant conditions. Since U speciation, and hence its toxicity, strongly depends on environmental pH, the present study aimed to investigate dose-dependent effects of U at pH 7.5. Arabidopsis thaliana plants (Mouse-ear Cress) were exposed for three days to different U concentrations at pH 7.5. In the roots, the increased capacities of ascorbate peroxidase and glutathione reductase indicate an important role for the ascorbate-glutathione cycle during U-induced stress. However, a significant decrease in the ascorbate redox state was observed after exposure to 75 and 100 µM U, indicating that those roots are severely stressed. In accordance with the roots, the ascorbate-glutathione cycle plays an important role in the antioxidative defence systems in A. thaliana leaves exposed to U at pH 7.5 as the ascorbate and glutathione biosynthesis were upregulated. In addition, small inductions of enzymes of the antioxidative defence system were observed at lower U concentrations to counteract the U-induced stress. However, at higher U concentrations it seems that the antioxidative defence system of the leaves collapses as reductions in enzyme activities and gene expression levels were observed. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Synergistic and Antagonistic Action of Phytochrome (Phy) A and PhyB during Seedling De-Etiolation in Arabidopsis thaliana
by Liang Su, Pei Hou, Meifang Song, Xu Zheng, Lin Guo, Yang Xiao, Lei Yan, Wanchen Li and Jianping Yang
Int. J. Mol. Sci. 2015, 16(6), 12199-12212; https://doi.org/10.3390/ijms160612199 - 28 May 2015
Cited by 25 | Viewed by 7371
Abstract
It has been reported that Arabidopsis phytochrome (phy) A and phyB are crucial photoreceptors that display synergistic and antagonistic action during seedling de-etiolation in multiple light signaling pathways. However, the functional relationship between phyA and phyB is not fully understood under different kinds [...] Read more.
It has been reported that Arabidopsis phytochrome (phy) A and phyB are crucial photoreceptors that display synergistic and antagonistic action during seedling de-etiolation in multiple light signaling pathways. However, the functional relationship between phyA and phyB is not fully understood under different kinds of light and in response to different intensities of such light. In this work, we compared hypocotyl elongation of the phyA-211 phyB-9 double mutant with the wild type, the phyA-211 and phyB-9 single mutants under different intensities of far-red (FR), red (R), blue (B) and white (W) light. We confirmed that phyA and phyB synergistically promote seedling de-etiolation in B-, B plus R-, W- and high R-light conditions. The correlation of endogenous ELONGATED HYPOCOTYL 5 (HY5) protein levels with the trend of hypocotyl elongation of all lines indicate that both phyA and phyB promote seedling photomorphogenesis in a synergistic manner in high-irradiance white light. Gene expression analyses of RBCS members and HY5 suggest that phyB and phyA act antagonistically on seedling development under FR light. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Functional Analysis of the Maize C-Repeat/DRE Motif-Binding Transcription Factor CBF3 Promoter in Response to Abiotic Stress
by Jinliang Liu, Fengting Wang, Gang Yu, Xianghui Zhang, Chengguo Jia, Jianchun Qin and Hongyu Pan
Int. J. Mol. Sci. 2015, 16(6), 12131-12146; https://doi.org/10.3390/ijms160612131 - 28 May 2015
Cited by 31 | Viewed by 7399
Abstract
The ZmCBF3 gene is a member of AP2/ERF transcription factor family, which is a large family of plant-specific transcription factors that share a well-conserved DNA-binding domain. To understand the regulatory mechanism of ZmCBF3 gene expression, we isolated and characterized the ZmCBF3 promoter (P [...] Read more.
The ZmCBF3 gene is a member of AP2/ERF transcription factor family, which is a large family of plant-specific transcription factors that share a well-conserved DNA-binding domain. To understand the regulatory mechanism of ZmCBF3 gene expression, we isolated and characterized the ZmCBF3 promoter (PZmCBF3). Three deletion fragments of PZmCBF3 were generated, C1–C3, from the translation start codon at position −1079, −638, and −234, and fused to the GUS reporter gene. Each deletion construct was analyzed by Agrobacterium-mediated stable transformation and expression in Arabidopsis thaliana. GUS expression assays indicated that the PZmCBF3 exhibited root-specific expression activity. A 234-bp fragment upstream of the ZmCBF3 gene conferred a high level of GUS activity in Arabidopsis. Some cis-acting elements involved in the down-regulation of gene expression were detected in the promoter, encompassing positions −1079 to −234. PZmCBF3 was activated by cold stress. The MYCCONSENSUSAT elements (CANNTG) were responsible for the ability of PZmCBF3 to respond to cold stress. The results of the present study suggest that PZmCBF3 might play a role in cold tolerance in maize. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
De Novo Assembly and Characterization of the Transcriptome of the Chinese Medicinal Herb, Gentiana rigescens
by Xiaodong Zhang, Andrew C. Allan, Caixia Li, Yuanzhong Wang and Qiuyang Yao
Int. J. Mol. Sci. 2015, 16(5), 11550-11573; https://doi.org/10.3390/ijms160511550 - 20 May 2015
Cited by 39 | Viewed by 8907
Abstract
Gentiana rigescens is an important medicinal herb in China. The main validated medicinal component gentiopicroside is synthesized in shoots, but is mainly found in the plant’s roots. The gentiopicroside biosynthetic pathway and its regulatory control remain to be elucidated. Genome resources of gentian [...] Read more.
Gentiana rigescens is an important medicinal herb in China. The main validated medicinal component gentiopicroside is synthesized in shoots, but is mainly found in the plant’s roots. The gentiopicroside biosynthetic pathway and its regulatory control remain to be elucidated. Genome resources of gentian are limited. Next-generation sequencing (NGS) technologies can aid in supplying global gene expression profiles. In this study we present sequence and transcript abundance data for the root and leaf transcriptome of G. rigescens, obtained using the Illumina Hiseq2000. Over fifty million clean reads were obtained from leaf and root libraries. This yields 76,717 unigenes with an average length of 753 bp. Among these, 33,855 unigenes were identified as putative homologs of annotated sequences in public protein and nucleotide databases. Digital abundance analysis identified 3306 unigenes differentially enriched between leaf and root. Unigenes found in both tissues were categorized according to their putative functional categories. Of the differentially expressed genes, over 130 were annotated as related to terpenoid biosynthesis. This work is the first study of global transcriptome analyses in gentian. These sequences and putative functional data comprise a resource for future investigation of terpenoid biosynthesis in Gentianaceae species and annotation of the gentiopicroside biosynthetic pathway and its regulatory mechanisms. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
Identification and Expression Analysis of Candidate Genes Associated with Defense Responses to Phytophthora capsici in Pepper Line “PI 201234”
by Pingyong Wang, Xiaodan Liu, Jinju Guo, Chen Liu, Nan Fu and Huolin Shen
Int. J. Mol. Sci. 2015, 16(5), 11417-11438; https://doi.org/10.3390/ijms160511417 - 18 May 2015
Cited by 20 | Viewed by 6150
Abstract
Phytophthora capsici (Leonian), classified as an oomycete, seriously threatens the production of pepper (Capsicum annuum). Current understanding of the defense responses in pepper to P. capsici is limited. In this study, RNA-sequencing analysis was utilized to identify differentially expressed genes in [...] Read more.
Phytophthora capsici (Leonian), classified as an oomycete, seriously threatens the production of pepper (Capsicum annuum). Current understanding of the defense responses in pepper to P. capsici is limited. In this study, RNA-sequencing analysis was utilized to identify differentially expressed genes in the resistant line “PI 201234”, with 1220 differentially expressed genes detected. Of those genes, 480 were up-regulated and 740 were down-regulated, with 211 candidate genes found to be involved in defense responses based on the gene annotations. Furthermore, the expression patterns of 12 candidate genes were further validated via quantitative real-time PCR (qPCR). These genes were found to be significantly up-regulated at different time points post-inoculation (6 hpi, 24 hpi, and 5 dpi) in the resistant line “PI 201234” and susceptible line “Qiemen”. Seven genes were found to be involved in cell wall modification, phytoalexin biosynthesis, symptom development, and phytohormone signaling pathways, thus possibly playing important roles in combating exogenous pathogens. The genes identified herein will provide a basis for further gene cloning and functional verification studies and will aid in an understanding of the regulatory mechanism of pepper resistance to P. capsici. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress
by Bin Bai, Jun Wu, Wen-Tao Sheng, Bo Zhou, Li-Jie Zhou, Wen Zhuang, Dong-Ping Yao and Qi-Yun Deng
Int. J. Mol. Sci. 2015, 16(5), 11398-11416; https://doi.org/10.3390/ijms160511398 - 18 May 2015
Cited by 69 | Viewed by 10325
Abstract
Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice [...] Read more.
Rice is highly sensitive to cold stress during reproductive developmental stages, and little is known about the mechanisms of cold responses in rice anther. Using the HiSeq™ 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Pei’ai64S) were analyzed at the fertility sensitive stage under cold stress. Approximately 243 million clean reads were obtained from four libraries and aligned against the oryza indica genome and 1497 and 5652 differentially expressed genes (DEGs) were identified in P64S and Y58S, respectively. Both gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted for these DEGs. Functional classification of DEGs was also carried out. The DEGs common to both genotypes were mainly involved in signal transduction, metabolism, transport, and transcriptional regulation. Most of the DEGs were unique for each comparison group. We observed that there were more differentially expressed MYB (Myeloblastosis) and zinc finger family transcription factors and signal transduction components such as calmodulin/calcium dependent protein kinases in the Y58S comparison group. It was also found that ribosome-related DEGs may play key roles in cold stress signal transduction. These results presented here would be particularly useful for further studies on investigating the molecular mechanisms of rice responses to cold stress. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Subcellular Sequestration and Impact of Heavy Metals on the Ultrastructure and Physiology of the Multicellular Freshwater Alga Desmidium swartzii
by Ancuela Andosch, Margit Höftberger, Cornelius Lütz and Ursula Lütz-Meindl
Int. J. Mol. Sci. 2015, 16(5), 10389-10410; https://doi.org/10.3390/ijms160510389 - 07 May 2015
Cited by 34 | Viewed by 6682 | Correction
Abstract
Due to modern life with increasing traffic, industrial production and agricultural practices, high amounts of heavy metals enter ecosystems and pollute soil and water. As a result, metals can be accumulated in plants and particularly in algae inhabiting peat bogs of low pH [...] Read more.
Due to modern life with increasing traffic, industrial production and agricultural practices, high amounts of heavy metals enter ecosystems and pollute soil and water. As a result, metals can be accumulated in plants and particularly in algae inhabiting peat bogs of low pH and high air humidity. In the present study, we investigated the impact and intracellular targets of aluminum, copper, cadmium, chromium VI and zinc on the filamentous green alga Desmidium swartzii, which is an important biomass producer in acid peat bogs. By means of transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS) it is shown that all metals examined are taken up into Desmidium readily, where they are sequestered in cell walls and/or intracellular compartments. They cause effects on cell ultrastructure to different degrees and additionally disturb photosynthetic activity and biomass production. Our study shows a clear correlation between toxicity of a metal and the ability of the algae to compartmentalize it intracellularly. Cadmium and chromium, which are not compartmentalized, exert the most toxic effects. In addition, this study shows that the filamentous alga Desmidium reacts more sensitively to aluminum and zinc when compared to its unicellular relative Micrasterias, indicating a severe threat to the ecosystem. Full article
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Article
Response of Different Genotypes of Faba Bean Plant to Drought Stress
by Manzer H. Siddiqui, Mutahhar Y. Al-Khaishany, Mohammed A. Al-Qutami, Mohamed H. Al-Whaibi, Anil Grover, Hayssam M. Ali, Mona S. Al-Wahibi and Najat A. Bukhari
Int. J. Mol. Sci. 2015, 16(5), 10214-10227; https://doi.org/10.3390/ijms160510214 - 05 May 2015
Cited by 132 | Viewed by 8996
Abstract
Drought stress is one of the major abiotic stresses that are a threat to crop production worldwide. Drought stress impairs the plants growth and yield. Therefore, the aim of the present experiment was to select the tolerant genotype/s on the basis of moprpho-physiological [...] Read more.
Drought stress is one of the major abiotic stresses that are a threat to crop production worldwide. Drought stress impairs the plants growth and yield. Therefore, the aim of the present experiment was to select the tolerant genotype/s on the basis of moprpho-physiological and biochemical characteristics of 10 Vicia faba genotypes (Zafar 1, Zafar 2, Shebam, Makamora, Espan, Giza Blanka, Giza 3, C4, C5 and G853) under drought stress. We studied the effect of different levels of drought stress i.e., (i) normal irrigation (ii) mild stress (iii) moderate stress, and (iv) severe stress on plant height (PH) plant−1, fresh weight (FW) and dry weight (DW) plant−1, area leaf−1, leaf relative water content (RWC), proline (Pro) content, total chlorophyll (Total Chl) content, electrolyte leakage (EL), malondialdehyde (MDA), hydrogen peroxide (H2O2) content, and activities of catalase (CAT), peroxidase (POD) and superoxide dismutase (SOD) of genotypes of faba bean. Drought stress reduced all growth parameters and Total Chl content of all genotypes. However, the deteriorating effect of drought stress on the growth performance of genotypes “C5” and “Zafar 1” were relatively low due to its better antioxidant enzymes activities (CAT, POD and SOD), and accumulation of Pro and Total Chl, and leaf RWC. In the study, genotype “C5” and “Zafar 1” were found to be relatively tolerant to drought stress and genotypes “G853” and “C4” were sensitive to drought stress. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Article
De Novo Transcriptome Sequencing of Low Temperature-Treated Phlox subulata and Analysis of the Genes Involved in Cold Stress
by Yanting Qu, Aimin Zhou, Xing Zhang, Huanwei Tang, Ming Liang, Hui Han and Yuhu Zuo
Int. J. Mol. Sci. 2015, 16(5), 9732-9748; https://doi.org/10.3390/ijms16059732 - 29 Apr 2015
Cited by 17 | Viewed by 6749
Abstract
Phlox subulata, a perennial herbaceous flower, can survive during the winter of northeast China, where the temperature can drop to −30 °C, suggesting that P. subulata is an ideal model for studying the molecular mechanisms of cold acclimation in plants. However, little [...] Read more.
Phlox subulata, a perennial herbaceous flower, can survive during the winter of northeast China, where the temperature can drop to −30 °C, suggesting that P. subulata is an ideal model for studying the molecular mechanisms of cold acclimation in plants. However, little is known about the gene expression profile of P. subulata under cold stress. Here, we examined changes in cold stress-related genes in P. subulata. We sequenced three cold-treated (CT) and control (CK) samples of P. subulata. After de novo assembly and quantitative assessment of the obtained reads, 99,174 unigenes were generated. Based on similarity searches with known proteins in public protein databases, 59,994 unigenes were functionally annotated. Among all differentially expressed genes (DEGs), 8302, 10,638 and 11,021 up-regulated genes and 9898, 17,876, and 12,358 down-regulated genes were identified after treatment at 4, 0, and −10 °C, respectively. Furthermore, 3417 up-regulated unigenes were expressed only in CT samples. Twenty major cold-related genes, including transcription factors, antioxidant enzymes, osmoregulation proteins, and Ca2+ and ABA signaling components, were identified, and their expression levels were estimated. Overall, this is the first transcriptome sequencing of this plant species under cold stress. Studies of DEGs involved in cold-related metabolic pathways may facilitate the discovery of cold-resistance genes. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
New Coumarin Derivatives and Other Constituents from the Stem Bark of Zanthoxylum avicennae: Effects on Neutrophil Pro-Inflammatory Responses
by Jih-Jung Chen, Chieh-Kai Yang, Yueh-Hsiung Kuo, Tsong-Long Hwang, Wen-Lung Kuo, Yun-Ping Lim, Ping-Jyun Sung, Tsung-Hsien Chang and Ming-Jen Cheng
Int. J. Mol. Sci. 2015, 16(5), 9719-9731; https://doi.org/10.3390/ijms16059719 - 29 Apr 2015
Cited by 21 | Viewed by 5813
Abstract
Three new coumarin derivatives, 8-formylalloxanthoxyletin (1), avicennone (2), and (Z)-avicennone (3), have been isolated from the stem bark of Zanthoxylum avicennae (Z. avicennae), together with 15 known compounds (418). [...] Read more.
Three new coumarin derivatives, 8-formylalloxanthoxyletin (1), avicennone (2), and (Z)-avicennone (3), have been isolated from the stem bark of Zanthoxylum avicennae (Z. avicennae), together with 15 known compounds (418). The structures of these new compounds were determined through spectroscopic and MS analyses. Compounds 1, 4, 9, 12, and 15 exhibited inhibition (half maximal inhibitory concentration (IC50) values ≤7.65 µg/mL) of superoxide anion generation by human neutrophils in response to formyl-l-methionyl-l-leucyl-l-phenylalanine/cytochalasin B (fMLP/CB). Compounds 1, 2, 4, 8 and 9 inhibited fMLP/CB-induced elastase release with IC50 values ≤8.17 µg/mL. This investigation reveals bioactive isolates (especially 1, 2, 4, 8, 9, 12 and 15) could be further developed as potential candidates for the treatment or prevention of various inflammatory diseases. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Overexpressing of OsAMT1-3, a High Affinity Ammonium Transporter Gene, Modifies Rice Growth and Carbon-Nitrogen Metabolic Status
by Aili Bao, Zhijun Liang, Zhuqing Zhao and Hongmei Cai
Int. J. Mol. Sci. 2015, 16(5), 9037-9063; https://doi.org/10.3390/ijms16059037 - 23 Apr 2015
Cited by 88 | Viewed by 7902
Abstract
AMT1-3 encodes the high affinity NH4+ transporter in rice roots and is predominantly expressed under nitrogen starvation. In order to evaluate the effect of AMT1-3 gene on rice growth, nitrogen absorption and metabolism, we generated AMT1-3-overexpressing [...] Read more.
AMT1-3 encodes the high affinity NH4+ transporter in rice roots and is predominantly expressed under nitrogen starvation. In order to evaluate the effect of AMT1-3 gene on rice growth, nitrogen absorption and metabolism, we generated AMT1-3-overexpressing plants and analyzed the growth phenotype, yield, carbon and nitrogen metabolic status, and gene expression profiles. Although AMT1-3 mRNA accumulated in transgenic plants, these plants displayed significant decreases in growth when compared to the wild-type plants. The nitrogen uptake assay using a 15N tracer revealed poor nitrogen uptake ability in AMT1-3-overexpressing plants. We found significant decreases in AMT1-3-overexpressing plant leaf carbon and nitrogen content accompanied with a higher leaf C/N ratio. Significant changes in soluble proteins and carbohydrates were also observed in AMT1-3-overexpressing plants. In addition, metabolite profile analysis demonstrated significant changes in individual sugars, organic acids and free amino acids. Gene expression analysis revealed distinct expression patterns of genes that participate in carbon and nitrogen metabolism. Additionally, the correlation between the metabolites and gene expression patterns was consistent in AMT1-3-overexpressing plants under both low and high nitrogen growth conditions. Therefore, we hypothesized that the carbon and nitrogen metabolic imbalance caused by AMT1-3 overexpressing attributed to the poor growth and yield of transgenic plants. Full article
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Article
Genome-Wide Identification and Evolution of HECT Genes in Soybean
by Xianwen Meng, Chen Wang, Siddiq Ur Rahman, Yaxu Wang, Ailan Wang and Shiheng Tao
Int. J. Mol. Sci. 2015, 16(4), 8517-8535; https://doi.org/10.3390/ijms16048517 - 16 Apr 2015
Cited by 14 | Viewed by 6826
Abstract
Proteins containing domains homologous to the E6-associated protein (E6-AP) carboxyl terminus (HECT) are an important class of E3 ubiquitin ligases involved in the ubiquitin proteasome pathway. HECT-type E3s play crucial roles in plant growth and development. However, current understanding of plant HECT genes [...] Read more.
Proteins containing domains homologous to the E6-associated protein (E6-AP) carboxyl terminus (HECT) are an important class of E3 ubiquitin ligases involved in the ubiquitin proteasome pathway. HECT-type E3s play crucial roles in plant growth and development. However, current understanding of plant HECT genes and their evolution is very limited. In this study, we performed a genome-wide analysis of the HECT domain-containing genes in soybean. Using high-quality genome sequences, we identified 19 soybean HECT genes. The predicted HECT genes were distributed unevenly across 15 of 20 chromosomes. Nineteen of these genes were inferred to be segmentally duplicated gene pairs, suggesting that in soybean, segmental duplications have made a significant contribution to the expansion of the HECT gene family. Phylogenetic analysis showed that these HECT genes can be divided into seven groups, among which gene structure and domain architecture was relatively well-conserved. The Ka/Ks ratios show that after the duplication events, duplicated HECT genes underwent purifying selection. Moreover, expression analysis reveals that 15 of the HECT genes in soybean are differentially expressed in 14 tissues, and are often highly expressed in the flowers and roots. In summary, this work provides useful information on which further functional studies of soybean HECT genes can be based. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Molecular Characterization of Sec2 Loci in Wheat—Secale africanum Derivatives Demonstrates Genomic Divergence of Secale Species
by Guangrong Li, Hongjun Zhang, Li Zhou, Dan Gao, Mengping Lei, Jie Zhang and Zujun Yang
Int. J. Mol. Sci. 2015, 16(4), 8324-8336; https://doi.org/10.3390/ijms16048324 - 14 Apr 2015
Cited by 4 | Viewed by 4760
Abstract
The unique 75 K γ-secalins encoded by Sec2 loci in Secale species is composed of almost half rye storage proteins. The chromosomal location of Sec2 loci in wild Secale species, Secale africanum, was carried out by the wheat—S. africanum derivatives, [...] Read more.
The unique 75 K γ-secalins encoded by Sec2 loci in Secale species is composed of almost half rye storage proteins. The chromosomal location of Sec2 loci in wild Secale species, Secale africanum, was carried out by the wheat—S. africanum derivatives, which were identified by genomic in situ hybridization and multi-color fluorescence in situ hybridization. The Sec2 gene-specific PCR analysis indicated that the S. cereale Sec2 was located on chromosome 2R, while the S. africanum Sec2 was localized on chromosome 6Rafr of S. africanum. A total of 38 Sec2 gene sequences were isolated from S. africanum, S. cereale and S. sylvestre by PCR-based cloning. Phylogenetic analysis showed that S. africanum Sec2 diverged from S. cereale Sec2 approximately 2–3 million years ago. The illegitimate recombination of chromosome 2R–6R involving the Sec2 loci region may accelerate sequence variation during evolutionary process from wild to cultivated Secale species. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Genetic Variability and Population Structure of Salvia lachnostachys: Implications for Breeding and Conservation Programs
by Marianna Erbano, Guilherme Schnell e Schühli and Élide Pereira dos Santos
Int. J. Mol. Sci. 2015, 16(4), 7839-7850; https://doi.org/10.3390/ijms16047839 - 08 Apr 2015
Cited by 38 | Viewed by 5886
Abstract
The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR) molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA [...] Read more.
The genetic diversity and population structure of Salvia lachnostachys Benth were assessed. Inter Simple Sequence Repeat (ISSR) molecular markers were used to investigate the restricted distribution of S. lachnostachys in Parana State, Brazil. Leaves of 73 individuals representing three populations were collected. DNA was extracted and submitted to PCR-ISSR amplification with nine tested primers. Genetic diversity parameters were evaluated. Our analysis indicated 95.6% polymorphic loci (stress value 0.02) with a 0.79 average Simpson’s index. The Nei-Li distance dendrogram and principal component analysis largely recovered the geographical origin of each sample. Four major clusters were recognized representing each collected population. Nei’s gene diversity and Shannon’s information index were 0.25 and 0.40 respectively. As is typical for outcrossing herbs, the majority of genetic variation occurred at the population level (81.76%). A high gene flow (Nm = 2.48) was observed with a correspondingly low fixation index. These values were generally similar to previous studies on congeneric species. The results of principal coordinate analysis (PCA) and of arithmetic average (UPGMA) were consistent and all three populations appear distinct as in STRUCTURE analysis. In addition, this analysis indicated a majority intrapopulation genetic variation. Despite the human pressure on natural populations our study found high levels of genetic diversity for S. lachnostachys. This was the first molecular assessment for this endemic species with medicinal proprieties and the results can guide for subsequent bioprospection, breeding programs or conservation actions. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)
by Giovanna Câmara Giudicelli, Geraldo Mäder and Loreta Brandão de Freitas
Int. J. Mol. Sci. 2015, 16(4), 7289-7303; https://doi.org/10.3390/ijms16047289 - 01 Apr 2015
Cited by 25 | Viewed by 6719
Abstract
DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, [...] Read more.
DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Identification and Functional Analysis of MicroRNAs and Their Targets in Platanus acerifolia under Lead (Pb) Stress
by Yuanlong Wang, Zhenli Zhao, Minjie Deng, Rongning Liu, Suyan Niu and Guoqiang Fan
Int. J. Mol. Sci. 2015, 16(4), 7098-7111; https://doi.org/10.3390/ijms16047098 - 30 Mar 2015
Cited by 24 | Viewed by 5824
Abstract
MicroRNAs (miRNAs) play important regulatory roles in development and stress responses in plants. Lead (Pb) is a non-essential element that is highly toxic to living organisms. Platanus acerifolia is grown as a street tree in cities throughout temperate regions for its importance in [...] Read more.
MicroRNAs (miRNAs) play important regulatory roles in development and stress responses in plants. Lead (Pb) is a non-essential element that is highly toxic to living organisms. Platanus acerifolia is grown as a street tree in cities throughout temperate regions for its importance in improving the urban ecological environment. MiRNAs that respond to abiotic stresses have been identified in plants; however, until now, the influence of Pb stress on P. acerifolia miRNAs has not been reported. To identify miRNAs and predict their target genes under Pb stress, two small RNA and two degradome libraries were constructed from Pb-treated and Pb-free leaves of P. acerifolia seedlings. After sequencing, 55 known miRNAs and 129 novel miRNAs were obtained, and 104 target genes for the miRNAs were identified by degradome sequencing. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to predict the functions of the targets. The expressions of eight differentially expressed miRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first report about P. acerifolia miRNAs and their target genes under Pb stress. This study has provided data for further research into molecular mechanisms involved in resistance of P. acerifolia to Pb stress. Full article
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Article
RNA-Seq Transcriptome Analysis of Maize Inbred Carrying Nicosulfuron-Tolerant and Nicosulfuron-Susceptible Alleles
by Xiaomin Liu, Xian Xu, Binghua Li, Xueqing Wang, Guiqi Wang and Moran Li
Int. J. Mol. Sci. 2015, 16(3), 5975-5989; https://doi.org/10.3390/ijms16035975 - 13 Mar 2015
Cited by 25 | Viewed by 8029
Abstract
Postemergence applications of nicosulfuron can cause great damage to certain maize inbred lines and hybrids. Variation among different responses to nicosulfuron may be attributed to differential rates of herbicide metabolism. We employed RNA-Seq analysis to compare transcriptome responses between nicosulfuron-treated and untreated in [...] Read more.
Postemergence applications of nicosulfuron can cause great damage to certain maize inbred lines and hybrids. Variation among different responses to nicosulfuron may be attributed to differential rates of herbicide metabolism. We employed RNA-Seq analysis to compare transcriptome responses between nicosulfuron-treated and untreated in both tolerant and susceptible maize plants. A total of 71.8 million paired end Illumina RNA-Seq reads were generated, representing the transcription of around 40,441 unique reads. About 345,171 gene ontology (GO) term assignments were conducted for the annotation in terms of biological process, cellular component and molecular function categories, and 6413 sequences with 108 enzyme commission numbers were assigned to 134 predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Digital gene expression profile (DGE) analysis using Solexa sequencing was performed within the susceptible and tolerant maize between the nicosulfuron-treated and untreated conditions, 13 genes were selected as the candidates most likely involved in herbicide metabolism, and quantitative RT-PCR validated the RNA-Seq results for eight genes. This transcriptome data may provide opportunities for the study of sulfonylurea herbicides susceptibility emergence of Zea mays. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Positive Selection and Functional Divergence of R2R3-MYB Paralogous Genes Expressed in Inflorescence Buds of Scutellaria Species (Labiatae)
by Bing-Hong Huang, Erli Pang, Yi-Wen Chen, Huifen Cao, Yu Ruan and Pei-Chun Liao
Int. J. Mol. Sci. 2015, 16(3), 5900-5921; https://doi.org/10.3390/ijms16035900 - 13 Mar 2015
Cited by 5 | Viewed by 6342
Abstract
Anthocyanin is the main pigment forming floral diversity. Several transcription factors that regulate the expression of anthocyanin biosynthetic genes belong to the R2R3-MYB family. Here we examined the transcriptomes of inflorescence buds of Scutellaria species (skullcaps), identified the expression R2R3-MYBs, [...] Read more.
Anthocyanin is the main pigment forming floral diversity. Several transcription factors that regulate the expression of anthocyanin biosynthetic genes belong to the R2R3-MYB family. Here we examined the transcriptomes of inflorescence buds of Scutellaria species (skullcaps), identified the expression R2R3-MYBs, and detected the genetic signatures of positive selection for adaptive divergence across the rapidly evolving skullcaps. In the inflorescence buds, seven R2R3-MYBs were identified. MYB11 and MYB16 were detected to be positively selected. The signature of positive selection on MYB genes indicated that species diversification could be affected by transcriptional regulation, rather than at the translational level. When comparing among the background lineages of Arabidopsis, tomato, rice, and Amborella, heterogeneous evolutionary rates were detected among MYB paralogs, especially between MYB13 and MYB19. Significantly different evolutionary rates were also evidenced by type-I functional divergence between MYB13 and MYB19, and the accelerated evolutionary rates in MYB19, implied the acquisition of novel functions. Another paralogous pair, MYB2/7 and MYB11, revealed significant radical amino acid changes, indicating divergence in the regulation of different anthocyanin-biosynthetic enzymes. Our findings not only showed that Scutellaria R2R3-MYBs are functionally divergent and positively selected, but also indicated the adaptive relevance of regulatory genes in floral diversification. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Genome-Wide Identification and Analysis of Drought-Responsive Genes and MicroRNAs in Tobacco
by Fuqiang Yin, Cheng Qin, Jian Gao, Ming Liu, Xirong Luo, Wenyou Zhang, Hongjun Liu, Xinhui Liao, Yaou Shen, Likai Mao, Zhiming Zhang, Haijian Lin, Thomas Lübberstedt and Guangtang Pan
Int. J. Mol. Sci. 2015, 16(3), 5714-5740; https://doi.org/10.3390/ijms16035714 - 12 Mar 2015
Cited by 30 | Viewed by 8510
Abstract
Drought stress response is a complex trait regulated at transcriptional and post-transcriptional levels in tobacco. Since the 1990s, many studies have shown that miRNAs act in many ways to regulate target expression in plant growth, development and stress response. The recent draft genome [...] Read more.
Drought stress response is a complex trait regulated at transcriptional and post-transcriptional levels in tobacco. Since the 1990s, many studies have shown that miRNAs act in many ways to regulate target expression in plant growth, development and stress response. The recent draft genome sequence of Nicotiana benthamiana has provided a framework for Digital Gene Expression (DGE) and small RNA sequencing to understand patterns of transcription in the context of plant response to environmental stress. We sequenced and analyzed three Digital Gene Expression (DGE) libraries from roots of normal and drought-stressed tobacco plants, and four small RNA populations from roots, stems and leaves of control or drought-treated tobacco plants, respectively. We identified 276 candidate drought responsive genes (DRGs) with sequence similarities to 64 known DRGs from other model plant crops, 82 were transcription factors (TFs) including WRKY, NAC, ERF and bZIP families. Of these tobacco DRGs, 54 differentially expressed DRGs included 21 TFs, which belonged to 4 TF families such as NAC (6), MYB (4), ERF (10), and bZIP (1). Additionally, we confirmed expression of 39 known miRNA families (122 members) and five conserved miRNA families, which showed differential regulation under drought stress. Targets of miRNAs were further surveyed based on a recently published study, of which ten targets were DRGs. An integrated gene regulatory network is proposed for the molecular mechanisms of tobacco root response to drought stress using differentially expressed DRGs, the changed expression profiles of miRNAs and their target transcripts. This network analysis serves as a reference for future studies on tobacco response stresses such as drought, cold and heavy metals. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Comprehensive Analysis Suggests Overlapping Expression of Rice ONAC Transcription Factors in Abiotic and Biotic Stress Responses
by Lijun Sun, Lei Huang, Yongbo Hong, Huijuan Zhang, Fengming Song and Dayong Li
Int. J. Mol. Sci. 2015, 16(2), 4306-4326; https://doi.org/10.3390/ijms16024306 - 17 Feb 2015
Cited by 44 | Viewed by 7675
Abstract
NAC (NAM/ATAF/CUC) transcription factors comprise a large plant-specific gene family that contains more than 149 members in rice. Extensive studies have revealed that NAC transcription factors not only play important roles in plant growth and development, but also have functions in regulation of [...] Read more.
NAC (NAM/ATAF/CUC) transcription factors comprise a large plant-specific gene family that contains more than 149 members in rice. Extensive studies have revealed that NAC transcription factors not only play important roles in plant growth and development, but also have functions in regulation of responses to biotic and abiotic stresses. However, biological functions for most of the members in the NAC family remain unknown. In this study, microarray data analyses revealed that a total of 63 ONAC genes exhibited overlapping expression patterns in rice under various abiotic (salt, drought, and cold) and biotic (infection by fungal, bacterial, viral pathogens, and parasitic plants) stresses. Thirty-eight ONAC genes exhibited overlapping expression in response to any two abiotic stresses, among which 16 of 30 selected ONAC genes were upregulated in response to exogenous ABA. Sixty-five ONAC genes showed overlapping expression patterns in response to any two biotic stresses. Results from the present study suggested that members of the ONAC genes with overlapping expression pattern may have pleiotropic biological functions in regulation of defense response against different abiotic and biotic stresses, which provide clues for further functional analysis of the ONAC genes in stress tolerance and pathogen resistance. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Characterisation of Two Oxidosqualene Cyclases Responsible for Triterpenoid Biosynthesis in Ilex asprella
by Xiasheng Zheng, Xiuxiu Luo, Guobing Ye, Ye Chen, Xiaoyu Ji, Lingling Wen, Yaping Xu, Hui Xu, Ruoting Zhan and Weiwen Chen
Int. J. Mol. Sci. 2015, 16(2), 3564-3578; https://doi.org/10.3390/ijms16023564 - 05 Feb 2015
Cited by 29 | Viewed by 9053
Abstract
Ilex asprella, a plant widely used as a folk herbal drug in southern China, produces and stores a large amount of triterpenoid saponins, most of which are of the α-amyrin type. In this study, two oxidosqualene cyclase (OSC) cDNAs, IaAS1 and IaAS2 [...] Read more.
Ilex asprella, a plant widely used as a folk herbal drug in southern China, produces and stores a large amount of triterpenoid saponins, most of which are of the α-amyrin type. In this study, two oxidosqualene cyclase (OSC) cDNAs, IaAS1 and IaAS2, were cloned from the I. asprella root. Functional characterisation was performed by heterologous expression in the yeast Saccharomyces cerevisiae. Analysis of the resulting products by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) showed that both genes encode a mixed amyrin synthase, producing α-amyrin and β-amyrin at different ratios. IaAS1, which mainly produces α-amyrin, is the second triterpene synthase so far identified in which the level of α-amyrin produced is ≥80% of total amyrin production. By contrast, IaAS2 mainly synthesises β-amyrin, with a yield of 95%. Gene expression patterns of these two amyrin synthases in roots and leaves of I. asprella were found to be consistent with the content patterns of total saponins. Finally, phylogenetic analysis and multiple sequence alignment of the two amyrin synthases against several known OSCs from other plants were conducted to further elucidate their evolutionary relationship. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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Article
A Ribosomal Protein AgRPS3aE from Halophilic Aspergillus glaucus Confers Salt Tolerance in Heterologous Organisms
by Xilong Liang, Yiling Liu, Lixia Xie, Xiaodan Liu, Yi Wei, Xiaoyang Zhou and Shihong Zhang
Int. J. Mol. Sci. 2015, 16(2), 3058-3070; https://doi.org/10.3390/ijms16023058 - 29 Jan 2015
Cited by 20 | Viewed by 6638
Abstract
High salt in soils is one of the abiotic stresses that significantly reduces crop yield, although saline lands are considered potential resources arable for agriculture. Currently, genetic engineering for enhancing salt tolerance is being tested as an efficient and viable strategy for crop [...] Read more.
High salt in soils is one of the abiotic stresses that significantly reduces crop yield, although saline lands are considered potential resources arable for agriculture. Currently, genetic engineering for enhancing salt tolerance is being tested as an efficient and viable strategy for crop improvement. We previously characterized a large subunit of the ribosomal protein RPL44, which is involved in osmotic stress in the extremely halophilic fungus Aspergillus glaucus. Here, we screened another ribosomal protein (AgRPS3aE) that also produced high-salt tolerance in yeast. Bioinformatics analysis indicated that AgRPS3aE encodes a 29.2 kDa small subunit of a ribosomal protein belonging to the RPS3Ae family in eukaryotes. To further confirm its protective function against salinity, we expressed AgRPS3aE in three heterologous systems, the filamentous fungus Magnaporthe oryzae and two model plants Arabidopsis and tobacco. Overexpression of AgRPS3aE in all tested transformants significantly alleviated stress symptoms compared with controls, suggesting that AgRPS3aE functions not only in fungi but also in plants. Considering that ribosomal proteins are housekeeping components in organisms from prokaryotes to eukaryotes, we propose that AgRPS3aE is one of the optimal genes for improving high-salt tolerance in crops. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Transcriptome Analysis of Methyl Jasmonate-Elicited Panax ginseng Adventitious Roots to Discover Putative Ginsenoside Biosynthesis and Transport Genes
by Hongzhe Cao, Mohammed Nuruzzaman, Hao Xiu, Jingjia Huang, Kunlu Wu, Xianghui Chen, Jijia Li, Li Wang, Ji-Hak Jeong, Sun-Jin Park, Fang Yang, Junli Luo and Zhiyong Luo
Int. J. Mol. Sci. 2015, 16(2), 3035-3057; https://doi.org/10.3390/ijms16023035 - 29 Jan 2015
Cited by 51 | Viewed by 8150
Abstract
The Panax ginseng C.A. Meyer belonging to the Araliaceae has long been used as an herbal medicine. Although public databases are presently available for this family, no methyl jasmonate (MeJA) elicited transcriptomic information was previously reported on this species, with the exception of [...] Read more.
The Panax ginseng C.A. Meyer belonging to the Araliaceae has long been used as an herbal medicine. Although public databases are presently available for this family, no methyl jasmonate (MeJA) elicited transcriptomic information was previously reported on this species, with the exception of a few expressed sequence tags (ESTs) using the traditional Sanger method. Here, approximately 53 million clean reads of adventitious root transcriptome were separately filtered via Illumina HiSeq™2000 from two samples treated with MeJA (Pg-MeJA) and equal volumes of solvent, ethanol (Pg-Con). Jointly, a total of 71,095 all-unigenes from both samples were assembled and annotated, and based on sequence similarity search with known proteins, a total of 56,668 unigenes was obtained. Out of these annotated unigenes, 54,920 were assigned to the NCBI non-redundant protein (Nr) database, 35,448 to the Swiss-prot database, 43,051 to gene ontology (GO), and 19,986 to clusters of orthologous groups (COG). Searching in the Kyoto encyclopedia of genes and genomes (KEGG) pathway database indicated that 32,200 unigenes were mapped to 128 KEGG pathways. Moreover, we obtained several genes showing a wide range of expression levels. We also identified a total of 749 ginsenoside biosynthetic enzyme genes and 12 promising pleiotropic drug resistance (PDR) genes related to ginsenoside transport. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Reactive Oxygen and Nitrogen Species in Defense/Stress Responses Activated by Chitosan in Sycamore Cultured Cells
by Massimo Malerba and Raffaella Cerana
Int. J. Mol. Sci. 2015, 16(2), 3019-3034; https://doi.org/10.3390/ijms16023019 - 29 Jan 2015
Cited by 34 | Viewed by 5526
Abstract
Chitosan (CHT) is a non-toxic and inexpensive compound obtained by deacetylation of chitin, the main component of the exoskeleton of arthropods as well as of the cell walls of many fungi. In agriculture CHT is used to control numerous diseases on various horticultural [...] Read more.
Chitosan (CHT) is a non-toxic and inexpensive compound obtained by deacetylation of chitin, the main component of the exoskeleton of arthropods as well as of the cell walls of many fungi. In agriculture CHT is used to control numerous diseases on various horticultural commodities but, although different mechanisms have been proposed, the exact mode of action of CHT is still unknown. In sycamore (Acer pseudoplatanus L.) cultured cells, CHT induces a set of defense/stress responses that includes production of H2O2 and nitric oxide (NO). We investigated the possible signaling role of these reactive molecules in some CHT-induced responses by means of inhibitors of production and/or scavengers. The results show that both reactive nitrogen and oxygen species are not only a mere symptom of stress conditions but are involved in the responses induced by CHT in sycamore cells. In particular, NO appears to be involved in a cell death form induced by CHT that shows apoptotic features like DNA fragmentation, increase in caspase-3-like activity and release of cytochrome c from the mitochondrion. On the contrary, reactive oxygen species (ROS) appear involved in a cell death form induced by CHT that does not show these apoptotic features but presents increase in lipid peroxidation. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Article
Transgenic Plants as Low-Cost Platform for Chemotherapeutic Drugs Screening
by Daniele Vergara, Stefania De Domenico, Michele Maffia, Gabriella Piro and Gian-Pietro Di Sansebastiano
Int. J. Mol. Sci. 2015, 16(1), 2174-2186; https://doi.org/10.3390/ijms16012174 - 20 Jan 2015
Cited by 9 | Viewed by 6620
Abstract
In this work we explored the possibility of using genetically modified Arabidopsis thaliana plants as a rapid and low-cost screening tool for evaluating human anticancer drugs action and efficacy. Here, four different inhibitors with a validated anticancer effect in humans and distinct mechanism [...] Read more.
In this work we explored the possibility of using genetically modified Arabidopsis thaliana plants as a rapid and low-cost screening tool for evaluating human anticancer drugs action and efficacy. Here, four different inhibitors with a validated anticancer effect in humans and distinct mechanism of action were screened in the plant model for their ability to interfere with the cytoskeletal and endomembrane networks. We used plants expressing a green fluorescent protein (GFP) tagged microtubule-protein (TUA6-GFP), and three soluble GFPs differently sorted to reside in the endoplasmic reticulum (GFPKDEL) or to accumulate in the vacuole through a COPII dependent (AleuGFP) or independent (GFPChi) mechanism. Our results demonstrated that drugs tested alone or in combination differentially influenced the monitored cellular processes including cytoskeletal organization and endomembrane trafficking. In conclusion, we demonstrated that A. thaliana plants are sensitive to the action of human chemotherapeutics and can be used for preliminary screening of drugs efficacy. The cost-effective subcellular imaging in plant cell may contribute to better clarify drugs subcellular targets and their anticancer effects. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Article
Molecular Characterization of a New Wheat-Thinopyrum intermedium Translocation Line with Resistance to Powdery Mildew and Stripe Rust
by Haixian Zhan, Xiaojun Zhang, Guangrong Li, Zhihui Pan, Jin Hu, Xin Li, Linyi Qiao, Juqing Jia, Huijuan Guo, Zhijian Chang and Zujun Yang
Int. J. Mol. Sci. 2015, 16(1), 2162-2173; https://doi.org/10.3390/ijms16012162 - 20 Jan 2015
Cited by 21 | Viewed by 7414
Abstract
A new wheat-Thinopyrum translocation line CH13-21 was selected from the progenies derived from a cross between wheat-Th. intermedium partial amphiploid TAI7047 and wheat line Mianyang11. CH13-21 was characterized by using genomic in situ hybridization (GISH), multicolor-GISH (mc-GISH), multicolor-fluorescence in situ hybridization [...] Read more.
A new wheat-Thinopyrum translocation line CH13-21 was selected from the progenies derived from a cross between wheat-Th. intermedium partial amphiploid TAI7047 and wheat line Mianyang11. CH13-21 was characterized by using genomic in situ hybridization (GISH), multicolor-GISH (mc-GISH), multicolor-fluorescence in situ hybridization (mc-FISH) and chromosome-specific molecular markers. When inoculated with stripe rust and powdery mildew isolates, CH13-21 displayed novel resistance to powdery mildew and stripe rust which inherited from its Thinopyrum parent. The chromosomal counting analyses indicated that CH13-21 has 42 chromosomes, with normal bivalent pairing at metaphase I of meiosis. GISH probed by Th. intermedium genomic DNA showed that CH13-21 contained a pair of wheat-Th. intermedium translocated chromosomes. Sequential mc-FISH analyses probed by pSc119.2 and pAs1 clearly revealed that chromosome arm 6BS of CH13-21 was replaced by Thinopyrum chromatin in the translocation chromosome. The molecular markers analysis further confirmed that the introduced Th. intermedium chromatin in CH13-21 belonged to the long arm of homoeologous group 6 chromosome. Therefore, CH13-21 was a new T6BS.6Ai#1L compensating Robertsonian translocation line. It concludes that CH13-21 is a new genetic resource for wheat breeding programs providing novel variation for disease resistances. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Variation and Genetic Structure in Platanus mexicana (Platanaceae) along Riparian Altitudinal Gradient
by Dulce M. Galván-Hernández, J. Armando Lozada-García, Norma Flores-Estévez, Jorge Galindo-González and S. Mario Vázquez-Torres
Int. J. Mol. Sci. 2015, 16(1), 2066-2077; https://doi.org/10.3390/ijms16012066 - 19 Jan 2015
Cited by 5 | Viewed by 5731
Abstract
Platanus mexicana is a dominant arboreal species of riparian ecosystems. These ecosystems are associated with altitudinal gradients that can generate genetic differences in the species, especially in the extremes of the distribution. However, studies on the altitudinal effect on genetic variation to riparian [...] Read more.
