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Special Issue "Plant Proteomic Research 2.0"

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

Deadline for manuscript submissions: closed (18 December 2018).

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Guest Editor
Prof. Dr. Setsuko Komatsu

Department of Environmental and Food Sciences, Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui, Fukui Prefecture 910-0028, Japan
Website | E-Mail
Phone: 81-766-29-2466
Interests: gel-free/label-free proteomics; plant physiology; crop, abiotic stress

Special Issue Information

Dear Colleagues,

This Special Issue is the continuation of our 2016 Special Issue, "Plant Proteomic Research" (https://www.mdpi.com/journal/ijms/special_issues/plant-proteomic).

Advancement in high-throughput “Omics” techniques has revolutionized plant molecular biology research. Proteomics offer one of the best options for the functional analysis of translated regions of the genome and generate much detail information about the intrinsic mechanism of plant stress response. Various proteomic approaches that are being exploited extensively for elucidating master regulator proteins, which play key roles in stress perception and signaling, largely involve gel-based and gel-free techniques including both label-based and label-free protein quantification. Nevertheless, the ultimate success of any proteomic strategy lies in the various factors including isolation of full component of proteins, separation, visualization and their accurate identification. Despite recent advancements, more emphasis needs to be given to the protein extraction protocols, especially for very low-abundant, as well as proteins with exceedingly large molecular weight. Thus, amalgamation of diverse MS techniques, complemented with genome-sequence data and modern bioinformatics analysis with improved sample preparation and fractionation strategies, offer a powerful tool to identify and characterize novel proteins and to follow temporal changes in protein relative abundances under adverse environmental conditions. Furthermore, post-translational modifications and protein-protein interactions provide deeper insight into protein molecular function. Authors are welcome to submit original research articles and reviews addressing recent advancements, as well as limitations of current proteomic techniques and their diverse applications to get new insights of plant molecular responses to various biotic and abiotic stressors. In addition, bioinformatic techniques are needed for proteomic analysis of plants without genome information. We will also welcome articles about proteomic research, such as meditational plants and so on, which have no genomic information.

Prof. Dr. Setsuko Komatsu
Guest Editor

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Keywords

  • plant proteomic research
  • methods, techniques and protocols of plant proteomics
  • applications of plant proteomics

Published Papers (30 papers)

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Editorial

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Open AccessEditorial
Plant Proteomic Research 2.0: Trends and Perspectives
Int. J. Mol. Sci. 2019, 20(10), 2495; https://doi.org/10.3390/ijms20102495
Received: 20 May 2019 / Accepted: 20 May 2019 / Published: 21 May 2019
Cited by 1 | PDF Full-text (189 KB) | HTML Full-text | XML Full-text
Abstract
Plants being sessile in nature are constantly exposed to environmental challenges resulting in substantial yield loss [...] Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available