Platanus mexicana is a dominant arboreal species of riparian ecosystems. These ecosystems are associated with altitudinal gradients that can generate genetic differences in the species, especially in the extremes of the distribution. However, studies on the altitudinal effect on genetic variation to riparian species are scarce. In Mexico, the population of P. mexicana along the Colipa River (Veracruz State) grows below its reported minimum altitude range, possibly the lowest where this tree grows. This suggests that altitude might be an important factor in population genetics differentiation. We examined the genetic variation and population structuring at four sites with different altitudes (70, 200, 600 and 1700 m a.s.l.) using ten inter-simple sequence repeats (ISSR) markers. The highest value for Shannon index and Nei’s gene diversity was obtained at 1700 m a.s.l. (He = 0.27, Ne = 1.47, I = 0.42) and polymorphism reached the top value at the middle altitude (% p = 88.57). Analysis of molecular variance (AMOVA) and STRUCTURE analysis indicated intrapopulation genetic differentiation. The arithmetic average (UPGMA) dendrogram identified 70 m a.s.l. as the most genetically distant site. The genetic structuring resulted from limited gene flow and genetic drift. This is the first report of genetic variation in populations of P. mexicana in Mexico. This research highlights its importance as a dominant species, and its ecological and evolutionary implications in altitudinal gradients of riparian ecosystems. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Isolation and Characterization of Six AP2/ERF Transcription Factor Genes in Chrysanthemum nankingense
by Chunyan Gao, Peiling Li, Aiping Song, Haibin Wang, Yinjie Wang, Liping Ren, Xiangyu Qi, Fadi Chen, Jiafu Jiang and Sumei Chen
Int. J. Mol. Sci. 2015, 16(1), 2052-2065; https://doi.org/10.3390/ijms16012052 - 19 Jan 2015
Cited by 22 | Viewed by 6658
Abstract
The AP2/ERF family of plant transcription factors (TFs) regulate a variety of developmental and physiological processes. Here, we report the isolation of six AP2/ERF TF family genes from Chrysanthemum nankingense. On the basis of sequence similarity, one of these belonged to the Ethylene [...] Read more.
The AP2/ERF family of plant transcription factors (TFs) regulate a variety of developmental and physiological processes. Here, we report the isolation of six AP2/ERF TF family genes from Chrysanthemum nankingense. On the basis of sequence similarity, one of these belonged to the Ethylene Responsive Factor (ERF) subfamily and the other five to the Dehydration Responsive Element Binding protein (DREB) subfamily. A transient expression experiment showed that all six AP2/ERF proteins localized to the nucleus. A yeast-one hybrid assay demonstrated that CnDREB1-1, 1-2 and 1-3 all function as transactivators, while CnERF1, CnDREB3-1 and 3-2 have no transcriptional activation ability. The transcription response of the six TFs in response to wounding, salinity and low temperature stress and treatment with abscisic acid (ABA), salicylic acid (SA) and jasmonic acid (JA) showed that CnERF1 was up-regulated by wounding and low temperature stress but suppressed by salinity stress. The transcription of CnDREB1-1, 1-2 and 1-3 was down-regulated by ABA and JA to varying degrees. CnDREB3-1 and 3-2 was moderately increased or decreased by wounding and SA treatment, suppressed by salinity stress and JA treatment, and enhanced by low temperature stress and ABA treatment. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
The Dynamics of DNA Methylation in Maize Roots under Pb Stress
by Haiping Ding, Jian Gao, Cheng Qin, Haixia Ma, Hong Huang, Pan Song, Xirong Luo, Haijian Lin, Ya'ou Shen, Guangtang Pan and Zhiming Zhang
Int. J. Mol. Sci. 2014, 15(12), 23537-23554; https://doi.org/10.3390/ijms151223537 - 17 Dec 2014
Cited by 37 | Viewed by 7720
Abstract
Plants adapt to adverse conditions through a series of physiological, cellular, and molecular processes, culminating in stress tolerance. However, little is known about the associated regulatory mechanisms at the epigenetic level in maize under lead (Pb) stress. Therefore, in this study, we aimed [...] Read more.
Plants adapt to adverse conditions through a series of physiological, cellular, and molecular processes, culminating in stress tolerance. However, little is known about the associated regulatory mechanisms at the epigenetic level in maize under lead (Pb) stress. Therefore, in this study, we aimed to compare DNA methylation profiles during the dynamic development of maize roots following Pb treatment to identify candidate genes involved in the response to Pb stress. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) was used to investigate the genome-wide DNA methylation patterns in maize roots under normal condition (A1) and 3 mM Pb(NO3)2 stress for 12 h (K2), 24 h (K3) and 48 h (K4). The results showed that the average methylation density was the highest in CpG islands (CGIs), followed by the intergenic regions. Within the gene body, the methylation density of the introns was higher than those of the UTRs and exons. In total, 3857 methylated genes were found in 4 tested samples, including 1805 differentially methylated genes for K2 versus A1, 1508 for K3 versus A1, and 1660 for K4 versus A1. Further analysis showed that 140 genes exhibited altered DNA methylation in all three comparisons, including some well-known stress-responsive transcription factors and proteins, such as MYB, AP2/ERF, bZIP, serine-threonine/tyrosine-proteins, pentatricopeptide repeat proteins, RING zinc finger proteins, F-box proteins, leucine-rich repeat proteins and tetratricopeptide repeat proteins. This study revealed the genome-scale DNA methylation patterns of maize roots in response to Pb exposure and identified candidate genes that potentially regulate root dynamic development under Pb stress at the methylation level. Full article
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Article
Shotgun Bisulfite Sequencing of the Betula platyphylla Genome Reveals the Tree’s DNA Methylation Patterning
by Chang Su, Chao Wang, Lin He, Chuanping Yang and Yucheng Wang
Int. J. Mol. Sci. 2014, 15(12), 22874-22886; https://doi.org/10.3390/ijms151222874 - 10 Dec 2014
Cited by 16 | Viewed by 7578
Abstract
DNA methylation plays a critical role in the regulation of gene expression. Most studies of DNA methylation have been performed in herbaceous plants, and little is known about the methylation patterns in tree genomes. In the present study, we generated a map of [...] Read more.
DNA methylation plays a critical role in the regulation of gene expression. Most studies of DNA methylation have been performed in herbaceous plants, and little is known about the methylation patterns in tree genomes. In the present study, we generated a map of methylated cytosines at single base pair resolution for Betula platyphylla (white birch) by bisulfite sequencing combined with transcriptomics to analyze DNA methylation and its effects on gene expression. We obtained a detailed view of the function of DNA methylation sequence composition and distribution in the genome of B. platyphylla. There are 34,460 genes in the whole genome of birch, and 31,297 genes are methylated. Conservatively, we estimated that 14.29% of genomic cytosines are methylcytosines in birch. Among the methylation sites, the CHH context accounts for 48.86%, and is the largest proportion. Combined transcriptome and methylation analysis showed that the genes with moderate methylation levels had higher expression levels than genes with high and low methylation. In addition, methylated genes are highly enriched for the GO subcategories of binding activities, catalytic activities, cellular processes, response to stimulus and cell death, suggesting that methylation mediates these pathways in birch trees. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Article
Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean
by Senlei Zhang, Youning Wang, Kexue Li, Yanmin Zou, Liang Chen and Xia Li
Int. J. Mol. Sci. 2014, 15(8), 13596-13614; https://doi.org/10.3390/ijms150813596 - 05 Aug 2014
Cited by 47 | Viewed by 8203
Abstract
As a warm climate species, soybean is highly sensitive to chilling temperatures. Exposure to chilling temperatures causes a significant reduction in the nitrogen fixation rate in soybean plants and subsequent yield loss. However, the molecular basis for the sensitivity of soybean to chilling [...] Read more.
As a warm climate species, soybean is highly sensitive to chilling temperatures. Exposure to chilling temperatures causes a significant reduction in the nitrogen fixation rate in soybean plants and subsequent yield loss. However, the molecular basis for the sensitivity of soybean to chilling is poorly understood. In this study, we identified cold-responsive miRNAs in nitrogen-fixing nodules of soybean. Upon chilling, the expression of gma-miR397a, gma-miR166u and gma-miR171p was greatly upregulated, whereas the expression of gma-miR169c, gma-miR159b, gma-miR319a/b and gma-miR5559 was significantly decreased. The target genes of these miRNAs were predicted and validated using 5' complementary DNA ends (5'-RACE) experiments, and qPCR analysis identified putative genes targeted by the cold-responsive miRNAs in response to chilling temperatures. Taken together, our results reveal that miRNAs may be involved in the protective mechanism against chilling injury in mature nodules of soybean. Full article
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Article
The Activity of Nodules of the Supernodulating Mutant Mtsunn Is not Limited by Photosynthesis under Optimal Growth Conditions
by Ricardo A. Cabeza, Annika Lingner, Rebecca Liese, Saad Sulieman, Mehmet Senbayram, Merle Tränkner, Klaus Dittert and Joachim Schulze
Int. J. Mol. Sci. 2014, 15(4), 6031-6045; https://doi.org/10.3390/ijms15046031 - 10 Apr 2014
Cited by 12 | Viewed by 8080
Abstract
Legumes match the nodule number to the N demand of the plant. When a mutation in the regulatory mechanism deprives the plant of that ability, an excessive number of nodules are formed. These mutants show low productivity in the fields, mainly due to [...] Read more.
Legumes match the nodule number to the N demand of the plant. When a mutation in the regulatory mechanism deprives the plant of that ability, an excessive number of nodules are formed. These mutants show low productivity in the fields, mainly due to the high carbon burden caused through the necessity to supply numerous nodules. The objective of this study was to clarify whether through optimal conditions for growth and CO2 assimilation a higher nodule activity of a supernodulating mutant of Medicago truncatula (M. truncatula) can be induced. Several experimental approaches reveal that under the conditions of our experiments, the nitrogen fixation of the supernodulating mutant, designated as sunn (super numeric nodules), was not limited by photosynthesis. Higher specific nitrogen fixation activity could not be induced through short- or long-term increases in CO2 assimilation around shoots. Furthermore, a whole plant P depletion induced a decline in nitrogen fixation, however this decline did not occur significantly earlier in sunn plants, nor was it more intense compared to the wild-type. However, a distinctly different pattern of nitrogen fixation during the day/night cycles of the experiment indicates that the control of N2 fixing activity of the large number of nodules is an additional problem for the productivity of supernodulating mutants. Full article
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Article
A Chrysanthemum Heat Shock Protein Confers Tolerance to Abiotic Stress
by Aiping Song, Xirong Zhu, Fadi Chen, Haishun Gao, Jiafu Jiang and Sumei Chen
Int. J. Mol. Sci. 2014, 15(3), 5063-5078; https://doi.org/10.3390/ijms15035063 - 21 Mar 2014
Cited by 78 | Viewed by 8482
Abstract
Heat shock proteins are associated with protection against various abiotic stresses. Here, the isolation of a chrysanthemum cDNA belonging to the HSP70 family is reported. The cDNA, designated CgHSP70, encodes a 647-residue polypeptide, of estimated molecular mass 70.90 kDa and pI 5.12. [...] Read more.
Heat shock proteins are associated with protection against various abiotic stresses. Here, the isolation of a chrysanthemum cDNA belonging to the HSP70 family is reported. The cDNA, designated CgHSP70, encodes a 647-residue polypeptide, of estimated molecular mass 70.90 kDa and pI 5.12. A sub-cellular localization assay indicated that the cDNA product is deposited in the cytoplasm and nucleus. The performance of Arabidopsis thaliana plants constitutively expressing CgHSP70 demonstrated that the gene enhances tolerance to heat, drought and salinity. When CgHSP70 was stably over-expressed in chrysanthemum, the plants showed an increased peroxidase (POD) activity, higher proline content and inhibited malondialdehyde (MDA) content. After heat stress, drought or salinity the transgenic plants were better able to recover, demonstrating CgHSP70 positive effect. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Article
New Insights on Plant Cell Elongation: A Role for Acetylcholine
by Gian-Pietro Di Sansebastiano, Silvia Fornaciari, Fabrizio Barozzi, Gabriella Piro and Laura Arru
Int. J. Mol. Sci. 2014, 15(3), 4565-4582; https://doi.org/10.3390/ijms15034565 - 17 Mar 2014
Cited by 32 | Viewed by 7497
Abstract
We investigated the effect of auxin and acetylcholine on the expression of the tomato expansin gene LeEXPA2, a specific expansin gene expressed in elongating tomato hypocotyl segments. Since auxin interferes with clathrin-mediated endocytosis, in order to regulate cellular and developmental responses we [...] Read more.
We investigated the effect of auxin and acetylcholine on the expression of the tomato expansin gene LeEXPA2, a specific expansin gene expressed in elongating tomato hypocotyl segments. Since auxin interferes with clathrin-mediated endocytosis, in order to regulate cellular and developmental responses we produced protoplasts from tomato elongating hypocotyls and followed the endocytotic marker, FM4-64, internalization in response to treatments. Tomato protoplasts were observed during auxin and acetylcholine treatments after transient expression of chimerical markers of volume-control related compartments such as vacuoles. Here we describe the contribution of auxin and acetylcholine to LeEXPA2 expression regulation and we support the hypothesis that a possible subcellular target of acetylcholine signal is the vesicular transport, shedding some light on the characterization of this small molecule as local mediator in the plant physiological response. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Article
Effect of Nitrate on Nodule and Root Growth of Soybean (Glycine max (L.) Merr.)
by Akinori Saito, Sayuri Tanabata, Takanari Tanabata, Seiya Tajima, Manabu Ueno, Shinji Ishikawa, Norikuni Ohtake, Kuni Sueyoshi and Takuji Ohyama
Int. J. Mol. Sci. 2014, 15(3), 4464-4480; https://doi.org/10.3390/ijms15034464 - 13 Mar 2014
Cited by 77 | Viewed by 8863
Abstract
The application of combined nitrogen, especially nitrate, to soybean plants is known to strongly inhibit nodule formation, growth and nitrogen fixation. In the present study, we measured the effects of supplying 5 mM nitrate on the growth of nodules, primary root, and lateral [...] Read more.
The application of combined nitrogen, especially nitrate, to soybean plants is known to strongly inhibit nodule formation, growth and nitrogen fixation. In the present study, we measured the effects of supplying 5 mM nitrate on the growth of nodules, primary root, and lateral roots under light at 28 °C or dark at 18 °C conditions. Photographs of the nodulated roots were periodically taken by a digital camera at 1-h intervals, and the size of the nodules was measured with newly developed computer software. Nodule growth was depressed approximately 7 h after the addition of nitrate under light conditions. The nodule growth rate under dark conditions was almost half that under light conditions, and nodule growth was further suppressed by the addition of 5 mM nitrate. Similar results were observed for the extending growth rate of the primary root as those for nodule growth supplied with 5 mM nitrate under light/dark conditions. In contrast, the growth of lateral roots was promoted by the addition of 5 mM nitrate. The 2D-PAGE profiles of nodule protein showed similar patterns between the 0 and 5 mM nitrate treatments, which suggested that metabolic integrity may be maintained with the 5 mM nitrate treatment. Further studies are required to confirm whether light or temperature condition may give the primary effect on the growth of nodules and roots. Full article
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Article
Isolation and Characterization of the Brassinosteroid Receptor Gene (GmBRI1) from Glycine max
by Miao Wang, Shi Sun, Cunxiang Wu, Tianfu Han and Qingyu Wang
Int. J. Mol. Sci. 2014, 15(3), 3871-3888; https://doi.org/10.3390/ijms15033871 - 04 Mar 2014
Cited by 21 | Viewed by 7338
Abstract
Brassinosteroids (BRs) constitute a group of steroidal phytohormones that contribute to a wide range of plant growth and development functions. The genetic modulation of BR receptor genes, which play major roles in the BR signaling pathway, can create semi-dwarf plants that have great [...] Read more.
Brassinosteroids (BRs) constitute a group of steroidal phytohormones that contribute to a wide range of plant growth and development functions. The genetic modulation of BR receptor genes, which play major roles in the BR signaling pathway, can create semi-dwarf plants that have great advantages in crop production. In this study, a brassinosteroid insensitive gene homologous with AtBRI1 and other BRIs was isolated from Glycine max and designated as GmBRI1. A bioinformatic analysis revealed that GmBRI1 shares a conserved kinase domain and 25 tandem leucine-rich repeats (LRRs) that are characteristic of a BR receptor for BR reception and reaction and bear a striking similarity in protein tertiary structure to AtBRI1. GmBRI1 transcripts were more abundant in soybean hypocotyls and could be upregulated in response to exogenous BR treatment. The transformation of GmBRI1 into the Arabidopsis dwarf mutant bri1-5 restored the phenotype, especially regarding pod size and plant height. Additionally, this complementation is a consequence of a restored BR signaling pathway demonstrated in the light/dark analysis, root inhibition assay and BR-response gene expression. Therefore, GmBRI1 functions as a BR receptor to alter BR-mediated signaling and is valuable for improving plant architecture and enhancing the yield of soybean. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Communication
A Proteomic Approach of Bradyrhizobium/Aeschynomene Root and Stem Symbioses Reveals the Importance of the fixA Locus for Symbiosis
by Nathanael Delmotte, Samuel Mondy, Benoit Alunni, Joel Fardoux, Clémence Chaintreuil, Julia A. Vorholt, Eric Giraud and Benjamin Gourion
Int. J. Mol. Sci. 2014, 15(3), 3660-3670; https://doi.org/10.3390/ijms15033660 - 28 Feb 2014
Cited by 13 | Viewed by 7780
Abstract
Rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. These associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. Most of our knowledge [...] Read more.
Rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. These associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. Most of our knowledge on the metabolism and the physiology of the bacteria during symbiosis derives from studying roots nodules of terrestrial plants. Here we used a proteomics approach to investigate the bacterial physiology of photosynthetic Bradyrhizobium sp. ORS278 during the symbiotic process with the semi aquatical plant Aeschynomene indica that forms root and stem nodules. We analyzed the proteomes of bacteria extracted from each type of nodule. First, we analyzed the bacteroid proteome at two different time points and found only minor variation between the bacterial proteomes of 2-week- and 3-week-old nodules. High conservation of the bacteroid proteome was also found when comparing stem nodules and root nodules. Among the stem nodule specific proteins were those related to the phototrophic ability of Bradyrhizobium sp. ORS278. Furthermore, we compared our data with those obtained during an extensive genetic screen previously published. The symbiotic role of four candidate genes which corresponding proteins were found massively produced in the nodules but not identified during this screening was examined. Mutant analysis suggested that in addition to the EtfAB system, the fixA locus is required for symbiotic efficiency. Full article
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Article
Plant Dependence on Rhizobia for Nitrogen Influences Induced Plant Defenses and Herbivore Performance
by Jennifer M. Dean, Mark C. Mescher and Consuelo M. De Moraes
Int. J. Mol. Sci. 2014, 15(1), 1466-1480; https://doi.org/10.3390/ijms15011466 - 21 Jan 2014
Cited by 42 | Viewed by 7480
Abstract
Symbiotic rhizobia induce many changes in legumes that could affect aboveground interactions with herbivores. We explored how changing the intensity of Bradyrhizobium japonicum, as modulated by soil nitrogen (N) levels, influenced the interaction between soybean (Glycine max) and herbivores of [...] Read more.
Symbiotic rhizobia induce many changes in legumes that could affect aboveground interactions with herbivores. We explored how changing the intensity of Bradyrhizobium japonicum, as modulated by soil nitrogen (N) levels, influenced the interaction between soybean (Glycine max) and herbivores of different feeding guilds. When we employed a range of fertilizer applications to manipulate soil N, plants primarily dependent on rhizobia for N exhibited increased root nodulation and higher levels of foliar ureides than plants given N fertilizer; yet all treatments maintained similar total N levels. Soybean podworm (Helicoverpa zea) larvae grew best on plants with the highest levels of rhizobia but, somewhat surprisingly, preferred to feed on high-N-fertilized plants when given a choice. Induction of the defense signaling compound jasmonic acid (JA) by H. zea feeding damage was highest in plants primarily dependent on rhizobia. Differences in rhizobial dependency on soybean did not appear to affect interactions with the phloem-feeding soybean aphid (Aphis glycines). Overall, our results suggest that rhizobia association can affect plant nutritional quality and the induction of defense signaling pathways and that these effects may influence herbivore feeding preferences and performance—though such effects may vary considerably for different classes of herbivores. Full article
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Article
Mutation in the pssA Gene Involved in Exopolysaccharide Synthesis Leads to Several Physiological and Symbiotic Defects in Rhizobium leguminosarum bv. trifolii
by Monika Janczarek and Kamila Rachwał
Int. J. Mol. Sci. 2013, 14(12), 23711-23735; https://doi.org/10.3390/ijms141223711 - 05 Dec 2013
Cited by 22 | Viewed by 7394
Abstract
The symbiotic nitrogen-fixing bacterium Rhizobium leguminosarum bv. trifolii 24.2 secretes large amounts of acidic exopolysaccharide (EPS), which plays a crucial role in establishment of effective symbiosis with clover. The biosynthesis of this heteropolymer is conducted by a multi-enzymatic complex located in the bacterial [...] Read more.
The symbiotic nitrogen-fixing bacterium Rhizobium leguminosarum bv. trifolii 24.2 secretes large amounts of acidic exopolysaccharide (EPS), which plays a crucial role in establishment of effective symbiosis with clover. The biosynthesis of this heteropolymer is conducted by a multi-enzymatic complex located in the bacterial inner membrane. PssA protein, responsible for the addition of glucose-1-phosphate to a polyprenyl phosphate carrier, is involved in the first step of EPS synthesis. In this work, we characterize R. leguminosarum bv. trifolii strain Rt270 containing a mini-Tn5 transposon insertion located in the 3'-end of the pssA gene. It has been established that a mutation in this gene causes a pleiotropic effect in rhizobial cells. This is confirmed by the phenotype of the mutant strain Rt270, which exhibits several physiological and symbiotic defects such as a deficiency in EPS synthesis, decreased motility and utilization of some nutrients, decreased sensitivity to several antibiotics, an altered extracellular protein profile, and failed host plant infection. The data of this study indicate that the protein product of the pssA gene is not only involved in EPS synthesis, but also required for proper functioning of Rhizobium leguminosarum bv. trifolii cells. Full article
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Article
Functional Diversity of Genes for the Biosynthesis of Paeoniflorin and Its Derivatives in Paeonia
by Yuan Yuan, Jun Yu, Chao Jiang, Minhui Li, Shufang Lin, Xumin Wang and Luqi Huang
Int. J. Mol. Sci. 2013, 14(9), 18502-18519; https://doi.org/10.3390/ijms140918502 - 09 Sep 2013
Cited by 23 | Viewed by 7865
Abstract
The Paeonia root, with or without bark, are considered vital traditional Chinese medicine materials; the examples are those of Bai Shao, Chi Shao, and Dan Pi. In this study, we examine 24 genes and their expressions involved in the biosynthesis of paeoniflorin and [...] Read more.
The Paeonia root, with or without bark, are considered vital traditional Chinese medicine materials; the examples are those of Bai Shao, Chi Shao, and Dan Pi. In this study, we examine 24 genes and their expressions involved in the biosynthesis of paeoniflorin and its derivatives, which are active compounds of the Paeonia root, in Paeonia lactiflora and P. suffruticosa, as well as other related plants, Punica granatum, Rhus radicans, and Coriaria nepalensis. Our phylogenetic analyses suggest that these genes have functional diversity, and analysis of the transcriptional level shows paeoniflorin and gallic acid biosynthesis-related genes exhibit different transcription profiles in flowers, carpels, bark-free roots, and bark of P. lactiflora. The correlation analysis of gene expression and active compound contents support the idea that hydroxymethylglutaryl-CoA synthase and phosphomevalonate kinase in the mevalonate pathway and 3-dehydroquinate dehydratase/shikimate dehydrogenase in shikimate biosynthesis are potentially closely related to the accumulation of paeoniflorin and benzoylpaeoniflorin. Coupling gene diversity with chemical analysis, we show that paeoniflorin and its derived aromatic amino acids are predominant in bark. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Biomolecular Characterization of Diazotrophs Isolated from the Tropical Soil in Malaysia
by Umme Aminun Naher, Radziah Othman, Mohammad Abdul Latif, Qurban Ali Panhwar, Puteri Aminatulhawa Megat Amaddin and Zulkifli H Shamsuddin
Int. J. Mol. Sci. 2013, 14(9), 17812-17829; https://doi.org/10.3390/ijms140917812 - 30 Aug 2013
Cited by 6 | Viewed by 7346
Abstract
This study was conducted to evaluate selected biomolecular characteristics of rice root-associated diazotrophs isolated from the Tanjong Karang rice irrigation project area of Malaysia. Soil and rice plant samples were collected from seven soil series belonging to order Inceptisol (USDA soil taxonomy). A [...] Read more.
This study was conducted to evaluate selected biomolecular characteristics of rice root-associated diazotrophs isolated from the Tanjong Karang rice irrigation project area of Malaysia. Soil and rice plant samples were collected from seven soil series belonging to order Inceptisol (USDA soil taxonomy). A total of 38 diazotrophs were isolated using a nitrogen-free medium. The biochemical properties of the isolated bacteria, such as nitrogenase activity, indoleacetic acid (IAA) production and sugar utilization, were measured. According to a cluster analysis of Jaccard’s similarity coefficients, the genetic similarities among the isolated diazotrophs ranged from 10% to 100%. A dendogram constructed using the unweighted pair-group method with arithmetic mean (UPGMA) showed that the isolated diazotrophs clustered into 12 groups. The genomic DNA rep-PCR data were subjected to a principal component analysis, and the first four principal components (PC) accounted for 52.46% of the total variation among the 38 diazotrophs. The 10 diazotrophs that tested highly positive in the acetylene reduction assay (ARA) were identified as Bacillus spp. (9 diazotrophs) and Burkholderia sp. (Sb16) using the partial 16S rRNA gene sequence analysis. In the analysis of the biochemical characteristics, three principal components were accounted for approximately 85% of the total variation among the identified diazotrophs. The examination of root colonization using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) proved that two of the isolated diazotrophs (Sb16 and Sb26) were able to colonize the surface and interior of rice roots and fixed 22%–24% of the total tissue nitrogen from the atmosphere. In general, the tropical soils (Inceptisols) of the Tanjong Karang rice irrigation project area in Malaysia harbor a diverse group of diazotrophs that exhibit a large variation of biomolecular characteristics. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Arbuscular Mycorrhizal Fungi and Plant Growth-Promoting Pseudomonads Increases Anthocyanin Concentration in Strawberry Fruits (Fragaria x ananassa var. Selva) in Conditions of Reduced Fertilization
by Guido Lingua, Elisa Bona, Paola Manassero, Francesco Marsano, Valeria Todeschini, Simone Cantamessa, Andrea Copetta, Giovanni D'Agostino, Elisa Gamalero and Graziella Berta
Int. J. Mol. Sci. 2013, 14(8), 16207-16225; https://doi.org/10.3390/ijms140816207 - 06 Aug 2013
Cited by 129 | Viewed by 11951
Abstract
Anthocyanins are a group of common phenolic compounds in plants. They are mainly detected in flowers and fruits, are believed to play different important roles such as in the attraction of animals and seed dispersal, and also in the increase of the antioxidant [...] Read more.
Anthocyanins are a group of common phenolic compounds in plants. They are mainly detected in flowers and fruits, are believed to play different important roles such as in the attraction of animals and seed dispersal, and also in the increase of the antioxidant response in tissues directly or indirectly affected by biotic or abiotic stress factors. As a major group of secondary metabolites in plants commonly consumed as food, they are of importance in both the food industry and human nutrition. It is known that arbuscular mycorrhizal (AM) fungi can influence the plant secondary metabolic pathways such as the synthesis of essential oils in aromatic plants, of secondary metabolites in roots, and increase flavonoid concentration. Plant Growth-Promoting Bacteria (PGPB) are able to increase plant growth, improving plant nutrition and supporting plant development under natural or stressed conditions. Various studies confirmed that a number of bacterial species living on and inside the root system are beneficial for plant growth, yield and crop quality. In this work it is shown that inoculation with AM fungi and/or with selected and tested Pseudomonas strains, under conditions of reduced fertilization, increases anthocyanin concentration in the fruits of strawberry. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Genetic Analysis of Health-Related Secondary Metabolites in a Brassica rapa Recombinant Inbred Line Population
by Hedayat Bagheri, Mohamed El-Soda, Hye Kyong Kim, Steffi Fritsche, Christian Jung and Mark G. M. Aarts
Int. J. Mol. Sci. 2013, 14(8), 15561-15577; https://doi.org/10.3390/ijms140815561 - 25 Jul 2013
Cited by 8 | Viewed by 8164
Abstract
The genetic basis of the wide variation for nutritional traits in Brassica rapa is largely unknown. A new Recombinant Inbred Line (RIL) population was profiled using High Performance Liquid Chromatography (HPLC) and Nuclear Magnetic Resonance (NMR) analysis to detect quantitative trait [...] Read more.
The genetic basis of the wide variation for nutritional traits in Brassica rapa is largely unknown. A new Recombinant Inbred Line (RIL) population was profiled using High Performance Liquid Chromatography (HPLC) and Nuclear Magnetic Resonance (NMR) analysis to detect quantitative trait loci (QTLs) controlling seed tocopherol and seedling metabolite concentrations. RIL population parent L58 had a higher level of glucosinolates and phenylpropanoids, whereas levels of sucrose, glucose and glutamate were higher in the other RIL population parent, R-o-18. QTL related to seed tocopherol (α-, β-, γ-, δ-, α-⁄γ- and total tocopherol) concentrations were detected on chromosomes A3, A6, A9 and A10, explaining 11%–35% of the respective variation. The locus on A3 co-locates with the BrVTE1gene, encoding tocopherol cyclase. NMR spectroscopy identified the presence of organic/amino acid, sugar/glucosinolate and aromatic compounds in seedlings. QTL positions were obtained for most of the identified compounds. Compared to previous studies, novel loci were found for glucosinolate concentrations. This work can be used to design markers for marker-assisted selection of nutritional compounds in B. rapa. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Protein Synthesis Inhibition Activity by Strawberry Tissue Protein Extracts during Plant Life Cycle and under Biotic and Abiotic Stresses
by Letizia Polito, Massimo Bortolotti, Daniele Mercatelli, Rossella Mancuso, Gianluca Baruzzi, Walther Faedi and Andrea Bolognesi
Int. J. Mol. Sci. 2013, 14(8), 15532-15545; https://doi.org/10.3390/ijms140815532 - 25 Jul 2013
Cited by 8 | Viewed by 8549
Abstract
Ribosome-inactivating proteins (RIPs), enzymes that are widely distributed in the plant kingdom, inhibit protein synthesis by depurinating rRNA and many other polynucleotidic substrates. Although RIPs show antiviral, antifungal, and insecticidal activities, their biological and physiological roles are not completely understood. Additionally, it has [...] Read more.
Ribosome-inactivating proteins (RIPs), enzymes that are widely distributed in the plant kingdom, inhibit protein synthesis by depurinating rRNA and many other polynucleotidic substrates. Although RIPs show antiviral, antifungal, and insecticidal activities, their biological and physiological roles are not completely understood. Additionally, it has been described that RIP expression is augmented under stressful conditions. In this study, we evaluated protein synthesis inhibition activity in partially purified basic proteins (hereafter referred to as RIP activity) from tissue extracts of Fragaria × ananassa (strawberry) cultivars with low (Dora) and high (Record) tolerance to root pathogens and fructification stress. Association between the presence of RIP activity and the crop management (organic or integrated soil), growth stage (quiescence, flowering, and fructification), and exogenous stress (drought) were investigated. RIP activity was found in every tissue tested (roots, rhizomes, leaves, buds, flowers, and fruits) and under each tested condition. However, significant differences in RIP distribution were observed depending on the soil and growth stage, and an increase in RIP activity was found in the leaves of drought-stressed plants. These results suggest that RIP expression and activity could represent a response mechanism against biotic and abiotic stresses and could be a useful tool in selecting stress-resistant strawberry genotypes. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Identification and Phylogenetic Analysis of a CC-NBS-LRR Encoding Gene Assigned on Chromosome 7B of Wheat
by Caiyan Gong, Shuanghe Cao, Renchun Fan, Bo Wei, Guiping Chen, Xianping Wang, Yiwen Li and Xiangqi Zhang
Int. J. Mol. Sci. 2013, 14(8), 15330-15347; https://doi.org/10.3390/ijms140815330 - 24 Jul 2013
Cited by 10 | Viewed by 7574
Abstract
Hexaploid wheat displays limited genetic variation. As a direct A and B genome donor of hexaploid wheat, tetraploid wheat represents an important gene pool for cultivated bread wheat. Many disease resistant genes express conserved domains of the nucleotide-binding site and leucine-rich repeats (NBS-LRR). [...] Read more.
Hexaploid wheat displays limited genetic variation. As a direct A and B genome donor of hexaploid wheat, tetraploid wheat represents an important gene pool for cultivated bread wheat. Many disease resistant genes express conserved domains of the nucleotide-binding site and leucine-rich repeats (NBS-LRR). In this study, we isolated a CC-NBS-LRR gene locating on chromosome 7B from durum wheat variety Italy 363, and designated it TdRGA-7Ba. Its open reading frame was 4014 bp, encoding a 1337 amino acid protein with a complete NBS domain and 18 LRR repeats, sharing 44.7% identity with the PM3B protein. TdRGA-7Ba expression was continuously seen at low levels and was highest in leaves. TdRGA-7Ba has another allele TdRGA-7Bb with a 4 bp deletion at position +1892 in other cultivars of tetraploid wheat. In Ae. speltoides, as a B genome progenitor, both TdRGA-7Ba and TdRGA-7Bb were detected. In all six species of hexaploid wheats (AABBDD), only TdRGA-7Bb existed. Phylogenic analysis showed that all TdRGA-7Bb type genes were grouped in one sub-branch. We speculate that TdRGA-7Bb was derived from a TdRGA-7Ba mutation, and it happened in Ae. speltoides. Both types of TdRGA-7B participated in tetraploid wheat formation. However, only the TdRGA-7Bb was retained in hexaploid wheat. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Impacts of pr-10a Overexpression at the Molecular and the Phenotypic Level
by Lea A. I. Vaas, Maja Marheine, Johannes Sikorski, Markus Göker and Heinz-Martin Schumacher
Int. J. Mol. Sci. 2013, 14(7), 15141-15166; https://doi.org/10.3390/ijms140715141 - 22 Jul 2013
Cited by 7 | Viewed by 7804
Abstract
Biotechnological approaches using genetic modifications such as homologous gene overexpression can be used to decode gene functions under well-defined circumstances. However, only the recording of the resulting phenotypes allows inferences about the impact of the modification on the organisms’ evolutionary, ecological or economic [...] Read more.
Biotechnological approaches using genetic modifications such as homologous gene overexpression can be used to decode gene functions under well-defined circumstances. However, only the recording of the resulting phenotypes allows inferences about the impact of the modification on the organisms’ evolutionary, ecological or economic performance. We here compare a potato wild-type cell line with two genetically engineered cell cultures homologously overexpressing Pathogenesis Related Protein 10a (pr-10a). A detailed analysis of the relative gene-expression patterns of pr-10a and its regulators sebf and pti4 over time provides insights into the molecular response of heterotrophic cells to distinct osmotic and salt-stress conditions. Furthermore, this system serves as an exemplar for the tracing of respiration kinetics as a faster and more sensitive alternative to the laborious and time-consuming recording of growth curves. The utility and characteristics of the resulting data type and the requirements for its appropriate analysis are figured out. It is demonstrated how this novel type of phenotypic information together with the gene-expression-data provides valuable insights into the effect of genetic modifications on the behaviour of cells on both the molecular and the macroscopic level. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Induced Production of 1-Methoxy-indol-3-ylmethyl Glucosinolate by Jasmonic Acid and Methyl Jasmonate in Sprouts and Leaves of Pak Choi (Brassica rapa ssp. chinensis)
by Melanie Wiesner, Franziska S. Hanschen, Monika Schreiner, Hansruedi Glatt and Rita Zrenner
Int. J. Mol. Sci. 2013, 14(7), 14996-15016; https://doi.org/10.3390/ijms140714996 - 18 Jul 2013
Cited by 61 | Viewed by 11490
Abstract
Pak choi plants (Brassica rapa ssp. chinensis) were treated with different signaling molecules methyl jasmonate, jasmonic acid, linolenic acid, and methyl salicylate and were analyzed for specific changes in their glucosinolate profile. Glucosinolate levels were quantified using HPLC-DAD-UV, with focus on [...] Read more.
Pak choi plants (Brassica rapa ssp. chinensis) were treated with different signaling molecules methyl jasmonate, jasmonic acid, linolenic acid, and methyl salicylate and were analyzed for specific changes in their glucosinolate profile. Glucosinolate levels were quantified using HPLC-DAD-UV, with focus on induction of indole glucosinolates and special emphasis on 1-methoxy-indol-3-ylmethyl glucosinolate. Furthermore, the effects of the different signaling molecules on indole glucosinolate accumulation were analyzed on the level of gene expression using semi-quantitative realtime RT-PCR of selected genes. The treatments with signaling molecules were performed on sprouts and mature leaves to determine ontogenetic differences in glucosinolate accumulation and related gene expression. The highest increase of indole glucosinolate levels, with considerable enhancement of the 1-methoxy-indol-3-ylmethyl glucosinolate content, was achieved with treatments of sprouts and mature leaves with methyl jasmonate and jasmonic acid. This increase was accompanied by increased expression of genes putatively involved in the indole glucosinolate biosynthetic pathway. The high levels of indole glucosinolates enabled the plant to preferentially produce the respective breakdown products after tissue damage. Thus, pak choi plants treated with methyl jasmonate or jasmonic acid, are a valuable tool to analyze the specific protection functions of 1-methoxy-indole-3-carbinole in the plants defense strategy in the future. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
MAEWEST Expression in Flower Development of Two Petunia Species
by Ana Lúcia A. Segatto, Andreia Carina Turchetto-Zolet, Lilian Cristina B. Aizza, Carolina C. Monte-Bello, Marcelo C. Dornelas, Rogerio Margis and Loreta B. Freitas
Int. J. Mol. Sci. 2013, 14(7), 13796-13807; https://doi.org/10.3390/ijms140713796 - 03 Jul 2013
Cited by 3 | Viewed by 9022
Abstract
Changes in flower morphology may influence the frequency and specificity of animal visitors. In Petunia (Solanaceae), adaptation to different pollinators is one of the factors leading to species diversification within the genus. This study provides evidence that differential expression patterns of MAWEWEST ( [...] Read more.
Changes in flower morphology may influence the frequency and specificity of animal visitors. In Petunia (Solanaceae), adaptation to different pollinators is one of the factors leading to species diversification within the genus. This study provides evidence that differential expression patterns of MAWEWEST (MAW) homologs in different Petunia species may be associated with adaptive changes in floral morphology. The Petunia × hybrida MAW gene belongs to the WOX (WUSCHEL-related homeobox) transcription factor family and has been identified as a controller of petal fusion during corolla formation. We analyzed the expression patterns of P. inflata and P. axillaris MAW orthologs (PiMAW and PaMAW, respectively) by reverse transcriptase polymerase chain reaction (RT-PCR), reverse transcription–quantitative PCR (qRT-PCR) and in situ hybridization in different tissues and different developmental stages of flowers in both species. The spatial expression patterns of PiMAW and PaMAW were similar in P. inflata and P. axillaris. Nevertheless, PaMAW expression level in P. axillaris was higher during the late bud development stage as compared to PiMAW in P. inflata. This work represents an expansion of petunia developmental research to wild accessions. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Early Phenylpropanoid Biosynthetic Steps in Cannabis sativa: Link between Genes and Metabolites
by Teresa Docimo, Roberto Consonni, Immacolata Coraggio and Monica Mattana
Int. J. Mol. Sci. 2013, 14(7), 13626-13644; https://doi.org/10.3390/ijms140713626 - 28 Jun 2013
Cited by 29 | Viewed by 10900
Abstract
Phenylalanine ammonia-lyase (PAL), Cinnamic acid 4-hydroxylase (C4H) and 4-Coumarate: CoA ligase (4CL) catalyze the first three steps of the general phenylpropanoid pathway whereas chalcone synthase (CHS) catalyzes the first specific step towards flavonoids production. This class of specialized metabolites has a wide range [...] Read more.
Phenylalanine ammonia-lyase (PAL), Cinnamic acid 4-hydroxylase (C4H) and 4-Coumarate: CoA ligase (4CL) catalyze the first three steps of the general phenylpropanoid pathway whereas chalcone synthase (CHS) catalyzes the first specific step towards flavonoids production. This class of specialized metabolites has a wide range of biological functions in plant development and defence and a broad spectrum of therapeutic activities for human health. In this study, we report the isolation of hemp PAL and 4CL cDNA and genomic clones. Through in silico analysis of their deduced amino acid sequences, more than an 80% identity with homologues genes of other plants was shown and phylogenetic relationships were highlighted. Quantitative expression analysis of the four above mentioned genes, PAL and 4CL enzymatic activities, lignin content and NMR metabolite fingerprinting in different Cannabis sativa tissues were evaluated. Furthermore, the use of different substrates to assay PAL and 4CL enzymatic activities indicated that different isoforms were active in different tissues. The diversity in secondary metabolites content observed in leaves (mainly flavonoids) and roots (mainly lignin) was discussed in relation to gene expression and enzymatic activities data. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Alleviation of Osmotic Stress Effects by Exogenous Application of Salicylic or Abscisic Acid on Wheat Seedlings
by Izabela Marcińska, Ilona Czyczyło-Mysza, Edyta Skrzypek, Maciej T. Grzesiak, Franciszek Janowiak, Maria Filek, Michał Dziurka, Kinga Dziurka, Piotr Waligórski, Katarzyna Juzoń, Katarzyna Cyganek and Stanisław Grzesiak
Int. J. Mol. Sci. 2013, 14(7), 13171-13193; https://doi.org/10.3390/ijms140713171 - 26 Jun 2013
Cited by 72 | Viewed by 9718
Abstract
The aim of the study was to assess the role of salicylic acid (SA) and abscisic acid (ABA) in osmotic stress tolerance of wheat seedlings. This was accomplished by determining the impact of the acids applied exogenously on seedlings grown under osmotic stress [...] Read more.
The aim of the study was to assess the role of salicylic acid (SA) and abscisic acid (ABA) in osmotic stress tolerance of wheat seedlings. This was accomplished by determining the impact of the acids applied exogenously on seedlings grown under osmotic stress in hydroponics. The investigation was unique in its comprehensiveness, examining changes under osmotic stress and other conditions, and testing a number of parameters simultaneously. In both drought susceptible (SQ1) and drought resistant (CS) wheat cultivars, significant physiological and biochemical changes were observed upon the addition of SA (0.05 mM) or ABA (0.1 μM) to solutions containing half-strength Hoagland medium and PEG 6000 (−0.75 MPa). The most noticeable result of supplementing SA or ABA to the medium (PEG + SA and PEG + ABA) was a decrease in the length of leaves and roots in both cultivars. While PEG treatment reduced gas exchange parameters, chlorophyll content in CS, and osmotic potential, and conversely, increased lipid peroxidation, soluble carbohydrates in SQ1, proline content in both cultivars and total antioxidants activity in SQ1, PEG + SA or PEG + ABA did not change the values of these parameters. Furthermore, PEG caused a two-fold increase of endogenous ABA content in SQ1 and a four-fold increase in CS. PEG + ABA increased endogenous ABA only in SQ1, whereas PEG + SA caused a greater increase of ABA content in both cultivars compared to PEG. In PEG-treated plants growing until the harvest, a greater decrease of yield components was observed in SQ1 than in CS. PEG + SA, and particularly PEG + ABA, caused a greater increase of these yield parameters in CS compared to SQ1. In conclusion, SA and ABA ameliorate, particularly in the tolerant wheat cultivar, the harmful effects and after effects of osmotic stress induced by PEG in hydroponics through better osmotic adjustment achieved by an increase in proline and carbohydrate content as well as by an increase in antioxidant activity. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Metabolomic-Based Study of the Leafy Gall, the Ecological Niche of the Phytopathogen Rhodococcus fascians, as a Potential Source of Bioactive Compounds
by Aminata P. Nacoulma, Olivier M. Vandeputte, Manuella De Lorenzi, Mondher El Jaziri and Pierre Duez
Int. J. Mol. Sci. 2013, 14(6), 12533-12549; https://doi.org/10.3390/ijms140612533 - 14 Jun 2013
Cited by 10 | Viewed by 9729
Abstract
Leafy gall is a plant hyperplasia induced upon Rhodococcus fascians infection. Previously, by genomic and transcriptomic analysis, it has been reported that, at the early stage of symptom development, both primary and secondary metabolisms are modified. The present study is based on the [...] Read more.