Research

Jump to: Editorial, Review

Open AccessArticle
Proteomics Reveal the Profiles of Color Change in Brunfelsia acuminata Flowers
Int. J. Mol. Sci. 2019, 20(8), 2000; https://doi.org/10.3390/ijms20082000
Received: 7 March 2019 / Revised: 12 April 2019 / Accepted: 21 April 2019 / Published: 23 April 2019
Cited by 1 | PDF Full-text (4544 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Brunfelsia acuminata is a popular ornamental plant with different colors resulted from the rapid change of color after blooming. The petals at day one (purple), day three (white and purple) and day five (white) were used to analyze the reason of flower color [...] Read more.
Brunfelsia acuminata is a popular ornamental plant with different colors resulted from the rapid change of color after blooming. The petals at day one (purple), day three (white and purple) and day five (white) were used to analyze the reason of flower color change by a comparative proteomics approach, gas chromatography coupled to a time-of-flight mass analyzer (GC-TOF-MS) and quantitative real-time PCR (qRT-PCR). The results showed that the 52 identified proteins were classified into eight functional groups, 6% of which were related to the anthocyanin metabolic pathway. The expression levels of all anthocyanin proteins from the first day to fifth day were remarkably down-regulated, which was consistent with the changing patterns of the key genes (CHS, CHI and F3′5′H) in petals. Simultaneously, the main floral volatile components including Linalool and 2-Hexenal (E) were identified, and the contents of 2-Hexenal at day five increased dramatically. Moreover, the content of flavonoids and total phenolic increased at day five. The majority of the proteins associated with stress defense and senescence proteins were up-regulated and the activities of peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) in the petals at day five were significantly higher than others. It was concluded that the competition in the precursors of metabolic pathways occurs and causes the flow of metabolite to the pathways of floral scent and lignin derived from the shikimate pathway or degrade into others. Therefore, the anthocyanin content significantly decreased, and the petal color changed from deep purple to white. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
The Major Storage Protein in Potato Tuber Is Mobilized by a Mechanism Dependent on Its Phosphorylation Status
Int. J. Mol. Sci. 2019, 20(8), 1889; https://doi.org/10.3390/ijms20081889
Received: 21 February 2019 / Revised: 5 April 2019 / Accepted: 13 April 2019 / Published: 17 April 2019
Cited by 1 | PDF Full-text (1546 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The role of the protein phosphorylation mechanism in the mobilization of vegetative storage proteins (VSPs) is totally unknown. Patatin is the major VSP of the potato (Solanum tuberosum L.) tuber that encompasses multiple differentially phosphorylated isoforms. In this study, temporal changes in [...] Read more.
The role of the protein phosphorylation mechanism in the mobilization of vegetative storage proteins (VSPs) is totally unknown. Patatin is the major VSP of the potato (Solanum tuberosum L.) tuber that encompasses multiple differentially phosphorylated isoforms. In this study, temporal changes in the phosphorylation status of patatin isoforms and their involvement in patatin mobilization are investigated using phosphoproteomic methods based on targeted two-dimensional electrophoresis (2-DE). High-resolution 2-DE profiles of patatin isoforms were obtained in four sequential tuber life cycle stages of Kennebec cultivar: endodormancy, bud break, sprouting and plant growth. In-gel multiplex identification of phosphorylated isoforms with Pro-Q Diamond phosphoprotein-specific stain revealed an increase in the number of phosphorylated isoforms after the tuber endodormancy stage. In addition, we found that the phosphorylation status of patatin isoforms significantly changed throughout the tuber life cycle (P < 0.05) using the chemical method of protein dephosphorylation with hydrogen fluoride-pyridine (HF-P) coupled to 2-DE. More specifically, patatin phosphorylation increased by 32% from endodormancy to the tuber sprouting stage and subsequently decreased together with patatin degradation. Patatin isoforms were not randomly mobilized because highly phosphorylated Kuras-isoforms were preferably degraded in comparison to less phosphorylated non-Kuras isoforms. These results lead us to conclude that patatin is mobilized by a mechanism dependent on the phosphorylation status of specific isoforms. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Molecular Responses of Maize Shoot to a Plant Derived Smoke Solution
Int. J. Mol. Sci. 2019, 20(6), 1319; https://doi.org/10.3390/ijms20061319
Received: 16 December 2018 / Revised: 14 February 2019 / Accepted: 5 March 2019 / Published: 15 March 2019
Cited by 1 | PDF Full-text (2238 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Plant-derived smoke has effects on plant growth. To find the molecular mechanism of plant-derived smoke on maize, a gel-free/label-free proteomic technique was used. The length of root and shoot were increased in maize by plant-derived smoke. Proteomic analysis revealed that 2000 ppm plant-derived [...] Read more.
Plant-derived smoke has effects on plant growth. To find the molecular mechanism of plant-derived smoke on maize, a gel-free/label-free proteomic technique was used. The length of root and shoot were increased in maize by plant-derived smoke. Proteomic analysis revealed that 2000 ppm plant-derived smoke changed the abundance of 69 proteins in 4-days old maize shoot. Proteins in cytoplasm, chloroplast, and cell membrane were altered by plant-derived smoke. Catalytic, signaling, and nucleotide binding proteins were changed. Proteins related to sucrose synthase, nucleotides, signaling, and glutathione were significantly increased; however, cell wall, lipids, photosynthetic, and amino acid degradations related proteins were decreased. Based on proteomic and immunoblot analyses, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) was decreased; however, RuBisCO activase was not changed by plant-derived smoke in maize shoot. Ascorbate peroxidase was not affected; however, peroxiredoxin was decreased by plant-derived smoke. Furthermore, the results from enzyme-activity and mRNA-expression analyses confirmed regulation of ascorbate peroxidase and the peroxiredoxinin reactive oxygen scavenging system. These results suggest that increases in sucrose synthase, nucleotides, signaling, and glutathione related proteins combined with regulation of reactive oxygen species and their scavenging system in response to plant-derived smoke may improve maize growth. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Identification of Candidate Ergosterol-Responsive Proteins Associated with the Plasma Membrane of Arabidopsis thaliana