Leafy gall is a plant hyperplasia induced upon Rhodococcus fascians infection. Previously, by genomic and transcriptomic analysis, it has been reported that, at the early stage of symptom development, both primary and secondary metabolisms are modified. The present study is based on the hypothesis that fully developed leafy gall, could represent a potential source of new bioactive compounds. Therefore, non-targeted metabolomic analysis of aqueous and chloroform extracts of leafy gall and non-infected tobacco was carried out by 1H-NMR coupled to principal component analysis (PCA) and orthogonal projections to latent structures-discriminant analysis (OPLS-DA). Polar metabolite profiling reflects modifications mainly in the primary metabolites and in some polyphenolics. In contrast, main modifications occurring in non-polar metabolites concern secondary metabolites, and gas chromatography and mass spectrometry (GC-MS) evidenced alterations in diterpenoids family. Analysis of crude extracts of leafy galls and non-infected tobacco leaves exhibited a distinct antiproliferative activity against all four tested human cancer cell lines. A bio-guided fractionation of chloroformic crude extract yield to semi-purified fractions, which inhibited proliferation of glioblastoma U373 cells with IC50 between 14.0 and 2.4 µg/mL. Discussion is focused on the consequence of these metabolic changes, with respect to plant defense mechanisms following infection. Considering the promising role of diterpenoid family as bioactive compounds, leafy gall may rather be a propitious source for drug discovery. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Combining Hexanoic Acid Plant Priming with Bacillus thuringiensis Insecticidal Activity against Colorado Potato Beetle
by Inmaculada García-Robles, Camila Ochoa-Campuzano, Emma Fernández-Crespo, Gemma Camañes, Amparo C. Martínez-Ramírez, Carmen González-Bosch, Pilar García-Agustín, Carolina Rausell and María Dolores Real
Int. J. Mol. Sci. 2013, 14(6), 12138-12156; https://doi.org/10.3390/ijms140612138 - 06 Jun 2013
Cited by 10 | Viewed by 9330
Abstract
Interaction between insect herbivores and host plants can be modulated by endogenous and exogenous compounds present in the source of food and might be successfully exploited in Colorado potato beetle (CPB) pest management. Feeding tests with CPB larvae reared on three solanaceous plants [...] Read more.
Interaction between insect herbivores and host plants can be modulated by endogenous and exogenous compounds present in the source of food and might be successfully exploited in Colorado potato beetle (CPB) pest management. Feeding tests with CPB larvae reared on three solanaceous plants (potato, eggplant and tomato) resulted in variable larval growth rates and differential susceptibility to Bacillus thuringiensis Cry3Aa toxin as a function of the host plant. An inverse correlation with toxicity was observed in Cry3Aa proteolytic patterns generated by CPB midgut brush-border membrane vesicles (BBMV) from Solanaceae-fed larvae, being the toxin most extensively proteolyzed on potato, followed by eggplant and tomato. We found that CPB cysteine proteases intestains may interact with Cry3Aa toxin and, in CPB BBMV from larvae fed all three Solanaceae, the toxin was able to compete for the hydrolysis of a papain substrate. In response to treatment with the JA-dependent plant inducer Hexanoic acid (Hx), we showed that eggplant reduced OPDA basal levels and both, potato and eggplant induced JA-Ile. CPB larvae feeding on Hx-induced plants exhibited enhanced Cry3Aa toxicity, which correlated with altered papain activity. Results indicated host-mediated effects on B. thuringiensis efficacy against CPB that can be enhanced in combination with Hx plant induction. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Use of Heat Stress Responsive Gene Expression Levels for Early Selection of Heat Tolerant Cabbage (Brassica oleracea L.)
by Hyun Ji Park, Won Yong Jung, Sang Sook Lee, Jun Ho Song, Suk-Yoon Kwon, HyeRan Kim, ChulWook Kim, Jun Cheul Ahn and Hye Sun Cho
Int. J. Mol. Sci. 2013, 14(6), 11871-11894; https://doi.org/10.3390/ijms140611871 - 04 Jun 2013
Cited by 41 | Viewed by 10352
Abstract
Cabbage is a relatively robust vegetable at low temperatures. However, at high temperatures, cabbage has disadvantages, such as reduced disease tolerance and lower yields. Thus, selection of heat-tolerant cabbage is an important goal in cabbage breeding. Easier or faster selection of superior varieties [...] Read more.
Cabbage is a relatively robust vegetable at low temperatures. However, at high temperatures, cabbage has disadvantages, such as reduced disease tolerance and lower yields. Thus, selection of heat-tolerant cabbage is an important goal in cabbage breeding. Easier or faster selection of superior varieties of cabbage, which are tolerant to heat and disease and have improved taste and quality, can be achieved with molecular and biological methods. We compared heat-responsive gene expression between a heat-tolerant cabbage line (HTCL), “HO”, and a heat-sensitive cabbage line (HSCL), “JK”, by Genechip assay. Expression levels of specific heat stress-related genes were increased in response to high-temperature stress, according to Genechip assays. We performed quantitative RT-PCR (qRT-PCR) to compare expression levels of these heat stress-related genes in four HTCLs and four HSCLs. Transcript levels for heat shock protein BoHsp70 and transcription factor BoGRAS (SCL13) were more strongly expressed only in all HTCLs compared to all HSCLs, showing much lower level expressions at the young plant stage under heat stress (HS). Thus, we suggest that expression levels of these genes may be early selection markers for HTCLs in cabbage breeding. In addition, several genes that are involved in the secondary metabolite pathway were differentially regulated in HTCL and HSCL exposed to heat stress. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Versatile Redox Chemistry Complicates Antioxidant Capacity Assessment: Flavonoids as Milieu-Dependent Anti- and Pro-Oxidants
by Vladimir Chobot, Lenka Kubicova, Gert Bachmann and Franz Hadacek
Int. J. Mol. Sci. 2013, 14(6), 11830-11841; https://doi.org/10.3390/ijms140611830 - 04 Jun 2013
Cited by 20 | Viewed by 7508
Abstract
Some antioxidants have been shown to possess additional pro-oxidant effects. Diverse methodologies exist for studying redox properties of synthetic and natural chemicals. The latter are substantial components of our diet. Exploration of their contribution to life-extending or -compromising effects is mandatory. Among reactive [...] Read more.
Some antioxidants have been shown to possess additional pro-oxidant effects. Diverse methodologies exist for studying redox properties of synthetic and natural chemicals. The latter are substantial components of our diet. Exploration of their contribution to life-extending or -compromising effects is mandatory. Among reactive oxygen species (ROS), hydroxyl radical (OH) is the most damaging species. Due to its short half-life, the assay has to contain a specific generation system. Plants synthesize flavonoids, phenolic compounds recognized as counter-agents to coronary heart disease. Their antioxidant activities are affected by their hydroxylation patterns. Moreover, in the plant, they mainly occur as glycosides. We chose three derivatives, quercetin, luteolin, and rutin, in attempts to explore their redox chemistry in contrasting hydrogen peroxide environments. Initial addition of hydrogen peroxide in high concentration or gradual development constituted a main factor affecting their redox chemical properties, especially in case of quercetin. Our study exemplifies that a combination of a chemical assay (deoxyribose degradation) with an electrochemical method (square-wave voltammetry) provides insightful data. The ambiguity of the tested flavonoids to act either as anti- or pro-oxidant may complicate categorization, but probably contributed to their evolution as components of a successful metabolic system that benefits both producer and consumer. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
The Physiological Importance of Glucosinolates on Plant Response to Abiotic Stress in Brassica
by María Del Carmen Martínez-Ballesta, Diego A. Moreno and Micaela Carvajal
Int. J. Mol. Sci. 2013, 14(6), 11607-11625; https://doi.org/10.3390/ijms140611607 - 30 May 2013
Cited by 253 | Viewed by 18970
Abstract
Glucosinolates, a class of secondary metabolites, mainly found in Brassicaceae, are affected by the changing environment. This review is focusing on the physiological significance of glucosinolates and their hydrolysis products in the plant response to different abiotic stresses. Special attention is paid to [...] Read more.
Glucosinolates, a class of secondary metabolites, mainly found in Brassicaceae, are affected by the changing environment. This review is focusing on the physiological significance of glucosinolates and their hydrolysis products in the plant response to different abiotic stresses. Special attention is paid to the crosstalk between some of the physiological processes involved in stress response and glucosinolate metabolism, with the resulting connection between both pathways in which signaling mechanisms glucosinolate may act as signals themselves. The function of glucosinolates, further than in defense switching, is discussed in terms of alleviating pathogen attack under abiotic stress. The fact that the exogenous addition of glucosinolate hydrolysis products may alleviate certain stress conditions through its effect on specific proteins is described in light of the recent reports, but the molecular mechanisms involved in this response merit further research. Finally, the transient allocation and re-distribution of glucosinolates as a response to environmental changes is summarized. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Oxidative and Molecular Responses in Capsicum annuum L. after Hydrogen Peroxide, Salicylic Acid and Chitosan Foliar Applications
by Laura Mejía-Teniente, Flor de Dalia Durán-Flores, Angela María Chapa-Oliver, Irineo Torres-Pacheco, Andrés Cruz-Hernández, Mario M. González-Chavira, Rosalía V. Ocampo-Velázquez and Ramón G. Guevara-González
Int. J. Mol. Sci. 2013, 14(5), 10178-10196; https://doi.org/10.3390/ijms140510178 - 15 May 2013
Cited by 83 | Viewed by 10621
Abstract
Hydrogen peroxide (H2O2) is an important ROS molecule (Reactive oxygen species) that serves as a signal of oxidative stress and activation of signaling cascades as a result of the early response of the plant to biotic stress. This response [...] Read more.
Hydrogen peroxide (H2O2) is an important ROS molecule (Reactive oxygen species) that serves as a signal of oxidative stress and activation of signaling cascades as a result of the early response of the plant to biotic stress. This response can also be generated with the application of elicitors, stable molecules that induce the activation of transduction cascades and hormonal pathways, which trigger induced resistance to environmental stress. In this work, we evaluated the endogenous H2O2 production caused by salicylic acid (SA), chitosan (QN), and H2O2 elicitors in Capsicum annuum L. Hydrogen peroxide production after elicitation, catalase (CAT) and phenylalanine ammonia lyase (PAL) activities, as well as gene expression analysis of cat1, pal, and pathogenesis-related protein 1 (pr1) were determined. Our results displayed that 6.7 and 10 mM SA concentrations, and, 14 and 18 mM H2O2 concentrations, induced an endogenous H2O2 and gene expression. QN treatments induced the same responses in lesser proportion than the other two elicitors. Endogenous H2O2 production monitored during several days, showed results that could be an indicator for determining application opportunity uses in agriculture for maintaining plant alert systems against a stress. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Microarray Analysis of Transcriptional Responses to Abscisic Acid and Salt Stress in Arabidopsis thaliana
by Yujia Liu, Xiaoyu Ji, Lei Zheng, Xianguang Nie and Yucheng Wang
Int. J. Mol. Sci. 2013, 14(5), 9979-9998; https://doi.org/10.3390/ijms14059979 - 10 May 2013
Cited by 29 | Viewed by 9379
Abstract
Abscisic acid (ABA) plays a crucial role in plant responses to abiotic stress. To investigate differences in plant responses to salt and ABA stimulus, differences in gene expression in Arabidopsis in response to salt and ABA were compared using an Agilent oligo microarray. [...] Read more.
Abscisic acid (ABA) plays a crucial role in plant responses to abiotic stress. To investigate differences in plant responses to salt and ABA stimulus, differences in gene expression in Arabidopsis in response to salt and ABA were compared using an Agilent oligo microarray. A total of 144 and 139 genes were significantly up- and downregulated, respectively, under NaCl stress, while 406 and 381 genes were significantly up- and downregulated, respectively, under ABA stress conditions. In addition, 31 genes were upregulated by both NaCl and ABA stresses, and 23 genes were downregulated by these stressors, suggesting that these genes may play similar roles in plant responses to salt and ABA stress. Gene ontology (GO) analysis revealed four subgroups of genes, including genes in the GO categories “Molecular transducer activity”, “Growth”, “Biological adhesion” and “Pigmentation”, which were expressed in response to ABA stress but not NaCl stress. In addition, genes that play specific roles during salt or ABA stress were identified. Our results may help elucidate differences in the response of plants to salt and ABA stress. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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365 KiB  
Article
Two Volatile Organic Compounds Trigger Plant Self-Defense against a Bacterial Pathogen and a Sucking Insect in Cucumber under Open Field Conditions
by Geun Cheol Song and Choong-Min Ryu
Int. J. Mol. Sci. 2013, 14(5), 9803-9819; https://doi.org/10.3390/ijms14059803 - 08 May 2013
Cited by 147 | Viewed by 12539
Abstract
Systemic acquired resistance (SAR) is a plant self-defense mechanism against a broad-range of pathogens and insect pests. Among chemical SAR triggers, plant and bacterial volatiles are promising candidates for use in pest management, as these volatiles are highly effective, inexpensive, and can be [...] Read more.
Systemic acquired resistance (SAR) is a plant self-defense mechanism against a broad-range of pathogens and insect pests. Among chemical SAR triggers, plant and bacterial volatiles are promising candidates for use in pest management, as these volatiles are highly effective, inexpensive, and can be employed at relatively low concentrations compared with agrochemicals. However, such volatiles have some drawbacks, including the high evaporation rate of these compounds after application in the open field, their negative effects on plant growth, and their inconsistent levels of effectiveness. Here, we demonstrate the effectiveness of volatile organic compound (VOC)-mediated induced resistance against both the bacterial angular leaf spot pathogen, Pseudononas syringae pv. lachrymans, and the sucking insect aphid, Myzus persicae, in the open field. Using the VOCs 3-pentanol and 2-butanone where fruit yields increased gave unexpectedly, a significant increase in the number of ladybird beetles, Coccinella septempunctata, a natural enemy of aphids. The defense-related gene CsLOX was induced by VOC treatment, indicating that triggering the oxylipin pathway in response to the emission of green leaf volatiles can recruit the natural enemy of aphids. These results demonstrate that VOCs may help prevent plant disease and insect damage by eliciting induced resistance, even in open fields. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Effects of (−)-Gallocatechin-3-Gallate on Tetrodotoxin-Resistant Voltage-Gated Sodium Channels in Rat Dorsal Root Ganglion Neurons
by Yan Zhang, Yan-Yan Jia, Jin-Lei Guo, Pei-Qing Liu and Jian-Min Jiang
Int. J. Mol. Sci. 2013, 14(5), 9779-9789; https://doi.org/10.3390/ijms14059779 - 07 May 2013
Cited by 6 | Viewed by 6895
Abstract
The (−)-gallocatechin-3-gallate (GCG) concentration in some tea beverages can account for as much as 50% of the total catechins. It has been shown that catechins have analgesic properties. Voltage-gated sodium channels (Nav) mediate neuronal action potentials. Tetrodotoxin inhibits all Nav isoforms, but Nav1.8 [...] Read more.
The (−)-gallocatechin-3-gallate (GCG) concentration in some tea beverages can account for as much as 50% of the total catechins. It has been shown that catechins have analgesic properties. Voltage-gated sodium channels (Nav) mediate neuronal action potentials. Tetrodotoxin inhibits all Nav isoforms, but Nav1.8 and Nav1.9 are relatively tetrodotoxin-resistant compared to other isoforms and functionally linked to nociception. In this study, the effects of GCG on tetrodotoxin-resistant Na+ currents were investigated in rat primary cultures of dorsal root ganglion neurons via the whole-cell patch-clamp technique. We found that 1 μM GCG reduced the amplitudes of peak current density of tetrodotoxin-resistant Na+ currents significantly. Furthermore, the inhibition was accompanied by a depolarizing shift of the activation voltage and a hyperpolarizing shift of steady-state inactivation voltage. The percentage block of GCG (1 μM) on tetrodotoxin-resistant Na+ current was 45.1% ± 1.1% in 10 min. In addition, GCG did not produce frequency-dependent block of tetrodotoxin-resistant Na+ currents at stimulation frequencies of 1 Hz, 2 Hz and 5 Hz. On the basis of these findings, we propose that GCG may be a potential analgesic agent. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
Antioxidant Systems from Pepper (Capsicum annuum L.): Involvement in the Response to Temperature Changes in Ripe Fruits
by Rosa M. Mateos, Ana Jiménez, Paloma Román, Félix Romojaro, Sierra Bacarizo, Marina Leterrier, Manuel Gómez, Francisca Sevilla, Luis A. Del Río, Francisco J. Corpas and José M. Palma
Int. J. Mol. Sci. 2013, 14(5), 9556-9580; https://doi.org/10.3390/ijms14059556 - 02 May 2013
Cited by 70 | Viewed by 10218
Abstract
Sweet pepper is susceptible to changes in the environmental conditions, especially temperatures below 15 °C. In this work, two sets of pepper fruits (Capsicum annuum L.) which underwent distinct temperature profiles in planta were investigated. Accordingly, two harvesting times corresponding to each [...] Read more.
Sweet pepper is susceptible to changes in the environmental conditions, especially temperatures below 15 °C. In this work, two sets of pepper fruits (Capsicum annuum L.) which underwent distinct temperature profiles in planta were investigated. Accordingly, two harvesting times corresponding to each set were established: Harvest 1, whose fruits developed and ripened at 14.9 °C as average temperature; and Harvest 2, with average temperature of 12.4 °C. The oxidative metabolism was analyzed in all fruits. Although total ascorbate content did not vary between Harvests, a shift from the reduced to the oxidized form (dehydroascorbate), accompanied by a higher ascorbate peroxidase activity, was observed in Harvest 2 with respect to Harvest 1. Moreover, a decrease of the ascorbate-generating enzymatic system, the γ-galactono-lactone dehydrogenase, was found at Harvest 2. The activity values of the NADP-dependent dehydrogenases analyzed seem to indicate that a lower NADPH synthesis may occur in fruits which underwent lower temperature conditions. In spite of the important changes observed in the oxidative metabolism in fruits subjected to lower temperature, no oxidative stress appears to occur, as indicated by the lipid peroxidation and protein oxidation profiles. Thus, the antioxidative systems of pepper fruits seem to be involved in the response against temperature changes. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Drought Stress Acclimation Imparts Tolerance to Sclerotinia sclerotiorum and Pseudomonas syringae in Nicotiana benthamiana
by Venkategowda Ramegowda, Muthappa Senthil-Kumar, Yasuhiro Ishiga, Amita Kaundal, Makarla Udayakumar and Kirankumar S. Mysore
Int. J. Mol. Sci. 2013, 14(5), 9497-9513; https://doi.org/10.3390/ijms14059497 - 02 May 2013
Cited by 80 | Viewed by 10477
Abstract
Acclimation of plants with an abiotic stress can impart tolerance to some biotic stresses. Such a priming response has not been widely studied. In particular, little is known about enhanced defense capacity of drought stress acclimated plants to fungal and bacterial pathogens. Here [...] Read more.
Acclimation of plants with an abiotic stress can impart tolerance to some biotic stresses. Such a priming response has not been widely studied. In particular, little is known about enhanced defense capacity of drought stress acclimated plants to fungal and bacterial pathogens. Here we show that prior drought acclimation in Nicotiana benthamiana plants imparts tolerance to necrotrophic fungus, Sclerotinia sclerotiorum, and also to hemi-biotrophic bacterial pathogen, Pseudomonas syringae pv. tabaci. S. sclerotiorum inoculation on N. benthamiana plants acclimated with drought stress lead to less disease-induced cell death compared to non-acclimated plants. Furthermore, inoculation of P. syringae pv. tabaci on N. benthamiana plants acclimated to moderate drought stress showed reduced disease symptoms. The levels of reactive oxygen species (ROS) in drought acclimated plants were highly correlated with disease resistance. Further, in planta growth of GFPuv expressing P. syringae pv. tabaci on plants pre-treated with methyl viologen showed complete inhibition of bacterial growth. Taken together, these experimental results suggested a role for ROS generated during drought acclimation in imparting tolerance against S. sclerotiorum and P. syringae pv. tabaci. We speculate that the generation of ROS during drought acclimation primed a defense response in plants that subsequently caused the tolerance against the pathogens tested. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Improved Nutritive Quality and Salt Resistance in Transgenic Maize by Simultaneously Overexpression of a Natural Lysine-Rich Protein Gene, SBgLR, and an ERF Transcription Factor Gene, TSRF1
by Meizhen Wang, Chen Liu, Shixue Li, Dengyun Zhu, Qian Zhao and Jingjuan Yu
Int. J. Mol. Sci. 2013, 14(5), 9459-9474; https://doi.org/10.3390/ijms14059459 - 29 Apr 2013
Cited by 30 | Viewed by 8037
Abstract
Maize (Zea mays L.), as one of the most important crops in the world, is deficient in lysine and tryptophan. Environmental conditions greatly impact plant growth, development and productivity. In this study, we used particle bombardment mediated co-transformation to obtain marker-free transgenic [...] Read more.
Maize (Zea mays L.), as one of the most important crops in the world, is deficient in lysine and tryptophan. Environmental conditions greatly impact plant growth, development and productivity. In this study, we used particle bombardment mediated co-transformation to obtain marker-free transgenic maize inbred X178 lines harboring a lysine-rich protein gene SBgLR from potato and an ethylene responsive factor (ERF) transcription factor gene, TSRF1, from tomato. Both of the target genes were successfully expressed and showed various expression levels in different transgenic lines. Analysis showed that the protein and lysine content in T1 transgenic maize seeds increased significantly. Compared to non-transformed maize, the protein and lysine content increased by 7.7% to 24.38% and 8.70% to 30.43%, respectively. Moreover, transgenic maize exhibited more tolerance to salt stress. When treated with 200 mM NaCl for 48 h, both non-transformed and transgenic plant leaves displayed wilting and losing green symptoms and dramatic increase of the free proline contents. However, the degree of control seedlings was much more serious than that of transgenic lines and much more increases of the free proline contents in the transgenic lines than that in the control seedlings were observed. Meanwhile, lower extent decreases of the chlorophyll contents were detected in the transgenic seedlings. Quantitative RT-PCR was performed to analyze the expression of ten stress-related genes, including stress responsive transcription factor genes, ZmMYB59 and ZmMYC1, proline synthesis related genes, ZmP5CS1 and ZmP5CS2, photosynthesis-related genes, ZmELIP, ZmPSI-N, ZmOEE, Zmrbcs and ZmPLAS, and one ABA biosynthesis related gene, ZmSDR. The results showed that with the exception of ZmP5CS1 and ZmP5CS2 in line 9–10 and 19–11, ZmMYC1 in line 19–11 and ZmSDR in line 19–11, the expression of other stress-related genes were inhibited in transgenic lines under normal conditions. After salt treatment, the expressions of the ten stress-related genes were significantly induced in both wild-type (WT) and transgenic lines. However, compared to WT, the increases of ZmP5CS1 in all these three transgenic lines and ZmP5CS2 in line 9–10 were less than WT plants. This study provides an effective approach of maize genetic engineering for improved nutritive quality and salt tolerance. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Characterization of Rice NADPH Oxidase Genes and Their Expression under Various Environmental Conditions
by Gang-Feng Wang, Wen-Qiang Li, Wen-Yan Li, Guo-Li Wu, Cong-Yi Zhou and Kun-Ming Chen
Int. J. Mol. Sci. 2013, 14(5), 9440-9458; https://doi.org/10.3390/ijms14059440 - 29 Apr 2013
Cited by 88 | Viewed by 9050
Abstract
Plasma membrane NADPH oxidases (Noxs) are key producers of reactive oxygen species under both normal and stress conditions in plants. We demonstrate that at least eleven genes in the genome of rice (Oryza sativa L.) were predicted to encode Nox proteins, including [...] Read more.
Plasma membrane NADPH oxidases (Noxs) are key producers of reactive oxygen species under both normal and stress conditions in plants. We demonstrate that at least eleven genes in the genome of rice (Oryza sativa L.) were predicted to encode Nox proteins, including nine genes (OsNox19) that encode typical Noxs and two that encode ancient Nox forms (ferric reduction oxidase 1 and 7, OsFRO1 and OsFRO7). Phylogenetic analysis divided the Noxs from nine plant species into six subfamilies, with rice Nox genes distributed among subfamilies I to V. Gene expression analysis using semi-quantitative RT-PCR and real-time qRT-PCR indicated that the expression of rice Nox genes depends on organs and environmental conditions. Exogenous calcium strongly stimulated the expression of OsNox3, OsNox5, OsNox7, and OsNox8, but depressed the expression of OsFRO1. Drought stress substantially upregulated the expression of OsNox13, OsNox5, OsNox9, and OsFRO1, but downregulated OsNox6. High temperature upregulated OsNox59, but significantly downregulated OsNox13 and OsFRO1. NaCl treatment increased the expression of OsNox2, OsNox8, OsFRO1, and OsFRO7, but decreased that of OsNox1, OsNox3, OsNox5, and OsNox6. These results suggest that the expression profiles of rice Nox genes have unique stress-response characteristics, reflecting their related but distinct functions in response to different environmental stresses. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Differential Activity of Plasma and Vacuolar Membrane Transporters Contributes to Genotypic Differences in Salinity Tolerance in a Halophyte Species, Chenopodium quinoa
by Edgar Bonales-Alatorre, Igor Pottosin, Lana Shabala, Zhong-Hua Chen, Fanrong Zeng, Sven-Erik Jacobsen and Sergey Shabala
Int. J. Mol. Sci. 2013, 14(5), 9267-9285; https://doi.org/10.3390/ijms14059267 - 29 Apr 2013
Cited by 88 | Viewed by 9056
Abstract
Halophytes species can be used as a highly convenient model system to reveal key ionic and molecular mechanisms that confer salinity tolerance in plants. Earlier, we reported that quinoa (Chenopodium quinoa Willd.), a facultative C3 halophyte species, can efficiently control the activity [...] Read more.
Halophytes species can be used as a highly convenient model system to reveal key ionic and molecular mechanisms that confer salinity tolerance in plants. Earlier, we reported that quinoa (Chenopodium quinoa Willd.), a facultative C3 halophyte species, can efficiently control the activity of slow (SV) and fast (FV) tonoplast channels to match specific growth conditions by ensuring that most of accumulated Na+ is safely locked in the vacuole (Bonales-Alatorre et al. (2013) Plant Physiology). This work extends these finding by comparing the properties of tonoplast FV and SV channels in two quinoa genotypes contrasting in their salinity tolerance. The work is complemented by studies of the kinetics of net ion fluxes across the plasma membrane of quinoa leaf mesophyll tissue. Our results suggest that multiple mechanisms contribute towards genotypic differences in salinity tolerance in quinoa. These include: (i) a higher rate of Na+ exclusion from leaf mesophyll; (ii) maintenance of low cytosolic Na+ levels; (iii) better K+ retention in the leaf mesophyll; (iv) a high rate of H+ pumping, which increases the ability of mesophyll cells to restore their membrane potential; and (v) the ability to reduce the activity of SV and FV channels under saline conditions. These mechanisms appear to be highly orchestrated, thus enabling the remarkable overall salinity tolerance of quinoa species. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Characteristic of the Pepper CaRGA2 Gene in Defense Responses against Phytophthora capsici Leonian
by Ying-Li Zhang, Qing-Li Jia, Da-Wei Li, Jun-E Wang, Yan-Xu Yin and Zhen-Hui Gong
Int. J. Mol. Sci. 2013, 14(5), 8985-9004; https://doi.org/10.3390/ijms14058985 - 25 Apr 2013
Cited by 40 | Viewed by 9607
Abstract
The most significant threat to pepper production worldwide is the Phytophthora blight, which is caused by the oomycete pathogen, Phytophthora capsici Leonian. In an effort to help control this disease, we isolated and characterized a P. capsici resistance gene, CaRGA2, from a [...] Read more.
The most significant threat to pepper production worldwide is the Phytophthora blight, which is caused by the oomycete pathogen, Phytophthora capsici Leonian. In an effort to help control this disease, we isolated and characterized a P. capsici resistance gene, CaRGA2, from a high resistant pepper (C. annuum CM334) and analyzed its function by the method of real-time PCR and virus-induced gene silencing (VIGS). The CaRGA2 has a full-length cDNA of 3,018 bp with 2,874 bp open reading frame (ORF) and encodes a 957-aa protein. The protein has a predicted molecular weight of 108.6 kDa, and the isoelectric point is 8.106. Quantitative real-time PCR indicated that CaRGA2 expression was rapidly induced by P. capsici. The gene expression pattern was different between the resistant and susceptible cultivars. CaRGA2 was quickly expressed in the resistant cultivar, CM334, and reached to a peak at 24 h after inoculation with P. capsici, five-fold higher than that of susceptible cultivar. Our results suggest that CaRGA2 has a distinct pattern of expression and plays a critical role in P. capsici stress tolerance. When the CaRGA2 gene was silenced via VIGS, the resistance level was clearly suppressed, an observation that was supported by semi-quantitative RT-PCR and detached leave inoculation. VIGS analysis revealed their importance in the surveillance to P. capsici in pepper. Our results support the idea that the CaRGA2 gene may show their response in resistance against P. capsici. These analyses will aid in an effort towards breeding for broad and durable resistance in economically important pepper cultivars. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
The Expression of Millettia pinnata Chalcone Isomerase in Saccharomyces cerevisiae Salt-Sensitive Mutants Enhances Salt-Tolerance
by Hui Wang, Tangjin Hu, Jianzi Huang, Xiang Lu, Baiqu Huang and Yizhi Zheng
Int. J. Mol. Sci. 2013, 14(5), 8775-8786; https://doi.org/10.3390/ijms14058775 - 24 Apr 2013
Cited by 27 | Viewed by 7820
Abstract
The present study demonstrates a new Millettia pinnata chalcone isomerase (MpCHI) whose transcription level in leaf was confirmed to be enhanced after being treated by seawater or NaCl (500 mM) via transcriptome sequencing and Real-Time Quantitative Reverse Transcription PCR (QRT-PCR) analyses. Its full [...] Read more.
The present study demonstrates a new Millettia pinnata chalcone isomerase (MpCHI) whose transcription level in leaf was confirmed to be enhanced after being treated by seawater or NaCl (500 mM) via transcriptome sequencing and Real-Time Quantitative Reverse Transcription PCR (QRT-PCR) analyses. Its full length cDNA (666 bp) was obtained by 3'-end and 5'-end Rapid Amplification of cDNA Ends (RACE). The analysis via NCBI BLAST indicates that both aminoacid sequence and nucleotide sequence of the MpCHI clone share high homology with other leguminous CHIs (73%–86%). Evolutionarily, the phylogenic analysis further revealed that the MpCHI is a close relative of leguminous CHIs. The MpCHI protein consists of 221 aminoacid (23.64 KDa), whose peptide length, amino acid residues of substrate-binding site and reactive site are very similar to other leguminous CHIs reported previously. Two pYES2-MpCHI transformed salt-sensitive Saccharomyces cerevisiae mutants (Δnha1 and Δnhx1) showed improved salt-tolerance significantly compared to pYES2-vector transformed yeast mutants, suggesting the MpCHI or the flavonoid biosynthesis pathway could regulate the resistance to salt stress in M. pinnata. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Characterization, Purification of Poncirin from Edible Citrus Ougan (Citrus reticulate cv. Suavissima) and Its Growth Inhibitory Effect on Human Gastric Cancer Cells SGC-7901
by Xiaoyan Zhu, Fenglei Luo, Yixiong Zheng, Jiukai Zhang, Jianzhen Huang, Chongde Sun, Xian Li and Kunsong Chen
Int. J. Mol. Sci. 2013, 14(5), 8684-8697; https://doi.org/10.3390/ijms14058684 - 24 Apr 2013
Cited by 31 | Viewed by 8339
Abstract
Poncirin is a bitter flavanone glycoside with various biological activities. Poncirin was isolated from four different tissues (flavedo, albedo, segment membrane, and juice sac) of Ougan fruit (Citrus reticulate cv. Suavissima). The highest content of poncirin was found in the albedo of [...] Read more.
Poncirin is a bitter flavanone glycoside with various biological activities. Poncirin was isolated from four different tissues (flavedo, albedo, segment membrane, and juice sac) of Ougan fruit (Citrus reticulate cv. Suavissima). The highest content of poncirin was found in the albedo of Ougan fruit (1.37 mg/g DW). High speed counter-current chromatography (HSCCC) combined with D101 resin chromatography was utilized for the separation and purification of poncirin from the albedo of Ougan fruit. After this two-step purification, poncirin purity increased from 0.14% to 96.56%. The chemical structure of the purified poncirin was identified by both HPLC-PDA and LC-MS. Poncirin showed a significant in vitro inhibitory effect on the growth of the human gastric cancer cells, SGC-7901, in a dose-dependent manner. Thus, poncirin from Ougan fruit, may be beneficial for gastric cancer prevention. The purification method demonstrated here will be useful for further studies on the pharmacological mechanism of poncirin activity, as well as for guiding the consumption of Ougan fruit. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Identifying Differentially Expressed Genes in Pollen from Self-Incompatible “Wuzishatangju” and Self-Compatible “Shatangju” Mandarins
by Hongxia Miao, Zixing Ye, Jaime A. Teixeira da Silva, Yonghua Qin and Guibing Hu
Int. J. Mol. Sci. 2013, 14(4), 8538-8555; https://doi.org/10.3390/ijms14048538 - 17 Apr 2013
Cited by 11 | Viewed by 7065
Abstract
Self-incompatibility (SI) is one of the important factors that can result in seedless fruit in Citrus. However, the molecular mechanism of SI in Citrus is not yet clear. In this study, two suppression subtractive hybridization (SSH) libraries (forward, F and reverse, R) [...] Read more.
Self-incompatibility (SI) is one of the important factors that can result in seedless fruit in Citrus. However, the molecular mechanism of SI in Citrus is not yet clear. In this study, two suppression subtractive hybridization (SSH) libraries (forward, F and reverse, R) were constructed to isolate differentially expressed genes in pollen from “Wuzishatangju” (SI) and “Shatangju” (self-compatibility, SC) mandarins. Four hundred and sixty-eight differentially expressed cDNA clones from 2077 positive clones were sequenced and identified. Differentially expressed ESTs are possibly involved in the SI reaction of “Wuzishatangju” by regulating pollen development, kinase activity, ubiquitin pathway, pollen-pistil interaction, and calcium ion binding. Twenty five SI candidate genes were obtained, six of which displayed specific expression patterns in various organs and stages after self- and cross-pollination. The expression level of the F-box gene (H304) and S1 (F78) in the pollen of “Wuzishatangju” was 5-fold higher than that in “Shatangju” pollen. The F-box gene, S1, UBE2, UBE3, RNaseHII, and PCP were obviously up-regulated in pistils at 3 d after self-pollination of “Wuzishatangju”, approximately 3-, 2-, 10-, 5-, 5-, and 2-fold higher, respectively than that at the same stage after cross-pollination of “Wuzishatangju” × “Shatangju” pistils. The potential involvement of these genes in the pollen SI reaction of “Wuzishatangju” is discussed. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Article
Detection of Quantitative Trait Loci (QTLs) for Resistances to Small Brown Planthopper and Rice Stripe Virus in Rice Using Recombinant Inbred Lines
by Qi Wang, Yuqiang Liu, Jinlong Hu, Yingxin Zhang, Kun Xie, Baoxiang Wang, Le Quang Tuyen, Zhaoqiang Song, Han Wu, Yanling Liu, Ling Jiang, Shijia Liu, Xianian Cheng, Chunming Wang, Huqu Zhai and Jianmin Wan
Int. J. Mol. Sci. 2013, 14(4), 8406-8421; https://doi.org/10.3390/ijms14048406 - 16 Apr 2013
Cited by 13 | Viewed by 8781
Abstract
Small brown planthopper (SBPH) and rice stripe virus (RSV) disease transmitted by SBPH cause serious damage to rice (Oryza sativa L.) in China. In the present study, we screened 312 rice accessions for resistance to SBPH. The indica variety, N22, is highly [...] Read more.
Small brown planthopper (SBPH) and rice stripe virus (RSV) disease transmitted by SBPH cause serious damage to rice (Oryza sativa L.) in China. In the present study, we screened 312 rice accessions for resistance to SBPH. The indica variety, N22, is highly resistant to SBPH. One hundred and eighty two recombinant inbred lines (RILs) derived from a cross of N22 and the highly susceptible variety, USSR5, were used for quantitative trait locus (QTL) analysis of resistances to SBPH and RSV. In a modified seedbox screening test, three QTLs for SBPH resistance, qSBPH2, qSBPH3 and qSBPH7.1, were mapped on chromosomes 2, 3 and 7, a total explaining 35.1% of the phenotypic variance. qSBPH7.2 and qSBPH11.2, conferring antibiosis against SBPH, were detected on chromosomes 7 and 11 and accounted for 20.7% of the total phenotypic variance. In addition, qSBPH5 and qSBPH7.3, expressing antixenosis to SBPH, were detected on chromosomes 5 and 7, explaining 23.9% of the phenotypic variance. qSBPH7.1, qSBPH7.2 and qSBPH7.3, located in the same region between RM234 and RM429 on chromosome 7, using three different phenotyping methods indicate that the locus or region plays a major role in conferring resistance to SBPH in N22. Moreover, three QTLs, qSTV4, qSTV11.1 and qSTV11.2, for RSV resistance were detected on chromosomes 4 and 11. qSTV11.1 and qSTV11.2 are located in the same region between RM287 and RM209 on chromosome 11. Molecular markers spanning these QTLs should be useful in the development of varieties with resistance to SBPH and RSV. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Two Common Bean Genotypes with Contrasting Response to Phosphorus Deficiency Show Variations in the microRNA 399-Mediated PvPHO2 Regulation within the PvPHR1 Signaling Pathway
by Mario Ramírez, Gerardo Flores-Pacheco, José Luis Reyes, Ana Luz Alvarez, Jean Jacques Drevon, Lourdes Girard and Georgina Hernández
Int. J. Mol. Sci. 2013, 14(4), 8328-8344; https://doi.org/10.3390/ijms14048328 - 16 Apr 2013
Cited by 32 | Viewed by 7213
Abstract
Crop production of the important legume, the common bean (Phaseolus vulgaris), is often limited by low phosphorus (P) in the soil. The genotypes, BAT477 and DOR364, of the common bean have contrasting responses to P starvation. Plants from the BAT477 [...] Read more.
Crop production of the important legume, the common bean (Phaseolus vulgaris), is often limited by low phosphorus (P) in the soil. The genotypes, BAT477 and DOR364, of the common bean have contrasting responses to P starvation. Plants from the BAT477 P deficiency tolerant genotype showed higher phosphate content and root biomass as compared to the DOR364 plants under P starvation. The PvPHR1 transcription factor-signaling pathway plays an essential role in the response to P starvation. PvPHO2, a negative regulator of this pathway, encodes an ubiquitin E2 conjugase that promotes degradation of P-responsive proteins and is the target gene of PvmiR399. PvPHO2 is downregulated in BAT477 plants under P deficiency, while such a response is not observed in P-starved DOR364 plants. Five putative PvmiR399 binding sites were identified in the 5' UTR region in both genotypes. While four sites showed an identical DNA sequence, the fifth (binding site of PvPHO2 one) showed three base changes and higher complementarity scores in DOR364 as compared to BAT477. Modified 5'RACE experiments indicated that PvmiR399 binding and/or processing was affected in DOR364 P-starved plants. We propose that a less efficient cleavage of the PvPHO2 mRNA directed by PvmiR399 would result in a higher PvPHO2-mediated degradation of P-responsive proteins in the DOR364 genotype with decreased P deficiency tolerance. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Proteins Involved in Distinct Phases of Cold Hardening Process in Frost Resistant Winter Barley (Hordeum vulgare L.) cv Luxor
by Iva Hlaváčková, Pavel Vítámvás, Jiří Šantrůček, Klára Kosová, Sylva Zelenková, Ilja Tom Prášil, Jaroslava Ovesná, Radovan Hynek and Milan Kodíček
Int. J. Mol. Sci. 2013, 14(4), 8000-8024; https://doi.org/10.3390/ijms14048000 - 12 Apr 2013
Cited by 36 | Viewed by 7819
Abstract
Winter barley is an economically important cereal crop grown in higher latitudes and altitudes where low temperatures represent an important environmental constraint limiting crop productivity. In this study changes in proteome of leaves and crowns in a frost tolerant winter barley cv. Luxor [...] Read more.
Winter barley is an economically important cereal crop grown in higher latitudes and altitudes where low temperatures represent an important environmental constraint limiting crop productivity. In this study changes in proteome of leaves and crowns in a frost tolerant winter barley cv. Luxor in relation to short and long term periods of cold followed by a brief frost treatment were studied in order to disclose proteins responsible for the cold hardening process in distinct plant tissues. The mentioned changes have been monitored using two dimensional difference gel electrophoresis (2D-DIGE) with subsequent peptide-mapping protein identification. Regarding approximately 600–700 distinct protein spots detected on 2D gels, there has been found at least a two-fold change after exposure to low temperatures in about 10% of proteins in leaves and 13% of proteins in crowns. Protein and nitrogen metabolic processes have been influenced by low temperature to a similar extent in both tissues while catabolism, carbohydrate metabolism and proteins involved in stress response have been more affected in crowns than in leaves. The range of changes in protein abundance was generally higher in leaves and chloroplast proteins were frequently affected which suggests a priority to protect photosynthetic apparatus. Overall, our data proved existence of slightly different response strategies to low temperature stress in crowns and leaves, i.e., tissues with different biological role. Moreover, there have been found several proteins with large increase in accumulation, e.g., 33 kDa oxygen evolving protein of photosystem II in leaves and “enhanced disease susceptibility 1” in crowns; these proteins might have potential to indicate an enhanced level of frost tolerance in barley. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Environmental Stresses Induce Misfolded Protein Aggregation in Plant Cells in a Microtubule-Dependent Manner
by Yuko Nakajima and Shunji Suzuki
Int. J. Mol. Sci. 2013, 14(4), 7771-7783; https://doi.org/10.3390/ijms14047771 - 10 Apr 2013
Cited by 46 | Viewed by 10180
Abstract
Misfolded protein aggregation in mammalian cells is one of the cellular responses to environmental stresses. However, the aggregation of misfolded proteins in plant cells exposed to environmental stresses is still poorly understood. Here, we report the misfolded protein aggregation in plant cells in [...] Read more.
Misfolded protein aggregation in mammalian cells is one of the cellular responses to environmental stresses. However, the aggregation of misfolded proteins in plant cells exposed to environmental stresses is still poorly understood. Here, we report the misfolded protein aggregation in plant cells in response to environmental stresses, including ultraviolet (UV) radiation, heat stress and cold stress. Treatment of grape and tobacco cultured cells with MG-132, a proteasome inhibitor, induced misfolded protein aggregation. All of the environmental stresses examined induced the endoplasmic reticulum (ER) stress response in the cells. The cells under ER stress showed aggregation of misfolded proteins. The misfolded protein aggregation was completely inhibited by treatment of the cells with trichostatin A or colchicine, suggesting that the misfolded proteins might be aggregated in plant cells in a microtubule-dependent manner. Detected aggregates were initially observed immediately after exposure to the environmental stresses (1 min after UV radiation, 5 min after heat stress exposure, and 15 min after cold stress exposure). Based on these findings, we hypothesize that environmental stresses induce misfolded protein aggregation in plant cells in a microtubule-dependent manner. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Plant Core Environmental Stress Response Genes Are Systemically Coordinated during Abiotic Stresses
by Achim Hahn, Joachim Kilian, Anne Mohrholz, Friederike Ladwig, Florian Peschke, Rebecca Dautel, Klaus Harter, Kenneth W. Berendzen and Dierk Wanke
Int. J. Mol. Sci. 2013, 14(4), 7617-7641; https://doi.org/10.3390/ijms14047617 - 08 Apr 2013
Cited by 49 | Viewed by 11427
Abstract
Studying plant stress responses is an important issue in a world threatened by global warming. Unfortunately, comparative analyses are hampered by varying experimental setups. In contrast, the AtGenExpress abiotic stress experiment displays intercomparability. Importantly, six of the nine stresses (wounding, genotoxic, oxidative, UV-B [...] Read more.
Studying plant stress responses is an important issue in a world threatened by global warming. Unfortunately, comparative analyses are hampered by varying experimental setups. In contrast, the AtGenExpress abiotic stress experiment displays intercomparability. Importantly, six of the nine stresses (wounding, genotoxic, oxidative, UV-B light, osmotic and salt) can be examined for their capacity to generate systemic signals between the shoot and root, which might be essential to regain homeostasis in Arabidopsis thaliana. We classified the systemic responses into two groups: genes that are regulated in the non-treated tissue only are defined as type I responsive and, accordingly, genes that react in both tissues are termed type II responsive. Analysis of type I and II systemic responses suggest distinct functionalities, but also significant overlap between different stresses. Comparison with salicylic acid (SA) and methyl-jasmonate (MeJA) responsive genes implies that MeJA is involved in the systemic stress response. Certain genes are predominantly responding in only one of the categories, e.g., WRKY genes respond mainly non-systemically. Instead, genes of the plant core environmental stress response (PCESR), e.g., ZAT10, ZAT12, ERD9 or MES9, are part of different response types. Moreover, several PCESR genes switch between the categories in a stress-specific manner. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Cadmium Tolerance and Removal from Cunninghamella elegans Related to the Polyphosphate Metabolism
by Marcos A. B. De Lima, Luciana De O. Franco, Patrícia M. De Souza, Aline E. Do Nascimento, Carlos A. A. Da Silva, Rita De C. C. Maia, Hercília M. L. Rolim and Galba M. C. Takaki
Int. J. Mol. Sci. 2013, 14(4), 7180-7192; https://doi.org/10.3390/ijms14047180 - 28 Mar 2013
Cited by 24 | Viewed by 6827
Abstract
The aim of the present work was to study the cadmium effects on growth, ultrastructure and polyphosphate metabolism, as well as to evaluate the metal removal and accumulation by Cunninghamella elegans (IFM 46109) growing in culture medium. The presence of cadmium reduced growth, [...] Read more.
The aim of the present work was to study the cadmium effects on growth, ultrastructure and polyphosphate metabolism, as well as to evaluate the metal removal and accumulation by Cunninghamella elegans (IFM 46109) growing in culture medium. The presence of cadmium reduced growth, and a longer lag phase was observed. However, the phosphate uptake from the culture medium increased 15% when compared to the control. Moreover, C. elegans removed 70%–81% of the cadmium added to the culture medium during its growth. The C. elegans mycelia showed a removal efficiency of 280 mg/g at a cadmium concentration of 22.10 mg/L, and the removal velocity of cadmium was 0.107 mg/h. Additionally, it was observed that cadmium induced vacuolization, the presence of electron dense deposits in vacuoles, cytoplasm and cell membranes, as well as the distinct behavior of polyphosphate fractions. The results obtained with C. elegans suggest that precipitation, vacuolization and polyphosphate fractions were associated to cadmium tolerance, and this species demonstrated a higher potential for bioremediation of heavy metals. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Transcriptional Analysis of Drought-Induced Genes in the Roots of a Tolerant Genotype of the Common Bean (Phaseolus vulgaris L.)
by Gustavo Henrique Recchia, Danielle Gregorio Gomes Caldas, Ana Luiza Ahern Beraldo, Márcio José Da Silva and Siu Mui Tsai
Int. J. Mol. Sci. 2013, 14(4), 7155-7179; https://doi.org/10.3390/ijms14047155 - 28 Mar 2013
Cited by 35 | Viewed by 8344
Abstract
In Brazil, common bean (Phaseolus vulgaris L.) productivity is severely affected by drought stress due to low technology cultivation systems. Our purpose was to identify differentially expressed genes in roots of a genotype tolerant to water deficit (BAT 477) when submitted to [...] Read more.
In Brazil, common bean (Phaseolus vulgaris L.) productivity is severely affected by drought stress due to low technology cultivation systems. Our purpose was to identify differentially expressed genes in roots of a genotype tolerant to water deficit (BAT 477) when submitted to an interruption of irrigation during its development. A SSH library was constructed taking as “driver” the genotype Carioca 80SH (susceptible to drought). After clustering and data mining, 1572 valid reads were obtained, resulting in 1120 ESTs (expressed sequence tags). We found sequences for transcription factors, carbohydrates metabolism, proline-rich proteins, aquaporins, chaperones and ubiquitins, all of them organized according to their biological processes. Our suppressive subtractive hybridization (SSH) library was validated through RT-qPCR experiment by assessing the expression patterns of 10 selected genes in both genotypes under stressed and control conditions. Finally, the expression patterns of 31 ESTs, putatively related to drought responses, were analyzed in a time-course experiment. Our results confirmed that such genes are more expressed in the tolerant genotype during stress; however, they are not exclusive, since different levels of these transcripts were also detected in the susceptible genotype. In addition, we observed a fluctuation in gene regulation over time for both the genotypes, which seem to adopt and adapt different strategies in order to develop tolerance against this stress. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Disruption of AtWNK8 Enhances Tolerance of Arabidopsis to Salt and Osmotic Stresses via Modulating Proline Content and Activities of Catalase and Peroxidase
by Baige Zhang, Kaidong Liu, Yan Zheng, Yingxiang Wang, Jinxiang Wang and Hong Liao
Int. J. Mol. Sci. 2013, 14(4), 7032-7047; https://doi.org/10.3390/ijms14047032 - 27 Mar 2013
Cited by 47 | Viewed by 9413
Abstract
With no lysine kinases (WNKs) play important roles in plant growth and development. However, its role in salt and osmotic stress tolerance is unclear. Here, we report that AtWNK8 is mainly expressed in primary root, hypocotyl, stamen and pistil and is induced by [...] Read more.
With no lysine kinases (WNKs) play important roles in plant growth and development. However, its role in salt and osmotic stress tolerance is unclear. Here, we report that AtWNK8 is mainly expressed in primary root, hypocotyl, stamen and pistil and is induced by NaCl and sorbitol treatment. Compared to the wild-type, the T-DNA knock-out wnk8 mutant was more tolerant to severe salinity and osmotic stresses, as indicated by 27% and 198% more fresh weight in the NaCl and sorbitol treatment, respectively. The wnk8 mutant also accumulated 1.43-fold more proline than the wild-type in the sorbitol treatment. Under NaCl and sorbitol stresses, catalase (CAT) activity in wnk8 mutant was 1.92- and 3.7-times of that in Col-0, respectively. Similarly, under salt and osmotic stress conditions, peroxidase (POD) activities in wnk8 mutant were 1.81- and 1.58-times of that in Col-0, respectively. Taken together, we revealed that maintaining higher CAT and POD activities might be one of the reasons that the disruption of AtWNK8 enhances the tolerance to salt stress, and accumulating more proline and higher activities of CAT and POD might result in the higher tolerance of WNK8 to osmotic stress. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Transgenerational, Dynamic Methylation of Stomata Genes in Response to Low Relative Humidity
by Penny J. Tricker, Carlos M. Rodríguez López, George Gibbings, Paul Hadley and Mike J. Wilkinson
Int. J. Mol. Sci. 2013, 14(4), 6674-6689; https://doi.org/10.3390/ijms14046674 - 26 Mar 2013
Cited by 44 | Viewed by 10523
Abstract
Transgenerational inheritance of abiotic stress-induced epigenetic modifications in plants has potential adaptive significance and might condition the offspring to improve the response to the same stress, but this is at least partly dependent on the potency, penetrance and persistence of the transmitted epigenetic [...] Read more.
Transgenerational inheritance of abiotic stress-induced epigenetic modifications in plants has potential adaptive significance and might condition the offspring to improve the response to the same stress, but this is at least partly dependent on the potency, penetrance and persistence of the transmitted epigenetic marks. We examined transgenerational inheritance of low Relative Humidity-induced DNA methylation for two gene loci in the stomatal developmental pathway in Arabidopsis thaliana and the abundance of associated short-interfering RNAs (siRNAs). Heritability of low humidity-induced methylation was more predictable and penetrative at one locus (SPEECHLESS, entropy ≤ 0.02; χ2 < 0.001) than the other (FAMA, entropy ≤ 0.17; χ2 ns). Methylation at SPEECHLESS correlated positively with the continued presence of local siRNAs (r2 = 0.87; p = 0.013) which, however, could be disrupted globally in the progeny under repeated stress. Transgenerational methylation and a parental low humidity-induced stomatal phenotype were heritable, but this was reversed in the progeny under repeated treatment in a previously unsuspected manner. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Identification of Amplified Fragment Length Polymorphism (AFLP) Markers Tightly Associated with Drought Stress Gene in Male Sterile and Fertile Salvia miltiorrhiza Bunge
by Yuejin Zhang, Lijun Guo, Zhiming Shu, Yiyue Sun, Yuanyuan Chen, Zongsuo Liang and Hongbo Guo
Int. J. Mol. Sci. 2013, 14(3), 6518-6528; https://doi.org/10.3390/ijms14036518 - 22 Mar 2013
Cited by 9 | Viewed by 7871
Abstract
Consistent grain yield in drought environment has attracted wide attention due to global climate change. However, the important drought-related traits/genes in crops have been rarely reported. Many near-isogenic lines (NILs) of male sterile and fertile Salvia miltiorrhiza have been obtained in our previous [...] Read more.
Consistent grain yield in drought environment has attracted wide attention due to global climate change. However, the important drought-related traits/genes in crops have been rarely reported. Many near-isogenic lines (NILs) of male sterile and fertile Salvia miltiorrhiza have been obtained in our previous work through testcross and backcross in continuous field experiments conducted in 2006–2009. Both segregating sterile and fertile populations were subjected to bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) with 384 and 170 primer combinations, respectively. One out of 14 AFLP markers (E9/M3246) was identified in treated fertile population as tightly linked to the drought stress gene with a recombination frequency of 6.98% and at a distance of 7.02 cM. One of 15 other markers (E2/M5357) was identified in a treated sterile population that is closely associated with the drought stress gene. It had a recombination frequency of 4.65% and at a distance of 4.66 cM. Interestingly, the E9/M3246 fragment was found to be identical to another AFLP fragment E11/M4208 that was tightly linked to the male sterile gene of S. miltiorrhiza with 95% identity and e-value 4 × 10−93. Blastn analysis suggested that the drought stress gene sequence showed higher identity with nucleotides in Arabidopsis chromosome 1–5. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Combinatorial Analysis of Secretory Immunoglobulin A (sIgA) Expression in Plants
by Paloma Juarez, Estefania Huet-Trujillo, Alejandro Sarrion-Perdigones, Erica Elvira Falconi, Antonio Granell and Diego Orzaez
Int. J. Mol. Sci. 2013, 14(3), 6205-6222; https://doi.org/10.3390/ijms14036205 - 18 Mar 2013
Cited by 25 | Viewed by 8608
Abstract
Delivery of secretory immunoglobulin A (sIgA) to mucosal surfaces as a passive immunotherapy agent is a promising strategy to prevent infectious diseases. Recombinant sIgA production in plants requires the co-expression of four transcriptional units encoding the light chain (LC), heavy chain (HC), joining [...] Read more.
Delivery of secretory immunoglobulin A (sIgA) to mucosal surfaces as a passive immunotherapy agent is a promising strategy to prevent infectious diseases. Recombinant sIgA production in plants requires the co-expression of four transcriptional units encoding the light chain (LC), heavy chain (HC), joining chain (JC) and secretory component (SC). As a way to optimize sIgA production in plants, we tested the combinatorial expression of 16 versions of a human sIgA against the VP8* rotavirus antigen in Nicotiana benthamiana, using the recently developed GoldenBraid multigene assembly system. Each sIgA version was obtained by combining one of the two types of HC (α1 and α2) with one of the two LC types (k and λ) and linking or not a KDEL peptide to the HC and/or SC. From the analysis of the anti-VP8* activity, it was concluded that those sIgA versions carrying HCα1 and LCλ provided the highest yields. Moreover, ER retention significantly increased antibody production, particularly when the KDEL signal was linked to the SC. Maximum expression levels of 32.5 μg IgA/g fresh weight (FW) were obtained in the best performing combination, with an estimated 33% of it in the form of a secretory complex. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
A Rice Immunophilin Gene, OsFKBP16-3, Confers Tolerance to Environmental Stress in Arabidopsis and Rice
by Hyun Ji Park, Sang Sook Lee, Young Nim You, Dae Hwa Yoon, Beom-Gi Kim, Jun Cheul Ahn and Hye Sun Cho
Int. J. Mol. Sci. 2013, 14(3), 5899-5919; https://doi.org/10.3390/ijms14035899 - 13 Mar 2013
Cited by 15 | Viewed by 9391
Abstract
The putative thylakoid lumen immunophilin, FKBP16-3, has not yet been characterized, although this protein is known to be regulated by thioredoxin and possesses a well-conserved CxxxC motif in photosynthetic organisms. Here, we characterized rice OsFKBP16-3 and examined the role of this gene in [...] Read more.
The putative thylakoid lumen immunophilin, FKBP16-3, has not yet been characterized, although this protein is known to be regulated by thioredoxin and possesses a well-conserved CxxxC motif in photosynthetic organisms. Here, we characterized rice OsFKBP16-3 and examined the role of this gene in the regulation of abiotic stress in plants. FKBP16-3s are well conserved in eukaryotic photosynthetic organisms, including the presence of a unique disulfide-forming CxxxC motif in their N-terminal regions. OsFKBP16-3 was mainly expressed in rice leaf tissues and was upregulated by various abiotic stresses, including salt, drought, high light, hydrogen peroxide, heat and methyl viologen. The chloroplast localization of OsFKBP16-3-GFP was confirmed through the transient expression of OsFKBP16-3 in Nicotiana benthamiana leaves. Transgenic Arabidopsis and transgenic rice plants that constitutively expressed OsFKBP16-3 exhibited increased tolerance to salinity, drought and oxidative stresses, but showed no change in growth or phenotype, compared with vector control plants, when grown under non-stressed conditions. This is the first report to demonstrate the potential role of FKBP16-3 in the environmental stress response, which may be regulated by a redox relay process in the thylakoid lumen, suggesting that artificial regulation of FKBP16-3 expression is a candidate for stress-tolerant crop breeding. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Water Deficit and Heat Affect the Tolerance to High Illumination in Hibiscus Plants
by Romualdo Muñoz and María José Quiles
Int. J. Mol. Sci. 2013, 14(3), 5432-5444; https://doi.org/10.3390/ijms14035432 - 07 Mar 2013
Cited by 18 | Viewed by 6779
Abstract
This work studies the effects of water deficit and heat, as well as the involvement of chlororespiration and the ferredoxin-mediated cyclic pathway, on the tolerance of photosynthesis to high light intensity in Hibiscus rosa-sinensis plants. Drought and heat resulted in the down–regulation of [...] Read more.
This work studies the effects of water deficit and heat, as well as the involvement of chlororespiration and the ferredoxin-mediated cyclic pathway, on the tolerance of photosynthesis to high light intensity in Hibiscus rosa-sinensis plants. Drought and heat resulted in the down–regulation of photosynthetic linear electron transport in the leaves, although only a slight decrease in variable fluorescence (Fv)/maximal fluorescence (Fm) was observed, indicating that the chloroplast was protected by mechanisms that dissipate excess excitation energy to prevent damage to the photosynthetic apparatus. The incubation of leaves from unstressed plants under high light intensity resulted in an increase of the activity of electron donation by nicotinamide adenine dinucleotide phosphate (NADPH) and ferredoxin to plastoquinone, but no increase was observed in plants exposed to water deficit, suggesting that cyclic electron transport was stimulated by high light only in control plants. In contrast, the activities of the chlororespiration enzymes (NADH dehydrogenase (NDH) complex and plastid terminal oxidase (PTOX)) increased after incubation under high light intensity in leaves of the water deficit plants, but not in control plants, suggesting that chlororespiration was stimulated in stressed plants. The results indicate that the relative importance of chlororespiration and the cyclic electron pathway in the tolerance of photosynthesis to high illumination differs under stress conditions. When plants were not subjected to stress, the contribution of chlororespiration to photosynthetic electron flow regulation was not relevant, and another pathway, such as the ferredoxin-mediated cyclic pathway, was more important. However, when plants were subjected to water deficit and heat, chlororespiration was probably essential. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Insight into Differential Responses of Upland and Paddy Rice to Drought Stress by Comparative Expression Profiling Analysis
by Xipeng Ding, Xiaokai Li and Lizhong Xiong
Int. J. Mol. Sci. 2013, 14(3), 5214-5238; https://doi.org/10.3390/ijms14035214 - 04 Mar 2013
Cited by 39 | Viewed by 7585
Abstract
In this study, the drought responses of two genotypes, IRAT109 and Zhenshan 97 (ZS97), representing upland and paddy rice, respectively, were systematically compared at the morphological, physiological and transcriptional levels. IRAT109 has better performance in traits related to drought avoidance, such as leaf [...] Read more.
In this study, the drought responses of two genotypes, IRAT109 and Zhenshan 97 (ZS97), representing upland and paddy rice, respectively, were systematically compared at the morphological, physiological and transcriptional levels. IRAT109 has better performance in traits related to drought avoidance, such as leaf rolling, root volumes, the ratio of leaf water loss and relative conductivity. At the transcriptional level, more genes were induced by drought in IRAT109 at the early drought stage, but more genes had dynamic expression patterns in ZS97 at different drought degrees. Under drought conditions, more genes related to reproductive development and establishment of localization were repressed in IRAT109, but more genes involved in degradation of cellular components were induced in ZS97. By checking the expression patterns of 36 drought-responsive genes (located in 14 quantitative trail loci [QTL] intervals) in ZS97, IRAT109 and near isogenic lines (NILs) of the QTL intervals, we found that more than half of these genes had their expression patterns or expression levels changed in the NILs when compared to that in ZS97 or IRAT109. Our results may provide valuable information for dissecting the genetic bases of traits related to drought resistance, as well as for narrowing the candidate genes for the traits. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Comparative Analysis of the Symbiotic Efficiency of Medicago truncatula and Medicago sativa under Phosphorus Deficiency
by Saad Sulieman, Joachim Schulze and Lam-Son Phan Tran
Int. J. Mol. Sci. 2013, 14(3), 5198-5213; https://doi.org/10.3390/ijms14035198 - 04 Mar 2013
Cited by 30 | Viewed by 8008
Abstract
Phosphorus (P)-deficiency is a major abiotic stress that limits legume growth in many types of soils. The relationship between Medicago and Sinorhizobium, is known to be affected by different environmental conditions. Recent reports have shown that, in combination with S. meliloti 2011, Medicago [...] Read more.
Phosphorus (P)-deficiency is a major abiotic stress that limits legume growth in many types of soils. The relationship between Medicago and Sinorhizobium, is known to be affected by different environmental conditions. Recent reports have shown that, in combination with S. meliloti 2011, Medicago truncatula had a lower symbiotic efficiency than Medicago sativa. However, little is known about how Medicago–Sinorhizobium is affected by P-deficiency at the whole-plant level. The objective of the present study was to compare and characterize the symbiotic efficiency of N2 fixation of M. truncatula and M. sativa grown in sand under P-limitation. Under this condition, M. truncatula exhibited a significantly higher rate of N2 fixation. The specific activity of the nodules was much higher in M. truncatula in comparison to M. sativa, partially as a result of an increase in electron allocation to N2 versus H+. Although the main organic acid, succinate, exhibited a strong tendency to decrease under P-deficiency, the more efficient symbiotic ability observed in M. truncatula coincided with an apparent increase in the content of malate in its nodules. Our results indicate that the higher efficiency of the M. truncatula symbiotic system is related to the ability to increase malate content under limited P-conditions. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Secretory Phospholipases A2 in Durum Wheat (Triticum durum Desf.): Gene Expression, Enzymatic Activity, and Relation to Drought Stress Adaptation
by Angelo Verlotta, Maria T. Liberatore, Luigi Cattivelli and Daniela Trono
Int. J. Mol. Sci. 2013, 14(3), 5146-5169; https://doi.org/10.3390/ijms14035146 - 01 Mar 2013
Cited by 28 | Viewed by 7280
Abstract
Phospholipases A2 (PLA2s) are known to mediate signaling cascades during plant growth and development, as well as biotic and abiotic stress responses. In this context, the present study provides extensive characterization of specific PLA2s in durum wheat, and [...] Read more.
Phospholipases A2 (PLA2s) are known to mediate signaling cascades during plant growth and development, as well as biotic and abiotic stress responses. In this context, the present study provides extensive characterization of specific PLA2s in durum wheat, and assesses their involvement in durum wheat response to drought stress. In durum wheat leaves, four full-length expressed sequences encoding putative PLA2s were isolated and characterized as belonging to the class of secretory PLA2s (sPLA2s): TdsPLA2I, TdsPLA2II, TdsPLA2III and TdsPLA2IV. PLA2 activity was also detected, the characteristics of which resemble those of previously characterized plant sPLA2s: strong preference for phospholipids; requirement for millimolar Ca2+ concentrations; optimal activity at basic pH; heat stability; and inhibition by the reducing agent dithiothreitol. With drought stress imposed at both the vegetative and reproductive stages, accumulation of TdsPLA2I and TdsPLA2III transcripts, and to a lesser extent of TdsPLA2IV transcript, paralleled increased PLA2 activity; both transcript levels and enzymatic activity decreased as a consequence of stress recovery. Consistently, free fatty acid analysis of drought-stressed leaves revealed increased linoleate, linolenate and palmitate contents, which were reversed by plant re-watering. Overall, these findings strongly suggest that there are inducible sPLA2 isoforms in durum wheat that have roles in orchestrating the plant response to drought stress. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Differential Protein Expression in Response to Abiotic Stress in Two Potato Species: Solanum commersonii Dun and Solanum tuberosum L.
by Raquel Folgado, Bart Panis, Kjell Sergeant, Jenny Renaut, Rony Swennen and Jean-Francois Hausman
Int. J. Mol. Sci. 2013, 14(3), 4912-4933; https://doi.org/10.3390/ijms14034912 - 01 Mar 2013
Cited by 36 | Viewed by 8347
Abstract
Better knowledge on responses to dehydration stress could help to improve the existing cryopreservation protocols for potato, since plant tissues processed for cryopreservation are often submitted to similar in vitro stress conditions. Cryopreservation (the best method of conservation for vegetatively propagated plants) of [...] Read more.
Better knowledge on responses to dehydration stress could help to improve the existing cryopreservation protocols for potato, since plant tissues processed for cryopreservation are often submitted to similar in vitro stress conditions. Cryopreservation (the best method of conservation for vegetatively propagated plants) of potato still needs to be standardized to make it available and to conserve the wide diversity of this crop. In the present work, the response to osmotic stress and chilling temperature was investigated in two potato species, Solanum tuberosum and its relative, frost-tolerant S. commersonii. After 14 days of exposure, different growth parameters, such as shoot length and number of leaves, were measured. Furthermore, differentially abundant proteins were identified after performing 2-fluorescence difference gel electrophoresis (2-DIGE) experiments, and soluble carbohydrates were analyzed by High Performance Anion Exchange Chromatography with Pulsed Amperometric Detection (HPAEC-PAD). The results show different responses in both species depending on the stress treatment. Focusing on the differences in growth parameters during the treatments, Solanum commersonii seems to be more affected than S. tuberosum cv. Désirée. At the molecular level, there are some differences and similarities between the two potato species studied that are dependent on the type of stressor. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
PG-2, a Potent AMP against Pathogenic Microbial Strains, from Potato (Solanum tuberosum L cv. Gogu Valley) Tubers Not Cytotoxic against Human Cells
by Jin-Young Kim, Ramamourthy Gopal, Sang Young Kim, Chang Ho Seo, Hyang Burm Lee, Hyeonsook Cheong and Yoonkyung Park
Int. J. Mol. Sci. 2013, 14(2), 4349-4360; https://doi.org/10.3390/ijms14024349 - 21 Feb 2013
Cited by 14 | Viewed by 8394
Abstract
In an earlier study, we isolated potamin-1 (PT-1), a 5.6-kDa trypsin-chymotrypsin protease inhibitor, from the tubers of a potato strain (Solanum tuberosum L cv. Gogu Valley). We established that PT-1 strongly inhibits pathogenic microbial strains, but not human bacterial strains, and that [...] Read more.
In an earlier study, we isolated potamin-1 (PT-1), a 5.6-kDa trypsin-chymotrypsin protease inhibitor, from the tubers of a potato strain (Solanum tuberosum L cv. Gogu Valley). We established that PT-1 strongly inhibits pathogenic microbial strains, but not human bacterial strains, and that its sequence shows 62% homology with a serine protease inhibitor. In the present study, we isolated an antifungal and antibacterial peptide with no cytotoxicity from tubers of the same potato strain. The peptide (peptide-G2, PG-2) was isolated using salt-extraction, ultrafiltration and reverse-phase high performance liquid chromatography (RP-HPLC). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) showed the protein to have a molecular mass of 3228.5 Da, while automated Edman degradation showed the N-terminal sequence of PG-2 to be LVKDNPLDISPKQVQALCTDLVIRCMCCC-. PG-2 exhibited antimicrobial activity against Candida albicans, a human pathogenic yeast strain, and Clavibacter michiganensis subsp. michiganensis, a plant late blight strain. PG-2 also showed antibacterial activity against Staphylococcus aureus, but did not lyse human red blood cells and was thermostable. Overall, these results suggest PG-2 may be a good candidate to serve as a natural antimicrobial agent, agricultural pesticide and/or food additive. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
Proteome Analysis of Rice (Oryza sativa L.) Mutants Reveals Differentially Induced Proteins during Brown Planthopper (Nilaparvata lugens) Infestation
by Jatinder Singh Sangha, Yolanda H. Chen, Jatinder Kaur, Wajahatullah Khan, Zainularifeen Abduljaleel, Mohammed S. Alanazi, Aaron Mills, Candida B. Adalla, John Bennett, Balakrishnan Prithiviraj, Gary C. Jahn and Hei Leung
Int. J. Mol. Sci. 2013, 14(2), 3921-3945; https://doi.org/10.3390/ijms14023921 - 15 Feb 2013
Cited by 28 | Viewed by 15838
Abstract
Although rice resistance plays an important role in controlling the brown planthopper (BPH), Nilaparvata lugens, not all varieties have the same level of protection against BPH infestation. Understanding the molecular interactions in rice defense response is an important tool to help to [...] Read more.
Although rice resistance plays an important role in controlling the brown planthopper (BPH), Nilaparvata lugens, not all varieties have the same level of protection against BPH infestation. Understanding the molecular interactions in rice defense response is an important tool to help to reveal unexplained processes that underlie rice resistance to BPH. A proteomics approach was used to explore how wild type IR64 and near-isogenic rice mutants with gain and loss of resistance to BPH respond during infestation. A total of 65 proteins were found markedly altered in wild type IR64 during BPH infestation. Fifty-two proteins associated with 11 functional categories were identified using mass spectrometry. Protein abundance was less altered at 2 and 14 days after infestation (DAI) (T1, T2, respectively), whereas higher protein levels were observed at 28 DAI (T3). This trend diminished at 34 DAI (T4). Comparative analysis of IR64 with mutants showed 22 proteins that may be potentially associated with rice resistance to the brown planthopper (BPH). Ten proteins were altered in susceptible mutant (D1131) whereas abundance of 12 proteins including S-like RNase, Glyoxalase I, EFTu1 and Salt stress root protein “RS1” was differentially changed in resistant mutant (D518). S-like RNase was found in greater quantities in D518 after BPH infestation but remained unchanged in IR64 and decreased in D1131. Taken together, this study shows a noticeable level of protein abundance in the resistant mutant D518 compared to the susceptible mutant D1131 that may be involved in rendering enhanced level of resistance against BPH. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Rapid and Sensitive Determination of Timosaponin AIII in Rat Plasma by LC-MS/MS and Its Pharmacokinetic Application
by Yanping Liu, Yiqiong Pu, Tong Zhang, Yue Ding, Bing Wang and Zhenzhen Cai
Int. J. Mol. Sci. 2013, 14(2), 3656-3670; https://doi.org/10.3390/ijms14023656 - 07 Feb 2013
Cited by 8 | Viewed by 6491
Abstract
A rapid sensitive and selective liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for determination of timosaponin AIII (TA-III) in rat plasma, using ginsenoside Re as an internal standard (IS). TA-III and the IS were detected in MRM mode with a negative ionization [...] Read more.
A rapid sensitive and selective liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for determination of timosaponin AIII (TA-III) in rat plasma, using ginsenoside Re as an internal standard (IS). TA-III and the IS were detected in MRM mode with a negative ionization electrospray mass spectrometer. The calibration curves were linear over the concentration ranges from 11.14 to 1114 ng/mL and the lower limit of quantification (LLOQ) was 11.14 ng/mL. Intra-day and inter-day precisions (RSD) were within 10%, and accuracy ranged from 6.4% to 9.1%. The extraction recovery at three concentrations ranged from 92.3% to 95.5%. The validated method was successfully applied to monitor the concentrations of TA-III in rat plasma after intragastric administration. The best fit pharmacokinetic model to estimate the pharmacokinetic parameters was a single compartment model with weight of 1/x2 for oral administration groups of rats for TA-III. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
Expression of a Functional Recombinant Human Basic Fibroblast Growth Factor from Transgenic Rice Seeds
by Na An, Jiquan Ou, Daiming Jiang, Liping Zhang, Jingru Liu, Kai Fu, Ying Dai and Daichang Yang
Int. J. Mol. Sci. 2013, 14(2), 3556-3567; https://doi.org/10.3390/ijms14023556 - 07 Feb 2013
Cited by 35 | Viewed by 8461
Abstract
Basic fibroblast growth factor (FGF-2) is an important member of the FGF gene family. It is widely used in clinical applications for scald and wound healing in order to stimulate cell proliferation. Further it is applied for inhibiting stem cell differentiation in cultures. [...] Read more.
Basic fibroblast growth factor (FGF-2) is an important member of the FGF gene family. It is widely used in clinical applications for scald and wound healing in order to stimulate cell proliferation. Further it is applied for inhibiting stem cell differentiation in cultures. Due to a shortage of plasma and low expression levels of recombinant rbFGF in conventional gene expression systems, we explored the production of recombinant rbFGF in rice grains (Oryza sativa bFGF, OsrbFGF). An expression level of up to 185.66 mg/kg in brown rice was obtained. A simple purification protocol was established with final recovery of 4.49% and resulting in a yield of OsrbFGF reaching up to 8.33 mg/kg OsrbFGF. The functional assay of OsrbFGF indicated that the stimulating cell proliferation activity on NIH/3T3 was the same as with commercialized rbFGF. Wound healing in vivo of OsrbFGF is equivalent to commercialized rbFGF. Our results indicate that rice endosperm is capable of expressing small molecular mass proteins, such as bFGF. This again demonstrates that rice endosperm is a promising system to express various biopharmaceutical proteins. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
A Novel Peroxidase CanPOD Gene of Pepper Is Involved in Defense Responses to Phytophtora capsici Infection as well as Abiotic Stress Tolerance
by Jun-E Wang, Ke-Ke Liu, Da-Wei Li, Ying-Li Zhang, Qian Zhao, Yu-Mei He and Zhen-Hui Gong
Int. J. Mol. Sci. 2013, 14(2), 3158-3177; https://doi.org/10.3390/ijms14023158 - 04 Feb 2013
Cited by 77 | Viewed by 9193
Abstract
Peroxidases are involved in many plant processes including plant defense responses to biotic and abiotic stresses. We isolated a novel peroxidase gene CanPOD from leaves of pepper cultivar A3. The full-length gene has a 1353-bp cDNA sequence and contains an open reading frame [...] Read more.
Peroxidases are involved in many plant processes including plant defense responses to biotic and abiotic stresses. We isolated a novel peroxidase gene CanPOD from leaves of pepper cultivar A3. The full-length gene has a 1353-bp cDNA sequence and contains an open reading frame (ORF) of 975-bp, which encodes a putative polypeptide of 324 amino acids with a theoretical protein size of 34.93 kDa. CanPOD showed diverse expression levels in different tissues of pepper plants. To evaluate the role of CanPOD in plant stress responses, the expression patterns of CanPOD were examined using Real-Time RT-PCR. The results indicated that CanPOD was significantly induced by Phytophtora capsici. Moreover, CanPOD was also up-regulated in leaves after salt and drought stress treatments. In addition, CanPOD expression was strongly induced by signaling hormones salicylic acid (SA). In contrast, CanPOD was not highly expressed after treatment with cold. Meanwhile, in order to further assess the role of gene CanPOD in defense response to P. capsici attack, we performed a loss-of-function experiment using the virus-induced gene silencing (VIGS) technique in pepper plants. In comparison to the control plant, the expression levels of CanPOD were obviously decreased in CanPOD-silenced pepper plants. Furthermore, we analyzed the effect of P. capsici on detached-leaves and found that the CanPOD-silenced plant leaves were highly susceptible to P. capsici infection. Taken together, our results suggested that CanPOD is involved in defense responses to P. capsici infection as well as abiotic stresses in pepper plants. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Antioxidant, Analgesic, Anti-Inflammatory, and Hepatoprotective Effects of the Ethanol Extract of Mahonia oiwakensis Stem
by Jung Chao, Jiunn-Wang Liao, Wen-Huang Peng, Meng-Shiou Lee, Li-Heng Pao and Hao-Yuan Cheng
Int. J. Mol. Sci. 2013, 14(2), 2928-2945; https://doi.org/10.3390/ijms14022928 - 30 Jan 2013
Cited by 43 | Viewed by 7708
Abstract
The aim of this study was to evaluate pharmacological properties of ethanol extracted from Mahonia oiwakensis Hayata stems (MOSEtOH). The pharmacological properties included antioxidant, analgesic, anti-inflammatory and hepatoprotective effects. The protoberberine alkaloid content of the MOSEtOH was analyzed by high-performance [...] Read more.
The aim of this study was to evaluate pharmacological properties of ethanol extracted from Mahonia oiwakensis Hayata stems (MOSEtOH). The pharmacological properties included antioxidant, analgesic, anti-inflammatory and hepatoprotective effects. The protoberberine alkaloid content of the MOSEtOH was analyzed by high-performance liquid chromatography (HPLC). The results revealed that three alkaloids, berberine, palmatine and jatrorrhizine, could be identified. Moreover, the MOSEtOH exhibited antioxidative activity using the DPPH assay (IC50, 0.743 mg/mL). The DPPH radical scavenging activity of MOSEtOH was five times higher that that of vitamin C. MOSEtOH was also found to inhibit pain induced by acetic acid, formalin, and carrageenan inflammation. Treatment with MOSEtOH (100 and 500 mg/kg) or silymarin (200 mg/kg) decreased the serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels compared with the CCl4-treated group. Histological evaluation showed that MOSEtOH reduced the degree of liver injury, including vacuolization, inflammation and necrosis of hepatocytes. The anti-inflammatory and hepatoprotective effect of MOSEtOH were found to be related to the modulation of antioxidant enzyme activity in the liver and decreases in malondialdehyde (MDA) level and nitric oxide (NO) contents. Our findings suggest that MOSEtOH has analgesic, anti-inflammatory and hepatoprotective effects. These effects support the use of MOSEtOH for relieving pain and inflammation in folk medicine. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
The Transcriptome of Brassica napus L. Roots under Waterlogging at the Seedling Stage
by Xiling Zou, Xiaoyu Tan, Chengwei Hu, Liu Zeng, Guangyuan Lu, Guiping Fu, Yong Cheng and Xuekun Zhang
Int. J. Mol. Sci. 2013, 14(2), 2637-2651; https://doi.org/10.3390/ijms14022637 - 28 Jan 2013
Cited by 48 | Viewed by 8719
Abstract
Although rapeseed (Brassica napus L.) is known to be affected by waterlogging, the genetic basis of waterlogging tolerance by rapeseed is largely unknown. In this study, the transcriptome under 0 h and 12 h of waterlogging was assayed in the roots of [...] Read more.
Although rapeseed (Brassica napus L.) is known to be affected by waterlogging, the genetic basis of waterlogging tolerance by rapeseed is largely unknown. In this study, the transcriptome under 0 h and 12 h of waterlogging was assayed in the roots of ZS9, a tolerant variety, using digital gene expression (DGE). A total of 4432 differentially expressed genes were identified, indicating that the response to waterlogging in rapeseed is complicated. The assignments of the annotated genes based on GO (Gene Ontology) revealed there were more genes induced under waterlogging in “oxidation reduction”, “secondary metabolism”, “transcription regulation”, and “translation regulation”; suggesting these four pathways are enhanced under waterlogging. Analysis of the 200 most highly expressed genes illustrated that 144 under normal conditions were down-regulated by waterlogging, while up to 191 under waterlogging were those induced in response to stress. The expression of genes involved under waterlogging is mediated by multiple levels of transcriptional, post-transcriptional, translational and post-translational regulation, including phosphorylation and protein degradation; in particular, protein degradation might be involved in the negative regulation in response to this stress. Our results provide new insight into the response to waterlogging and will help to identify important candidate genes. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Yeast α-Glucosidase Inhibitory Phenolic Compounds Isolated from Gynura medica Leaf
by Chao Tan, Qunxing Wang, Chunhua Luo, Sai Chen, Qianyuan Li and Peng Li
Int. J. Mol. Sci. 2013, 14(2), 2551-2558; https://doi.org/10.3390/ijms14022551 - 28 Jan 2013
Cited by 45 | Viewed by 7144
Abstract
Gynura medica leaf extract contains significant amounts of flavonols and phenolic acids and exhibits powerful hypoglycemic activity against diabetic rats in vivo. However, the hypoglycemic active constituents that exist in the plant have not been fully elaborated. The purpose of this study [...] Read more.
Gynura medica leaf extract contains significant amounts of flavonols and phenolic acids and exhibits powerful hypoglycemic activity against diabetic rats in vivo. However, the hypoglycemic active constituents that exist in the plant have not been fully elaborated. The purpose of this study is to isolate and elaborate the hypoglycemic activity compounds against inhibition the yeast α-glucosidase in vitro. Seven phenolic compounds including five flavonols and two phenolic acids were isolated from the leaf of G. medica. Their structures were identified by the extensive NMR and mass spectral analyses as: kaempferol (1), quercetin (2), kaempferol-3-O-β-D-glucopyranoside (3), kaempferol-3-O-rutinoside (4), rutin (5), chlorogenic acid (6) and 3,5-dicaffeoylquinic acid methyl ester (7). All of the compounds except 1 and 3 were isolated for the first time from G. medica. Compounds 17 were also assayed for their hypoglycemic activity against yeast α-glucosidase in vitro. All of the compounds except 1 and 6 showed good yeast α-glucosidase inhibitory activity with the IC50 values of 1.67 mg/mL, 1.46 mg/mL, 0.38 mg/mL, 0.10 mg/mL and 0.53 mg/mL, respectively. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
The Combination of Catechin and Epicatechin Gallate from Fructus Crataegi Potentiates β-Lactam Antibiotics Against Methicillin-Resistant Staphylococcus aureus (MRSA) in Vitro and in Vivo
by Rongxin Qin, Kangkang Xiao, Bin Li, Weiwei Jiang, Wei Peng, Jiang Zheng and Hong Zhou
Int. J. Mol. Sci. 2013, 14(1), 1802-1821; https://doi.org/10.3390/ijms14011802 - 16 Jan 2013
Cited by 57 | Viewed by 9519
Abstract
Fructus crataegi (hawthorn) is the common name of all plant species in the genus Crataegus of the Rosaceae family. In the present study, three monomers of (+)-catechin (C), (−)-epicatechin gallate (ECg) and (−)-epigallocatechin (EGC) were isolated from the hawthorn under the guide of [...] Read more.
Fructus crataegi (hawthorn) is the common name of all plant species in the genus Crataegus of the Rosaceae family. In the present study, three monomers of (+)-catechin (C), (−)-epicatechin gallate (ECg) and (−)-epigallocatechin (EGC) were isolated from the hawthorn under the guide of antibacterial sensitization activity. The bioactivity of the composite fraction in enhancing the antibacterial effect of oxacillin against methicillin-resistant Staphylococcus aureus (MRSA) was greater than that of the individual monomer of the hawthorn extract in vitro. Two-fold dilution and checkerboard methods were used to analyze antibacterial activity and screen for the combination and proportion of monomers with the best bioactivity. The result showed that C (128 mg/L) combined with ECg (16 mg/L) had the greatest effect and the combination also reduced the bacterial load in blood of septic mice challenged with a sublethal dose of MRSA, increased daunomycin accumulation within MRSA and down-regulated the mRNA expression of norA, norC and abcA, three important efflux pumps of MRSA. In summary, C and ECg enhanced the antibacterial effect of β-lactam antibiotics against MRSA in vitro and in vivo, which might be related to the increased accumulation of antibiotics within MRSA via suppression of important efflux pumps’ gene expression. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
Mitochondrial Cytochrome c Oxidase and F1Fo-ATPase Dysfunction in Peppers (Capsicum annuum L.) with Cytoplasmic Male Sterility and Its Association with orf507 and Ψatp6-2 Genes
by Jiaojiao Ji, Wei Huang, Chuanchuan Yin and Zhenhui Gong
Int. J. Mol. Sci. 2013, 14(1), 1050-1068; https://doi.org/10.3390/ijms14011050 - 07 Jan 2013
Cited by 43 | Viewed by 8188
Abstract
Cytoplasmic male sterility (CMS) in pepper (Capsicum annuum L.) has been associated with novel genes in the mitochondria, such as orf507 and Ψatp6-2. Plant sterility has been proved to result from the rearrangement of the mitochondrial genome. Previous studies have demonstrated [...] Read more.
Cytoplasmic male sterility (CMS) in pepper (Capsicum annuum L.) has been associated with novel genes in the mitochondria, such as orf507 and Ψatp6-2. Plant sterility has been proved to result from the rearrangement of the mitochondrial genome. Previous studies have demonstrated that orf507 is co-transcribed with the cox II gene, and Ψatp6-2 is truncated at the 3' region of the atp6-2 that is found in the maintainer line. Until this time, little has been known about the relationship between the novel gene and the function of its corresponding enzyme in mitochondria from the CMS pepper line. Moreover, the aberrant function of the mitochondrial enzymes is seldom reported in pepper. In this study, we observed that anther abortion occurred after the tetrad stage in the CMS line (HW203A), which was accompanied by premature programmed cell death (PCD) in the tapetum. The spatiotemporal expression patterns of orf507 and Ψatp6-2 were analyzed together with the corresponding enzyme activities to investigate the interactions of the genes and mitochondrial enzymes. The two genes were both highly expressed in the anther. The orf507 was down-regulated in HW203A (CMS line), with nearly no expression in HW203B (the maintainer line). In contrast, the cytochrome c oxidase activity in HW203A showed the opposite trend, reaching its highest peak at the tetrad stage when compared with HW203B at the same stage. The Ψatp6-2 in the CMS line was also down-regulated, but it was up-regulated in the maintainer line. The corresponding F1Fo-ATPase activity in the CMS line was gradually decreased along with the development of the anther, which showed the same trend for Ψatp6-2 gene expression. On the contrary, with up-regulated gene expression of atp6-2 in the maintainer line, the F1Fo-ATPase activity sharply decreased after the initial development stage, but gradually increased following the tetrad stage, which was contrary to what happened in the CMS line. Taken together, all these results may provide evidence for the involvement of aberrant mitochondrial cytochrome c oxidase and F1Fo-ATPase in CMS pepper anther abortion. Moreover, the novel orf507 and Ψatp6-2 genes in the mitochondria may be involved in the dysfunction of the cytochrome c oxidase and F1Fo-ATPase, respectively, which are responsible for the abortion of anthers in the CMS line. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Enhancement of Palmarumycins C12 and C13 Production in Liquid Culture of Endophytic Fungus Berkleasmium sp. Dzf12 after Treatments with Metal Ions
by Yan Mou, Haiyu Luo, Ziling Mao, Tijiang Shan, Weibo Sun, Kaiyi Zhou and Ligang Zhou
Int. J. Mol. Sci. 2013, 14(1), 979-998; https://doi.org/10.3390/ijms14010979 - 07 Jan 2013
Cited by 19 | Viewed by 7115
Abstract
The influences of eight metal ions (i.e., Na+, Ca2+, Ag+, Co2+, Cu2+, Al3+, Zn2+, and Mn4+) on mycelia growth and palmarumycins C12 and C [...] Read more.
The influences of eight metal ions (i.e., Na+, Ca2+, Ag+, Co2+, Cu2+, Al3+, Zn2+, and Mn4+) on mycelia growth and palmarumycins C12 and C13 production in liquid culture of the endophytic fungus Berkleasmium sp. Dzf12 were investigated. Three metal ions, Ca2+, Cu2+ and Al3+ were exhibited as the most effective to enhance mycelia growth and palmarumycin production. When calcium ion (Ca2+) was applied to the medium at 10.0 mmol/L on day 3, copper ion (Cu2+) to the medium at 1.0 mmol/L on day 3, aluminum ion (Al3+) to the medium at 2.0 mmol/L on day 6, the maximal yields of palmarumycins C12 plus C13 were obtained as 137.57 mg/L, 146.28 mg/L and 156.77 mg/L, which were 3.94-fold, 4.19-fold and 4.49-fold in comparison with that (34.91 mg/L) of the control, respectively. Al3+ favored palmarumycin C12 production when its concentration was higher than 4 mmol/L. Ca2+ had an improving effect on mycelia growth of Berkleasmium sp. Dzf12. The combination effects of Ca2+, Cu2+ and Al3+ on palmarumycin C13 production were further studied by employing a statistical method based on the central composite design (CCD) and response surface methodology (RSM). By solving the quadratic regression equation between palmarumycin C13 and three metal ions, the optimal concentrations of Ca2+, Cu2+ and Al3+ in medium for palmarumycin C13 production were determined as 7.58, 1.36 and 2.05 mmol/L, respectively. Under the optimum conditions, the predicted maximum palmarumycin C13 yield reached 208.49 mg/L. By optimizing the combination of Ca2+, Cu2+ and Al3+ in medium, palmarumycin C13 yield was increased to 203.85 mg/L, which was 6.00-fold in comparison with that (33.98 mg/L) in the original basal medium. The results indicate that appropriate metal ions (i.e., Ca2+, Cu2+ and Al3+) could enhance palmarumycin production. Application of the metal ions should be an effective strategy for palmarumycin production in liquid culture of the endophytic fungus Berkleasmium sp. Dzf12. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
The Voltage-Dependent Anion Channel 1 (AtVDAC1) Negatively Regulates Plant Cold Responses during Germination and Seedling Development in Arabidopsis and Interacts with Calcium Sensor CBL1
by Zhi-Yong Li, Zhao-Shi Xu, Guang-Yuan He, Guang-Xiao Yang, Ming Chen, Lian-Cheng Li and Youzhi Ma
Int. J. Mol. Sci. 2013, 14(1), 701-713; https://doi.org/10.3390/ijms14010701 - 04 Jan 2013
Cited by 41 | Viewed by 8281
Abstract
The voltage-dependent anion channel (VDAC), a highly conserved major mitochondrial outer membrane protein, plays crucial roles in energy metabolism and metabolite transport. However, knowledge about the roles of the VDAC family in plants is limited. In this study, we investigated the expression pattern [...] Read more.