Int. J. Mol. Sci. 2019, 20(6), 1302; https://doi.org/10.3390/ijms20061302
Received: 27 January 2019 / Revised: 23 February 2019 / Accepted: 3 March 2019 / Published: 14 March 2019
Cited by 1 | PDF Full-text (2567 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The impact of fungal diseases on crop production negatively reflects on sustainable food production and overall economic health. Ergosterol is the major sterol component in fungal membranes and regarded as a general elicitor or microbe-associated molecular pattern (MAMP) molecule. Although plant responses to [...] Read more.
The impact of fungal diseases on crop production negatively reflects on sustainable food production and overall economic health. Ergosterol is the major sterol component in fungal membranes and regarded as a general elicitor or microbe-associated molecular pattern (MAMP) molecule. Although plant responses to ergosterol have been reported, the perception mechanism is still unknown. Here, Arabidopsis thaliana protein fractions were used to identify those differentially regulated following ergosterol treatment; additionally, they were subjected to affinity-based chromatography enrichment strategies to capture and categorize ergosterol-interacting candidate proteins using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Mature plants were treated with 250 nM ergosterol over a 24 h period, and plasma membrane-associated fractions were isolated. In addition, ergosterol was immobilized on two different affinity-based systems to capture interacting proteins/complexes. This resulted in the identification of defense-related proteins such as chitin elicitor receptor kinase (CERK), non-race specific disease resistance/harpin-induced (NDR1/HIN1)-like protein, Ras-related proteins, aquaporins, remorin protein, leucine-rich repeat (LRR)- receptor like kinases (RLKs), G-type lectin S-receptor-like serine/threonine-protein kinase (GsSRK), and glycosylphosphatidylinositol (GPI)-anchored protein. Furthermore, the results elucidated unknown signaling responses to this MAMP, including endocytosis, and other similarities to those previously reported for bacterial flagellin, lipopolysaccharides, and fungal chitin. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Proteomics Analysis to Identify Proteins and Pathways Associated with the Novel Lesion Mimic Mutant E40 in Rice Using iTRAQ-Based Strategy
Int. J. Mol. Sci. 2019, 20(6), 1294; https://doi.org/10.3390/ijms20061294
Received: 25 February 2019 / Revised: 9 March 2019 / Accepted: 11 March 2019 / Published: 14 March 2019
Cited by 1 | PDF Full-text (1892 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A novel rice lesion mimic mutant (LMM) was isolated from the mutant population of Japonica rice cultivar Hitomebore generated by ethyl methane sulfonate (EMS) treatment. Compared with the wild-type (WT), the mutant, tentatively designated E40, developed necrotic lesions over the whole growth period [...] Read more.
A novel rice lesion mimic mutant (LMM) was isolated from the mutant population of Japonica rice cultivar Hitomebore generated by ethyl methane sulfonate (EMS) treatment. Compared with the wild-type (WT), the mutant, tentatively designated E40, developed necrotic lesions over the whole growth period along with detectable changes in several important agronomic traits including lower height, fewer tillers, lower yield, and premature death. To understand the molecular mechanism of mutation-induced phenotypic differences in E40, a proteomics-based approach was used to identify differentially accumulated proteins between E40 and WT. Proteomic data from isobaric tags for relative and absolute quantitation (iTRAQ) showed that 233 proteins were significantly up- or down-regulated in E40 compared with WT. These proteins are involved in diverse biological processes, but phenylpropanoid biosynthesis was the only up-regulated pathway. Differential expression of the genes encoding some candidate proteins with significant up- or down-regulation in E40 were further verified by qPCR. Consistent with the proteomic results, substance and energy flow in E40 shifted from basic metabolism to secondary metabolism, mainly phenylpropanoid biosynthesis, which is likely involved in the formation of leaf spots. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Comparative Transcriptome Analysis Reveals the Transcriptional Alterations in Growth- and Development-Related Genes in Sweet Potato Plants Infected and Non-Infected by SPFMV, SPV2, and SPVG
Int. J. Mol. Sci. 2019, 20(5), 1012; https://doi.org/10.3390/ijms20051012
Received: 28 December 2018 / Revised: 31 January 2019 / Accepted: 10 February 2019 / Published: 26 February 2019
Cited by 1 | PDF Full-text (5012 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Field co-infection of multiple viruses results in considerable losses in the yield and quality of storage roots in sweet potato. However, little is known about the molecular mechanisms underlying developmental disorders of sweet potato subjected to co-infection by multiple viruses. Here, a comparative [...] Read more.
Field co-infection of multiple viruses results in considerable losses in the yield and quality of storage roots in sweet potato. However, little is known about the molecular mechanisms underlying developmental disorders of sweet potato subjected to co-infection by multiple viruses. Here, a comparative transcriptomic analysis was performed to reveal the transcriptional alterations in sweet potato plants infected (VCSP) and non-infected (VFSP) by Sweet potato mild mottle virus (SPFMV), Sweet potato virus Y (SPV2) and Sweet potato virus G (SPVG). A total of 1580 and 12,566 differentially expressed genes (DEGs) were identified in leaves and storage roots of VFSP and VCSP plants, respectively. In leaves, 707 upregulated and 773 downregulated genes were identified, whereas 5653 upregulated and 6913 downregulated genes were identified in storage roots. Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in chloroplast and photosynthesis and brassinosteroid (BR) biosynthesis in leaves and the vitamin biosynthetic process in storage roots was inhibited by co-infection of three viruses: SPFMV, SPV2, and SPVG. This was likely closely related to better photosynthesis and higher contents of Vitamin C (Vc) in storage roots of VFSP than that of VCSP. While some genes involved in ribosome and secondary metabolite-related pathways in leaves and alanine, aspartate, and glutamate metabolism in storage roots displayed higher expression in VCSP than in VFSP. Quantitative real-time PCR analysis demonstrated that the expression patterns of 26 DEGs, including 16 upregulated genes and 10 downregulated genes were consistent with the RNA-seq data from VFSP and VCSP. Taken together, this study integrates the results of morphology, physiology, and comparative transcriptome analyses in leaves and storage roots of VCSP and VFSP to reveal transcriptional alterations in growth- and development-related genes, providing new insight into the molecular mechanisms underlying developmental disorders of sweet potato subjected to co-infection by multiple viruses. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Application of Data-Independent Acquisition Approach to Study the Proteome Change from Early to Later Phases of Tomato Pathogenesis Responses