The voltage-dependent anion channel (VDAC), a highly conserved major mitochondrial outer membrane protein, plays crucial roles in energy metabolism and metabolite transport. However, knowledge about the roles of the VDAC family in plants is limited. In this study, we investigated the expression pattern of VDAC1 in Arabidopsis and found that cold stress promoted the accumulation of VDAC1 transcripts in imbibed seeds and mature plants. Overexpression of VDAC1 reduced tolerance to cold stress in Arabidopsis. Phenotype analysis of VDAC1 T-DNA insertion mutant plants indicated that a vdac1 mutant line had faster germination kinetics under cold treatment and showed enhanced tolerance to freezing. The yeast two-hybrid system revealed that VDAC1 interacts with CBL1, a calcium sensor in plants. Like the vdac1, a cbl1 mutant also exhibited a higher seed germination rate. We conclude that both VDAC1 and CBL1 regulate cold stress responses during seed germination and plant development. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
Chemical Constituents from Andrographis echioides and Their Anti-Inflammatory Activity
by De-Yang Shen, Shin-Hun Juang, Ping-Chung Kuo, Guan-Jhong Huang, Yu-Yi Chan, Amooru G. Damu and Tian-Shung Wu
Int. J. Mol. Sci. 2013, 14(1), 496-514; https://doi.org/10.3390/ijms14010496 - 27 Dec 2012
Cited by 17 | Viewed by 7701
Abstract
Phytochemical investigation of the whole plants of Andrographis echioides afforded two new 2'-oxygenated flavonoids (1) and (2), two new phenyl glycosides (3) and (4), along with 37 known structures. The structures of new compounds were elucidated [...] Read more.
Phytochemical investigation of the whole plants of Andrographis echioides afforded two new 2'-oxygenated flavonoids (1) and (2), two new phenyl glycosides (3) and (4), along with 37 known structures. The structures of new compounds were elucidated by spectral analysis and chemical transformation studies. Among the isolated compounds, (12) and (619) were subjected into the examination for their iNOS inhibitory bioactivity. The structure-activity relationships of the flavonoids for their inhibition of NO production were also discussed. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
Wheat Drought-Responsive Grain Proteome Analysis by Linear and Nonlinear 2-DE and MALDI-TOF Mass Spectrometry
by Shan-Shan Jiang, Xiao-Na Liang, Xin Li, Shun-Li Wang, Dong-Wen Lv, Chao-Ying Ma, Xiao-Hui Li, Wu-Jun Ma and Yue-Ming Yan
Int. J. Mol. Sci. 2012, 13(12), 16065-16083; https://doi.org/10.3390/ijms131216065 - 29 Nov 2012
Cited by 68 | Viewed by 9412
Abstract
A comparative proteomic analysis of drought-responsive proteins during grain development of two wheat varieties Kauz (strong resistance to drought stress) and Janz (sensitive to drought stress) was performed by using linear and nonlinear 2-DE and MALDI-TOF mass spectrometry technologies. Results revealed that the [...] Read more.
A comparative proteomic analysis of drought-responsive proteins during grain development of two wheat varieties Kauz (strong resistance to drought stress) and Janz (sensitive to drought stress) was performed by using linear and nonlinear 2-DE and MALDI-TOF mass spectrometry technologies. Results revealed that the nonlinear 2-DE had much higher resolution than the linear 2-DE. A total of 153 differentially expressed protein spots were detected by both 2-DE maps, of which 122 protein spots were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified differential proteins were mainly involved in carbohydrate metabolism (26%), detoxification and defense (23%), and storage proteins (17%). Some key proteins demonstrated significantly different expression patterns between the two varieties. In particular, catalase isozyme 1, WD40 repeat protein, LEA and alpha-amylase inhibitors displayed an upregulated expression pattern in Kauz, whereas they were downregulated or unchanged in Janz. Small and large subunit ADP glucose pyrophosphorylase, ascorbate peroxidase and G beta-like protein were all downregulated under drought stress in Janz, but had no expression changes in Kauz. Sucrose synthase and triticin precursor showed an upregulated expression pattern under water deficits in both varieties, but their upregulation levels were much higher in Kauz than in Janz. These differentially expressed proteins could be related to the biochemical pathways for stronger drought resistance of Kauz. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Article
The Characterization of SaPIN2b, a Plant Trichome-Localized Proteinase Inhibitor from Solanum americanum
by Ming Luo, Ling-Wen Ding, Zhi-Juan Ge, Zhen-Yu Wang, Bo-Lun Hu, Xiao-Bei Yang, Qiao-Yang Sun and Zeng-Fu Xu
Int. J. Mol. Sci. 2012, 13(11), 15162-15176; https://doi.org/10.3390/ijms131115162 - 16 Nov 2012
Cited by 15 | Viewed by 6500
Abstract
Proteinase inhibitors play an important role in plant resistance of insects and pathogens. In this study, we characterized the serine proteinase inhibitor SaPIN2b, which is constitutively expressed in Solanum americanum trichomes and contains two conserved motifs of the proteinase inhibitor II (PIN2) family. [...] Read more.
Proteinase inhibitors play an important role in plant resistance of insects and pathogens. In this study, we characterized the serine proteinase inhibitor SaPIN2b, which is constitutively expressed in Solanum americanum trichomes and contains two conserved motifs of the proteinase inhibitor II (PIN2) family. The recombinant SaPIN2b (rSaPIN2b), which was expressed in Escherichia coli, was demonstrated to be a potent proteinase inhibitor against a panel of serine proteinases, including subtilisin A, chymotrypsin and trypsin. Moreover, rSaPIN2b also effectively inhibited the proteinase activities of midgut trypsin-like proteinases that were extracted from the devastating pest Helicoverpa armigera. Furthermore, the overexpression of SaPIN2b in transgenic tobacco plants resulted in enhanced resistance against H. armigera. Taken together, our results demonstrated that SaPIN2b is a potent serine proteinase inhibitor that may act as a protective protein in plant defense against insect attacks. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Apoptosis Induction of Human Prostate Carcinoma DU145 Cells by Diallyl Disulfide via Modulation of JNK and PI3K/AKT Signaling Pathways
by Dong Yeok Shin, Gi-Young Kim, Jun Hyuk Lee, Byung Tae Choi, Young Hyun Yoo and Yung Hyun Choi
Int. J. Mol. Sci. 2012, 13(11), 14158-14171; https://doi.org/10.3390/ijms131114158 - 02 Nov 2012
Cited by 43 | Viewed by 7859
Abstract
Diallyl disulfide (DADS), a sulfur compound derived from garlic, has various biological properties, such as anticancer, antiangiogenic and anti-inflammatory effects. However, the mechanisms of action underlying the compound's anticancer activity have not been fully elucidated. In this study, the apoptotic effects of DADS [...] Read more.
Diallyl disulfide (DADS), a sulfur compound derived from garlic, has various biological properties, such as anticancer, antiangiogenic and anti-inflammatory effects. However, the mechanisms of action underlying the compound's anticancer activity have not been fully elucidated. In this study, the apoptotic effects of DADS were investigated in DU145 human prostate carcinoma cells. Our results showed that DADS markedly inhibited the growth of the DU145 cells by induction of apoptosis. Apoptosis was accompanied by modulation of Bcl-2 and inhibitor of apoptosis protein (IAP) family proteins, depolarization of the mitochondrial membrane potential (MMP, ΔΨm) and proteolytic activation of caspases. We also found that the expression of death-receptor 4 (DR4) and Fas ligand (FasL) proteins was increased and that the level of intact Bid proteins was down-regulated by DADS. Moreover, treatment with DADS induced phosphorylation of mitogen-activated protein kinases (MAPKs), including extracellular-signal regulating kinase (ERK), p38 MAPK and c-Jun N-terminal kinase (JNK). A specific JNK inhibitor, SP600125, significantly blocked DADS-induced-apoptosis, whereas inhibitors of the ERK (PD98059) and p38 MAPK (SB203580) had no effect. The induction of apoptosis was also accompanied by inactivation of phosphatidylinositol 3-kinase (PI3K)/Akt and the PI3K inhibitor LY29004 significantly increased DADS-induced cell death. These findings provide evidence demonstrating that the proapoptotic effect of DADS is mediated through the activation of JNK and the inhibition of the PI3K/Akt signaling pathway in DU145 cells. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
Transcriptomic Analysis of Phenotypic Changes in Birch (Betula platyphylla) Autotetraploids
by Huai-Zhi Mu, Zi-Jia Liu, Lin Lin, Hui-Yu Li, Jing Jiang and Gui-Feng Liu
Int. J. Mol. Sci. 2012, 13(10), 13012-13029; https://doi.org/10.3390/ijms131013012 - 11 Oct 2012
Cited by 49 | Viewed by 7491
Abstract
Plant breeders have focused much attention on polyploid trees because of their importance to forestry. To evaluate the impact of intraspecies genome duplication on the transcriptome, a series of Betula platyphylla autotetraploids and diploids were generated from four full-sib families. The phenotypes and [...] Read more.
Plant breeders have focused much attention on polyploid trees because of their importance to forestry. To evaluate the impact of intraspecies genome duplication on the transcriptome, a series of Betula platyphylla autotetraploids and diploids were generated from four full-sib families. The phenotypes and transcriptomes of these autotetraploid individuals were compared with those of diploid trees. Autotetraploids were generally superior in breast-height diameter, volume, leaf, fruit and stoma and were generally inferior in height compared to diploids. Transcriptome data revealed numerous changes in gene expression attributable to autotetraploidization, which resulted in the upregulation of 7052 unigenes and the downregulation of 3658 unigenes. Pathway analysis revealed that the biosynthesis and signal transduction of indoleacetate (IAA) and ethylene were altered after genome duplication, which may have contributed to phenotypic changes. These results shed light on variations in birch autotetraploidization and help identify important genes for the genetic engineering of birch trees. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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767 KiB  
Article
Genetic Diversity and Population Structure: Implications for Conservation of Wild Soybean (Glycine soja Sieb. et Zucc) Based on Nuclear and Chloroplast Microsatellite Variation
by Shuilian He, Yunsheng Wang, Sergei Volis, Dezhu Li and Tingshuang Yi
Int. J. Mol. Sci. 2012, 13(10), 12608-12628; https://doi.org/10.3390/ijms131012608 - 03 Oct 2012
Cited by 56 | Viewed by 9746
Abstract
Wild soybean (Glycine soja Sieb. et Zucc) is the most important germplasm resource for soybean breeding, and is currently subject to habitat loss, fragmentation and population decline. In order to develop successful conservation strategies, a total of 604 wild soybean accessions from [...] Read more.
Wild soybean (Glycine soja Sieb. et Zucc) is the most important germplasm resource for soybean breeding, and is currently subject to habitat loss, fragmentation and population decline. In order to develop successful conservation strategies, a total of 604 wild soybean accessions from 43 locations sampled across its range in China, Japan and Korea were analyzed using 20 nuclear (nSSRs) and five chloroplast microsatellite markers (cpSSRs) to reveal its genetic diversity and population structure. Relatively high nSSR diversity was found in wild soybean compared with other self-pollinated species, and the region of middle and lower reaches of Yangtze River (MDRY) was revealed to have the highest genetic diversity. However, cpSSRs suggested that Korea is a center of diversity. High genetic differentiation and low gene flow among populations were detected, which is consistent with the predominant self-pollination of wild soybean. Two main clusters were revealed by MCMC structure reconstruction and phylogenetic dendrogram, one formed by a group of populations from northwestern China (NWC) and north China (NC), and the other including northeastern China (NEC), Japan, Korea, MDRY, south China (SC) and southwestern China (SWC). Contrib analyses showed that southwestern China makes the greatest contribution to the total diversity and allelic richness, and is worthy of being given conservation priority. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Microsatellite Mutation Rate during Allohexaploidization of Newly Resynthesized Wheat
by Jiangtao Luo, Ming Hao, Li Zhang, Jixiang Chen, Lianquan Zhang, Zhongwei Yuan, Zehong Yan, Youliang Zheng, Huaigang Zhang, Yang Yen and Dengcai Liu
Int. J. Mol. Sci. 2012, 13(10), 12533-12543; https://doi.org/10.3390/ijms131012533 - 01 Oct 2012
Cited by 16 | Viewed by 7468
Abstract
Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and [...] Read more.
Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH) populations were made from 241 interspecific F1 haploid hybrids between Triticum turgidum L. and Aegilops tauschii (Coss.) through spontaneous chromosome doubling via unreduced gametes. Mutation events were studied at 160 SSR loci in the S1 generation (the first generation after chromosome doubling) of the three SynDH populations. Of the 148260 SSR alleles investigated in S1 generation, only one mutation (changed number of repeats) was confirmed with a mutation rate of 6.74 × 10−6. This mutation most likely occurred in the respective F1 hybrid. In comparison with previously reported data, our results suggested that allohexaploidization of wheat did not increase SSR mutation rate. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
SIG1, a Sigma Factor for the Chloroplast RNA Polymerase, Differently Associates with Multiple DNA Regions in the Chloroplast Chromosomes in Vivo
by Mitsumasa Hanaoka, Maiko Kato, Misato Anma and Kan Tanaka
Int. J. Mol. Sci. 2012, 13(10), 12182-12194; https://doi.org/10.3390/ijms131012182 - 25 Sep 2012
Cited by 22 | Viewed by 7959
Abstract
Chloroplasts have their own DNA and gene expression systems. Transcription in chloroplasts is regulated by two types of RNA polymerase, nuclear-encoded plastid RNA polymerase (NEP) and plastid-encoded plastid RNA polymerase (PEP), and multiple sigma factors for PEP. To study transcriptional regulation in chloroplasts, [...] Read more.
Chloroplasts have their own DNA and gene expression systems. Transcription in chloroplasts is regulated by two types of RNA polymerase, nuclear-encoded plastid RNA polymerase (NEP) and plastid-encoded plastid RNA polymerase (PEP), and multiple sigma factors for PEP. To study transcriptional regulation in chloroplasts, a molecular genetic approach has extensively been used. However, this method may include indirect effects, and it cannot be applied to the analysis of factors essential to survival. These limitations make understanding specific regulation by transcription factors difficult. Chromatin immunoprecipitation (ChIP) is a powerful and useful tool for obtaining information on transcription-factor binding sites; it can directly detect dynamic changes in their interaction patterns in vivo. To further understand transcriptional regulation in chloroplasts, we here established a ChIP-based method in Arabidopsis thaliana and analyzed the binding pattern of a chloroplast sigma factor, SIG1. We found that SIG1 specifically binds to newly identified target promoters as well as to a set of promoters of genes whose mRNA expression is dependent on OsSIG1 in rice and that this binding changed in response to high-light stress. These results suggested that the ChIP-based approach is very useful in understanding transcriptional regulation of chloroplast genes and can overcome several problems posed by conventional methods. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Ethyl Gallate Induces Apoptosis of HL-60 Cells by Promoting the Expression of Caspases-8, -9, -3, Apoptosis-Inducing Factor and Endonuclease G
by Woong-Hyun Kim, Hyun-Ok Song, Hwa-Jung Choi, Ho-Il Bang, Du-Young Choi and Hyun Park
Int. J. Mol. Sci. 2012, 13(9), 11912-11922; https://doi.org/10.3390/ijms130911912 - 20 Sep 2012
Cited by 23 | Viewed by 7417
Abstract
Many phytochemicals have been recognized to have potential therapeutic efficacy in cancer treatment. In this study, we investigated ethyl gallate (EG) for possible proapoptotic effects in the human promyelocytic leukemia cell line, HL-60. We examined cell viability, morphological changes, DNA content and fragmentation, [...] Read more.
Many phytochemicals have been recognized to have potential therapeutic efficacy in cancer treatment. In this study, we investigated ethyl gallate (EG) for possible proapoptotic effects in the human promyelocytic leukemia cell line, HL-60. We examined cell viability, morphological changes, DNA content and fragmentation, and expression of apoptosis-related proteins for up to 48 h after EG treatment. The results showed that EG induced morphological changes and DNA fragmentation and reduced HL-60 cell viability in a dose-dependent and time-dependent manner. Western blotting analysis indicated that EG-mediated HL-60 apoptosis mainly occurred through the mitochondrial pathway, as shown by the release of cytochrome c, apoptosis-inducing factor (AIF), and endonuclease G (Endo G), as well as the upregulation of Bcl-2-associated X protein (Bax). EG also activated the death receptor-dependent pathway of apoptosis by enhancing the expression of caspases-8, -9, and -3 and the Bcl-2 interacting domain (Bid). Collectively, our results showed that EG induces apoptosis in HL-60 via mitochondrial-mediated pathways. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
Determination and Analysis of Ustiloxins A and B by LC-ESI-MS and HPLC in False Smut Balls of Rice
by Tijiang Shan, Weibo Sun, Hao Liu, Shan Gao, Shiqiong Lu, Mingan Wang, Wenxian Sun, Zhiyi Chen, Shu Wang and Ligang Zhou
Int. J. Mol. Sci. 2012, 13(9), 11275-11287; https://doi.org/10.3390/ijms130911275 - 10 Sep 2012
Cited by 45 | Viewed by 7471
Abstract
Ustiloxins are cyclopeptide mycotoxins produced by the pathogenic fungus Villosiclava virens of rice false smut. Ustiloxins A and B as two main mycotoxins were determined conveniently by LC-ESI-MS in the water extract from rice false smut balls which were mostly composed of the [...] Read more.
Ustiloxins are cyclopeptide mycotoxins produced by the pathogenic fungus Villosiclava virens of rice false smut. Ustiloxins A and B as two main mycotoxins were determined conveniently by LC-ESI-MS in the water extract from rice false smut balls which were mostly composed of the chlamydospores and mycelia of the pathogen. Both ustiloxins A and B in the water extract were also quantitatively analyzed by HPLC. This is the first report on the determination and analysis of ustiloxins A and B simultaneously by LC-ESI-MS and HPLC in false smut balls of rice. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
The Opuntia streptacantha OpsHSP18 Gene Confers Salt and Osmotic Stress Tolerance in Arabidopsis thaliana
by Silvia Salas-Muñoz, Gracia Gómez-Anduro, Pablo Delgado-Sánchez, Margarita Rodríguez-Kessler and Juan Francisco Jiménez-Bremont
Int. J. Mol. Sci. 2012, 13(8), 10154-10175; https://doi.org/10.3390/ijms130810154 - 15 Aug 2012
Cited by 10 | Viewed by 9064
Abstract
Abiotic stress limits seed germination, plant growth, flowering and fruit quality, causing economic decrease. Small Heat Shock Proteins (sHSPs) are chaperons with roles in stress tolerance. Herein, we report the functional characterization of a cytosolic class CI sHSP (OpsHSP18) from Opuntia streptacantha during [...] Read more.
Abiotic stress limits seed germination, plant growth, flowering and fruit quality, causing economic decrease. Small Heat Shock Proteins (sHSPs) are chaperons with roles in stress tolerance. Herein, we report the functional characterization of a cytosolic class CI sHSP (OpsHSP18) from Opuntia streptacantha during seed germination in Arabidopsis thaliana transgenic lines subjected to different stress and hormone treatments. The over-expression of the OpsHSP18 gene in A. thaliana increased the seed germination rate under salt (NaCl) and osmotic (glucose and mannitol) stress, and in ABA treatments, compared with WT. On the other hand, the over-expression of the OpsHSP18 gene enhanced tolerance to salt (150 mM NaCl) and osmotic (274 mM mannitol) stress in Arabidopsis seedlings treated during 14 and 21 days, respectively. These plants showed increased survival rates (52.00 and 73.33%, respectively) with respect to the WT (18.75 and 53.75%, respectively). Thus, our results show that OpsHSP18 gene might have an important role in abiotic stress tolerance, in particular in seed germination and survival rate of Arabidopsis plants under unfavorable conditions. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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546 KiB  
Article
RNA-Mediated Gene Silencing Signals Are Not Graft Transmissible from the Rootstock to the Scion in Greenhouse-Grown Apple Plants Malus sp.
by Henryk Flachowsky, Conny Tränkner, Iris Szankowski, Sascha Waidmann, Magda-Viola Hanke, Dieter Treutter and Thilo C. Fischer
Int. J. Mol. Sci. 2012, 13(8), 9992-10009; https://doi.org/10.3390/ijms13089992 - 10 Aug 2012
Cited by 26 | Viewed by 8393
Abstract
RNA silencing describes the sequence specific degradation of RNA targets. Silencing is a non-cell autonomous event that is graft transmissible in different plant species. The present study is the first report on systemic acquired dsRNA-mediated gene silencing of transgenic and endogenous gene sequences [...] Read more.
RNA silencing describes the sequence specific degradation of RNA targets. Silencing is a non-cell autonomous event that is graft transmissible in different plant species. The present study is the first report on systemic acquired dsRNA-mediated gene silencing of transgenic and endogenous gene sequences in a woody plant like apple. Transgenic apple plants overexpressing a hairpin gene construct of the gusA reporter gene were produced. These plants were used as rootstocks and grafted with scions of the gusA overexpressing transgenic apple clone T355. After grafting, we observed a reduction of the gusA gene expression in T355 scions in vitro, but not in T355 scions grown in the greenhouse. Similar results were obtained after silencing of the endogenous Mdans gene in apple that is responsible for anthocyanin biosynthesis. Subsequently, we performed grafting experiments with Mdans silenced rootstocks and red leaf scions of TNR31-35 in order to evaluate graft transmitted silencing of the endogenous Mdans. The results obtained suggested a graft transmission of silencing signals in in vitro shoots. In contrast, no graft transmission of dsRNA-mediated gene silencing signals was detectable in greenhouse-grown plants and in plants grown in an insect protection tent. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Communication
Neuroprotective Effects of Triterpene Glycosides from Glycine max against Glutamate Induced Toxicity in Primary Cultured Rat Cortical Cells
by Hyung-In Moon and Jai-Heon Lee
Int. J. Mol. Sci. 2012, 13(8), 9642-9648; https://doi.org/10.3390/ijms13089642 - 02 Aug 2012
Cited by 7 | Viewed by 6210
Abstract
To examine the neuroprotective effects of Glycine max, we tested its protection against the glutamate-induced toxicity in primary cortical cultured neurons. In order to clarify the neuroprotective mechanism(s) of this observed effect, isolation was performed to seek and identify active fractions and [...] Read more.
To examine the neuroprotective effects of Glycine max, we tested its protection against the glutamate-induced toxicity in primary cortical cultured neurons. In order to clarify the neuroprotective mechanism(s) of this observed effect, isolation was performed to seek and identify active fractions and components. From such fractionation, two triterpene glycosides, 3-O-[α-L-rhamnopyranosyl(1-2)-β-D-glucopyranosyl(1-2)-β-D-glucuronopyranosyl]olean-12-en-3β,22β,24-triol (1) and 3-O-[β-D-glucopyranosyl(1-2)-β-D-galactopyranosyl(1-2)-β-D-glucuronopyranosyl]olean-12-en-3β,22β,24-triol (2) were isolated with the methanol extracts with of air-dried Glycine max. Among these compounds, compound 2 exhibited significant neuroprotective activities against glutamate-induced toxicity, exhibiting cell viability of about 50% at concentrations ranging from 0.1 μM to 10 μM. Therefore, the neuroprotective effect of Glycine max might be due to the inhibition of glutamate-induced toxicity by triterpene glycosides. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
Molecular Characterization and Comparative Sequence Analysis of Defense-Related Gene, Oryza rufipogon Receptor-Like Protein Kinase 1
by Yee-Song Law, Ranganath Gudimella, Beng-Kah Song, Wickneswari Ratnam and Jennifer Ann Harikrishna
Int. J. Mol. Sci. 2012, 13(7), 9343-9362; https://doi.org/10.3390/ijms13079343 - 24 Jul 2012
Cited by 6 | Viewed by 8826
Abstract
Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within [...] Read more.
Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structural prediction of extra cellular domains, cluster analysis and comparative gene expression. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
HR4 Gene Is Induced in the Arabidopsis-Trichoderma atroviride Beneficial Interaction
by Jorge Sáenz-Mata and Juan Francisco Jiménez-Bremont
Int. J. Mol. Sci. 2012, 13(7), 9110-9128; https://doi.org/10.3390/ijms13079110 - 20 Jul 2012
Cited by 16 | Viewed by 10766
Abstract
Plants are constantly exposed to microbes, for this reason they have evolved sophisticated strategies to perceive and identify biotic interactions. Thus, plants have large collections of so-called resistance (R) proteins that recognize specific microbe factors as signals of invasion. One of these proteins [...] Read more.
Plants are constantly exposed to microbes, for this reason they have evolved sophisticated strategies to perceive and identify biotic interactions. Thus, plants have large collections of so-called resistance (R) proteins that recognize specific microbe factors as signals of invasion. One of these proteins is codified by the Arabidopsis thaliana HR4 gene in the Col-0 ecotype that is homologous to RPW8 genes present in the Ms-0 ecotype. In this study, we investigated the expression patterns of the HR4 gene in Arabidopsis seedlings interacting with the beneficial fungus Trichoderma atroviride. We observed the induction of the HR4 gene mainly at 96 hpi when the fungus interaction was established. Furthermore, we found that the HR4 gene was differentially regulated in interactions with the beneficial bacterium Pseudomonas fluorescens and the pathogenic bacterium P. syringae. When hormone treatments were applied to A. thaliana (Col-0), each hormone treatment induced changes in HR4 gene expression. On the other hand, the expression of the RPW8.1 and RPW8.2 genes of Arabidopsis ecotype Ms-0 in interaction with T. atroviride was assessed. Interestingly, these genes are interaction-responsive; in particular, the RPW8.1 gene shows a very high level of expression in the later stages of interaction. These results indicate that HR4 and RPW8 genes could play a role in the establishment of Arabidopsis interactions with beneficial microbes. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Curcumin Inhibits Glutamate Release from Rat Prefrontal Nerve Endings by Affecting Vesicle Mobilization
by Tzu Yu Lin, Cheng Wei Lu, Shu Kuei Huang and Su Jane Wang
Int. J. Mol. Sci. 2012, 13(7), 9097-9109; https://doi.org/10.3390/ijms13079097 - 20 Jul 2012
Cited by 18 | Viewed by 6959
Abstract
Curcumin, one of the major constituents of Curcuma longa, has been shown to inhibit depolarization-evoked glutamate release from rat prefrontocortical nerve terminals by reducing voltage-dependent Ca2+ entry. This study showed that curcumin inhibited ionomycin-induced glutamate release and KCl-evoked FM1-43 release, suggesting [...] Read more.
Curcumin, one of the major constituents of Curcuma longa, has been shown to inhibit depolarization-evoked glutamate release from rat prefrontocortical nerve terminals by reducing voltage-dependent Ca2+ entry. This study showed that curcumin inhibited ionomycin-induced glutamate release and KCl-evoked FM1-43 release, suggesting that some steps after Ca2+ entry are regulated by curcumin. Furthermore, disrupting the cytoskeleton organization using cytochalasin D abolished the inhibitory action of curcumin on ionomycin-induced glutamate release. Mitogen-activated protein kinase kinase (MEK) inhibition also prevented the inhibitory effect of curcumin on ionomycin-induced glutamate release. Western blot analyses showed that curcumin decreased the ionomycin-induced phosphorylation of extracellular signal-regulated kinase 1 and 2 (ERK1/2) and synaptic vesicle-associated protein synapsin I, the main presynaptic target of ERK. These results show that curcumin-mediated inhibition of glutamate release involves modulating downstream events by controlling synaptic vesicle recruitment and exocytosis, possibly through a decrease of MAPK/ERK activation and synapsin I phosphorylation, thereby decreasing synaptic vesicle availability for exocytosis. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Article
Involvement of Disperse Repetitive Sequences in Wheat/Rye Genome Adjustment
by Diana Tomás, Miguel Bento, Wanda Viegas and Manuela Silva
Int. J. Mol. Sci. 2012, 13(7), 8549-8561; https://doi.org/10.3390/ijms13078549 - 10 Jul 2012
Cited by 3 | Viewed by 7568
Abstract
The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat [...] Read more.
The union of different genomes in the same nucleus frequently results in hybrid genotypes with improved genome plasticity related to both genome remodeling events and changes in gene expression. Most modern cereal crops are polyploid species. Triticale, synthesized by the cross between wheat and rye, constitutes an excellent model to study polyploidization functional implications. We intend to attain a deeper knowledge of dispersed repetitive sequence involvement in parental genome reshuffle in triticale and in wheat-rye addition lines that have the entire wheat genome plus each rye chromosome pair. Through Random Amplified Polymorphic DNA (RAPD) analysis with OPH20 10-mer primer we unraveled clear alterations corresponding to the loss of specific bands from both parental genomes. Moreover, the sequential nature of those events was revealed by the increased absence of rye-origin bands in wheat-rye addition lines in comparison with triticale. Remodeled band sequencing revealed that both repetitive and coding genome domains are affected in wheat-rye hybrid genotypes. Additionally, the amplification and sequencing of pSc20H internal segments showed that the disappearance of parental bands may result from restricted sequence alterations and unraveled the involvement of wheat/rye related repetitive sequences in genome adjustment needed for hybrid plant stabilization. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
DsHsp90 Is Involved in the Early Response of Dunaliella salina to Environmental Stress
by Si-Jia Wang, Ming-Jie Wu, Xiang-Jun Chen, Yan Jiang and Yong-Bin Yan
Int. J. Mol. Sci. 2012, 13(7), 7963-7979; https://doi.org/10.3390/ijms13077963 - 27 Jun 2012
Cited by 20 | Viewed by 7707
Abstract
Heat shock protein 90 (Hsp90) is a molecular chaperone highly conserved across the species from prokaryotes to eukaryotes. Hsp90 is essential for cell viability under all growth conditions and is proposed to act as a hub of the signaling network and protein homeostasis [...] Read more.
Heat shock protein 90 (Hsp90) is a molecular chaperone highly conserved across the species from prokaryotes to eukaryotes. Hsp90 is essential for cell viability under all growth conditions and is proposed to act as a hub of the signaling network and protein homeostasis of the eukaryotic cells. By interacting with various client proteins, Hsp90 is involved in diverse physiological processes such as signal transduction, cell mobility, heat shock response and osmotic stress response. In this research, we cloned the dshsp90 gene encoding a polypeptide composed of 696 amino acids from the halotolerant unicellular green algae Dunaliella salina. Sequence alignment indicated that DsHsp90 belonged to the cytosolic Hsp90A family. Further biophysical and biochemical studies of the recombinant protein revealed that DsHsp90 possessed ATPase activity and existed as a dimer with similar percentages of secondary structures to those well-studied Hsp90As. Analysis of the nucleotide sequence of the cloned genomic DNA fragment indicated that dshsp90 contained 21 exons interrupted by 20 introns, which is much more complicated than the other plant hsp90 genes. The promoter region of dshsp90 contained putative cis-acting stress responsive elements and binding sites of transcriptional factors that respond to heat shock and salt stress. Further experimental research confirmed that dshsp90 was upregulated quickly by heat and salt shock in the D. salina cells. These findings suggested that dshsp90 might serve as a component of the early response system of the D. salina cells against environmental stresses. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Introgression Between Cultivars and Wild Populations of Momordica charantia L. (Cucurbitaceae) in Taiwan
by Pei-Chun Liao, Chi-Chu Tsai, Chang-Hung Chou and Yu-Chung Chiang
Int. J. Mol. Sci. 2012, 13(5), 6469-6491; https://doi.org/10.3390/ijms13056469 - 24 May 2012
Cited by 20 | Viewed by 8540
Abstract
The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native [...] Read more.
The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM). Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Simple and Rapid Molecular Techniques for Identification of Amylose Levels in Rice Varieties
by Acga Cheng, Ismanizan Ismail, Mohamad Osman and Habibuddin Hashim
Int. J. Mol. Sci. 2012, 13(5), 6156-6166; https://doi.org/10.3390/ijms13056156 - 18 May 2012
Cited by 18 | Viewed by 8732
Abstract
The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as an [...] Read more.
The polymorphisms of Waxy (Wx) microsatellite and G-T single-nucleotide polymorphism (SNP) in the Wx gene region were analyzed using simplified techniques in fifteen rice varieties. A rapid and reliable electrophoresis method, MetaPhor agarose gel electrophoresis (MAGE), was effectively employed as an alternative to polyacrylamide gel electrophoresis (PAGE) for separating Wx microsatellite alleles. The amplified products containing the Wx microsatellite ranged from 100 to 130 bp in length. Five Wx microsatellite alleles, namely (CT)10, (CT)11, (CT)16, (CT)17, and (CT)18 were identified. Of these, (CT)11 and (CT)17 were the predominant classes among the tested varieties. All varieties with an apparent amylose content higher than 24% were associated with the shorter repeat alleles; (CT)10 and (CT)11, while varieties with 24% or less amylose were associated with the longer repeat alleles. All varieties with intermediate and high amylose content had the sequence AGGTATA at the 5'-leader intron splice site, while varieties with low amylose content had the sequence AGTTATA. The G-T polymorphism was further verified by the PCR-AccI cleaved amplified polymorphic sequence (CAPS) method, in which only genotypes containing the AGGTATA sequence were cleaved by AccI. Hence, varieties with desirable amylose levels can be developed rapidly using the Wx microsatellite and G-T SNP, along with MAGE. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Combinatorial Signal Integration by APETALA2/Ethylene Response Factor (ERF)-Transcription Factors and the Involvement of AP2-2 in Starvation Response
by Marc Oliver Vogel, Deborah Gomez-Perez, Nina Probst and Karl-Josef Dietz
Int. J. Mol. Sci. 2012, 13(5), 5933-5951; https://doi.org/10.3390/ijms13055933 - 16 May 2012
Cited by 16 | Viewed by 8676
Abstract
Transcription factors of the APETALA 2/Ethylene Response Factor (AP2/ERF)-family have been implicated in diverse processes during development, stress acclimation and retrograde signaling. Fifty-three leaf-expressed AP2/ERFs were screened for their transcriptional response to abscisic acid (ABA), 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), methylviologen (MV), sucrose and high or [...] Read more.
Transcription factors of the APETALA 2/Ethylene Response Factor (AP2/ERF)-family have been implicated in diverse processes during development, stress acclimation and retrograde signaling. Fifty-three leaf-expressed AP2/ERFs were screened for their transcriptional response to abscisic acid (ABA), 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), methylviologen (MV), sucrose and high or low light, respectively, and revealed high reactivity to these effectors. Six of them (AP2-2, ARF14, CEJ1, ERF8, ERF11, RAP2.5) were selected for combinatorial response analysis to ABA, DCMU and high light. Additive, synergistic and antagonistic effects demonstrated that these transcription factors are components of multiple signaling pathways. AP2-2 (At1g79700) was subjected to an in depth study. AP2-2 transcripts were high under conditions linked to limited carbohydrate availability and stress and down-regulated in extended light phase, high light or in the presence of sugar. ap2-2 knock out plants had unchanged metabolite profiles and transcript levels of co-expressed genes in extended darkness. However, ap2-2 revealed more efficient germination and faster early growth under high sugar, osmotic or salinity stress, but the difference was abolished in the absence of sugar or during subsequent growth. It is suggested that AP2-2 is involved in mediating starvation-related and hormonal signals. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Expression of Selected Ginkgo biloba Heat Shock Protein Genes After Cold Treatment Could Be Induced by Other Abiotic Stress
by Fuliang Cao, Hua Cheng, Shuiyuan Cheng, Linling Li, Feng Xu, Wanwen Yu and Honghui Yuan
Int. J. Mol. Sci. 2012, 13(5), 5768-5788; https://doi.org/10.3390/ijms13055768 - 15 May 2012
Cited by 27 | Viewed by 8304
Abstract
Heat shock proteins (HSPs) play various stress-protective roles in plants. In this study, three HSP genes were isolated from a suppression subtractive hybridization (SSH) cDNA library of Ginkgo biloba leaves treated with cold stress. Based on the molecular weight, the three genes were [...] Read more.
Heat shock proteins (HSPs) play various stress-protective roles in plants. In this study, three HSP genes were isolated from a suppression subtractive hybridization (SSH) cDNA library of Ginkgo biloba leaves treated with cold stress. Based on the molecular weight, the three genes were designated GbHSP16.8, GbHSP17 and GbHSP70. The full length of the three genes were predicted to encode three polypeptide chains containing 149 amino acids (Aa), 152 Aa, and 657 Aa, and their corresponding molecular weights were predicted as follows: 16.67 kDa, 17.39 kDa, and 71.81 kDa respectively. The three genes exhibited distinctive expression patterns in different organs or development stages. GbHSP16.8 and GbHSP70 showed high expression levels in leaves and a low level in gynoecia, GbHSP17 showed a higher transcription in stamens and lower level in fruit. This result indicates that GbHSP16.8 and GbHSP70 may play important roles in Ginkgo leaf development and photosynthesis, and GbHSP17 may play a positive role in pollen maturation. All three GbHSPs were up-regulated under cold stress, whereas extreme heat stress only caused up-regulation of GbHSP70, UV-B treatment resulted in up-regulation of GbHSP16.8 and GbHSP17, wounding treatment resulted in up-regulation of GbHSP16.8 and GbHSP70, and abscisic acid (ABA) treatment caused up-regulation of GbHSP70 primarily. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Genetic Diversity of the Endemic and Medicinally Important Plant Rheum officinale as Revealed by Inter-Simpe Sequence Repeat (ISSR) Markers
by Xu-Mei Wang, Xiao-Qi Hou, Yu-Qu Zhang, Rui Yang, Shi-Fang Feng, Yan Li and Yi Ren
Int. J. Mol. Sci. 2012, 13(3), 3900-3915; https://doi.org/10.3390/ijms13033900 - 22 Mar 2012
Cited by 54 | Viewed by 8601
Abstract
Rheum officinale Baill., an important but endangered medicinal herb, is endemic to China. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 12 populations of R. officinale. Thirteen selected primers yielded 189 bright and discernible bands, [...] Read more.
Rheum officinale Baill., an important but endangered medicinal herb, is endemic to China. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 12 populations of R. officinale. Thirteen selected primers yielded 189 bright and discernible bands, with an average of 14.54 per primer. The genetic diversity was low at the population level, but pretty high at the species level (H = 0.1008, I = 0.1505, PPB = 28.95% vs. H = 0.3341, I = 0.5000, PPB = 95.24%, respectively) by POPGENE analysis. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly among populations (74.38%), in line with the limited gene flow (Nm = 0.2766) among populations. Mantel test revealed a significant correlation between genetic and geographic distances (r = 0.5381, P = 0.002), indicating the role of geographic isolation in shaping the present population genetic structure. Both Bayesian analysis and UPGMA cluster analysis demonstrated the similar results. Our results imply that the conservation efforts should aim to preserve all the extant populations of this endangered species, and cultivation is proposed in this study. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Expression Analysis of Four Peroxiredoxin Genes from Tamarix hispida in Response to Different Abiotic Stresses and Exogenous Abscisic Acid (ABA)
by Caiqiu Gao, Kaimin Zhang, Guiyan Yang and Yucheng Wang
Int. J. Mol. Sci. 2012, 13(3), 3751-3764; https://doi.org/10.3390/ijms13033751 - 21 Mar 2012
Cited by 20 | Viewed by 6888
Abstract
Peroxiredoxins (Prxs) are a recently discovered family of antioxidant enzymes that catalyze the reduction of peroxides and alkyl peroxides. In this study, four Prx genes (named as ThPrxII, ThPrxIIE, ThPrxIIF, and Th2CysPrx) were cloned from Tamarix hispida. Their [...] Read more.
Peroxiredoxins (Prxs) are a recently discovered family of antioxidant enzymes that catalyze the reduction of peroxides and alkyl peroxides. In this study, four Prx genes (named as ThPrxII, ThPrxIIE, ThPrxIIF, and Th2CysPrx) were cloned from Tamarix hispida. Their expression profiles in response to stimulus of NaCl, NaHCO3, PEG, CdCl2 and abscisic acid (ABA) in roots, stems and leaves of T. hispida were investigated using real-time RT-PCR. The results showed that the four ThPrxs were all expressed in roots, stems and leaves. Furthermore, the transcript levels of ThPrxIIE and ThPrxII were the lowest and the highest, respectively, in all tissue types. All the ThPrx genes were induced by both NaCl and NaHCO3 and reached their highest expression levels at the onset of stress in roots. Under PEG and CdCl2 stress, the expression patterns of these ThPrxs showed temporal and spatial specificity. The expressions of the ThPrxs were all differentially regulated by ABA, indicating that they are all involved in the ABA signaling pathway. These findings reveal a complex regulation of Prxs that is dependent on the type of Prx, tissue, and the signaling molecule. The divergence of the stress-dependent transcriptional regulation of the ThPrx gene family in T. hispida may provide an essential basis for the elucidation of Prx function in future work. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Expression Analysis of an R3-Type MYB Transcription Factor CPC-LIKE MYB4 (TRICHOMELESS2) and CPL4-Related Transcripts in Arabidopsis
by Rumi Tominaga-Wada and Yuka Nukumizu
Int. J. Mol. Sci. 2012, 13(3), 3478-3491; https://doi.org/10.3390/ijms13033478 - 13 Mar 2012
Cited by 47 | Viewed by 8350
Abstract
The CAPRICE (CPC)-like MYB gene family encodes R3-type MYB transcription factors in Arabidopsis. There are six additional CPC-like MYB sequences in the Arabidopsis genome, including TRYPTICHON (TRY), ENHANCER OF TRY AND CPC1 and 2 (ETC1 and [...] Read more.
The CAPRICE (CPC)-like MYB gene family encodes R3-type MYB transcription factors in Arabidopsis. There are six additional CPC-like MYB sequences in the Arabidopsis genome, including TRYPTICHON (TRY), ENHANCER OF TRY AND CPC1 and 2 (ETC1 and ETC2), ENHANCER OF TRY AND CPC3/CPC-LIKE MYB3 (ETC3/CPL3), and TRICHOMELESS1 and 2 (TCL1 and TCL2). We independently identified CPC-LIKE MYB4 (CPL4), which was found to be identical to TCL2. RT-PCR analysis showed that CPL4 is strongly expressed in shoots, including true leaves, but not in roots. Promoter-GUS analyses indicated that CPL4 is specifically expressed in leaf blades. Although CPC expression was repressed in 35S::ETC1, 35S::ETC2 and 35S::CPL3 backgrounds, CPL4 expression was not affected by ETC1, ETC2 or CPL3 over-expression. Notably, several chimeric transcripts may result from inter-genic alternative splicing of CPL4 and ETC2, two tandemly repeated genes on chromosome II. At least two chimeric transcripts named CPL4-α and CPL4-β are expected to encode complete CPC-like MYB proteins. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Homologous NF-YC2 Subunit from Arabidopsis and Tobacco Is Activated by Photooxidative Stress and Induces Flowering
by Dieter Hackenberg, Ulrich Keetman and Bernhard Grimm
Int. J. Mol. Sci. 2012, 13(3), 3458-3477; https://doi.org/10.3390/ijms13033458 - 13 Mar 2012
Cited by 74 | Viewed by 9736
Abstract
The transcription factor NF-Y consists of the three subunits A, B and C, which are encoded in Arabidopsis in large gene families. The multiplicity of the genes implies that NF-Y may act in diverse combinations of each subunit for the transcriptional control. We [...] Read more.
The transcription factor NF-Y consists of the three subunits A, B and C, which are encoded in Arabidopsis in large gene families. The multiplicity of the genes implies that NF-Y may act in diverse combinations of each subunit for the transcriptional control. We aimed to assign a function in stress response and plant development to NF-YC subunits by analyzing the expression of NF-Y genes and exploitation of nf-y mutants. Among the subunit family, NF-YC2 showed the strongest inducibility towards oxidative stress, e.g. photodynamic, light, oxidative, heat and drought stress. A tobacco NF-YC homologous gene was found to be inducible by photooxidative stress generated by an accumulation of the tetrapyrrole metabolite, coproporphyrin. Despite the stress induction, an Arabidopsis nf-yc2 mutant and NF-YC2 overexpressors did not show phenotypical differences compared to wild-type seedlings in response to photooxidative stress. This can be explained by the compensatory potential of other members of the NF-YC family. However, NF-YC2 overexpression leads to an early flowering phenotype that is correlated with increased FLOWERING LOCUS T-transcript levels. It is proposed that NF-YC2 functions in floral induction and is a candidate gene among the NF-Y family for the transcriptional activation upon oxidative stress. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Arabidopsis Serine Decarboxylase Mutants Implicate the Roles of Ethanolamine in Plant Growth and Development
by Yerim Kwon, Si-in Yu, Hyoungseok Lee, Joung Han Yim, Jian-Kang Zhu and Byeong-ha Lee
Int. J. Mol. Sci. 2012, 13(3), 3176-3188; https://doi.org/10.3390/ijms13033176 - 07 Mar 2012
Cited by 37 | Viewed by 10006
Abstract
Ethanolamine is important for synthesis of choline, phosphatidylethanolamine (PE) and phosphatidylcholine (PC) in plants. The latter two phospholipids are the major phospholipids in eukaryotic membranes. In plants, ethanolamine is mainly synthesized directly from serine by serine decarboxylase. Serine decarboxylase is unique to plants [...] Read more.
Ethanolamine is important for synthesis of choline, phosphatidylethanolamine (PE) and phosphatidylcholine (PC) in plants. The latter two phospholipids are the major phospholipids in eukaryotic membranes. In plants, ethanolamine is mainly synthesized directly from serine by serine decarboxylase. Serine decarboxylase is unique to plants and was previously shown to have highly specific activity to L-serine. While serine decarboxylase was biochemically characterized, its functions and importance in plants were not biologically elucidated due to the lack of serine decarboxylase mutants. Here we characterized an Arabidopsis mutant defective in serine decarboxylase, named atsdc-1 (Arabidopsis thaliana serine decarboxylase-1). The atsdc-1 mutants showed necrotic lesions in leaves, multiple inflorescences, sterility in flower, and early flowering in short day conditions. These defects were rescued by ethanolamine application to atsdc-1, suggesting the roles of ethanolamine as well as serine decarboxylase in plant development. In addition, molecular analysis of serine decarboxylase suggests that Arabidopsis serine decarboxylase is cytosol-localized and expressed in all tissue. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Identification and Characterization of MicroRNAs from Barley (Hordeum vulgare L.) by High-Throughput Sequencing
by Shuzuo Lv, Xiaojun Nie, Le Wang, Xianghong Du, Siddanagouda S. Biradar, Xiaoou Jia and Song Weining
Int. J. Mol. Sci. 2012, 13(3), 2973-2984; https://doi.org/10.3390/ijms13032973 - 06 Mar 2012
Cited by 81 | Viewed by 9652
Abstract
MicroRNAs (miRNAs) are a class of endogenous RNAs that regulates the gene expression involved in various biological and metabolic processes. Barley is one of the most important cereal crops worldwide and is a model organism for genetic and genomic studies in Triticeae species. [...] Read more.
MicroRNAs (miRNAs) are a class of endogenous RNAs that regulates the gene expression involved in various biological and metabolic processes. Barley is one of the most important cereal crops worldwide and is a model organism for genetic and genomic studies in Triticeae species. However, the miRNA research in barley has lagged behind other model species in grass family. To obtain more information of miRNA genes in barley, we sequenced a small RNA library created from a pool of equal amounts of RNA from four different tissues using Solexa sequencing. In addition to 126 conserved miRNAs (58 families), 133 novel miRNAs belonging to 50 families were identified from this sequence data set. The miRNA* sequences of 15 novel miRNAs were also discovered, suggesting the additional evidence for existence of these miRNAs. qRT-PCR was used to examine the expression pattern of six randomly selected miRNAs. Some miRNAs involved in drought and salt stress response were also identified. Furthermore, the potential targets of these putative miRNAs were predicted using the psRNATarget tools. Our results significantly increased the number of novel miRNAs in barley, which should be useful for further investigation into the biological functions and evolution of miRNAs in barley and other species. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Article
Expression Analysis of MYC Genes from Tamarix hispida in Response to Different Abiotic Stresses
by Xiaoyu Ji, Yucheng Wang and Guifeng Liu
Int. J. Mol. Sci. 2012, 13(2), 1300-1313; https://doi.org/10.3390/ijms13021300 - 25 Jan 2012
Cited by 10 | Viewed by 7579
Abstract
The MYC genes are a group of transcription factors containing both bHLH and ZIP motifs that play important roles in the regulation of abscisic acid (ABA)-responsive genes. In the present study, to investigate the roles of MYC genes under NaCl, osmotic and ABA [...] Read more.
The MYC genes are a group of transcription factors containing both bHLH and ZIP motifs that play important roles in the regulation of abscisic acid (ABA)-responsive genes. In the present study, to investigate the roles of MYC genes under NaCl, osmotic and ABA stress conditions, nine MYC genes were cloned from Tamarix hispida. Real-time reverse-transcriptase (RT)-PCR showed that all nine MYC genes were expressed in root, stem and leaf tissues, but that the levels of the transcripts of these genes in the various tissues differed notably. The MYC genes were highly induced in the roots in response to ABA, NaCl and osmotic stresses after 3 h; however, in the stem and leaf tissues, MYC genes were highly induced only when exposed to these stresses for 6 h. In addition, most of these MYC genes were highly expressed in roots in comparison with stems and leaves. Furthermore, the MYC genes were more highly induced in roots than in stem and leaf tissues, indicating that these genes may play roles in stress responses mainly in the roots rather than the stems and leaves. The results of this present study suggest that MYCs are involved in salt and osmotic stress tolerances and are controlled by the ABA signal transduction pathway. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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130 KiB  
Article
Assessment of Genetic Diversity of Bermudagrass (Cynodon dactylon) Using ISSR Markers
by Tayebeh Mohammadi Farsani, Nematollah Etemadi, Badraldin Ebrahim Sayed-Tabatabaei and Majid Talebi
Int. J. Mol. Sci. 2012, 13(1), 383-392; https://doi.org/10.3390/ijms13010383 - 29 Dec 2011
Cited by 36 | Viewed by 10283
Abstract
Bermudagrass (Cynodon spp.) is a major turfgrass for home lawns, public parks, golf courses and sport fields and is known to have originated in the Middle East. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between [...] Read more.
Bermudagrass (Cynodon spp.) is a major turfgrass for home lawns, public parks, golf courses and sport fields and is known to have originated in the Middle East. Morphological and physiological characteristics are not sufficient to differentiate some bermudagrass genotypes because the differences between them are often subtle and subjected to environmental influences. In this study, twenty seven bermudagrass accessions and introductions, mostly from different parts of Iran, were assayed by inter-simple sequence repeat (ISSR) markers to differentiate and explore their genetic relationships. Fourteen ISSR primers amplified 389 fragments of which 313 (80.5%) were polymorphic. The average polymorphism information content (PIC) was 0.328, which shows that the majority of primers are informative. Cluster analysis using the un-weighted paired group method with arithmetic average (UPGMA) method and Jaccard’s similarity coefficient (r = 0.828) grouped the accessions into six main clusters according to some degree to geographical origin, their chromosome number and some morphological characteristics. It can be concluded that there exists a wide genetic base of bermudograss in Iran and that ISSR markers are effective in determining genetic diversity and relationships among them. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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572 KiB  
Article
Transient Co-Expression of Post-Transcriptional Gene Silencing Suppressors for Increased in Planta Expression of a Recombinant Anthrax Receptor Fusion Protein
by Lucas Arzola, Junxing Chen, Kittipong Rattanaporn, James M. Maclean and Karen A. McDonald
Int. J. Mol. Sci. 2011, 12(8), 4975-4990; https://doi.org/10.3390/ijms12084975 - 05 Aug 2011
Cited by 28 | Viewed by 9378
Abstract
Potential epidemics of infectious diseases and the constant threat of bioterrorism demand rapid, scalable, and cost-efficient manufacturing of therapeutic proteins. Molecular farming of tobacco plants provides an alternative for the recombinant production of therapeutics. We have developed a transient production platform that uses [...] Read more.
Potential epidemics of infectious diseases and the constant threat of bioterrorism demand rapid, scalable, and cost-efficient manufacturing of therapeutic proteins. Molecular farming of tobacco plants provides an alternative for the recombinant production of therapeutics. We have developed a transient production platform that uses Agrobacterium infiltration of Nicotiana benthamiana plants to express a novel anthrax receptor decoy protein (immunoadhesin), CMG2-Fc. This chimeric fusion protein, designed to protect against the deadly anthrax toxins, is composed of the von Willebrand factor A (VWA) domain of human capillary morphogenesis 2 (CMG2), an effective anthrax toxin receptor, and the Fc region of human immunoglobulin G (IgG). We evaluated, in N. benthamiana intact plants and detached leaves, the expression of CMG2-Fc under the control of the constitutive CaMV 35S promoter, and the co-expression of CMG2-Fc with nine different viral suppressors of post-transcriptional gene silencing (PTGS): p1, p10, p19, p21, p24, p25, p38, 2b, and HCPro. Overall, transient CMG2-Fc expression was higher on intact plants than detached leaves. Maximum expression was observed with p1 co-expression at 3.5 days post-infiltration (DPI), with a level of 0.56 g CMG2-Fc per kg of leaf fresh weight and 1.5% of the total soluble protein, a ten-fold increase in expression when compared to absence of suppression. Co-expression with the p25 PTGS suppressor also significantly increased the CMG2-Fc expression level after just 3.5 DPI. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming)
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127 KiB  
Article
Interactions of Antibiotics and Methanolic Crude Extracts of Afzelia Africana (Smith.) Against Drug Resistance Bacterial Isolates
by Olayinka Aiyegoro, Adekanmi Adewusi, Sunday Oyedemi, David Akinpelu and Anthony Okoh
Int. J. Mol. Sci. 2011, 12(7), 4477-4487; https://doi.org/10.3390/ijms12074477 - 13 Jul 2011
Cited by 29 | Viewed by 8405
Abstract
Infection due to multidrug resistance pathogens is difficult to manage due to bacterial virulence factors and because of a relatively limited choice of antimicrobial agents. Thus, it is imperative to discover fresh antimicrobials or new practices that are effective for the treatment of [...] Read more.
Infection due to multidrug resistance pathogens is difficult to manage due to bacterial virulence factors and because of a relatively limited choice of antimicrobial agents. Thus, it is imperative to discover fresh antimicrobials or new practices that are effective for the treatment of infectious diseases caused by drug-resistant microorganisms. The objective of this experiment is to investigate for synergistic outcomes when crude methanolic extract of the stem bark of Afzelia africana and antibiotics were combined against a panel of antibiotic resistant bacterial strains that have been implicated in infections. Standard microbiological protocols were used to determine the minimum inhibitory concentrations (MICs) of the extract and antibiotics, as well as to investigate the effect of combinations of the methanolic extract of A. africana stem bark and selected antibiotics using the time-kill assay method. The extract of Afzelia africana exhibited antibacterial activities against both Gram-negative and Gram-positive bacteria made up of environmental and standard strains at a screening concentration of 5 mg/mL. The MICs of the crude extracts and the antibiotics varied between 1 μg/mL and 5.0 mg/mL. Overall, synergistic response constituted about 63.79% of all manner of combinations of extract and antibiotics against all test organisms; antagonism was not detected among the 176 tests carried out. The extract from A. africana stem bark showed potentials of synergy in combination with antibiotics against strains of pathogenic bacteria. The detection of synergy between the extract and antibiotics demonstrates the potential of this plant as a source of antibiotic resistance modulating compounds. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming)
351 KiB  
Article
Membrane-Based Inverse Transition Cycling: An Improved Means for Purifying Plant-Derived Recombinant Protein-Elastin-Like Polypeptide Fusions
by Hoang Trong Phan and Udo Conrad
Int. J. Mol. Sci. 2011, 12(5), 2808-2821; https://doi.org/10.3390/ijms12052808 - 29 Apr 2011
Cited by 38 | Viewed by 10979
Abstract
Elastin-like peptide (ELP) was fused to two different avian flu H5N1 antigens and expressed in transgenic tobacco plants. The presence of the ELP tag enhanced the accumulation of the heterologous proteins in the tobacco leaves. An effective membrane-based Inverse Transition Cycling was developed [...] Read more.
Elastin-like peptide (ELP) was fused to two different avian flu H5N1 antigens and expressed in transgenic tobacco plants. The presence of the ELP tag enhanced the accumulation of the heterologous proteins in the tobacco leaves. An effective membrane-based Inverse Transition Cycling was developed to recover the ELPylated antigens and antibodies from plant material. The functionality of both the ELPylated neuraminidase and an ELPylated nanobody was demonstrated. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming)
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Review

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1007 KiB  
Review
Gibberellic Acid: A Key Phytohormone for Spikelet Fertility in Rice Grain Production
by Choon-Tak Kwon and Nam-Chon Paek
Int. J. Mol. Sci. 2016, 17(5), 794; https://doi.org/10.3390/ijms17050794 - 23 May 2016
Cited by 44 | Viewed by 8773
Abstract
The phytohormone gibberellic acid (GA) has essential signaling functions in multiple processes during plant development. In the “Green Revolution”, breeders developed high-yield rice cultivars that exhibited both semi-dwarfism and altered GA responses, thus improving grain production. Most studies of GA have concentrated on [...] Read more.
The phytohormone gibberellic acid (GA) has essential signaling functions in multiple processes during plant development. In the “Green Revolution”, breeders developed high-yield rice cultivars that exhibited both semi-dwarfism and altered GA responses, thus improving grain production. Most studies of GA have concentrated on germination and cell elongation, but GA also has a pivotal role in floral organ development, particularly in stamen/anther formation. In rice, GA signaling plays an important role in spikelet fertility; however, the molecular genetic and biochemical mechanisms of GA in male fertility remain largely unknown. Here, we review recent progress in understanding the network of GA signaling and its connection with spikelet fertility, which is tightly associated with grain productivity in cereal crops. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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504 KiB  
Review
Molecular Mechanisms of Floral Boundary Formation in Arabidopsis
by Hongyang Yu and Tengbo Huang
Int. J. Mol. Sci. 2016, 17(3), 317; https://doi.org/10.3390/ijms17030317 - 02 Mar 2016
Cited by 11 | Viewed by 7204 | Correction
Abstract
Boundary formation is a crucial developmental process in plant organogenesis. Boundaries separate cells with distinct identities and act as organizing centers to control the development of adjacent organs. In flower development, initiation of floral primordia requires the formation of the meristem-to-organ (M–O) boundaries [...] Read more.
Boundary formation is a crucial developmental process in plant organogenesis. Boundaries separate cells with distinct identities and act as organizing centers to control the development of adjacent organs. In flower development, initiation of floral primordia requires the formation of the meristem-to-organ (M–O) boundaries and floral organ development depends on the establishment of organ-to-organ (O–O) boundaries. Studies in this field have revealed a suite of genes and regulatory pathways controlling floral boundary formation. Many of these genes are transcription factors that interact with phytohormone pathways. This review will focus on the functions and interactions of the genes that play important roles in the floral boundaries and discuss the molecular mechanisms that integrate these regulatory pathways to control the floral boundary formation. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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1106 KiB  
Review
Plant Adaptation to Multiple Stresses during Submergence and Following Desubmergence
by Bishal Gole Tamang and Takeshi Fukao
Int. J. Mol. Sci. 2015, 16(12), 30164-30180; https://doi.org/10.3390/ijms161226226 - 17 Dec 2015
Cited by 97 | Viewed by 11858
Abstract
Plants require water for growth and development, but excessive water negatively affects their productivity and viability. Flash floods occasionally result in complete submergence of plants in agricultural and natural ecosystems. When immersed in water, plants encounter multiple stresses including low oxygen, low light, [...] Read more.
Plants require water for growth and development, but excessive water negatively affects their productivity and viability. Flash floods occasionally result in complete submergence of plants in agricultural and natural ecosystems. When immersed in water, plants encounter multiple stresses including low oxygen, low light, nutrient deficiency, and high risk of infection. As floodwaters subside, submerged plants are abruptly exposed to higher oxygen concentration and greater light intensity, which can induce post-submergence injury caused by oxidative stress, high light, and dehydration. Recent studies have emphasized the significance of multiple stress tolerance in the survival of submergence and prompt recovery following desubmergence. A mechanistic understanding of acclimation responses to submergence at molecular and physiological levels can contribute to the deciphering of the regulatory networks governing tolerance to other environmental stresses that occur simultaneously or sequentially in the natural progress of a flood event. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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634 KiB  
Review
Phenolic Phytoalexins in Rice: Biological Functions and Biosynthesis
by Man-Ho Cho and Sang-Won Lee
Int. J. Mol. Sci. 2015, 16(12), 29120-29133; https://doi.org/10.3390/ijms161226152 - 07 Dec 2015
Cited by 85 | Viewed by 9332
Abstract
Phytoalexins are inducible secondary metabolites possessing antimicrobial activity against phytopathogens. Rice produces a wide array of phytoalexins in response to pathogen attacks and environmental stresses. With few exceptions, most phytoalexins identified in rice are diterpenoid compounds. Until very recently, flavonoid sakuranetin was the [...] Read more.
Phytoalexins are inducible secondary metabolites possessing antimicrobial activity against phytopathogens. Rice produces a wide array of phytoalexins in response to pathogen attacks and environmental stresses. With few exceptions, most phytoalexins identified in rice are diterpenoid compounds. Until very recently, flavonoid sakuranetin was the only known phenolic phytoalexin in rice. However, recent studies have shown that phenylamides are involved in defense against pathogen attacks in rice. Phenylamides are amine-conjugated phenolic acids that are induced by pathogen infections and abiotic stresses including ultra violet (UV) radiation in rice. Stress-induced phenylamides, such as N-trans-cinnamoyltryptamine, N-p-coumaroylserotonin and N-cinnamoyltyramine, have been reported to possess antimicrobial activities against rice bacterial and fungal pathogens, an indication of their direct inhibitory roles against invading pathogens. This finding suggests that phenylamides act as phytoalexins in rice and belong to phenolic phytoalexins along with sakuranetin. Phenylamides also have been implicated in cell wall reinforcement for disease resistance and allelopathy of rice. Synthesis of phenolic phytoalexins is stimulated by phytopathogen attacks and abiotic challenges including UV radiation. Accumulating evidence has demonstrated that biosynthetic pathways including the shikimate, phenylpropanoid and arylmonoamine pathways are coordinately activated for phenolic phytoalexin synthesis, and related genes are induced by biotic and abiotic stresses in rice. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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720 KiB  
Review
Carbon Fluxes between Primary Metabolism and Phenolic Pathway in Plant Tissues under Stress
by Sofia Caretto, Vito Linsalata, Giovanni Colella, Giovanni Mita and Vincenzo Lattanzio
Int. J. Mol. Sci. 2015, 16(11), 26378-26394; https://doi.org/10.3390/ijms161125967 - 04 Nov 2015
Cited by 220 | Viewed by 11380
Abstract
Higher plants synthesize an amazing diversity of phenolic secondary metabolites. Phenolics are defined secondary metabolites or natural products because, originally, they were considered not essential for plant growth and development. Plant phenolics, like other natural compounds, provide the plant with specific adaptations to [...] Read more.
Higher plants synthesize an amazing diversity of phenolic secondary metabolites. Phenolics are defined secondary metabolites or natural products because, originally, they were considered not essential for plant growth and development. Plant phenolics, like other natural compounds, provide the plant with specific adaptations to changing environmental conditions and, therefore, they are essential for plant defense mechanisms. Plant defensive traits are costly for plants due to the energy drain from growth toward defensive metabolite production. Being limited with environmental resources, plants have to decide how allocate these resources to various competing functions. This decision brings about trade-offs, i.e., promoting some functions by neglecting others as an inverse relationship. Many studies have been carried out in order to link an evaluation of plant performance (in terms of growth rate) with levels of defense-related metabolites. Available results suggest that environmental stresses and stress-induced phenolics could be linked by a transduction pathway that involves: (i) the proline redox cycle; (ii) the stimulated oxidative pentose phosphate pathway; and, in turn, (iii) the reduced growth of plant tissues. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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1379 KiB  
Review
Small RNAs in Plant Responses to Abiotic Stresses: Regulatory Roles and Study Methods
by Yee-Shan Ku, Johanna Wing-Hang Wong, Zeta Mui, Xuan Liu, Jerome Ho-Lam Hui, Ting-Fung Chan and Hon-Ming Lam
Int. J. Mol. Sci. 2015, 16(10), 24532-24554; https://doi.org/10.3390/ijms161024532 - 15 Oct 2015
Cited by 34 | Viewed by 7438
Abstract
To survive under abiotic stresses in the environment, plants trigger a reprogramming of gene expression, by transcriptional regulation or translational regulation, to turn on protective mechanisms. The current focus of research on how plants cope with abiotic stresses has transitioned from transcriptomic analyses [...] Read more.
To survive under abiotic stresses in the environment, plants trigger a reprogramming of gene expression, by transcriptional regulation or translational regulation, to turn on protective mechanisms. The current focus of research on how plants cope with abiotic stresses has transitioned from transcriptomic analyses to small RNA investigations. In this review, we have summarized and evaluated the current methodologies used in the identification and validation of small RNAs and their targets, in the context of plant responses to abiotic stresses. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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769 KiB  
Review
Constituents and Pharmacological Activities of Myrcia (Myrtaceae): A Review of an Aromatic and Medicinal Group of Plants
by Márcia Moraes Cascaes, Giselle Maria Skelding Pinheiro Guilhon, Eloisa Helena de Aguiar Andrade, Maria Das Graças Bichara Zoghbi and Lourivaldo Da Silva Santos
Int. J. Mol. Sci. 2015, 16(10), 23881-23904; https://doi.org/10.3390/ijms161023881 - 09 Oct 2015
Cited by 67 | Viewed by 11479
Abstract
Myrcia is one of the largest genera of the economically important family Myrtaceae. Some of the species are used in folk medicine, such as a group known as “pedra-hume-caá” or “pedra-ume-caá” or “insulina vegetal” (insulin plant) that it is used for the treatment [...] Read more.
Myrcia is one of the largest genera of the economically important family Myrtaceae. Some of the species are used in folk medicine, such as a group known as “pedra-hume-caá” or “pedra-ume-caá” or “insulina vegetal” (insulin plant) that it is used for the treatment of diabetes. The species are an important source of essential oils, and most of the chemical studies on Myrcia describe the chemical composition of the essential oils, in which mono- and sesquiterpenes are predominant. The non-volatile compounds isolated from Myrcia are usually flavonoids, tannins, acetophenone derivatives and triterpenes. Anti-inflammatory, antinociceptive, antioxidant, antimicrobial activities have been described to Myrcia essential oils, while hypoglycemic, anti-hemorrhagic and antioxidant activities were attributed to the extracts. Flavonoid glucosides and acetophenone derivatives showed aldose reductase and α-glucosidase inhibition, and could explain the traditional use of Myrcia species to treat diabetes. Antimicrobial and anti-inflammatory are some of the activities observed for other isolated compounds from Myrcia. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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1087 KiB  
Review
Critical Issues in the Study of Magnesium Transport Systems and Magnesium Deficiency Symptoms in Plants
by Natsuko I. Kobayashi and Keitaro Tanoi
Int. J. Mol. Sci. 2015, 16(9), 23076-23093; https://doi.org/10.3390/ijms160923076 - 23 Sep 2015
Cited by 46 | Viewed by 10351
Abstract
Magnesium (Mg) is the second most abundant cation in living cells. Over 300 enzymes are known to be Mg-dependent, and changes in the Mg concentration significantly affects the membrane potential. As Mg becomes deficient, starch accumulation and chlorosis, bridged by the generation of [...] Read more.
Magnesium (Mg) is the second most abundant cation in living cells. Over 300 enzymes are known to be Mg-dependent, and changes in the Mg concentration significantly affects the membrane potential. As Mg becomes deficient, starch accumulation and chlorosis, bridged by the generation of reactive oxygen species, are commonly found in Mg-deficient young mature leaves. These defects further cause the inhibition of photosynthesis and finally decrease the biomass. Recently, transcriptome analysis has indicated the transcriptinal downregulation of chlorophyll apparatus at the earlier stages of Mg deficiency, and also the potential involvement of complicated networks relating to hormonal signaling and circadian oscillation. However, the processes of the common symptoms as well as the networks between Mg deficiency and signaling are not yet fully understood. Here, for the purpose of defining the missing pieces, several problems are considered and explained by providing an introduction to recent reports on physiological and transcriptional responses to Mg deficiency. In addition, it has long been unclear whether the Mg deficiency response involves the modulation of Mg2+ transport system. In this review, the current status of research on Mg2+ transport and the relating transporters are also summarized. Especially, the rapid progress in physiological characterization of the plant MRS2 gene family as well as the fundamental investigation about the molecular mechanism of the action of bacterial CorA proteins are described. Full article
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956 KiB  
Review
Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective
by Klára Kosová, Pavel Vítámvás, Milan Oldřich Urban, Miroslav Klíma, Amitava Roy and Ilja Tom Prášil
Int. J. Mol. Sci. 2015, 16(9), 20913-20942; https://doi.org/10.3390/ijms160920913 - 01 Sep 2015
Cited by 99 | Viewed by 9056
Abstract
Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an [...] Read more.
Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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2854 KiB  
Review
Disease Resistance Gene Analogs (RGAs) in Plants
by Manoj Kumar Sekhwal, Pingchuan Li, Irene Lam, Xiue Wang, Sylvie Cloutier and Frank M. You
Int. J. Mol. Sci. 2015, 16(8), 19248-19290; https://doi.org/10.3390/ijms160819248 - 14 Aug 2015
Cited by 194 | Viewed by 19788
Abstract
Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens’ resistance. Well-known RGAs are nucleotide binding [...] Read more.
Plants have developed effective mechanisms to recognize and respond to infections caused by pathogens. Plant resistance gene analogs (RGAs), as resistance (R) gene candidates, have conserved domains and motifs that play specific roles in pathogens’ resistance. Well-known RGAs are nucleotide binding site leucine rich repeats, receptor like kinases, and receptor like proteins. Others include pentatricopeptide repeats and apoplastic peroxidases. RGAs can be detected using bioinformatics tools based on their conserved structural features. Thousands of RGAs have been identified from sequenced plant genomes. High-density genome-wide RGA genetic maps are useful for designing diagnostic markers and identifying quantitative trait loci (QTL) or markers associated with plant disease resistance. This review focuses on recent advances in structures and mechanisms of RGAs, and their identification from sequenced genomes using bioinformatics tools. Applications in enhancing fine mapping and cloning of plant disease resistance genes are also discussed. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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1071 KiB  
Review
Gene Networks Involved in Hormonal Control of Root Development in Arabidopsis thaliana: A Framework for Studying Its Disturbance by Metal Stress
by Stefanie De Smet, Ann Cuypers, Jaco Vangronsveld and Tony Remans
Int. J. Mol. Sci. 2015, 16(8), 19195-19224; https://doi.org/10.3390/ijms160819195 - 14 Aug 2015
Cited by 51 | Viewed by 23714
Abstract
Plant survival under abiotic stress conditions requires morphological and physiological adaptations. Adverse soil conditions directly affect root development, although the underlying mechanisms remain largely to be discovered. Plant hormones regulate normal root growth and mediate root morphological responses to abiotic stress. Hormone synthesis, [...] Read more.
Plant survival under abiotic stress conditions requires morphological and physiological adaptations. Adverse soil conditions directly affect root development, although the underlying mechanisms remain largely to be discovered. Plant hormones regulate normal root growth and mediate root morphological responses to abiotic stress. Hormone synthesis, signal transduction, perception and cross-talk create a complex network in which metal stress can interfere, resulting in root growth alterations. We focus on Arabidopsis thaliana, for which gene networks in root development have been intensively studied, and supply essential terminology of anatomy and growth of roots. Knowledge of gene networks, mechanisms and interactions related to the role of plant hormones is reviewed. Most knowledge has been generated for auxin, the best-studied hormone with a pronounced primary role in root development. Furthermore, cytokinins, gibberellins, abscisic acid, ethylene, jasmonic acid, strigolactones, brassinosteroids and salicylic acid are discussed. Interactions between hormones that are of potential importance for root growth are described. This creates a framework that can be used for investigating the impact of abiotic stress factors on molecular mechanisms related to plant hormones, with the limited knowledge of the effects of the metals cadmium, copper and zinc on plant hormones and root development included as case example. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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2474 KiB  
Review
Route and Regulation of Zinc, Cadmium, and Iron Transport in Rice Plants (Oryza sativa L.) during Vegetative Growth and Grain Filling: Metal Transporters, Metal Speciation, Grain Cd Reduction and Zn and Fe Biofortification
by Tadakatsu Yoneyama, Satoru Ishikawa and Shu Fujimaki
Int. J. Mol. Sci. 2015, 16(8), 19111-19129; https://doi.org/10.3390/ijms160819111 - 13 Aug 2015
Cited by 130 | Viewed by 16061
Abstract
Zinc (Zn) and iron (Fe) are essential but are sometimes deficient in humans, while cadmium (Cd) is toxic if it accumulates in the liver and kidneys at high levels. All three are contained in the grains of rice, a staple cereal. Zn and [...] Read more.
Zinc (Zn) and iron (Fe) are essential but are sometimes deficient in humans, while cadmium (Cd) is toxic if it accumulates in the liver and kidneys at high levels. All three are contained in the grains of rice, a staple cereal. Zn and Fe concentrations in rice grains harvested under different levels of soil/hydroponic metals are known to change only within a small range, while Cd concentrations show greater changes. To clarify the mechanisms underlying such different metal contents, we synthesized information on the routes of metal transport and accumulation in rice plants by examining metal speciation, metal transporters, and the xylem-to-phloem transport system. At grain-filling, Zn and Cd ascending in xylem sap are transferred to the phloem by the xylem-to-phloem transport system operating at stem nodes. Grain Fe is largely derived from the leaves by remobilization. Zn and Fe concentrations in phloem-sap and grains are regulated within a small range, while Cd concentrations vary depending on xylem supply. Transgenic techniques to increase concentrations of the metal chelators (nicotianamine, 2′-deoxymugineic acid) are useful in increasing grain Zn and Fe concentrations. The elimination of OsNRAMP5 Cd-uptake transporter and the enhancement of root cell vacuolar Cd sequestration reduce uptake and root-to-shoot transport, respectively, resulting in a reduction of grain Cd accumulation. Full article
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Review
Current Understanding of the Interplay between Phytohormones and Photosynthesis under Environmental Stress
by Mayank Anand Gururani, Tapan Kumar Mohanta and Hanhong Bae
Int. J. Mol. Sci. 2015, 16(8), 19055-19085; https://doi.org/10.3390/ijms160819055 - 13 Aug 2015
Cited by 106 | Viewed by 8484
Abstract
Abiotic stress accounts for huge crop losses every year across the globe. In plants, the photosynthetic machinery gets severely damaged at various levels due to adverse environmental conditions. Moreover, the reactive oxygen species (ROS) generated as a result of stress further promote the [...] Read more.
Abiotic stress accounts for huge crop losses every year across the globe. In plants, the photosynthetic machinery gets severely damaged at various levels due to adverse environmental conditions. Moreover, the reactive oxygen species (ROS) generated as a result of stress further promote the photosynthetic damage by inhibiting the repair system of photosystem II. Earlier studies have suggested that phytohormones are not only required for plant growth and development, but they also play a pivotal role in regulating plants’ responses to different abiotic stress conditions. Although, phytohormones have been studied in great detail in the past, their influence on the photosynthetic machinery under abiotic stress has not been studied. One of the major factors that limits researchers fromelucidating the precise roles of phytohormones is the highly complex nature of hormonal crosstalk in plants. Another factor that needs to be elucidated is the method used for assessing photosynthetic damage in plants that are subjected to abiotic stress. Here, we review the current understanding on the role of phytohormones in the photosynthetic machinery under various abiotic stress conditions and discuss the potential areas for further research. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Review
Physiological and Molecular Aspects of Tolerance to Environmental Constraints in Grain and Forage Legumes
by Adnane Bargaz, Mainassara Zaman-Allah, Mohamed Farissi, Mohamed Lazali, Jean-Jacques Drevon, Rim T. Maougal and Carlsson Georg
Int. J. Mol. Sci. 2015, 16(8), 18976-19008; https://doi.org/10.3390/ijms160818976 - 13 Aug 2015
Cited by 35 | Viewed by 7171
Abstract
Despite the agronomical and environmental advantages of the cultivation of legumes, their production is limited by various environmental constraints such as water or nutrient limitation, frost or heat stress and soil salinity, which may be the result of pedoclimatic conditions, intensive use of [...] Read more.
Despite the agronomical and environmental advantages of the cultivation of legumes, their production is limited by various environmental constraints such as water or nutrient limitation, frost or heat stress and soil salinity, which may be the result of pedoclimatic conditions, intensive use of agricultural lands, decline in soil fertility and environmental degradation. The development of more sustainable agroecosystems that are resilient to environmental constraints will therefore require better understanding of the key mechanisms underlying plant tolerance to abiotic constraints. This review provides highlights of legume tolerance to abiotic constraints with a focus on soil nutrient deficiencies, drought, and salinity. More specifically, recent advances in the physiological and molecular levels of the adaptation of grain and forage legumes to abiotic constraints are discussed. Such adaptation involves complex multigene controlled-traits which also involve multiple sub-traits that are likely regulated under the control of a number of candidate genes. This multi-genetic control of tolerance traits might also be multifunctional, with extended action in response to a number of abiotic constraints. Thus, concrete efforts are required to breed for multifunctional candidate genes in order to boost plant stability under various abiotic constraints. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Review
Effect of Heavy Metals in Plants of the Genus Brassica
by Miguel P. Mourato, Inês N. Moreira, Inês Leitão, Filipa R. Pinto, Joana R. Sales and Luisa Louro Martins
Int. J. Mol. Sci. 2015, 16(8), 17975-17998; https://doi.org/10.3390/ijms160817975 - 04 Aug 2015
Cited by 189 | Viewed by 12970
Abstract
Several species from the Brassica genus are very important agricultural crops in different parts of the world and are also known to be heavy metal accumulators. There have been a large number of studies regarding the tolerance, uptake and defense mechanism in several [...] Read more.
Several species from the Brassica genus are very important agricultural crops in different parts of the world and are also known to be heavy metal accumulators. There have been a large number of studies regarding the tolerance, uptake and defense mechanism in several of these species, notably Brassica juncea and B. napus, against the stress induced by heavy metals. Numerous studies have also been published about the capacity of these species to be used for phytoremediation purposes but with mixed results. This review will focus on the latest developments in the study of the uptake capacity, oxidative damage and biochemical and physiological tolerance and defense mechanisms to heavy metal toxicity on six economically important species: B. juncea, B. napus, B. oleracea, B. carinata, B. rapa and B. nigra. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Review
Ethanol versus Phytochemicals in Wine: Oral Cancer Risk in a Light Drinking Perspective
by Elena M. Varoni, Giovanni Lodi and Marcello Iriti
Int. J. Mol. Sci. 2015, 16(8), 17029-17047; https://doi.org/10.3390/ijms160817029 - 27 Jul 2015
Cited by 21 | Viewed by 7867
Abstract
This narrative review aims to summarize the current controversy on the balance between ethanol and phytochemicals in wine, focusing on light drinking and oral cancer. Extensive literature search included PUBMED and EMBASE databases to identify in human studies and systematic reviews (up to [...] Read more.
This narrative review aims to summarize the current controversy on the balance between ethanol and phytochemicals in wine, focusing on light drinking and oral cancer. Extensive literature search included PUBMED and EMBASE databases to identify in human studies and systematic reviews (up to March 2015), which contributed to elucidate this issue. Independently from the type of beverage, meta-analyses considering light drinking (≤1 drinks/day or ≤12.5 g/day of ethanol) reported relative risks (RR) for oral, oro-pharyngeal, or upper aero-digestive tract cancers, ranging from 1.0 to 1.3. One meta-analysis measured the overall wine-specific RR, which corresponded to 2.1. Although little evidence exists on light wine intake, phytochemicals seem not to affect oral cancer risk, being probably present below the effective dosages and/or due to their low bioavailability. As expected, the risk of oral cancer, even in light drinking conditions, increases when associated with smoking habit and high-risk genotypes of alcohol and aldehyde dehydrogenases. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism 2015)
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Review
Network Candidate Genes in Breeding for Drought Tolerant Crops
by Christoph Tim Krannich, Lisa Maletzki, Christina Kurowsky and Renate Horn
Int. J. Mol. Sci. 2015, 16(7), 16378-16400; https://doi.org/10.3390/ijms160716378 - 17 Jul 2015
Cited by 53 | Viewed by 8712
Abstract
Climate change leading to increased periods of low water availability as well as increasing demands for food in the coming years makes breeding for drought tolerant crops a high priority. Plants have developed diverse strategies and mechanisms to survive drought stress. However, most [...] Read more.
Climate change leading to increased periods of low water availability as well as increasing demands for food in the coming years makes breeding for drought tolerant crops a high priority. Plants have developed diverse strategies and mechanisms to survive drought stress. However, most of these represent drought escape or avoidance strategies like early flowering or low stomatal conductance that are not applicable in breeding for crops with high yields under drought conditions. Even though a great deal of research is ongoing, especially in cereals, in this regard, not all mechanisms involved in drought tolerance are yet understood. The identification of candidate genes for drought tolerance that have a high potential to be used for breeding drought tolerant crops represents a challenge. Breeding for drought tolerant crops has to focus on acceptable yields under water-limited conditions and not on survival. However, as more and more knowledge about the complex networks and the cross talk during drought is available, more options are revealed. In addition, it has to be considered that conditioning a crop for drought tolerance might require the production of metabolites and might cost the plants energy and resources that cannot be used in terms of yield. Recent research indicates that yield penalty exists and efficient breeding for drought tolerant crops with acceptable yields under well-watered and drought conditions might require uncoupling yield penalty from drought tolerance. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Review
Plant MYB Transcription Factors: Their Role in Drought Response Mechanisms
by Elena Baldoni, Annamaria Genga and Eleonora Cominelli
Int. J. Mol. Sci. 2015, 16(7), 15811-15851; https://doi.org/10.3390/ijms160715811 - 13 Jul 2015
Cited by 305 | Viewed by 17194
Abstract
Water scarcity is one of the major causes of poor plant performance and limited crop yields worldwide and it is the single most common cause of severe food shortage in developing countries. Several molecular networks involved in stress perception, signal transduction and stress [...] Read more.
Water scarcity is one of the major causes of poor plant performance and limited crop yields worldwide and it is the single most common cause of severe food shortage in developing countries. Several molecular networks involved in stress perception, signal transduction and stress responses in plants have been elucidated so far. Transcription factors are major players in water stress signaling. In recent years, different MYB transcription factors, mainly in Arabidopsis thaliana (L.) Heynh. but also in some crops, have been characterized for their involvement in drought response. For some of them there is evidence supporting a specific role in response to water stress, such as the regulation of stomatal movement, the control of suberin and cuticular waxes synthesis and the regulation of flower development. Moreover, some of these genes have also been characterized for their involvement in other abiotic or biotic stresses, an important feature considering that in nature, plants are often simultaneously subjected to multiple rather than single environmental perturbations. This review summarizes recent studies highlighting the role of the MYB family of transcription factors in the adaptive responses to drought stress. The practical application value of MYBs in crop improvement, such as stress tolerance engineering, is also discussed. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Review
Function of ABA in Stomatal Defense against Biotic and Drought Stresses
by Chae Woo Lim, Woonhee Baek, Jangho Jung, Jung-Hyun Kim and Sung Chul Lee
Int. J. Mol. Sci. 2015, 16(7), 15251-15270; https://doi.org/10.3390/ijms160715251 - 06 Jul 2015
Cited by 342 | Viewed by 26893
Abstract
The plant hormone abscisic acid (ABA) regulates many key processes involved in plant development and adaptation to biotic and abiotic stresses. Under stress conditions, plants synthesize ABA in various organs and initiate defense mechanisms, such as the regulation of stomatal aperture and expression [...] Read more.
The plant hormone abscisic acid (ABA) regulates many key processes involved in plant development and adaptation to biotic and abiotic stresses. Under stress conditions, plants synthesize ABA in various organs and initiate defense mechanisms, such as the regulation of stomatal aperture and expression of defense-related genes conferring resistance to environmental stresses. The regulation of stomatal opening and closure is important to pathogen defense and control of transpirational water loss. Recent studies using a combination of approaches, including genetics, physiology, and molecular biology, have contributed considerably to our understanding of ABA signal transduction. A number of proteins associated with ABA signaling and responses—especially ABA receptors—have been identified. ABA signal transduction initiates signal perception by ABA receptors and transfer via downstream proteins, including protein kinases and phosphatases. In the present review, we focus on the function of ABA in stomatal defense against biotic and abiotic stresses, through analysis of each ABA signal component and the relationships of these components in the complex network of interactions. In particular, two ABA signal pathway models in response to biotic and abiotic stress were proposed, from stress signaling to stomatal closure, involving the pyrabactin resistance (PYR)/PYR-like (PYL) or regulatory component of ABA receptor (RCAR) family proteins, 2C-type protein phosphatases, and SnRK2-type protein kinases. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Review
Ascorbate Peroxidase and Catalase Activities and Their Genetic Regulation in Plants Subjected to Drought and Salinity Stresses
by Adriano Sofo, Antonio Scopa, Maria Nuzzaci and Antonella Vitti
Int. J. Mol. Sci. 2015, 16(6), 13561-13578; https://doi.org/10.3390/ijms160613561 - 12 Jun 2015
Cited by 487 | Viewed by 18933
Abstract
Hydrogen peroxide (H2O2), an important relatively stable non-radical reactive oxygen species (ROS) is produced by normal aerobic metabolism in plants. At low concentrations, H2O2 acts as a signal molecule involved in the regulation of specific biological/physiological [...] Read more.
Hydrogen peroxide (H2O2), an important relatively stable non-radical reactive oxygen species (ROS) is produced by normal aerobic metabolism in plants. At low concentrations, H2O2 acts as a signal molecule involved in the regulation of specific biological/physiological processes (photosynthetic functions, cell cycle, growth and development, plant responses to biotic and abiotic stresses). Oxidative stress and eventual cell death in plants can be caused by excess H2O2 accumulation. Since stress factors provoke enhanced production of H2O2 in plants, severe damage to biomolecules can be possible due to elevated and non-metabolized cellular H2O2. Plants are endowed with H2O2-metabolizing enzymes such as catalases (CAT), ascorbate peroxidases (APX), some peroxiredoxins, glutathione/thioredoxin peroxidases, and glutathione sulfo-transferases. However, the most notably distinguished enzymes are CAT and APX since the former mainly occurs in peroxisomes and does not require a reductant for catalyzing a dismutation reaction. In particular, APX has a higher affinity for H2O2 and reduces it to H2O in chloroplasts, cytosol, mitochondria and peroxisomes, as well as in the apoplastic space, utilizing ascorbate as specific electron donor. Based on recent reports, this review highlights the role of H2O2 in plants experiencing water deficit and salinity and synthesizes major outcomes of studies on CAT and APX activity and genetic regulation in drought- and salt-stressed plants. Full article
(This article belongs to the Special Issue Abiotic Stress and Gene Networks in Plants)
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Review
Starting to Gel: How Arabidopsis Seed Coat Epidermal Cells Produce Specialized Secondary Cell Walls
by Cătălin Voiniciuc, Bo Yang, Maximilian Heinrich-Wilhelm Schmidt, Markus Günl and Björn Usadel
Int. J. Mol. Sci. 2015, 16(2), 3452-3473; https://doi.org/10.3390/ijms16023452 - 04 Feb 2015
Cited by 89 | Viewed by 12093
Abstract
For more than a decade, the Arabidopsis seed coat epidermis (SCE) has been used as a model system to study the synthesis, secretion and modification of cell wall polysaccharides, particularly pectin. Our detailed re-evaluation of available biochemical data highlights that Arabidopsis seed mucilage [...] Read more.
For more than a decade, the Arabidopsis seed coat epidermis (SCE) has been used as a model system to study the synthesis, secretion and modification of cell wall polysaccharides, particularly pectin. Our detailed re-evaluation of available biochemical data highlights that Arabidopsis seed mucilage is more than just pectin. Typical secondary wall polymers such as xylans and heteromannans are also present in mucilage. Despite their low abundance, these components appear to play essential roles in controlling mucilage properties, and should be further investigated. We also provide a comprehensive community resource by re-assessing the mucilage phenotypes of almost 20 mutants using the same conditions. We conduct an in-depth functional evaluation of all the SCE genes described in the literature and propose a revised model for mucilage production. Further investigation of SCE cells will improve our understanding of plant cell walls. Full article
(This article belongs to the Special Issue Plant Molecular Biology)
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Review
Responses to Oxidative and Heavy Metal Stresses in Cyanobacteria: Recent Advances
by Corinne Cassier-Chauvat and Franck Chauvat
Int. J. Mol. Sci. 2015, 16(1), 871-886; https://doi.org/10.3390/ijms16010871 - 31 Dec 2014
Cited by 76 | Viewed by 9458
Abstract
Cyanobacteria, the only known prokaryotes that perform oxygen-evolving photosynthesis, are receiving strong attention in basic and applied research. In using solar energy, water, CO2 and mineral salts to produce a large amount of biomass for the food chain, cyanobacteria constitute the first [...] Read more.
Cyanobacteria, the only known prokaryotes that perform oxygen-evolving photosynthesis, are receiving strong attention in basic and applied research. In using solar energy, water, CO2 and mineral salts to produce a large amount of biomass for the food chain, cyanobacteria constitute the first biological barrier against the entry of toxics into the food chain. In addition, cyanobacteria have the potential for the solar-driven carbon-neutral production of biofuels. However, cyanobacteria are often challenged by toxic reactive oxygen species generated under intense illumination, i.e., when their production of photosynthetic electrons exceeds what they need for the assimilation of inorganic nutrients. Furthermore, in requiring high amounts of various metals for growth, cyanobacteria are also frequently affected by drastic changes in metal availabilities. They are often challenged by heavy metals, which are increasingly spread out in the environment through human activities, and constitute persistent pollutants because they cannot be degraded. Consequently, it is important to analyze the protection against oxidative and metal stresses in cyanobacteria because these ancient organisms have developed most of these processes, a large number of which have been conserved during evolution. This review summarizes what is known regarding these mechanisms, emphasizing on their crosstalk. Full article
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Review
Formins: Linking Cytoskeleton and Endomembranes in Plant Cells
by Fatima Cvrčková, Denisa Oulehlová and Viktor Žárský
Int. J. Mol. Sci. 2015, 16(1), 1-18; https://doi.org/10.3390/ijms16010001 - 23 Dec 2014
Cited by 18 | Viewed by 9730
Abstract
The cytoskeleton plays a central part in spatial organization of the plant cytoplasm, including the endomebrane system. However, the mechanisms involved are so far only partially understood. Formins (FH2 proteins), a family of evolutionarily conserved proteins sharing the FH2 domain whose dimer can [...] Read more.