Int. J. Mol. Sci. 2019, 20(4), 863; https://doi.org/10.3390/ijms20040863
Received: 27 December 2018 / Revised: 11 February 2019 / Accepted: 12 February 2019 / Published: 17 February 2019
Cited by 1 | PDF Full-text (1505 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Plants and pathogens are entangled in a continual arms race. Plants have evolved dynamic defence and immune mechanisms to resist infection and enhance immunity for second wave attacks from the same or different types of pathogenic species. In addition to evolutionarily and physiological [...] Read more.
Plants and pathogens are entangled in a continual arms race. Plants have evolved dynamic defence and immune mechanisms to resist infection and enhance immunity for second wave attacks from the same or different types of pathogenic species. In addition to evolutionarily and physiological changes, plant-pathogen interaction is also highly dynamic at the molecular level. Recently, an emerging quantitative mass spectrometry-based proteomics approach named data-independent acquisition (DIA), has been developed for the analysis of the proteome in a high-throughput fashion. In this study, the DIA approach was applied to quantitatively trace the change in the plant proteome from the early to the later stage of pathogenesis progression. This study revealed that at the early stage of the pathogenesis response, proteins directly related to the chaperon were regulated for the defence proteins. At the later stage, not only the defence proteins but also a set of the pathogen-associated molecular pattern-triggered immunity (PTI) and effector triggered immunity (ETI)-related proteins were highly induced. Our findings show the dynamics of the plant regulation of pathogenesis at the protein level and demonstrate the potential of using the DIA approach for tracing the dynamics of the plant proteome during pathogenesis responses. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Proteomic Analysis of the Effect of Inorganic and Organic Chemicals on Silver Nanoparticles in Wheat
Int. J. Mol. Sci. 2019, 20(4), 825; https://doi.org/10.3390/ijms20040825
Received: 16 December 2018 / Revised: 4 February 2019 / Accepted: 7 February 2019 / Published: 14 February 2019
Cited by 2 | PDF Full-text (2256 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Production and utilization of nanoparticles (NPs) are increasing due to their positive and stimulating effects on biological systems. Silver (Ag) NPs improve seed germination, photosynthetic efficiency, plant growth, and antimicrobial activities. In this study, the effects of chemo-blended Ag NPs on wheat were [...] Read more.
Production and utilization of nanoparticles (NPs) are increasing due to their positive and stimulating effects on biological systems. Silver (Ag) NPs improve seed germination, photosynthetic efficiency, plant growth, and antimicrobial activities. In this study, the effects of chemo-blended Ag NPs on wheat were investigated using the gel-free/label-free proteomic technique. Morphological analysis revealed that chemo-blended Ag NPs resulted in the increase of shoot length, shoot fresh weight, root length, and root fresh weight. Proteomic analysis indicated that proteins related to photosynthesis and protein synthesis were increased, while glycolysis, signaling, and cell wall related proteins were decreased. Proteins related to redox and mitochondrial electron transport chain were also decreased. Glycolysis associated proteins such as glyceraldehyde-3-phosphate dehydrogenase increased as well as decreased, while phosphoenol pyruvate carboxylase was decreased. Antioxidant enzyme activities such as superoxide dismutase, catalase, and peroxidase were promoted in response to the chemo-blended Ag NPs. These results suggested that chemo-blended Ag NPs promoted plant growth and development through regulation of energy metabolism by suppression of glycolysis. Number of grains/spike, 100-grains weight, and yield of wheat were stimulated with chemo-blended Ag NPs. Morphological study of next generational wheat plants depicted normal growth, and no toxic effects were observed. Therefore, morphological, proteomic, yield, and next generation results revealed that chemo-blended Ag NPs may promote plant growth and development through alteration in plant metabolism. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
New Insights on Arabidopsis thaliana Root Adaption to Ammonium Nutrition by the Use of a Quantitative Proteomic Approach
Int. J. Mol. Sci. 2019, 20(4), 814; https://doi.org/10.3390/ijms20040814
Received: 22 January 2019 / Revised: 31 January 2019 / Accepted: 5 February 2019 / Published: 14 February 2019
Cited by 2 | PDF Full-text (1384 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Nitrogen is an essential element for plant nutrition. Nitrate and ammonium are the two major inorganic nitrogen forms available for plant growth. Plant preference for one or the other form depends on the interplay between plant genetic background and environmental variables. Ammonium-based fertilization [...] Read more.
Nitrogen is an essential element for plant nutrition. Nitrate and ammonium are the two major inorganic nitrogen forms available for plant growth. Plant preference for one or the other form depends on the interplay between plant genetic background and environmental variables. Ammonium-based fertilization has been shown less environmentally harmful compared to nitrate fertilization, because of reducing, among others, nitrate leaching and nitrous oxide emissions. However, ammonium nutrition may become a stressful situation for a wide range of plant species when the ion is present at high concentrations. Although studied for long time, there is still an important lack of knowledge to explain plant tolerance or sensitivity towards ammonium nutrition. In this context, we performed a comparative proteomic study in roots of Arabidopsis thaliana plants grown under exclusive ammonium or nitrate supply. We identified and quantified 68 proteins with differential abundance between both conditions. These proteins revealed new potential important players on root response to ammonium nutrition, such as H+-consuming metabolic pathways to regulate pH homeostasis and specific secondary metabolic pathways like brassinosteroid and glucosinolate biosynthetic pathways. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Proteomic Analysis of the Resistance Mechanisms in Sugarcane during Sporisorium scitamineum Infection