The cytoskeleton plays a central part in spatial organization of the plant cytoplasm, including the endomebrane system. However, the mechanisms involved are so far only partially understood. Formins (FH2 proteins), a family of evolutionarily conserved proteins sharing the FH2 domain whose dimer can nucleate actin, mediate the co-ordination between actin and microtubule cytoskeletons in multiple eukaryotic lineages including plants. Moreover, some plant formins contain transmembrane domains and participate in anchoring cytoskeletal structures to the plasmalemma, and possibly to other membranes. Direct or indirect membrane association is well documented even for some fungal and metazoan formins lacking membrane insertion motifs, and FH2 proteins have been shown to associate with endomembranes and modulate their dynamics in both fungi and metazoans. Here we summarize the available evidence suggesting that formins participate in membrane trafficking and endomembrane, especially ER, organization also in plants. We propose that, despite some methodological pitfalls inherent to in vivo studies based on (over)expression of truncated and/or tagged proteins, formins are beginning to emerge as candidates for the so far somewhat elusive link between the plant cytoskeleton and the endomembrane system. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Review
Contribution of Chitinase A’s C-Terminal Vacuolar Sorting Determinant to the Study of Soluble Protein Compartmentation
by Egidio Stigliano, Gian-Pietro Di Sansebastiano and Jean-Marc Neuhaus
Int. J. Mol. Sci. 2014, 15(6), 11030-11039; https://doi.org/10.3390/ijms150611030 - 18 Jun 2014
Cited by 14 | Viewed by 6529
Abstract
Plant chitinases have been studied for their importance in the defense of crop plants from pathogen attacks and for their peculiar vacuolar sorting determinants. A peculiarity of the sequence of many family 19 chitinases is the presence of a C-terminal extension that [...] Read more.
Plant chitinases have been studied for their importance in the defense of crop plants from pathogen attacks and for their peculiar vacuolar sorting determinants. A peculiarity of the sequence of many family 19 chitinases is the presence of a C-terminal extension that seems to be important for their correct recognition by the vacuole sorting machinery. The 7 amino acids long C-terminal vacuolar sorting determinant (CtVSD) of tobacco chitinase A is necessary and sufficient for the transport to the vacuole. This VSD shares no homology with other CtVSDs such as the phaseolin’s tetrapeptide AFVY (AlaPheValTyr) and it is also sorted by different mechanisms. While a receptor for this signal has not yet been convincingly identified, the research using the chitinase CtVSD has been very informative, leading to the observation of phenomena otherwise difficult to observe such as the presence of separate vacuoles in differentiating cells and the existence of a Golgi-independent route to the vacuole. Thanks to these new insights in the endoplasmic reticulum (ER)-to-vacuole transport, GFPChi (Green Fluorescent Protein carrying the chitinase A CtVSD) and other markers based on chitinase signals will continue to help the investigation of vacuolar biogenesis in plants. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Review
Transport Pathways—Proton Motive Force Interrelationship in Durum Wheat Mitochondria
by Daniela Trono, Maura N. Laus, Mario Soccio and Donato Pastore
Int. J. Mol. Sci. 2014, 15(5), 8186-8215; https://doi.org/10.3390/ijms15058186 - 09 May 2014
Cited by 12 | Viewed by 8796
Abstract
In durum wheat mitochondria (DWM) the ATP-inhibited plant mitochondrial potassium channel (PmitoKATP) and the plant uncoupling protein (PUCP) are able to strongly reduce the proton motive force (pmf) to control mitochondrial production of reactive oxygen species; under these conditions, mitochondrial carriers [...] Read more.
In durum wheat mitochondria (DWM) the ATP-inhibited plant mitochondrial potassium channel (PmitoKATP) and the plant uncoupling protein (PUCP) are able to strongly reduce the proton motive force (pmf) to control mitochondrial production of reactive oxygen species; under these conditions, mitochondrial carriers lack the driving force for transport and should be inactive. However, unexpectedly, DWM uncoupling by PmitoKATP neither impairs the exchange of ADP for ATP nor blocks the inward transport of Pi and succinate. This uptake may occur via the plant inner membrane anion channel (PIMAC), which is physiologically inhibited by membrane potential, but unlocks its activity in de-energized mitochondria. Probably, cooperation between PIMAC and carriers may accomplish metabolite movement across the inner membrane under both energized and de-energized conditions. PIMAC may also cooperate with PmitoKATP to transport ammonium salts in DWM. Interestingly, this finding may trouble classical interpretation of in vitro mitochondrial swelling; instead of free passage of ammonia through the inner membrane and proton symport with Pi, that trigger metabolite movements via carriers, transport of ammonium via PmitoKATP and that of the counteranion via PIMAC may occur. Here, we review properties, modulation and function of the above reported DWM channels and carriers to shed new light on the control that they exert on pmf and vice-versa. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Review
Degradation of Organelles or Specific Organelle Components via Selective Autophagy in Plant Cells
by Simon Michaeli and Gad Galili
Int. J. Mol. Sci. 2014, 15(5), 7624-7638; https://doi.org/10.3390/ijms15057624 - 05 May 2014
Cited by 46 | Viewed by 10844
Abstract
Macroautophagy (hereafter referred to as autophagy) is a cellular mechanism dedicated to the degradation and recycling of unnecessary cytosolic components by their removal to the lytic compartment of the cell (the vacuole in plants). Autophagy is generally induced by stresses causing energy deprivation [...] Read more.
Macroautophagy (hereafter referred to as autophagy) is a cellular mechanism dedicated to the degradation and recycling of unnecessary cytosolic components by their removal to the lytic compartment of the cell (the vacuole in plants). Autophagy is generally induced by stresses causing energy deprivation and its operation occurs by special vesicles, termed autophagosomes. Autophagy also operates in a selective manner, recycling specific components, such as organelles, protein aggregates or even specific proteins, and selective autophagy is implicated in both cellular housekeeping and response to stresses. In plants, selective autophagy has recently been shown to degrade mitochondria, plastids and peroxisomes, or organelle components such as the endoplasmic-reticulum (ER) membrane and chloroplast-derived proteins such as Rubisco. This ability places selective-autophagy as a major factor in cellular steady-state maintenance, both under stress and favorable environmental conditions. Here we review the recent advances documented in plants for this cellular process and further discuss its impact on plant physiology. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Review
Delivering of Proteins to the Plant Vacuole—An Update
by Cláudia Pereira, Susana Pereira and José Pissarra
Int. J. Mol. Sci. 2014, 15(5), 7611-7623; https://doi.org/10.3390/ijms15057611 - 05 May 2014
Cited by 31 | Viewed by 7414
Abstract
Trafficking of soluble cargo to the vacuole is far from being a closed issue as it can occur by different routes and involve different intermediates. The textbook view of proteins being sorted at the post-Golgi level to the lytic vacuole via the pre-vacuole [...] Read more.
Trafficking of soluble cargo to the vacuole is far from being a closed issue as it can occur by different routes and involve different intermediates. The textbook view of proteins being sorted at the post-Golgi level to the lytic vacuole via the pre-vacuole or to the protein storage vacuole mediated by dense vesicles is now challenged as novel routes are being disclosed and vacuoles with intermediate characteristics described. The identification of Vacuolar Sorting Determinants is a key signature to understand protein trafficking to the vacuole. Despite the long established vacuolar signals, some others have been described in the last few years, with different properties that can be specific for some cells or some types of vacuoles. There are also reports of proteins having two different vacuolar signals and their significance is questionable: a way to increase the efficiency of the sorting or different sorting depending on the protein roles in a specific context? Along came the idea of differential vacuolar sorting, suggesting a possible specialization of the trafficking pathways according to the type of cell and specific needs. In this review, we show the recent advances in the field and focus on different aspects of protein trafficking to the vacuoles. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Review
Autophagy-Related Direct Membrane Import from ER/Cytoplasm into the Vacuole or Apoplast: A Hidden Gateway also for Secondary Metabolites and Phytohormones?
by Ivan Kulich and Viktor Žárský
Int. J. Mol. Sci. 2014, 15(5), 7462-7474; https://doi.org/10.3390/ijms15057462 - 29 Apr 2014
Cited by 26 | Viewed by 8343
Abstract
Transportation of low molecular weight cargoes into the plant vacuole represents an essential plant cell function. Several lines of evidence indicate that autophagy-related direct endoplasmic reticulum (ER) to vacuole (and also, apoplast) transport plays here a more general role than expected. This route [...] Read more.
Transportation of low molecular weight cargoes into the plant vacuole represents an essential plant cell function. Several lines of evidence indicate that autophagy-related direct endoplasmic reticulum (ER) to vacuole (and also, apoplast) transport plays here a more general role than expected. This route is regulated by autophagy proteins, including recently discovered involvement of the exocyst subcomplex. Traffic from ER into the vacuole bypassing Golgi apparatus (GA) acts not only in stress-related cytoplasm recycling or detoxification, but also in developmentally-regulated biopolymer and secondary metabolite import into the vacuole (or apoplast), exemplified by storage proteins and anthocyanins. We propose that this pathway is relevant also for some phytohormones’ (e.g., auxin, abscisic acid (ABA) and salicylic acid (SA)) degradation. We hypothesize that SA is not only an autophagy inducer, but also a cargo for autophagy-related ER to vacuole membrane container delivery and catabolism. ER membrane localized enzymes will potentially enhance the area of biosynthetic reactive surfaces, and also, abundant ER localized membrane importers (e.g., ABC transporters) will internalize specific molecular species into the autophagosome biogenesis domain of ER. Such active ER domains may create tubular invaginations of tonoplast into the vacuoles as import intermediates. Packaging of cargos into the ER-derived autophagosome-like containers might be an important mechanism of vacuole and exosome biogenesis and cytoplasm protection against toxic metabolites. A new perspective on metabolic transformations intimately linked to membrane trafficking in plants is emerging. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Review
The Role of Symbiotic Nitrogen Fixation in Sustainable Production of Biofuels
by Bandana Biswas and Peter M. Gresshoff
Int. J. Mol. Sci. 2014, 15(5), 7380-7397; https://doi.org/10.3390/ijms15057380 - 29 Apr 2014
Cited by 61 | Viewed by 11956
Abstract
With the ever-increasing population of the world (expected to reach 9.6 billion by 2050), and altered life style, comes an increased demand for food, fuel and fiber. However, scarcity of land, water and energy accompanied by climate change means that to produce enough [...] Read more.
With the ever-increasing population of the world (expected to reach 9.6 billion by 2050), and altered life style, comes an increased demand for food, fuel and fiber. However, scarcity of land, water and energy accompanied by climate change means that to produce enough to meet the demands is getting increasingly challenging. Today we must use every avenue from science and technology available to address these challenges. The natural process of symbiotic nitrogen fixation, whereby plants such as legumes fix atmospheric nitrogen gas to ammonia, usable by plants can have a substantial impact as it is found in nature, has low environmental and economic costs and is broadly established. Here we look at the importance of symbiotic nitrogen fixation in the production of biofuel feedstocks; how this process can address major challenges, how improving nitrogen fixation is essential, and what we can do about it. Full article
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Review
No Stress! Relax! Mechanisms Governing Growth and Shape in Plant Cells
by Gea Guerriero, Jean-Francois Hausman and Giampiero Cai
Int. J. Mol. Sci. 2014, 15(3), 5094-5114; https://doi.org/10.3390/ijms15035094 - 21 Mar 2014
Cited by 51 | Viewed by 13374
Abstract
The mechanisms through which plant cells control growth and shape are the result of the coordinated action of many events, notably cell wall stress relaxation and turgor-driven expansion. The scalar nature of turgor pressure would drive plant cells to assume spherical shapes; however, [...] Read more.
The mechanisms through which plant cells control growth and shape are the result of the coordinated action of many events, notably cell wall stress relaxation and turgor-driven expansion. The scalar nature of turgor pressure would drive plant cells to assume spherical shapes; however, this is not the case, as plant cells show an amazing variety of morphologies. Plant cell walls are dynamic structures that can display alterations in matrix polysaccharide composition and concentration, which ultimately affect the wall deformation rate. The wide varieties of plant cell shapes, spanning from elongated cylinders (as pollen tubes) and jigsaw puzzle-like epidermal cells, to very long fibres and branched stellate leaf trichomes, can be understood if the underlying mechanisms regulating wall biosynthesis and cytoskeletal dynamics are addressed. This review aims at gathering the available knowledge on the fundamental mechanisms regulating expansion, growth and shape in plant cells by putting a special emphasis on the cell wall-cytoskeleton system continuum. In particular, we discuss from a molecular point of view the growth mechanisms characterizing cell types with strikingly different geometries and describe their relationship with primary walls. The purpose, here, is to provide the reader with a comprehensive overview of the multitude of events through which plant cells manage to expand and control their final shapes. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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376 KiB  
Review
Calcium Imaging Perspectives in Plants
by Chidananda Nagamangala Kanchiswamy, Mickael Malnoy, Andrea Occhipinti and Massimo E. Maffei
Int. J. Mol. Sci. 2014, 15(3), 3842-3859; https://doi.org/10.3390/ijms15033842 - 04 Mar 2014
Cited by 40 | Viewed by 12100
Abstract
The calcium ion (Ca2+) is a versatile intracellular messenger. It provides dynamic regulation of a vast array of gene transcriptions, protein kinases, transcription factors and other complex downstream signaling cascades. For the past six decades, intracellular Ca2+ concentration has been [...] Read more.
The calcium ion (Ca2+) is a versatile intracellular messenger. It provides dynamic regulation of a vast array of gene transcriptions, protein kinases, transcription factors and other complex downstream signaling cascades. For the past six decades, intracellular Ca2+ concentration has been significantly studied and still many studies are under way. Our understanding of Ca2+ signaling and the corresponding physiological phenomenon is growing exponentially. Here we focus on the improvements made in the development of probes used for Ca2+ imaging and expanding the application of Ca2+ imaging in plant science research. Full article
(This article belongs to the Special Issue Plant Cell Compartmentation and Volume Control)
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Review
Advanced Knowledge of Three Important Classes of Grape Phenolics: Anthocyanins, Stilbenes and Flavonols
by Riccardo Flamini, Fulvio Mattivi, Mirko De Rosso, Panagiotis Arapitsas and Luigi Bavaresco
Int. J. Mol. Sci. 2013, 14(10), 19651-19669; https://doi.org/10.3390/ijms141019651 - 27 Sep 2013
Cited by 283 | Viewed by 18780
Abstract
Grape is qualitatively and quantitatively very rich in polyphenols. In particular, anthocyanins, flavonols and stilbene derivatives play very important roles in plant metabolism, thanks to their peculiar characteristics. Anthocyanins are responsible for the color of red grapes and wines and confer organoleptic characteristics [...] Read more.
Grape is qualitatively and quantitatively very rich in polyphenols. In particular, anthocyanins, flavonols and stilbene derivatives play very important roles in plant metabolism, thanks to their peculiar characteristics. Anthocyanins are responsible for the color of red grapes and wines and confer organoleptic characteristics on the wine. They are used for chemotaxonomic studies and to evaluate the polyphenolic ripening stage of grape. They are natural colorants, have antioxidant, antimicrobial and anticarcinogenic activity, exert protective effects on the human cardiovascular system, and are used in the food and pharmaceutical industries. Stilbenes are vine phytoalexins present in grape berries and associated with the beneficial effects of drinking wine. The principal stilbene, resveratrol, is characterized by anticancer, antioxidant, anti-inflammatory and cardioprotective activity. Resveratrol dimers and oligomers also occur in grape, and are synthetized by the vine as active defenses against exogenous attack, or produced by extracellular enzymes released from pathogens in an attempt to eliminate undesirable toxic compounds. Flavonols are a ubiquitous class of flavonoids with photo-protection and copigmentation (together with anthocyanins) functions. The lack of expression of the enzyme flavonoid 3',5'-hydroxylase in white grapes restricts the presence of these compounds to quercetin, kaempferol and isorhamnetin derivatives, whereas red grapes usually also contain myricetin, laricitrin and syringetin derivatives. In the last ten years, the technological development of analytical instrumentation, particularly mass spectrometry, has led to great improvements and further knowledge of the chemistry of these compounds. In this review, the biosynthesis and biological role of these grape polyphenols are briefly introduced, together with the latest knowledge of their chemistry. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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602 KiB  
Review
Biochemistry and Molecular Biology of Carotenoid Biosynthesis in Chili Peppers (Capsicum spp.)
by María Del Rocío Gómez-García and Neftalí Ochoa-Alejo
Int. J. Mol. Sci. 2013, 14(9), 19025-19053; https://doi.org/10.3390/ijms140919025 - 16 Sep 2013
Cited by 146 | Viewed by 17838
Abstract
Capsicum species produce fruits that synthesize and accumulate carotenoid pigments, which are responsible for the fruits’ yellow, orange and red colors. Chili peppers have been used as an experimental model for studying the biochemical and molecular aspects of carotenoid biosynthesis. Most reports refer [...] Read more.
Capsicum species produce fruits that synthesize and accumulate carotenoid pigments, which are responsible for the fruits’ yellow, orange and red colors. Chili peppers have been used as an experimental model for studying the biochemical and molecular aspects of carotenoid biosynthesis. Most reports refer to the characterization of carotenoids and content determination in chili pepper fruits from different species, cultivars, varieties or genotypes. The types and levels of carotenoids differ between different chili pepper fruits, and they are also influenced by environmental conditions. Yellow-orange colors of chili pepper fruits are mainly due to the accumulation of α- and β-carotene, zeaxanthin, lutein and β-cryptoxanthin. Carotenoids such as capsanthin, capsorubin and capsanthin-5,6-epoxide confer the red colors. Chromoplasts are the sites of carotenoid pigment synthesis and storage. According to the most accepted theory, the synthesis of carotenoids in chili peppers is controlled by three loci: c1, c2 and y. Several enzymes participating in carotenoid biosynthesis in chili pepper fruits have been isolated and characterized, and the corresponding gene sequences have been reported. However, there is currently limited information on the molecular mechanisms that regulate this biosynthetic pathway. Approaches to gain more knowledge of the regulation of carotenoid biosynthesis are discussed. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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1191 KiB  
Review
Berry Phenolics of Grapevine under Challenging Environments
by António Teixeira, José Eiras-Dias, Simone D. Castellarin and Hernâni Gerós
Int. J. Mol. Sci. 2013, 14(9), 18711-18739; https://doi.org/10.3390/ijms140918711 - 11 Sep 2013
Cited by 334 | Viewed by 21425
Abstract
Plant phenolics have been for many years a theme of major scientific and applied interest. Grape berry phenolics contribute to organoleptic properties, color and protection against environmental challenges. Climate change has already caused significant warming in most grape-growing areas of the world, and [...] Read more.
Plant phenolics have been for many years a theme of major scientific and applied interest. Grape berry phenolics contribute to organoleptic properties, color and protection against environmental challenges. Climate change has already caused significant warming in most grape-growing areas of the world, and the climatic conditions determine, to a large degree, the grape varieties that can be cultivated as well as wine quality. In particular, heat, drought and light/UV intensity severely affect phenolic metabolism and, thus, grape composition and development. In the variety Chardonnay, water stress increases the content of flavonols and decreases the expression of genes involved in biosynthesis of stilbene precursors. Also, polyphenolic profile is greatly dependent on genotype and environmental interactions. This review deals with the diversity and biosynthesis of phenolic compounds in the grape berry, from a general overview to a more detailed level, where the influence of environmental challenges on key phenolic metabolism pathways is approached. The full understanding of how and when specific phenolic compounds accumulate in the berry, and how the varietal grape berry metabolism responds to the environment is of utmost importance to adjust agricultural practices and thus, modify wine profile. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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790 KiB  
Review
Green Leaf Volatiles: A Plant’s Multifunctional Weapon against Herbivores and Pathogens
by Alessandra Scala, Silke Allmann, Rossana Mirabella, Michel A. Haring and Robert C. Schuurink
Int. J. Mol. Sci. 2013, 14(9), 17781-17811; https://doi.org/10.3390/ijms140917781 - 30 Aug 2013
Cited by 328 | Viewed by 26150
Abstract
Plants cannot avoid being attacked by an almost infinite number of microorganisms and insects. Consequently, they arm themselves with molecular weapons against their attackers. Plant defense responses are the result of a complex signaling network, in which the hormones jasmonic acid (JA), salicylic [...] Read more.
Plants cannot avoid being attacked by an almost infinite number of microorganisms and insects. Consequently, they arm themselves with molecular weapons against their attackers. Plant defense responses are the result of a complex signaling network, in which the hormones jasmonic acid (JA), salicylic acid (SA) and ethylene (ET) are the usual suspects under the magnifying glass when researchers investigate host-pest interactions. However, Green Leaf Volatiles (GLVs), C6 molecules, which are very quickly produced and/or emitted upon herbivory or pathogen infection by almost every green plant, also play an important role in plant defenses. GLVs are semiochemicals used by insects to find their food or their conspecifics. They have also been reported to be fundamental in indirect defenses and to have a direct effect on pests, but these are not the only roles of GLVs. These volatiles, being probably one of the fastest weapons exploited, are also able to directly elicit or prime plant defense responses. Moreover, GLVs, via crosstalk with phytohormones, mostly JA, can influence the outcome of the plant’s defense response against pathogens. For all these reasons GLVs should be considered as co-protagonists in the play between plants and their attackers. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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836 KiB  
Review
Plant Flavonoids—Biosynthesis, Transport and Involvement in Stress Responses
by Elisa Petrussa, Enrico Braidot, Marco Zancani, Carlo Peresson, Alberto Bertolini, Sonia Patui and Angelo Vianello
Int. J. Mol. Sci. 2013, 14(7), 14950-14973; https://doi.org/10.3390/ijms140714950 - 17 Jul 2013
Cited by 472 | Viewed by 23363
Abstract
This paper aims at analysing the synthesis of flavonoids, their import and export in plant cell compartments, as well as their involvement in the response to stress, with particular reference to grapevine (Vitis vinifera L.). A multidrug and toxic compound extrusion (MATE) [...] Read more.
This paper aims at analysing the synthesis of flavonoids, their import and export in plant cell compartments, as well as their involvement in the response to stress, with particular reference to grapevine (Vitis vinifera L.). A multidrug and toxic compound extrusion (MATE) as well as ABC transporters have been demonstrated in the tonoplast of grape berry, where they perform a flavonoid transport. The involvement of a glutathione S-transferase (GST) gene has also been inferred. Recently, a putative flavonoid carrier, similar to mammalian bilitranslocase (BTL), has been identified in both grape berry skin and pulp. In skin the pattern of BTL expression increases from véraison to harvest, while in the pulp its expression reaches the maximum at the early ripening stage. Moreover, the presence of BTL in vascular bundles suggests its participation in long distance transport of flavonoids. In addition, the presence of a vesicular trafficking in plants responsible for flavonoid transport is discussed. Finally, the involvement of flavonoids in the response to stress is described. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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2081 KiB  
Review
Modulation of Phytoalexin Biosynthesis in Engineered Plants for Disease Resistance
by Philippe Jeandet, Christophe Clément, Eric Courot and Sylvain Cordelier
Int. J. Mol. Sci. 2013, 14(7), 14136-14170; https://doi.org/10.3390/ijms140714136 - 08 Jul 2013
Cited by 120 | Viewed by 16760
Abstract
Phytoalexins are antimicrobial substances of low molecular weight produced by plants in response to infection or stress, which form part of their active defense mechanisms. Starting in the 1950’s, research on phytoalexins has begun with biochemistry and bio-organic chemistry, resulting in the determination [...] Read more.
Phytoalexins are antimicrobial substances of low molecular weight produced by plants in response to infection or stress, which form part of their active defense mechanisms. Starting in the 1950’s, research on phytoalexins has begun with biochemistry and bio-organic chemistry, resulting in the determination of their structure, their biological activity as well as mechanisms of their synthesis and their catabolism by microorganisms. Elucidation of the biosynthesis of numerous phytoalexins has permitted the use of molecular biology tools for the exploration of the genes encoding enzymes of their synthesis pathways and their regulators. Genetic manipulation of phytoalexins has been investigated to increase the disease resistance of plants. The first example of a disease resistance resulting from foreign phytoalexin expression in a novel plant has concerned a phytoalexin from grapevine which was transferred to tobacco. Transformations were then operated to investigate the potential of other phytoalexin biosynthetic genes to confer resistance to pathogens. Unexpectedly, engineering phytoalexins for disease resistance in plants seem to have been limited to exploiting only a few phytoalexin biosynthetic genes, especially those encoding stilbenes and some isoflavonoids. Research has rather focused on indirect approaches which allow modulation of the accumulation of phytoalexin employing transcriptional regulators or components of upstream regulatory pathways. Genetic approaches using gain- or less-of functions in phytoalexin engineering together with modulation of phytoalexin accumulation through molecular engineering of plant hormones and defense-related marker and elicitor genes have been reviewed. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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537 KiB  
Review
Biosynthetic Pathway and Health Benefits of Fucoxanthin, an Algae-Specific Xanthophyll in Brown Seaweeds
by Koji Mikami and Masashi Hosokawa
Int. J. Mol. Sci. 2013, 14(7), 13763-13781; https://doi.org/10.3390/ijms140713763 - 02 Jul 2013
Cited by 166 | Viewed by 23296
Abstract
Fucoxanthin is the main carotenoid produced in brown algae as a component of the light-harvesting complex for photosynthesis and photoprotection. In contrast to the complete elucidation of the carotenoid biosynthetic pathways in red and green algae, the biosynthetic pathway of fucoxanthin in brown [...] Read more.
Fucoxanthin is the main carotenoid produced in brown algae as a component of the light-harvesting complex for photosynthesis and photoprotection. In contrast to the complete elucidation of the carotenoid biosynthetic pathways in red and green algae, the biosynthetic pathway of fucoxanthin in brown algae is not fully understood. Recently, two models for the fucoxanthin biosynthetic pathway have been proposed in unicellular diatoms; however, there is no such information for the pathway in brown seaweeds to date. Here, we propose a biosynthetic pathway for fucoxanthin in the brown seaweed, Ectocarpus siliculosus, derived from comparison of carotenogenic genes in its sequenced genome with those in the genomes of two diatoms, Thalassiosira pseudonana and Phaeodactylum tricornutum. Currently, fucoxanthin is receiving attention, due to its potential benefits for human health. Therefore, new knowledge regarding the medical and nutraceutical properties of fucoxanthin from brown seaweeds is also summarized here. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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869 KiB  
Review
Putative Genes Involved in Saikosaponin Biosynthesis in Bupleurum Species
by Tsai-Yun Lin, Chung-Yi Chiou and Shu-Jiau Chiou
Int. J. Mol. Sci. 2013, 14(6), 12806-12826; https://doi.org/10.3390/ijms140612806 - 19 Jun 2013
Cited by 33 | Viewed by 11479
Abstract
Alternative medicinal agents, such as the herb Bupleurum, are increasingly used in modern medicine to supplement synthetic drugs. First, we present a review of the currently known effects of triterpene saponins-saikosaponins of Bupleurum species. The putative biosynthetic pathway of saikosaponins in Bupleurum species [...] Read more.
Alternative medicinal agents, such as the herb Bupleurum, are increasingly used in modern medicine to supplement synthetic drugs. First, we present a review of the currently known effects of triterpene saponins-saikosaponins of Bupleurum species. The putative biosynthetic pathway of saikosaponins in Bupleurum species is summarized, followed by discussions on identification and characterization of genes involved in the biosynthesis of saikosaponins. The purpose is to provide a brief review of gene extraction, functional characterization of isolated genes and assessment of expression patterns of genes encoding enzymes in the process of saikosaponin production in Bupleurum species, mainly B. kaoi. We focus on the effects of MeJA on saikosaponin production, transcription patterns of genes involved in biosynthesis and on functional depiction. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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539 KiB  
Review
Sesquiterpenoids Lactones: Benefits to Plants and People
by Martin Chadwick, Harriet Trewin, Frances Gawthrop and Carol Wagstaff
Int. J. Mol. Sci. 2013, 14(6), 12780-12805; https://doi.org/10.3390/ijms140612780 - 19 Jun 2013
Cited by 458 | Viewed by 31528
Abstract
Sesquiterpenoids, and specifically sesquiterpene lactones from Asteraceae, may play a highly significant role in human health, both as part of a balanced diet and as pharmaceutical agents, due to their potential for the treatment of cardiovascular disease and cancer. This review highlights the [...] Read more.
Sesquiterpenoids, and specifically sesquiterpene lactones from Asteraceae, may play a highly significant role in human health, both as part of a balanced diet and as pharmaceutical agents, due to their potential for the treatment of cardiovascular disease and cancer. This review highlights the role of sesquiterpene lactones endogenously in the plants that produce them, and explores mechanisms by which they interact in animal and human consumers of these plants. Several mechanisms are proposed for the reduction of inflammation and tumorigenesis at potentially achievable levels in humans. Plants can be classified by their specific array of produced sesquiterpene lactones, showing high levels of translational control. Studies of folk medicines implicate sesquiterpene lactones as the active ingredient in many treatments for other ailments such as diarrhea, burns, influenza, and neurodegradation. In addition to the anti-inflammatory response, sesquiterpene lactones have been found to sensitize tumor cells to conventional drug treatments. This review explores the varied ecological roles of sesquiterpenes in the plant producer, depending upon the plant and the compound. These include allelopathy with other plants, insects, and microbes, thereby causing behavioural or developmental modification to these secondary organisms to the benefit of the sesquiterpenoid producer. Some sesquiterpenoid lactones are antimicrobial, disrupting the cell wall of fungi and invasive bacteria, whereas others protect the plant from environmental stresses that would otherwise cause oxidative damage. Many of the compounds are effective due to their bitter flavor, which has obvious implications for human consumers. The implications of sesquiterpenoid lactone qualities for future crop production are discussed. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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896 KiB  
Review
Towards a Molecular Understanding of the Biosynthesis of Amaryllidaceae Alkaloids in Support of Their Expanding Medical Use
by Adam M. Takos and Fred Rook
Int. J. Mol. Sci. 2013, 14(6), 11713-11741; https://doi.org/10.3390/ijms140611713 - 31 May 2013
Cited by 74 | Viewed by 19692
Abstract
The alkaloids characteristically produced by the subfamily Amaryllidoideae of the Amaryllidaceae, bulbous plant species that include well know genera such as Narcissus (daffodils) and Galanthus (snowdrops), are a source of new pharmaceutical compounds. Presently, only the Amaryllidaceae alkaloid galanthamine, an acetylcholinesterase inhibitor used [...] Read more.
The alkaloids characteristically produced by the subfamily Amaryllidoideae of the Amaryllidaceae, bulbous plant species that include well know genera such as Narcissus (daffodils) and Galanthus (snowdrops), are a source of new pharmaceutical compounds. Presently, only the Amaryllidaceae alkaloid galanthamine, an acetylcholinesterase inhibitor used to treat symptoms of Alzheimer’s disease, is produced commercially as a drug from cultivated plants. However, several Amaryllidaceae alkaloids have shown great promise as anti-cancer drugs, but their further clinical development is restricted by their limited commercial availability. Amaryllidaceae species have a long history of cultivation and breeding as ornamental bulbs, and phytochemical research has focussed on the diversity in alkaloid content and composition. In contrast to the available pharmacological and phytochemical data, ecological, physiological and molecular aspects of the Amaryllidaceae and their alkaloids are much less explored and the identity of the alkaloid biosynthetic genes is presently unknown. An improved molecular understanding of Amaryllidaceae alkaloid biosynthesis would greatly benefit the rational design of breeding programs to produce cultivars optimised for the production of pharmaceutical compounds and enable biotechnology based approaches. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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725 KiB  
Review
Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research
by Man-Wah Li, Xinpeng Qi, Meng Ni and Hon-Ming Lam
Int. J. Mol. Sci. 2013, 14(6), 11444-11483; https://doi.org/10.3390/ijms140611444 - 29 May 2013
Cited by 7 | Viewed by 11527
Abstract
Abiotic and biotic stresses lead to massive reprogramming of different life processes and are the major limiting factors hampering crop productivity. Omics-based research platforms allow for a holistic and comprehensive survey on crop stress responses and hence may bring forth better crop improvement [...] Read more.
Abiotic and biotic stresses lead to massive reprogramming of different life processes and are the major limiting factors hampering crop productivity. Omics-based research platforms allow for a holistic and comprehensive survey on crop stress responses and hence may bring forth better crop improvement strategies. Since high-throughput approaches generate considerable amounts of data, bioinformatics tools will play an essential role in storing, retrieving, sharing, processing, and analyzing them. Genomic and functional genomic studies in crops still lag far behind similar studies in humans and other animals. In this review, we summarize some useful genomics and bioinformatics resources available to crop scientists. In addition, we also discuss the major challenges and advancements in the “-omics” studies, with an emphasis on their possible impacts on crop stress research and crop improvement. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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286 KiB  
Review
Integrated -Omics: A Powerful Approach to Understanding the Heterogeneous Lignification of Fibre Crops
by Gea Guerriero, Kjell Sergeant and Jean-François Hausman
Int. J. Mol. Sci. 2013, 14(6), 10958-10978; https://doi.org/10.3390/ijms140610958 - 24 May 2013
Cited by 44 | Viewed by 9460
Abstract
Lignin and cellulose represent the two main components of plant secondary walls and the most abundant polymers on Earth. Quantitatively one of the principal products of the phenylpropanoid pathway, lignin confers high mechanical strength and hydrophobicity to plant walls, thus enabling erect growth [...] Read more.
Lignin and cellulose represent the two main components of plant secondary walls and the most abundant polymers on Earth. Quantitatively one of the principal products of the phenylpropanoid pathway, lignin confers high mechanical strength and hydrophobicity to plant walls, thus enabling erect growth and high-pressure water transport in the vessels. Lignin is characterized by a high natural heterogeneity in its composition and abundance in plant secondary cell walls, even in the different tissues of the same plant. A typical example is the stem of fibre crops, which shows a lignified core enveloped by a cellulosic, lignin-poor cortex. Despite the great value of fibre crops for humanity, however, still little is known on the mechanisms controlling their cell wall biogenesis, and particularly, what regulates their spatially-defined lignification pattern. Given the chemical complexity and the heterogeneous composition of fibre crops’ secondary walls, only the use of multidisciplinary approaches can convey an integrated picture and provide exhaustive information covering different levels of biological complexity. The present review highlights the importance of combining high throughput -omics approaches to get a complete understanding of the factors regulating the lignification heterogeneity typical of fibre crops. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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1044 KiB  
Review
Plant Defense against Insect Herbivores
by Joel Fürstenberg-Hägg, Mika Zagrobelny and Søren Bak
Int. J. Mol. Sci. 2013, 14(5), 10242-10297; https://doi.org/10.3390/ijms140510242 - 16 May 2013
Cited by 565 | Viewed by 38049
Abstract
Plants have been interacting with insects for several hundred million years, leading to complex defense approaches against various insect feeding strategies. Some defenses are constitutive while others are induced, although the insecticidal defense compound or protein classes are often similar. Insect herbivory induce [...] Read more.
Plants have been interacting with insects for several hundred million years, leading to complex defense approaches against various insect feeding strategies. Some defenses are constitutive while others are induced, although the insecticidal defense compound or protein classes are often similar. Insect herbivory induce several internal signals from the wounded tissues, including calcium ion fluxes, phosphorylation cascades and systemic- and jasmonate signaling. These are perceived in undamaged tissues, which thereafter reinforce their defense by producing different, mostly low molecular weight, defense compounds. These bioactive specialized plant defense compounds may repel or intoxicate insects, while defense proteins often interfere with their digestion. Volatiles are released upon herbivory to repel herbivores, attract predators or for communication between leaves or plants, and to induce defense responses. Plants also apply morphological features like waxes, trichomes and latices to make the feeding more difficult for the insects. Extrafloral nectar, food bodies and nesting or refuge sites are produced to accommodate and feed the predators of the herbivores. Meanwhile, herbivorous insects have adapted to resist plant defenses, and in some cases even sequester the compounds and reuse them in their own defense. Both plant defense and insect adaptation involve metabolic costs, so most plant-insect interactions reach a stand-off, where both host and herbivore survive although their development is suboptimal. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Review
Physiological, Biochemical, and Molecular Mechanisms of Heat Stress Tolerance in Plants
by Mirza Hasanuzzaman, Kamrun Nahar, Md. Mahabub Alam, Rajib Roychowdhury and Masayuki Fujita
Int. J. Mol. Sci. 2013, 14(5), 9643-9684; https://doi.org/10.3390/ijms14059643 - 03 May 2013
Cited by 1359 | Viewed by 59960
Abstract
High temperature (HT) stress is a major environmental stress that limits plant growth, metabolism, and productivity worldwide. Plant growth and development involve numerous biochemical reactions that are sensitive to temperature. Plant responses to HT vary with the degree and duration of HT and [...] Read more.
High temperature (HT) stress is a major environmental stress that limits plant growth, metabolism, and productivity worldwide. Plant growth and development involve numerous biochemical reactions that are sensitive to temperature. Plant responses to HT vary with the degree and duration of HT and the plant type. HT is now a major concern for crop production and approaches for sustaining high yields of crop plants under HT stress are important agricultural goals. Plants possess a number of adaptive, avoidance, or acclimation mechanisms to cope with HT situations. In addition, major tolerance mechanisms that employ ion transporters, proteins, osmoprotectants, antioxidants, and other factors involved in signaling cascades and transcriptional control are activated to offset stress-induced biochemical and physiological alterations. Plant survival under HT stress depends on the ability to perceive the HT stimulus, generate and transmit the signal, and initiate appropriate physiological and biochemical changes. HT-induced gene expression and metabolite synthesis also substantially improve tolerance. The physiological and biochemical responses to heat stress are active research areas, and the molecular approaches are being adopted for developing HT tolerance in plants. This article reviews the recent findings on responses, adaptation, and tolerance to HT at the cellular, organellar, and whole plant levels and describes various approaches being taken to enhance thermotolerance in plants. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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247 KiB  
Review
Improving Pharmaceutical Protein Production in Oryza sativa
by Yu-Chieh Kuo, Chia-Chun Tan, Jung-Ting Ku, Wei-Cho Hsu, Sung-Chieh Su, Chung-An Lu and Li-Fen Huang
Int. J. Mol. Sci. 2013, 14(5), 8719-8739; https://doi.org/10.3390/ijms14058719 - 24 Apr 2013
Cited by 40 | Viewed by 8910
Abstract
Application of plant expression systems in the production of recombinant proteins has several advantages, such as low maintenance cost, absence of human pathogens, and possession of complex post-translational glycosylation capabilities. Plants have been successfully used to produce recombinant cytokines, vaccines, antibodies, and other [...] Read more.
Application of plant expression systems in the production of recombinant proteins has several advantages, such as low maintenance cost, absence of human pathogens, and possession of complex post-translational glycosylation capabilities. Plants have been successfully used to produce recombinant cytokines, vaccines, antibodies, and other proteins, and rice (Oryza sativa) is a potential plant used as recombinant protein expression system. After successful transformation, transgenic rice cells can be either regenerated into whole plants or grown as cell cultures that can be upscaled into bioreactors. This review summarizes recent advances in the production of different recombinant protein produced in rice and describes their production methods as well as methods to improve protein yield and quality. Glycosylation and its impact in plant development and protein production are discussed, and several methods of improving yield and quality that have not been incorporated in rice expression systems are also proposed. Finally, different bioreactor options are explored and their advantages are analyzed. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
859 KiB  
Review
Endoplasmic Reticulum (ER) Stress Response and Its Physiological Roles in Plants
by Yan Deng, Renu Srivastava and Stephen H. Howell
Int. J. Mol. Sci. 2013, 14(4), 8188-8212; https://doi.org/10.3390/ijms14048188 - 15 Apr 2013
Cited by 85 | Viewed by 14922
Abstract
The endoplasmic reticulum (ER) stress response is a highly conserved mechanism that results from the accumulation of unfolded or misfolded proteins in the ER. The response plays an important role in allowing plants to sense and respond to adverse environmental conditions, such as [...] Read more.
The endoplasmic reticulum (ER) stress response is a highly conserved mechanism that results from the accumulation of unfolded or misfolded proteins in the ER. The response plays an important role in allowing plants to sense and respond to adverse environmental conditions, such as heat stress, salt stress and pathogen infection. Since the ER is a well-controlled microenvironment for proper protein synthesis and folding, it is highly susceptible to stress conditions. Accumulation of unfolded or misfolded proteins activates a signaling pathway, called the unfolded protein response (UPR), which acts to relieve ER stress and, if unsuccessful, leads to cell death. Plants have two arms of the UPR signaling pathway, an arm involving the proteolytic processing of membrane-associated basic leucine zipper domain (bZIP) transcription factors and an arm involving RNA splicing factor, IRE1, and its mRNA target. These signaling pathways play an important role in determining the cell’s fate in response to stress conditions. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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589 KiB  
Review
Role of Homeodomain Leucine Zipper (HD-Zip) IV Transcription Factors in Plant Development and Plant Protection from Deleterious Environmental Factors
by William Chew, Maria Hrmova and Sergiy Lopato
Int. J. Mol. Sci. 2013, 14(4), 8122-8147; https://doi.org/10.3390/ijms14048122 - 12 Apr 2013
Cited by 69 | Viewed by 10647
Abstract
Homeobox genes comprise an important group of genes that are responsible for regulation of developmental processes. These genes determine cell differentiation and cell fate in all eukaryotic organisms, starting from the early stages of embryo development. Homeodomain leucine zipper (HD-Zip) transcription factors are [...] Read more.
Homeobox genes comprise an important group of genes that are responsible for regulation of developmental processes. These genes determine cell differentiation and cell fate in all eukaryotic organisms, starting from the early stages of embryo development. Homeodomain leucine zipper (HD-Zip) transcription factors are unique to the plant kingdom. Members of the HD-Zip IV subfamily have a complex domain topology and can bind several cis-elements with overlapping sequences. Many of the reported HD-Zip IV genes were shown to be specifically or preferentially expressed in plant epidermal or sub-epidermal cells. HD-Zip IV TFs were found to be associated with differentiation and maintenance of outer cell layers, and regulation of lipid biosynthesis and transport. Insights about the role of these proteins in plant cuticle formation, and hence their possible involvement in plant protection from pathogens and abiotic stresses has just started to emerge. These roles make HD-Zip IV proteins an attractive tool for genetic engineering of crop plants. To this end, there is a need for in-depth studies to further clarify the function of each HD-Zip IV subfamily member in commercially important plant species. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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579 KiB  
Review
Plant bZIP Transcription Factors Responsive to Pathogens: A Review
by Murilo S. Alves, Silvana P. Dadalto, Amanda B. Gonçalves, Gilza B. De Souza, Vanessa A. Barros and Luciano G. Fietto
Int. J. Mol. Sci. 2013, 14(4), 7815-7828; https://doi.org/10.3390/ijms14047815 - 10 Apr 2013
Cited by 211 | Viewed by 13004
Abstract
Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are master regulators of many central developmental and physiological processes, including morphogenesis, seed formation, abiotic and biotic stress responses. Modulation of the expression patterns of [...] Read more.
Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are master regulators of many central developmental and physiological processes, including morphogenesis, seed formation, abiotic and biotic stress responses. Modulation of the expression patterns of bZIP genes and changes in their activity often contribute to the activation of various signaling pathways and regulatory networks of different physiological processes. However, most advances in the study of plant bZIP transcription factors are related to their involvement in abiotic stress and development. In contrast, there are few examples of functional research with regard to biotic stress, particularly in the defense against pathogens. In this review, we summarize the recent progress revealing the role of bZIP transcription factors in the biotic stress responses of several plant species, from Arabidopsis to cotton. Moreover, we summarize the interacting partners of bZIP proteins in molecular responses during pathogen attack and the key components of the signal transduction pathways with which they physically interact during plant defense responses. Lastly, we focus on the recent advances regarding research on the functional role of bZIPs in major agricultural cultivars and examine the studies performed in this field. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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401 KiB  
Review
A Dual Role of Strigolactones in Phosphate Acquisition and Utilization in Plants
by Olaf Czarnecki, Jun Yang, David J. Weston, Gerald A. Tuskan and Jin-Gui Chen
Int. J. Mol. Sci. 2013, 14(4), 7681-7701; https://doi.org/10.3390/ijms14047681 - 09 Apr 2013
Cited by 97 | Viewed by 13158
Abstract
Phosphorus, acquired in the form of phosphate (Pi), is one of the primary macronutrients for plants but is least available in the soil. Pi deficiency is a major factor limiting plant growth, development and reproduction. Plants have developed a complex signaling network to [...] Read more.
Phosphorus, acquired in the form of phosphate (Pi), is one of the primary macronutrients for plants but is least available in the soil. Pi deficiency is a major factor limiting plant growth, development and reproduction. Plants have developed a complex signaling network to respond to Pi deficiency. The recent discovery of strigolactones, a new class of plant hormones, has led to an emerging signaling module illustrating the integrated control of Pi acquisition, plant-microbe symbiotic interactions and plant architecture. This review article focuses on the recent findings of plant responses and roles of strigolactones to Pi deficiency. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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1124 KiB  
Review
Plant High-Affinity Potassium (HKT) Transporters Involved in Salinity Tolerance: Structural Insights to Probe Differences in Ion Selectivity
by Shane Waters, Matthew Gilliham and Maria Hrmova
Int. J. Mol. Sci. 2013, 14(4), 7660-7680; https://doi.org/10.3390/ijms14047660 - 09 Apr 2013
Cited by 92 | Viewed by 11511
Abstract
High-affinity Potassium Transporters (HKTs) belong to an important class of integral membrane proteins (IMPs) that facilitate cation transport across the plasma membranes of plant cells. Some members of the HKT protein family have been shown to be critical for salinity tolerance in commercially [...] Read more.