Int. J. Mol. Sci. 2019, 20(3), 569; https://doi.org/10.3390/ijms20030569
Received: 11 December 2018 / Revised: 26 January 2019 / Accepted: 27 January 2019 / Published: 29 January 2019
Cited by 1 | PDF Full-text (3266 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Smut disease is caused by Sporisorium scitamineum, an important sugarcane fungal pathogen causing an extensive loss in yield and sugar quality. The available literature suggests that there are two types of smut resistance mechanisms: external resistance by physical or chemical barriers and [...] Read more.
Smut disease is caused by Sporisorium scitamineum, an important sugarcane fungal pathogen causing an extensive loss in yield and sugar quality. The available literature suggests that there are two types of smut resistance mechanisms: external resistance by physical or chemical barriers and intrinsic internal resistance mechanisms operating at host–pathogen interaction at cellular and molecular levels. The nature of smut resistance mechanisms, however, remains largely unknown. The present study investigated the changes in proteome occurring in two sugarcane varieties with contrasting susceptibility to smut—F134 and NCo310—at whip development stage after S. scitamineum infection. Total proteins from pathogen inoculated and uninoculated (control) leaves were separated by two-dimensional gel electrophoresis (2D-PAGE). Protein identification was performed using BLASTp and tBLASTn against NCBI nonredundant protein databases and EST databases, respectively. A total of thirty proteins spots representing differentially expressed proteins (DEPs), 16 from F134 and 14 from NCo310, were identified and analyzed by MALDI-TOF/TOF MS. In F134, 4 DEPs were upregulated and nine were downregulated, while, nine were upregulated and three were downregulated in NCo310. The DEPs were associated with DNA binding, metabolic processes, defense, stress response, photorespiration, protein refolding, chloroplast, nucleus and plasma membrane. Finally, the expression of CAT, SOD, and PAL with recognized roles in S. scitamineum infection in both sugarcane verities were analyzed by real-time quantitative PCR (RT-qPCR) technique. Identification of genes critical for smut resistance in sugarcane will increase our knowledge of S. scitamineum-sugarcane interaction and help to develop molecular and conventional breeding strategies for variety improvement. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Comparative Phosphoproteomic Analysis of Barley Embryos with Different Dormancy during Imbibition
Int. J. Mol. Sci. 2019, 20(2), 451; https://doi.org/10.3390/ijms20020451
Received: 17 December 2018 / Revised: 16 January 2019 / Accepted: 17 January 2019 / Published: 21 January 2019
Cited by 1 | PDF Full-text (1282 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Dormancy is the mechanism that allows seeds to become temporally quiescent in order to select the right time and place to germinate. Like in other species, in barley, grain dormancy is gradually reduced during after-ripening. Phosphosignaling networks in barley grains were investigated by [...] Read more.
Dormancy is the mechanism that allows seeds to become temporally quiescent in order to select the right time and place to germinate. Like in other species, in barley, grain dormancy is gradually reduced during after-ripening. Phosphosignaling networks in barley grains were investigated by a large-scale analysis of phosphoproteins to examine potential changes in response pathways to after-ripening. We used freshly harvested (FH) and after-ripened (AR) barley grains which showed different dormancy levels. The LC-MS/MS analysis identified 2346 phosphopeptides in barley embryos, with 269 and 97 of them being up- or downregulated during imbibition, respectively. A number of phosphopeptides were differentially regulated between FH and AR samples, suggesting that phosphoproteomic profiles were quite different between FH and AR grains. Motif analysis suggested multiple protein kinases including SnRK2 and MAPK could be involved in such a difference between FH and AR samples. Taken together, our results revealed phosphosignaling pathways in barley grains during the water imbibition process. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Organ-Specific Analysis of Morus alba Using a Gel-Free/Label-Free Proteomic Technique
Int. J. Mol. Sci. 2019, 20(2), 365; https://doi.org/10.3390/ijms20020365
Received: 15 December 2018 / Revised: 14 January 2019 / Accepted: 15 January 2019 / Published: 16 January 2019
Cited by 1 | PDF Full-text (5467 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Morus alba is an important medicinal plant that is used to treat human diseases. The leaf, branch, and root of Morus can be applied as antidiabetic, antioxidant, and anti-inflammatory medicines, respectively. To explore the molecular mechanisms underlying the various pharmacological functions within different [...] Read more.
Morus alba is an important medicinal plant that is used to treat human diseases. The leaf, branch, and root of Morus can be applied as antidiabetic, antioxidant, and anti-inflammatory medicines, respectively. To explore the molecular mechanisms underlying the various pharmacological functions within different parts of Morus, organ-specific proteomics were performed. Protein profiles of the Morus leaf, branch, and root were determined using a gel-free/label-free proteomic technique. In the Morus leaf, branch, and root, a total of 492, 414, and 355 proteins were identified, respectively, including 84 common proteins. In leaf, the main function was related to protein degradation, photosynthesis, and redox ascorbate/glutathione metabolism. In branch, the main function was related to protein synthesis/degradation, stress, and redox ascorbate/glutathione metabolism. In root, the main function was related to protein synthesis/degradation, stress, and cell wall. Additionally, organ-specific metabolites and antioxidant activities were analyzed. These results revealed that flavonoids were highly accumulated in Morus root compared with the branch and leaf. Accordingly, two root-specific proteins named chalcone flavanone isomerase and flavonoid 3,5-hydroxylase were accumulated in the flavonoid pathway. Consistent with this finding, the content of the total flavonoids was higher in root compared to those detected in branch and leaf. These results suggest that the flavonoids in Morus root might be responsible for its biological activity and the root is the main part for flavonoid biosynthesis in Morus. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Quantitative Proteomic Analysis of Castor (Ricinus communis L.) Seeds During Early Imbibition Provided Novel Insights into Cold Stress Response
Int. J. Mol. Sci. 2019, 20(2), 355; https://doi.org/10.3390/ijms20020355
Received: 19 December 2018 / Revised: 8 January 2019 / Accepted: 8 January 2019 / Published: 16 January 2019
Cited by 1 | PDF Full-text (2564 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Early planting is one of the strategies used to increase grain yield in temperate regions. However, poor cold tolerance in castor inhibits seed germination, resulting in lower seedling emergence and biomass. Here, the elite castor variety Tongbi 5 was used to identify the [...] Read more.
Early planting is one of the strategies used to increase grain yield in temperate regions. However, poor cold tolerance in castor inhibits seed germination, resulting in lower seedling emergence and biomass. Here, the elite castor variety Tongbi 5 was used to identify the differential abundance protein species (DAPS) between cold stress (4 °C) and control conditions (30 °C) imbibed seeds. As a result, 127 DAPS were identified according to isobaric tag for relative and absolute quantification (iTRAQ) strategy. These DAPS were mainly involved in carbohydrate and energy metabolism, translation and posttranslational modification, stress response, lipid transport and metabolism, and signal transduction. Enzyme-linked immunosorbent assays (ELISA) demonstrated that the quantitative proteomics data collected here were reliable. This study provided some invaluable insights into the cold stress responses of early imbibed castor seeds: (1) up-accumulation of all DAPS involved in translation might confer cold tolerance by promoting protein synthesis; (2) stress-related proteins probably protect the cell against damage caused by cold stress; (3) up-accumulation of key DAPS associated with fatty acid biosynthesis might facilitate resistance or adaptation of imbibed castor seeds to cold stress by the increased content of unsaturated fatty acid (UFA). The data has been deposited to the ProteomeXchange with identifier PXD010043. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Open AccessArticle
Quantitative Proteomic Analysis of the Response to Cold Stress in Jojoba, a Tropical Woody Crop
Int. J. Mol. Sci. 2019, 20(2), 243; https://doi.org/10.3390/ijms20020243
Received: 12 September 2018 / Revised: 1 January 2019 / Accepted: 3 January 2019 / Published: 9 January 2019
Cited by 2 | PDF Full-text (10459 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Jojoba (Simmondsia chinensis) is a semi-arid, oil-producing industrial crop that have been widely cultivated in tropical arid region. Low temperature is one of the major environmental stress that impair jojoba’s growth, development and yield and limit introduction of jojoba in the [...] Read more.
Jojoba (Simmondsia chinensis) is a semi-arid, oil-producing industrial crop that have been widely cultivated in tropical arid region. Low temperature is one of the major environmental stress that impair jojoba’s growth, development and yield and limit introduction of jojoba in the vast temperate arid areas. To get insight into the molecular mechanisms of the cold stress response of jojoba, a combined physiological and quantitative proteomic analysis was conducted. Under cold stress, the photosynthesis was repressed, the level of malondialdehyde (MDA), relative electrolyte leakage (REL), soluble sugars, superoxide dismutase (SOD) and phenylalanine ammonia-lyase (PAL) were increased in jojoba leaves. Of the 2821 proteins whose abundance were determined, a total of 109 differentially accumulated proteins (DAPs) were found and quantitative real time PCR (qRT-PCR) analysis of the coding genes for 7 randomly selected DAPs were performed for validation. The identified DAPs were involved in various physiological processes. Functional classification analysis revealed that photosynthesis, adjustment of cytoskeleton and cell wall, lipid metabolism and transport, reactive oxygen species (ROS) scavenging and carbohydrate metabolism were closely associated with the cold stress response. Some cold-induced proteins, such as cold-regulated 47 (COR47), staurosporin and temperature sensitive 3-like a (STT3a), phytyl ester synthase 1 (PES1) and copper/zinc superoxide dismutase 1, might play important roles in cold acclimation in jojoba seedlings. Our work provided important data to understand the plant response to the cold stress in tropical woody crops. Full article
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Open AccessArticle
Quantitative Proteomics of Potato Leaves Infected with Phytophthora infestans Provides Insights into Coordinated and Altered Protein Expression during Early and Late Disease Stages
Int. J. Mol. Sci. 2019, 20(1), 136; https://doi.org/10.3390/ijms20010136
Received: 11 November 2018 / Revised: 19 December 2018 / Accepted: 24 December 2018 / Published: 1 January 2019
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Abstract
In order to get a better understanding of protein association during Solanum tuberosum (cv. Sarpo Mira)–Phytophthora infestans incompatible interaction, we investigated the proteome dynamics of cv. Sarpo Mira, after foliar application of zoospore suspension from P. infestans isolate, at three key time-points: [...] Read more.
In order to get a better understanding of protein association during Solanum tuberosum (cv. Sarpo Mira)–Phytophthora infestans incompatible interaction, we investigated the proteome dynamics of cv. Sarpo Mira, after foliar application of zoospore suspension from P. infestans isolate, at three key time-points: zero hours post inoculation (hpi) (Control), 48 hpi (EI), and 120 hpi (LI); divided into early and late disease stages by the tandem mass tagging (TMT) method. A total of 1229 differentially-expressed proteins (DEPs) were identified in cv. Sarpo Mira in a pairwise comparison of the two disease stages, including commonly shared DEPs, specific DEPs in early and late disease stages, respectively. Over 80% of the changes in protein abundance were up-regulated in the early stages of infection, whereas more DEPs (61%) were down-regulated in the later disease stage. Expression patterns, functional category, and enrichment tests highlighted significant coordination and enrichment of cell wall-associated defense response proteins during the early stage of infection. The late stage was characterized by a cellular protein modification process, membrane protein complex formation, and cell death induction. These results, together with phenotypic observations, provide further insight into the molecular mechanism of P. infestans resistance in potatos. Full article
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Open AccessArticle
Proteome Map of Pea (Pisum sativum L.) Embryos Containing Different Amounts of Residual Chlorophylls