High-affinity Potassium Transporters (HKTs) belong to an important class of integral membrane proteins (IMPs) that facilitate cation transport across the plasma membranes of plant cells. Some members of the HKT protein family have been shown to be critical for salinity tolerance in commercially important crop species, particularly in grains, through exclusion of Na+ ions from sensitive shoot tissues in plants. However, given the number of different HKT proteins expressed in plants, it is likely that different members of this protein family perform in a range of functions. Plant breeders and biotechnologists have attempted to manipulate HKT gene expression through genetic engineering and more conventional plant breeding methods to improve the salinity tolerance of commercially important crop plants. Successful manipulation of a biological trait is more likely to be effective after a thorough understanding of how the trait, genes and proteins are interconnected at the whole plant level. This article examines the current structural and functional knowledge relating to plant HKTs and how their structural features may explain their transport selectivity. We also highlight specific areas where new knowledge of plant HKT transporters is needed. Our goal is to present how knowledge of the structure of HKT proteins is helpful in understanding their function and how this understanding can be an invaluable experimental tool. As such, we assert that accurate structural information of plant IMPs will greatly inform functional studies and will lead to a deeper understanding of plant nutrition, signalling and stress tolerance, all of which represent factors that can be manipulated to improve agricultural productivity. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Review
A Review of the “Omics” Approach to Biomarkers of Oxidative Stress in Oryza sativa
by Nyuk Ling Ma, Zaidah Rahmat and Su Shiung Lam
Int. J. Mol. Sci. 2013, 14(4), 7515-7541; https://doi.org/10.3390/ijms14047515 - 08 Apr 2013
Cited by 36 | Viewed by 12399
Abstract
Physiological and ecological constraints that cause the slow growth and depleted production of crops have raised a major concern in the agriculture industry as they represent a possible threat of short food supply in the future. The key feature that regulates the stress [...] Read more.
Physiological and ecological constraints that cause the slow growth and depleted production of crops have raised a major concern in the agriculture industry as they represent a possible threat of short food supply in the future. The key feature that regulates the stress signaling pathway is always related to the reactive oxygen species (ROS). The accumulation of ROS in plant cells would leave traces of biomarkers at the genome, proteome, and metabolome levels, which could be identified with the recent technological breakthrough coupled with improved performance of bioinformatics. This review highlights the recent breakthrough in molecular strategies (comprising transcriptomics, proteomics, and metabolomics) in identifying oxidative stress biomarkers and the arising opportunities and obstacles observed in research on biomarkers in rice. The major issue in incorporating bioinformatics to validate the biomarkers from different omic platforms for the use of rice-breeding programs is also discussed. The development of powerful techniques for identification of oxidative stress-related biomarkers and the integration of data from different disciplines shed light on the oxidative response pathways in plants. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Review
A Central Role for Thiols in Plant Tolerance to Abiotic Stress
by Lyuben Zagorchev, Charlotte E. Seal, Ilse Kranner and Mariela Odjakova
Int. J. Mol. Sci. 2013, 14(4), 7405-7432; https://doi.org/10.3390/ijms14047405 - 02 Apr 2013
Cited by 325 | Viewed by 21668
Abstract
Abiotic stress poses major problems to agriculture and increasing efforts are being made to understand plant stress response and tolerance mechanisms and to develop new tools that underpin successful agriculture. However, the molecular mechanisms of plant stress tolerance are not fully understood, and [...] Read more.
Abiotic stress poses major problems to agriculture and increasing efforts are being made to understand plant stress response and tolerance mechanisms and to develop new tools that underpin successful agriculture. However, the molecular mechanisms of plant stress tolerance are not fully understood, and the data available is incomplete and sometimes contradictory. Here, we review the significance of protein and non-protein thiol compounds in relation to plant tolerance of abiotic stress. First, the roles of the amino acids cysteine and methionine, are discussed, followed by an extensive discussion of the low-molecular-weight tripeptide, thiol glutathione, which plays a central part in plant stress response and oxidative signalling and of glutathione-related enzymes, including those involved in the biosynthesis of non-protein thiol compounds. Special attention is given to the glutathione redox state, to phytochelatins and to the role of glutathione in the regulation of the cell cycle. The protein thiol section focuses on glutaredoxins and thioredoxins, proteins with oxidoreductase activity, which are involved in protein glutathionylation. The review concludes with a brief overview of and future perspectives for the involvement of plant thiols in abiotic stress tolerance. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Review
The Critical Role of Potassium in Plant Stress Response
by Min Wang, Qingsong Zheng, Qirong Shen and Shiwei Guo
Int. J. Mol. Sci. 2013, 14(4), 7370-7390; https://doi.org/10.3390/ijms14047370 - 02 Apr 2013
Cited by 1082 | Viewed by 46582
Abstract
Agricultural production continues to be constrained by a number of biotic and abiotic factors that can reduce crop yield quantity and quality. Potassium (K) is an essential nutrient that affects most of the biochemical and physiological processes that influence plant growth and metabolism. [...] Read more.
Agricultural production continues to be constrained by a number of biotic and abiotic factors that can reduce crop yield quantity and quality. Potassium (K) is an essential nutrient that affects most of the biochemical and physiological processes that influence plant growth and metabolism. It also contributes to the survival of plants exposed to various biotic and abiotic stresses. The following review focuses on the emerging role of K in defending against a number of biotic and abiotic stresses, including diseases, pests, drought, salinity, cold and frost and waterlogging. The availability of K and its effects on plant growth, anatomy, morphology and plant metabolism are discussed. The physiological and molecular mechanisms of K function in plant stress resistance are reviewed. This article also evaluates the potential for improving plant stress resistance by modifying K fertilizer inputs and highlights the future needs for research about the role of K in agriculture. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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563 KiB  
Review
Impact of Cell Wall Composition on Maize Resistance to Pests and Diseases
by Rogelio Santiago, Jaime Barros-Rios and Rosa A. Malvar
Int. J. Mol. Sci. 2013, 14(4), 6960-6980; https://doi.org/10.3390/ijms14046960 - 27 Mar 2013
Cited by 105 | Viewed by 14622
Abstract
In cereals, the primary cell wall is built of a skeleton of cellulosic microfibrils embedded in a matrix of hemicelluloses and smaller amounts of pectins, glycoproteins and hydroxycinnamates. Later, during secondary wall development, p-coumaryl, coniferyl and sinapyl alcohols are copolymerized to form [...] Read more.
In cereals, the primary cell wall is built of a skeleton of cellulosic microfibrils embedded in a matrix of hemicelluloses and smaller amounts of pectins, glycoproteins and hydroxycinnamates. Later, during secondary wall development, p-coumaryl, coniferyl and sinapyl alcohols are copolymerized to form mixed lignins. Several of these cell wall components show a determinative role in maize resistance to pest and diseases. However, defense mechanisms are very complex and vary among the same plant species, different tissues or even the same tissue at different developmental stages. Thus, it is important to highlight that the role of the cell wall components needs to be tested in diverse genotypes and specific tissues where the feeding or attacking by the pathogen takes place. Understanding the role of cell wall constituents as defense mechanisms may allow modifications of crops to withstand pests and diseases. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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444 KiB  
Review
Alternative Oxidase: A Mitochondrial Respiratory Pathway to Maintain Metabolic and Signaling Homeostasis during Abiotic and Biotic Stress in Plants
by Greg C. Vanlerberghe
Int. J. Mol. Sci. 2013, 14(4), 6805-6847; https://doi.org/10.3390/ijms14046805 - 26 Mar 2013
Cited by 511 | Viewed by 26964
Abstract
Alternative oxidase (AOX) is a non-energy conserving terminal oxidase in the plant mitochondrial electron transport chain. While respiratory carbon oxidation pathways, electron transport, and ATP turnover are tightly coupled processes, AOX provides a means to relax this coupling, thus providing a degree of [...] Read more.
Alternative oxidase (AOX) is a non-energy conserving terminal oxidase in the plant mitochondrial electron transport chain. While respiratory carbon oxidation pathways, electron transport, and ATP turnover are tightly coupled processes, AOX provides a means to relax this coupling, thus providing a degree of metabolic homeostasis to carbon and energy metabolism. Beside their role in primary metabolism, plant mitochondria also act as “signaling organelles”, able to influence processes such as nuclear gene expression. AOX activity can control the level of potential mitochondrial signaling molecules such as superoxide, nitric oxide and important redox couples. In this way, AOX also provides a degree of signaling homeostasis to the organelle. Evidence suggests that AOX function in metabolic and signaling homeostasis is particularly important during stress. These include abiotic stresses such as low temperature, drought, and nutrient deficiency, as well as biotic stresses such as bacterial infection. This review provides an introduction to the genetic and biochemical control of AOX respiration, as well as providing generalized examples of how AOX activity can provide metabolic and signaling homeostasis. This review also examines abiotic and biotic stresses in which AOX respiration has been critically evaluated, and considers the overall role of AOX in growth and stress tolerance. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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436 KiB  
Review
Protein Contribution to Plant Salinity Response and Tolerance Acquisition
by Klára Kosová, Ilja T. Prášil and Pavel Vítámvás
Int. J. Mol. Sci. 2013, 14(4), 6757-6789; https://doi.org/10.3390/ijms14046757 - 26 Mar 2013
Cited by 159 | Viewed by 12854
Abstract
The review is focused on plant proteome response to salinity with respect to physiological aspects of plant salt stress response. The attention is paid to both osmotic and ionic effects of salinity stress on plants with respect to several protein functional groups. Therefore, [...] Read more.
The review is focused on plant proteome response to salinity with respect to physiological aspects of plant salt stress response. The attention is paid to both osmotic and ionic effects of salinity stress on plants with respect to several protein functional groups. Therefore, the role of individual proteins involved in signalling, changes in gene expression, protein biosynthesis and degradation and the resulting changes in protein relative abundance in proteins involved in energy metabolism, redox metabolism, stress- and defence-related proteins, osmolyte metabolism, phytohormone, lipid and secondary metabolism, mechanical stress-related proteins as well as protein posttranslational modifications are discussed. Differences between salt-sensitive (glycophytes) and salt-tolerant (halophytes) plants are analysed with respect to differential salinity tolerance. In conclusion, contribution of proteomic studies to understanding plant salinity tolerance is summarised and discussed. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Review
The Influence of Metal Stress on the Availability and Redox State of Ascorbate, and Possible Interference with Its Cellular Functions
by An Bielen, Tony Remans, Jaco Vangronsveld and Ann Cuypers
Int. J. Mol. Sci. 2013, 14(3), 6382-6413; https://doi.org/10.3390/ijms14036382 - 20 Mar 2013
Cited by 85 | Viewed by 8667
Abstract
Worldwide, metals have been distributed to excessive levels in the environment due to industrial and agricultural activities. Plants growing on soils contaminated with excess levels of metals experience a disturbance of the cellular redox balance, which leads to an augmentation of reactive oxygen [...] Read more.
Worldwide, metals have been distributed to excessive levels in the environment due to industrial and agricultural activities. Plants growing on soils contaminated with excess levels of metals experience a disturbance of the cellular redox balance, which leads to an augmentation of reactive oxygen species (ROS). Even though the increased ROS levels can cause cellular damage, controlled levels play an important role in modulating signaling networks that control physiological processes and stress responses. Plants control ROS levels using their antioxidative defense system both under non-stress conditions, as well as under stress conditions such as exposure to excess metals. Ascorbate (AsA) is a well-known and important component of the plant’s antioxidative system. As primary antioxidant, it can reduce ROS directly and indirectly via ascorbate peroxidase in the ascorbate–glutathione cycle. Furthermore, AsA fulfills an essential role in physiological processes, some of which are disturbed by excess metals. In this review, known direct effects of excess metals on AsA biosynthesis and functioning will be discussed, as well as the possible interference of metals with the role of AsA in physiological and biochemical processes. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Review
Structure, Function and Networks of Transcription Factors Involved in Abiotic Stress Responses
by Søren Lindemose, Charlotte O'Shea, Michael Krogh Jensen and Karen Skriver
Int. J. Mol. Sci. 2013, 14(3), 5842-5878; https://doi.org/10.3390/ijms14035842 - 13 Mar 2013
Cited by 256 | Viewed by 19827
Abstract
Transcription factors (TFs) are master regulators of abiotic stress responses in plants. This review focuses on TFs from seven major TF families, known to play functional roles in response to abiotic stresses, including drought, high salinity, high osmolarity, temperature extremes and the phytohormone [...] Read more.
Transcription factors (TFs) are master regulators of abiotic stress responses in plants. This review focuses on TFs from seven major TF families, known to play functional roles in response to abiotic stresses, including drought, high salinity, high osmolarity, temperature extremes and the phytohormone ABA. Although ectopic expression of several TFs has improved abiotic stress tolerance in plants, fine-tuning of TF expression and protein levels remains a challenge to avoid crop yield loss. To further our understanding of TFs in abiotic stress responses, emerging gene regulatory networks based on TFs and their direct targets genes are presented. These revealed components shared between ABA-dependent and independent signaling as well as abiotic and biotic stress signaling. Protein structure analysis suggested that TFs hubs of large interactomes have extended regions with protein intrinsic disorder (ID), referring to their lack of fixed tertiary structures. ID is now an emerging topic in plant science. Furthermore, the importance of the ubiquitin-proteasome protein degradation systems and modification by sumoylation is also apparent from the interactomes. Therefore; TF interaction partners such as E3 ubiquitin ligases and TF regions with ID represent future targets for engineering improved abiotic stress tolerance in crops. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Review
Structural Biology of a Major Signaling Network that Regulates Plant Abiotic Stress: The CBL-CIPK Mediated Pathway
by María José Sánchez-Barrena, Martín Martínez-Ripoll and Armando Albert
Int. J. Mol. Sci. 2013, 14(3), 5734-5749; https://doi.org/10.3390/ijms14035734 - 12 Mar 2013
Cited by 52 | Viewed by 11375
Abstract
The Arabidopsis SOS2 family of twenty-six protein kinases (CIPKs), their interacting activators, the SOS3 family of ten calcium-binding proteins (CBLs) and protein phosphatases type 2C (PP2C), function together in decoding calcium signals elicited by different environmental stimuli. Biochemical data suggest that stable CBL-CIPK [...] Read more.
The Arabidopsis SOS2 family of twenty-six protein kinases (CIPKs), their interacting activators, the SOS3 family of ten calcium-binding proteins (CBLs) and protein phosphatases type 2C (PP2C), function together in decoding calcium signals elicited by different environmental stimuli. Biochemical data suggest that stable CBL-CIPK or CIPK-PP2C complexes may be regulating the activity of various substrates controlling ion homeostasis. The available structural information provides a general regulatory mechanism in which calcium perception by CBLs and kinase activation is coupled. The structural basis of this molecular mechanism and the specificity of the network is reviewed and discussed in detail. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Review
Cold Signaling and Cold Response in Plants
by Kenji Miura and Tsuyoshi Furumoto
Int. J. Mol. Sci. 2013, 14(3), 5312-5337; https://doi.org/10.3390/ijms14035312 - 06 Mar 2013
Cited by 360 | Viewed by 20405
Abstract
Plants are constantly exposed to a variety of environmental stresses. Freezing or extremely low temperature constitutes a key factor influencing plant growth, development and crop productivity. Plants have evolved a mechanism to enhance tolerance to freezing during exposure to periods of low, but [...] Read more.
Plants are constantly exposed to a variety of environmental stresses. Freezing or extremely low temperature constitutes a key factor influencing plant growth, development and crop productivity. Plants have evolved a mechanism to enhance tolerance to freezing during exposure to periods of low, but non-freezing temperatures. This phenomenon is called cold acclimation. During cold acclimation, plants develop several mechanisms to minimize potential damages caused by low temperature. Cold response is highly complex process that involves an array of physiological and biochemical modifications. Furthermore, alterations of the expression patterns of many genes, proteins and metabolites in response to cold stress have been reported. Recent studies demonstrate that post-transcriptional and post-translational regulations play a role in the regulation of cold signaling. In this review article, recent advances in cold stress signaling and tolerance are highlighted. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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527 KiB  
Review
Metabolomics as a Tool to Investigate Abiotic Stress Tolerance in Plants
by Vicent Arbona, Matías Manzi, Carlos De Ollas and Aurelio Gómez-Cadenas
Int. J. Mol. Sci. 2013, 14(3), 4885-4911; https://doi.org/10.3390/ijms14034885 - 01 Mar 2013
Cited by 455 | Viewed by 26546
Abstract
Metabolites reflect the integration of gene expression, protein interaction and other different regulatory processes and are therefore closer to the phenotype than mRNA transcripts or proteins alone. Amongst all –omics technologies, metabolomics is the most transversal and can be applied to different organisms [...] Read more.
Metabolites reflect the integration of gene expression, protein interaction and other different regulatory processes and are therefore closer to the phenotype than mRNA transcripts or proteins alone. Amongst all –omics technologies, metabolomics is the most transversal and can be applied to different organisms with little or no modifications. It has been successfully applied to the study of molecular phenotypes of plants in response to abiotic stress in order to find particular patterns associated to stress tolerance. These studies have highlighted the essential involvement of primary metabolites: sugars, amino acids and Krebs cycle intermediates as direct markers of photosynthetic dysfunction as well as effectors of osmotic readjustment. On the contrary, secondary metabolites are more specific of genera and species and respond to particular stress conditions as antioxidants, Reactive Oxygen Species (ROS) scavengers, coenzymes, UV and excess radiation screen and also as regulatory molecules. In addition, the induction of secondary metabolites by several abiotic stress conditions could also be an effective mechanism of cross-protection against biotic threats, providing a link between abiotic and biotic stress responses. Moreover, the presence/absence and relative accumulation of certain metabolites along with gene expression data provides accurate markers (mQTL or MWAS) for tolerant crop selection in breeding programs. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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872 KiB  
Review
Low Oxygen Response Mechanisms in Green Organisms
by Valeria Banti, Beatrice Giuntoli, Silvia Gonzali, Elena Loreti, Leonardo Magneschi, Giacomo Novi, Eleonora Paparelli, Sandro Parlanti, Chiara Pucciariello, Antonietta Santaniello and Pierdomenico Perata
Int. J. Mol. Sci. 2013, 14(3), 4734-4761; https://doi.org/10.3390/ijms14034734 - 27 Feb 2013
Cited by 85 | Viewed by 11634
Abstract
Low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. Both plants and algae respond to low oxygen by resetting their metabolism. The shift from mitochondrial respiration to fermentation is the hallmark of [...] Read more.
Low oxygen stress often occurs during the life of green organisms, mostly due to the environmental conditions affecting oxygen availability. Both plants and algae respond to low oxygen by resetting their metabolism. The shift from mitochondrial respiration to fermentation is the hallmark of anaerobic metabolism in most organisms. This involves a modified carbohydrate metabolism coupled with glycolysis and fermentation. For a coordinated response to low oxygen, plants exploit various molecular mechanisms to sense when oxygen is either absent or in limited amounts. In Arabidopsis thaliana, a direct oxygen sensing system has recently been discovered, where a conserved N-terminal motif on some ethylene responsive factors (ERFs), targets the fate of the protein under normoxia/hypoxia. In Oryza sativa, this same group of ERFs drives physiological and anatomical modifications that vary in relation to the genotype studied. The microalga Chlamydomonas reinhardtii responses to low oxygen seem to have evolved independently of higher plants, posing questions on how the fermentative metabolism is modulated. In this review, we summarize the most recent findings related to these topics, highlighting promising developments for the future. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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Review
Regulation of Translation Initiation under Biotic and Abiotic Stresses
by Sira Echevarría-Zomeño, Emilio Yángüez, Nuria Fernández-Bautista, Ana B. Castro-Sanz, Alejandro Ferrando and M. Mar Castellano
Int. J. Mol. Sci. 2013, 14(3), 4670-4683; https://doi.org/10.3390/ijms14034670 - 26 Feb 2013
Cited by 37 | Viewed by 8571
Abstract
Plants have developed versatile strategies to deal with the great variety of challenging conditions they are exposed to. Among them, the regulation of translation is a common target to finely modulate gene expression both under biotic and abiotic stress situations. Upon environmental challenges, [...] Read more.
Plants have developed versatile strategies to deal with the great variety of challenging conditions they are exposed to. Among them, the regulation of translation is a common target to finely modulate gene expression both under biotic and abiotic stress situations. Upon environmental challenges, translation is regulated to reduce the consumption of energy and to selectively synthesize proteins involved in the proper establishment of the tolerance response. In the case of viral infections, the situation is more complex, as viruses have evolved unconventional mechanisms to regulate translation in order to ensure the production of the viral encoded proteins using the plant machinery. Although the final purpose is different, in some cases, both plants and viruses share common mechanisms to modulate translation. In others, the mechanisms leading to the control of translation are viral- or stress-specific. In this paper, we review the different mechanisms involved in the regulation of translation initiation under virus infection and under environmental stress in plants. In addition, we describe the main features within the viral RNAs and the cellular mRNAs that promote their selective translation in plants undergoing biotic and abiotic stress situations. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
256 KiB  
Review
Agriculture and Bioactives: Achieving Both Crop Yield and Phytochemicals
by Lina García-Mier, Ramón G. Guevara-González, Víctor M. Mondragón-Olguín, Beatriz Del Rocío Verduzco-Cuellar and Irineo Torres-Pacheco
Int. J. Mol. Sci. 2013, 14(2), 4203-4222; https://doi.org/10.3390/ijms14024203 - 20 Feb 2013
Cited by 44 | Viewed by 9581
Abstract
Plants are fundamental elements of the human diet, either as direct sources of nutrients or indirectly as feed for animals. During the past few years, the main goal of agriculture has been to increase yield in order to provide the food that is [...] Read more.
Plants are fundamental elements of the human diet, either as direct sources of nutrients or indirectly as feed for animals. During the past few years, the main goal of agriculture has been to increase yield in order to provide the food that is needed by a growing world population. As important as yield, but commonly forgotten in conventional agriculture, is to keep and, if it is possible, to increase the phytochemical content due to their health implications. Nowadays, it is necessary to go beyond this, reconciling yield and phytochemicals that, at first glance, might seem in conflict. This can be accomplished through reviewing food requirements, plant consumption with health implications, and farming methods. The aim of this work is to show how both yield and phytochemicals converge into a new vision of agricultural management in a framework of integrated agricultural practices. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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Review
The Role of F-Box Proteins during Viral Infection
by Régis Lopes Correa, Fernanda Prieto Bruckner, Renan De Souza Cascardo and Poliane Alfenas-Zerbini
Int. J. Mol. Sci. 2013, 14(2), 4030-4049; https://doi.org/10.3390/ijms14024030 - 18 Feb 2013
Cited by 18 | Viewed by 7178
Abstract
The F-box domain is a protein structural motif of about 50 amino acids that mediates protein–protein interactions. The F-box protein is one of the four components of the SCF (SKp1, Cullin, F-box protein) complex, which mediates ubiquitination of proteins targeted for degradation by [...] Read more.
The F-box domain is a protein structural motif of about 50 amino acids that mediates protein–protein interactions. The F-box protein is one of the four components of the SCF (SKp1, Cullin, F-box protein) complex, which mediates ubiquitination of proteins targeted for degradation by the proteasome, playing an essential role in many cellular processes. Several discoveries have been made on the use of the ubiquitin–proteasome system by viruses of several families to complete their infection cycle. On the other hand, F-box proteins can be used in the defense response by the host. This review describes the role of F-box proteins and the use of the ubiquitin–proteasome system in virus–host interactions. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
347 KiB  
Review
Flavonoids as Antioxidants and Developmental Regulators: Relative Significance in Plants and Humans
by Cecilia Brunetti, Martina Di Ferdinando, Alessio Fini, Susanna Pollastri and Massimiliano Tattini
Int. J. Mol. Sci. 2013, 14(2), 3540-3555; https://doi.org/10.3390/ijms14023540 - 07 Feb 2013
Cited by 370 | Viewed by 17258
Abstract
Phenylpropanoids, particularly flavonoids have been recently suggested as playing primary antioxidant functions in the responses of plants to a wide range of abiotic stresses. Furthermore, flavonoids are effective endogenous regulators of auxin movement, thus behaving as developmental regulators. Flavonoids are capable of controlling [...] Read more.
Phenylpropanoids, particularly flavonoids have been recently suggested as playing primary antioxidant functions in the responses of plants to a wide range of abiotic stresses. Furthermore, flavonoids are effective endogenous regulators of auxin movement, thus behaving as developmental regulators. Flavonoids are capable of controlling the development of individual organs and the whole-plant; and, hence, to contribute to stress-induced morphogenic responses of plants. The significance of flavonoids as scavengers of reactive oxygen species (ROS) in humans has been recently questioned, based on the observation that the flavonoid concentration in plasma and most tissues is too low to effectively reduce ROS. Instead, flavonoids may play key roles as signaling molecules in mammals, through their ability to interact with a wide range of protein kinases, including mitogen-activated protein kinases (MAPK), that supersede key steps of cell growth and differentiation. Here we discuss about the relative significance of flavonoids as reducing agents and signaling molecules in plants and humans. We show that structural features conferring ROS-scavenger ability to flavonoids are also required to effectively control developmental processes in eukaryotic cells. Full article
(This article belongs to the Special Issue Molecular Research in Plant Secondary Metabolism)
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341 KiB  
Review
Natural Products as a Source for Treating Neglected Parasitic Diseases
by Dieudonné Ndjonka, Ludmila Nakamura Rapado, Ariel M. Silber, Eva Liebau and Carsten Wrenger
Int. J. Mol. Sci. 2013, 14(2), 3395-3439; https://doi.org/10.3390/ijms14023395 - 06 Feb 2013
Cited by 125 | Viewed by 12859
Abstract
Infectious diseases caused by parasites are a major threat for the entire mankind, especially in the tropics. More than 1 billion people world-wide are directly exposed to tropical parasites such as the causative agents of trypanosomiasis, leishmaniasis, schistosomiasis, lymphatic filariasis and onchocerciasis, which [...] Read more.
Infectious diseases caused by parasites are a major threat for the entire mankind, especially in the tropics. More than 1 billion people world-wide are directly exposed to tropical parasites such as the causative agents of trypanosomiasis, leishmaniasis, schistosomiasis, lymphatic filariasis and onchocerciasis, which represent a major health problem, particularly in impecunious areas. Unlike most antibiotics, there is no “general” antiparasitic drug available. Here, the selection of antiparasitic drugs varies between different organisms. Some of the currently available drugs are chemically de novo synthesized, however, the majority of drugs are derived from natural sources such as plants which have subsequently been chemically modified to warrant higher potency against these human pathogens. In this review article we will provide an overview of the current status of plant derived pharmaceuticals and their chemical modifications to target parasite-specific peculiarities in order to interfere with their proliferation in the human host. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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407 KiB  
Review
Activation of Defense Mechanisms against Pathogens in Mosses and Flowering Plants
by Inés Ponce de León and Marcos Montesano
Int. J. Mol. Sci. 2013, 14(2), 3178-3200; https://doi.org/10.3390/ijms14023178 - 04 Feb 2013
Cited by 91 | Viewed by 10934
Abstract
During evolution, plants have developed mechanisms to cope with and adapt to different types of stress, including microbial infection. Once the stress is sensed, signaling pathways are activated, leading to the induced expression of genes with different roles in defense. Mosses (Bryophytes) are [...] Read more.
During evolution, plants have developed mechanisms to cope with and adapt to different types of stress, including microbial infection. Once the stress is sensed, signaling pathways are activated, leading to the induced expression of genes with different roles in defense. Mosses (Bryophytes) are non-vascular plants that diverged from flowering plants more than 450 million years ago, allowing comparative studies of the evolution of defense-related genes and defensive metabolites produced after microbial infection. The ancestral position among land plants, the sequenced genome and the feasibility of generating targeted knock-out mutants by homologous recombination has made the moss Physcomitrella patens an attractive model to perform functional studies of plant genes involved in stress responses. This paper reviews the current knowledge of inducible defense mechanisms in P. patens and compares them to those activated in flowering plants after pathogen assault, including the reinforcement of the cell wall, ROS production, programmed cell death, activation of defense genes and synthesis of secondary metabolites and defense hormones. The knowledge generated in P. patens together with comparative studies in flowering plants will help to identify key components in plant defense responses and to design novel strategies to enhance resistance to biotic stress. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
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232 KiB  
Review
Production of Pharmaceutical Proteins in Solanaceae Food Crops
by Maria Manuela Rigano, Giorgio De Guzman, Amanda M. Walmsley, Luigi Frusciante and Amalia Barone
Int. J. Mol. Sci. 2013, 14(2), 2753-2773; https://doi.org/10.3390/ijms14022753 - 29 Jan 2013
Cited by 27 | Viewed by 7083
Abstract
The benefits of increased safety and cost-effectiveness make vegetable crops appropriate systems for the production and delivery of pharmaceutical proteins. In particular, Solanaceae edible crops could be inexpensive biofactories for oral vaccines and other pharmaceutical proteins that can be ingested as minimally processed [...] Read more.
The benefits of increased safety and cost-effectiveness make vegetable crops appropriate systems for the production and delivery of pharmaceutical proteins. In particular, Solanaceae edible crops could be inexpensive biofactories for oral vaccines and other pharmaceutical proteins that can be ingested as minimally processed extracts or as partially purified products. The field of crop plant biotechnology is advancing rapidly due to novel developments in genetic and genomic tools being made available today for the scientific community. In this review, we briefly summarize data now available regarding genomic resources for the Solanaceae family. In addition, we describe novel strategies developed for the expression of foreign proteins in vegetable crops and the utilization of these techniques to manufacture pharmaceutical proteins. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
591 KiB  
Review
The Twenty-Year Story of a Plant-Based Vaccine Against Hepatitis B: Stagnation or Promising Prospects?
by Tomasz Pniewski
Int. J. Mol. Sci. 2013, 14(1), 1978-1998; https://doi.org/10.3390/ijms14011978 - 21 Jan 2013
Cited by 24 | Viewed by 15378
Abstract
Hepatitis B persists as a common human disease despite effective vaccines having been employed for almost 30 years. Plants were considered as alternative sources of vaccines, to be mainly orally administered. Despite 20-year attempts, no real anti-HBV plant-based vaccine has been developed. Immunization [...] Read more.
Hepatitis B persists as a common human disease despite effective vaccines having been employed for almost 30 years. Plants were considered as alternative sources of vaccines, to be mainly orally administered. Despite 20-year attempts, no real anti-HBV plant-based vaccine has been developed. Immunization trials, based on ingestion of raw plant tissue and conjugated with injection or exclusively oral administration of lyophilized tissue, were either impractical or insufficient due to oral tolerance acquisition. Plant-produced purified HBV antigens were highly immunogenic when injected, but their yields were initially insufficient for practical purposes. However, knowledge and technology have progressed, hence new plant-derived anti-HBV vaccines can be proposed today. All HBV antigens can be efficiently produced in stable or transient expression systems. Processing of injection vaccines has been developed and needs only to be successfully completed. Purified antigens can be used for injection in an equivalent manner to the present commercial vaccines. Although oral vaccines require improvement, plant tissue, lyophilized or extracted and converted into tablets, etc., may serve as a boosting vaccine. Preliminary data indicate also that both vaccines can be combined in an effective parenteral-oral immunization procedure. A partial substitution of injection vaccines with oral formulations still offers good prospects for economically viable and efficacious anti-HBV plant-based vaccines. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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316 KiB  
Review
Dual Targeting and Retrograde Translocation: Regulators of Plant Nuclear Gene Expression Can Be Sequestered by Plastids
by Kirsten Krause, Svenja Oetke and Karin Krupinska
Int. J. Mol. Sci. 2012, 13(9), 11085-11101; https://doi.org/10.3390/ijms130911085 - 06 Sep 2012
Cited by 32 | Viewed by 9754
Abstract
Changes in the developmental or metabolic state of plastids can trigger profound changes in the transcript profiles of nuclear genes. Many nuclear transcription factors were shown to be controlled by signals generated in the organelles. In addition to the many different compounds for [...] Read more.
Changes in the developmental or metabolic state of plastids can trigger profound changes in the transcript profiles of nuclear genes. Many nuclear transcription factors were shown to be controlled by signals generated in the organelles. In addition to the many different compounds for which an involvement in retrograde signaling is discussed, accumulating evidence suggests a role for proteins in plastid-to-nucleus communication. These proteins might be sequestered in the plastids before they act as transcriptional regulators in the nucleus. Indeed, several proteins exhibiting a dual localization in the plastids and the nucleus are promising candidates for such a direct signal transduction involving regulatory protein storage in the plastids. Among such proteins, the nuclear transcription factor WHIRLY1 stands out as being the only protein for which an export from plastids and translocation to the nucleus has been experimentally demonstrated. Other proteins, however, strongly support the notion that this pathway might be more common than currently believed. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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354 KiB  
Review
Molecular Tools for Exploring Polyploid Genomes in Plants
by Riccardo Aversano, Maria Raffaella Ercolano, Immacolata Caruso, Carlo Fasano, Daniele Rosellini and Domenico Carputo
Int. J. Mol. Sci. 2012, 13(8), 10316-10335; https://doi.org/10.3390/ijms130810316 - 17 Aug 2012
Cited by 40 | Viewed by 12258
Abstract
Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid [...] Read more.
Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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630 KiB  
Review
Molecular Mechanisms of Epigenetic Variation in Plants
by Ryo Fujimoto, Taku Sasaki, Ryo Ishikawa, Kenji Osabe, Takahiro Kawanabe and Elizabeth S. Dennis
Int. J. Mol. Sci. 2012, 13(8), 9900-9922; https://doi.org/10.3390/ijms13089900 - 08 Aug 2012
Cited by 50 | Viewed by 9721
Abstract
Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve [...] Read more.
Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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498 KiB  
Review
Multiple Mechanisms and Challenges for the Application of Allopolyploidy in Plants
by Kenji Osabe, Takahiro Kawanabe, Taku Sasaki, Ryo Ishikawa, Keiichi Okazaki, Elizabeth S. Dennis, Tomohiko Kazama and Ryo Fujimoto
Int. J. Mol. Sci. 2012, 13(7), 8696-8721; https://doi.org/10.3390/ijms13078696 - 13 Jul 2012
Cited by 22 | Viewed by 9945
Abstract
An allopolyploid is an individual having two or more complete sets of chromosomes derived from different species. Generation of allopolyploids might be rare because of the need to overcome limitations such as co-existing populations of parental lines, overcoming hybrid incompatibility, gametic non-reduction, and [...] Read more.
An allopolyploid is an individual having two or more complete sets of chromosomes derived from different species. Generation of allopolyploids might be rare because of the need to overcome limitations such as co-existing populations of parental lines, overcoming hybrid incompatibility, gametic non-reduction, and the requirement for chromosome doubling. However, allopolyploids are widely observed among plant species, so allopolyploids have succeeded in overcoming these limitations and may have a selective advantage. As techniques for making allopolyploids are developed, we can compare transcription, genome organization, and epigenetic modifications between synthesized allopolyploids and their direct parental lines or between several generations of allopolyploids. It has been suggested that divergence of transcription caused either genetically or epigenetically, which can contribute to plant phenotype, is important for the adaptation of allopolyploids. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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173 KiB  
Review
Recent Molecular Advances on Downstream Plant Responses to Abiotic Stress
by Sávio Pinho Dos Reis, Aline Medeiros Lima and Cláudia Regina Batista De Souza
Int. J. Mol. Sci. 2012, 13(7), 8628-8647; https://doi.org/10.3390/ijms13078628 - 11 Jul 2012
Cited by 141 | Viewed by 9927
Abstract
Abiotic stresses such as extremes of temperature and pH, high salinity and drought, comprise some of the major factors causing extensive losses to crop production worldwide. Understanding how plants respond and adapt at cellular and molecular levels to continuous environmental changes is a [...] Read more.
Abiotic stresses such as extremes of temperature and pH, high salinity and drought, comprise some of the major factors causing extensive losses to crop production worldwide. Understanding how plants respond and adapt at cellular and molecular levels to continuous environmental changes is a pre-requisite for the generation of resistant or tolerant plants to abiotic stresses. In this review we aimed to present the recent advances on mechanisms of downstream plant responses to abiotic stresses and the use of stress-related genes in the development of genetically engineered crops. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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901 KiB  
Review
Glutamine Synthetase in Legumes: Recent Advances in Enzyme Structure and Functional Genomics
by Marco Betti, Margarita García-Calderón, Carmen M. Pérez-Delgado, Alfredo Credali, Guillermo Estivill, Francisco Galván, José M. Vega and Antonio J. Márquez
Int. J. Mol. Sci. 2012, 13(7), 7994-8024; https://doi.org/10.3390/ijms13077994 - 28 Jun 2012
Cited by 46 | Viewed by 10227
Abstract
Glutamine synthetase (GS) is the key enzyme involved in the assimilation of ammonia derived either from nitrate reduction, N2 fixation, photorespiration or asparagine breakdown. A small gene family is encoding for different cytosolic (GS1) or plastidic (GS2) isoforms in legumes. We summarize [...] Read more.
Glutamine synthetase (GS) is the key enzyme involved in the assimilation of ammonia derived either from nitrate reduction, N2 fixation, photorespiration or asparagine breakdown. A small gene family is encoding for different cytosolic (GS1) or plastidic (GS2) isoforms in legumes. We summarize here the recent advances carried out concerning the quaternary structure of GS, as well as the functional relationship existing between GS2 and processes such as nodulation, photorespiration and water stress, in this latter case by means of proline production. Functional genomic analysis using GS2-minus mutant reveals the key role of GS2 in the metabolic control of the plants and, more particularly, in carbon metabolism. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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189 KiB  
Review
Mitogen-Activated Protein (MAP) Kinases in Plant Metal Stress: Regulation and Responses in Comparison to Other Biotic and Abiotic Stresses
by Kelly Opdenakker, Tony Remans, Jaco Vangronsveld and Ann Cuypers
Int. J. Mol. Sci. 2012, 13(6), 7828-7853; https://doi.org/10.3390/ijms13067828 - 21 Jun 2012
Cited by 107 | Viewed by 10603
Abstract
Exposure of plants to toxic concentrations of metals leads to disruption of the cellular redox status followed by an accumulation of reactive oxygen species (ROS). ROS, like hydrogen peroxide, can act as signaling molecules in the cell and induce signaling via mitogen-activated protein [...] Read more.
Exposure of plants to toxic concentrations of metals leads to disruption of the cellular redox status followed by an accumulation of reactive oxygen species (ROS). ROS, like hydrogen peroxide, can act as signaling molecules in the cell and induce signaling via mitogen-activated protein kinase (MAPK) cascades. MAPK cascades are evolutionary conserved signal transduction modules, able to convert extracellular signals to appropriate cellular responses. In this review, our current understanding about MAPK signaling in plant metal stress is discussed. However, this knowledge is scarce compared to research into the role of MAPK signaling in the case of other abiotic and biotic stresses. ROS production is a common response induced by different stresses and undiscovered analogies may exist with metal stress. Therefore, further attention is given to MAPK signaling in other biotic and abiotic stresses and its interplay with other signaling pathways to create a framework in which the involvement of MAPK signaling in metal stress may be studied. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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106 KiB  
Review
Recent Advances of Flowering Locus T Gene in Higher Plants
by Feng Xu, Xiaofeng Rong, Xiaohua Huang and Shuiyuan Cheng
Int. J. Mol. Sci. 2012, 13(3), 3773-3781; https://doi.org/10.3390/ijms13033773 - 21 Mar 2012
Cited by 26 | Viewed by 8800
Abstract
Flowering Locus T (FT) can promote flowering in the plant photoperiod pathway and also facilitates vernalization flowering pathways and other ways to promote flowering. The expression of products of the FT gene is recognized as important parts of the flowering hormone [...] Read more.
Flowering Locus T (FT) can promote flowering in the plant photoperiod pathway and also facilitates vernalization flowering pathways and other ways to promote flowering. The expression of products of the FT gene is recognized as important parts of the flowering hormone and can induce flowering by long-distance transportation. In the present study, many FT-like genes were isolated, and the transgenic results show that FT gene can promote flowering in plants. This paper reviews the progress of the FT gene and its expression products to provide meaningful information for further studies of the functions of FT genes. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
337 KiB  
Review
Recombinant Cytokines from Plants
by Agnieszka Sirko, Tomas Vaněk, Anna Góra-Sochacka and Patrycja Redkiewicz
Int. J. Mol. Sci. 2011, 12(6), 3536-3552; https://doi.org/10.3390/ijms12063536 - 03 Jun 2011
Cited by 31 | Viewed by 10009
Abstract
Plant-based platforms have been successfully applied for the last two decades for the efficient production of pharmaceutical proteins. The number of commercialized products biomanufactured in plants is, however, rather discouraging. Cytokines are small glycosylated polypeptides used in the treatment of cancer, immune disorders [...] Read more.
Plant-based platforms have been successfully applied for the last two decades for the efficient production of pharmaceutical proteins. The number of commercialized products biomanufactured in plants is, however, rather discouraging. Cytokines are small glycosylated polypeptides used in the treatment of cancer, immune disorders and various other related diseases. Because the clinical use of cytokines is limited by high production costs they are good candidates for plant-made pharmaceuticals. Several research groups explored the possibilities of cost-effective production of animal cytokines in plant systems. This review summarizes recent advances in this field. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming)
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204 KiB  
Review
Evolution of Plant-Made Pharmaceuticals
by David R. Thomas, Claire A. Penney, Amrita Majumder and Amanda M. Walmsley
Int. J. Mol. Sci. 2011, 12(5), 3220-3236; https://doi.org/10.3390/ijms12053220 - 17 May 2011
Cited by 42 | Viewed by 12724
Abstract
The science and policy of pharmaceuticals produced and/or delivered by plants has evolved over the past twenty-one years from a backyard remedy to regulated, purified products. After seemingly frozen at Phase I human clinical trials with six orally delivered plant-made vaccines not progressing [...] Read more.
The science and policy of pharmaceuticals produced and/or delivered by plants has evolved over the past twenty-one years from a backyard remedy to regulated, purified products. After seemingly frozen at Phase I human clinical trials with six orally delivered plant-made vaccines not progressing past this stage over seven years, plant-made pharmaceuticals have made a breakthrough with several purified plant-based products advancing to Phase II trials and beyond. Though fraught with the usual difficulties of pharmaceutical development, pharmaceuticals made by plants have achieved pertinent milestones albeit slowly compared to other pharmaceutical production systems and are now at the cusp of reaching the consumer. Though the current economic climate begs for cautious investment as opposed to trail blazing, it is perhaps a good time to look to the future of plant-made pharmaceutical technology to assist in planning for future developments in order not to slow this technology’s momentum. To encourage continued progress, we highlight the advances made so far by this technology, particularly the change in paradigms, comparing developmental timelines, and summarizing the current status and future possibilities of plant-made pharmaceuticals. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming)
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1 pages, 149 KiB  
Correction
Correction: Yu, H.; et al. Molecular Mechanisms of Floral Boundary Formation in Arabidopsis. Int. J. Mol. Sci. 2016, 17, 317
by Hongyang Yu and Tengbo Huang
Int. J. Mol. Sci. 2018, 19(7), 1845; https://doi.org/10.3390/ijms19071845 - 22 Jun 2018
Cited by 2 | Viewed by 2285
Abstract
The authors wish to make the following correction to their paper [1].[...] Full article
(This article belongs to the Special Issue Plant Molecular Biology)
984 KiB  
Letter
Global Profiling of Various Metabolites in Platycodon grandiflorum by UPLC-QTOF/MS
by Jae Won Lee, Seung-Heon Ji, Geum-Soog Kim, Kyung-Sik Song, Yurry Um, Ok Tae Kim, Yi Lee, Chang Pyo Hong, Dong-Ho Shin, Chang-Kug Kim, Seung-Eun Lee, Young-Sup Ahn and Dae-Young Lee
Int. J. Mol. Sci. 2015, 16(11), 26786-26796; https://doi.org/10.3390/ijms161125993 - 09 Nov 2015
Cited by 31 | Viewed by 7485
Abstract
In this study, a method of metabolite profiling based on UPLC-QTOF/MS was developed to analyze Platycodon grandiflorum. In the optimal UPLC, various metabolites, including major platycosides, were separated well in 15 min. The metabolite extraction protocols were also optimized by selecting a [...] Read more.
In this study, a method of metabolite profiling based on UPLC-QTOF/MS was developed to analyze Platycodon grandiflorum. In the optimal UPLC, various metabolites, including major platycosides, were separated well in 15 min. The metabolite extraction protocols were also optimized by selecting a solvent for use in the study, the ratio of solvent to sample and sonication time. This method was used to profile two different parts of P. grandiflorum, i.e., the roots of P. grandiflorum (PR) and the stems and leaves of P. grandiflorum (PS), in the positive and negative ion modes. As a result, PR and PS showed qualitatively and quantitatively different metabolite profiles. Furthermore, their metabolite compositions differed according to individual plant samples. These results indicate that the UPLC-QTOF/MS-based profiling method is a good tool to analyze various metabolites in P. grandiflorum. This metabolomics approach can also be applied to evaluate the overall quality of P. grandiflorum, as well as to discriminate the cultivars for the medicinal plant industry. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences)
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