Int. J. Mol. Sci. 2018, 19(12), 4066; https://doi.org/10.3390/ijms19124066
Received: 7 November 2018 / Revised: 11 December 2018 / Accepted: 13 December 2018 / Published: 15 December 2018
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Abstract
Due to low culturing costs and high seed protein contents, legumes represent the main global source of food protein. Pea (Pisum sativum L.) is one of the major legume crops, impacting both animal feed and human nutrition. Therefore, the quality of pea [...] Read more.
Due to low culturing costs and high seed protein contents, legumes represent the main global source of food protein. Pea (Pisum sativum L.) is one of the major legume crops, impacting both animal feed and human nutrition. Therefore, the quality of pea seeds needs to be ensured in the context of sustainable crop production and nutritional efficiency. Apparently, changes in seed protein patterns might directly affect both of these aspects. Thus, here, we address the pea seed proteome in detail and provide, to the best of our knowledge, the most comprehensive annotation of the functions and intracellular localization of pea seed proteins. To address possible intercultivar differences, we compared seed proteomes of yellow- and green-seeded pea cultivars in a comprehensive case study. The analysis revealed totally 1938 and 1989 nonredundant proteins, respectively. Only 35 and 44 proteins, respectively, could be additionally identified after protamine sulfate precipitation (PSP), potentially indicating the high efficiency of our experimental workflow. Totally 981 protein groups were assigned to 34 functional classes, which were to a large extent differentially represented in yellow and green seeds. Closer analysis of these differences by processing of the data in KEGG and String databases revealed their possible relation to a higher metabolic status and reduced longevity of green seeds. Full article
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Open AccessArticle
iTRAQ-Based Quantitative Proteomic Analysis of Embryogenic and Non-embryogenic Calli Derived from a Maize (Zea mays L.) Inbred Line Y423
Int. J. Mol. Sci. 2018, 19(12), 4004; https://doi.org/10.3390/ijms19124004
Received: 13 November 2018 / Revised: 3 December 2018 / Accepted: 7 December 2018 / Published: 12 December 2018
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Abstract
Somatic embryos (SE) have potential to rapidly form a whole plant. Generally, SE is thought to be derived from embryogenic calli (EC). However, in maize, not only embryogenic calli (EC, can generate SE) but also nonembryogenic calli (NEC, can’t generate SE) can be [...] Read more.
Somatic embryos (SE) have potential to rapidly form a whole plant. Generally, SE is thought to be derived from embryogenic calli (EC). However, in maize, not only embryogenic calli (EC, can generate SE) but also nonembryogenic calli (NEC, can’t generate SE) can be induced from immature embryos. In order to understand the differences between EC and NEC and the mechanism of EC, which can easily form SE in maize, differential abundance protein species (DAPS) of EC and NEC from the maize inbred line Y423 were identified by using the isobaric tags for relative and absolute quantification (iTRAQ) proteomic technology. We identified 632 DAPS in EC compared with NEC. The results of bioinformatics analysis showed that EC development might be related to accumulation of pyruvate caused by the DAPS detected in some pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, tricarboxylic acid (TCA) cycle, fatty acid metabolism and phenylpropanoid biosynthesis. Based on the differentially accumulated proteins in EC and NEC, a series of DAPS related with pyruvate biosynthesis and suppression of acetyl-CoA might be responsible for the differences between EC and NEC cells. Furthermore, we speculate that the decreased abundance of enzymes/proteins involved in phenylpropanoid biosynthesis pathway in the EC cells results in reducing of lignin substances, which might affect the maize callus morphology. Full article
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Open AccessArticle
Proteomics Analysis Reveals That Caspase-Like and Metacaspase-Like Activities Are Dispensable for Activation of Proteases Involved in Early Response to Biotic Stress in Triticum aestivum L.
Int. J. Mol. Sci. 2018, 19(12), 3991; https://doi.org/10.3390/ijms19123991
Received: 8 November 2018 / Revised: 4 December 2018 / Accepted: 8 December 2018 / Published: 11 December 2018
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Abstract
Plants, including Triticum aestivum L., are constantly attacked by various pathogens which induce immune responses. Immune processes in plants are tightly regulated by proteases from different families within their degradome. In this study, a wheat degradome was characterized. Using profile hidden Markov model [...] Read more.
Plants, including Triticum aestivum L., are constantly attacked by various pathogens which induce immune responses. Immune processes in plants are tightly regulated by proteases from different families within their degradome. In this study, a wheat degradome was characterized. Using profile hidden Markov model (HMMer) algorithm and Pfam database, comprehensive analysis of the T. aestivum genome revealed a large number of proteases (1544 in total) belonging to the five major protease families: serine, cysteine, threonine, aspartic, and metallo-proteases. Mass-spectrometry analysis revealed a 30% difference between degradomes of distinct wheat cultivars (Khakasskaya and Darya), and infection by biotrophic (Puccinia recondita Rob. ex Desm f. sp. tritici) or necrotrophic (Stagonospora nodorum) pathogens induced drastic changes in the presence of proteolytic enzymes. This study shows that an early immune response to biotic stress is associated with the same core of proteases from the C1, C48, C65, M24, M41, S10, S9, S8, and A1 families. Further liquid chromatography-mass spectrometry (LC-MS) analysis of the detected protease-derived peptides revealed that infection by both pathogens enhances overall proteolytic activity in wheat cells and leads to activation of proteolytic cascades. Moreover, sites of proteolysis were identified within the proteases, which probably represent targets of autocatalytic activation, or hydrolysis by another protease within the proteolytic cascades. Although predicted substrates of metacaspase-like and caspase-like proteases were similar in biotrophic and necrotrophic infections, proteolytic activation of proteases was not found to be associated with metacaspase-like and caspase-like activities. These findings indicate that the response of T. aestivum to biotic stress is regulated by unique mechanisms. Full article
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Open AccessArticle
iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism Underlying the Weakening of Carbon Metabolism in Chlorotic Tea Leaves
Int. J. Mol. Sci. 2018, 19(12), 3943; https://doi.org/10.3390/ijms19123943
Received: 7 November 2018 / Revised: 3 December 2018 / Accepted: 5 December 2018 / Published: 7 December 2018
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Abstract
To uncover mechanism of highly weakened carbon metabolism in chlorotic tea (Camellia sinensis) plants, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic analyses were employed to study the differences in protein expression profiles in chlorophyll-deficient and normal green leaves in [...] Read more.
To uncover mechanism of highly weakened carbon metabolism in chlorotic tea (Camellia sinensis) plants, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic analyses were employed to study the differences in protein expression profiles in chlorophyll-deficient and normal green leaves in the tea plant cultivar “Huangjinya”. A total of 2110 proteins were identified in “Huangjinya”, and 173 proteins showed differential accumulations between the chlorotic and normal green leaves. Of these, 19 proteins were correlated with RNA expression levels, based on integrated analyses of the transcriptome and proteome. Moreover, the results of our analysis of differentially expressed proteins suggested that primary carbon metabolism (i.e., carbohydrate synthesis and transport) was inhibited in chlorotic tea leaves. The differentially expressed genes and proteins combined with photosynthetic phenotypic data indicated that 4-coumarate-CoA ligase (4CL) showed a major effect on repressing flavonoid metabolism, and abnormal developmental chloroplast inhibited the accumulation of chlorophyll and flavonoids because few carbon skeletons were provided as a result of a weakened primary carbon metabolism. Additionally, a positive feedback mechanism was verified at the protein level (Mg chelatase and chlorophyll b reductase) in the chlorophyll biosynthetic pathway, which might effectively promote the accumulation of chlorophyll b in response to the demand for this pigment in the cells of chlorotic tea leaves in weakened carbon metabolism. Full article
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Open AccessArticle
Comparative Proteomic Analysis Reveals Elevated Capacity for Photosynthesis in Polyphenol Oxidase Expression-Silenced Clematis terniflora DC. Leaves
Int. J. Mol. Sci. 2018, 19(12), 3897; https://doi.org/10.3390/ijms19123897
Received: 21 September 2018 / Revised: 1 December 2018 / Accepted: 2 December 2018 / Published: 5 December 2018
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Abstract
Polyphenol oxidase (PPO) catalyzes the o-hydroxylation of monophenols and oxidation of o-diphenols to quinones. Although the effects of PPO on plant physiology were recently proposed, little has been done to explore the inherent molecular mechanisms. To explore the in vivo physiological functions of [...] Read more.
Polyphenol oxidase (PPO) catalyzes the o-hydroxylation of monophenols and oxidation of o-diphenols to quinones. Although the effects of PPO on plant physiology were recently proposed, little has been done to explore the inherent molecular mechanisms. To explore the in vivo physiological functions of PPO, a model with decreased PPO expression and enzymatic activity was constructed on Clematis terniflora DC. using virus-induced gene silencing (VIGS) technology. Proteomics was performed to identify the differentially expressed proteins (DEPs) in the model (VC) and empty vector-carrying plants (VV) untreated or exposed to high levels of UV-B and dark (HUV-B+D). Following integration, it was concluded that the DEPs mainly functioned in photosynthesis, glycolysis, and redox in the PPO silence plants. Mapman analysis showed that the DEPs were mainly involved in light reaction and Calvin cycle in photosynthesis. Further analysis illustrated that the expression level of adenosine triphosphate (ATP) synthase, the content of chlorophyll, and the photosynthesis rate were increased in VC plants compared to VV plants pre- and post HUV-B+D. These results indicate that the silence of PPO elevated the plant photosynthesis by activating the glycolysis process, regulating Calvin cycle and providing ATP for energy metabolism. This study provides a prospective approach for increasing crop yield in agricultural production. Full article
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Open AccessArticle
Characterization of Heterotrimeric G Protein γ4 Subunit in Rice
Int. J. Mol. Sci. 2018, 19(11), 3596; https://doi.org/10.3390/ijms19113596
Received: 27 September 2018 / Revised: 5 November 2018 / Accepted: 9 November 2018 / Published: 14 November 2018
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Abstract
Heterotrimeric G proteins are the molecule switch that transmits information from external signals to intracellular target proteins in mammals and yeast cells. In higher plants, heterotrimeric G proteins regulate plant architecture. Rice harbors one canonical α subunit gene (RGA1), four extra-large [...] Read more.
Heterotrimeric G proteins are the molecule switch that transmits information from external signals to intracellular target proteins in mammals and yeast cells. In higher plants, heterotrimeric G proteins regulate plant architecture. Rice harbors one canonical α subunit gene (RGA1), four extra-large GTP-binding protein genes (XLGs), one canonical β-subunit gene (RGB1), and five γ-subunit genes (tentatively designated RGG1, RGG2, RGG3/GS3/Mi/OsGGC1, RGG4/DEP1/DN1/qPE9-1/OsGGC3, and RGG5/OsGGC2) as components of the heterotrimeric G protein complex. Among the five γ-subunit genes, RGG1 encodes the canonical γ-subunit, RGG2 encodes a plant-specific type of γ-subunit with additional amino acid residues at the N-terminus, and the remaining three γ-subunit genes encode atypical γ-subunits with cysteine-rich C-termini. We characterized the RGG4/DEP1/DN1/qPE9-1/OsGGC3 gene product Gγ4 in the wild type (WT) and truncated protein Gγ4∆Cys in the RGG4/DEP1/DN1/qPE9-1/OsGGC3 mutant, Dn1-1, as littele information regarding the native Gγ4 and Gγ4∆Cys proteins is currently available. Based on liquid chromatography-tandem mass spectrometry analysis, immunoprecipitated Gγ4 candidates were confirmed as actual Gγ4. Similar to α-(Gα) and β-subunits (Gβ), Gγ4 was enriched in the plasma membrane fraction and accumulated in the developing leaf sheath. As RGG4/DEP1/DN1/qPE9-1/OsGGC3 mutants exhibited dwarfism, tissues that accumulated Gγ4 corresponded to the abnormal tissues observed in RGG4/DEP1/DN1/qPE9-1/OsGGC3 mutants. Full article
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Open AccessArticle
Identification of Heterotrimeric G Protein γ3 Subunit in Rice Plasma Membrane
Int. J. Mol. Sci. 2018, 19(11), 3591; https://doi.org/10.3390/ijms19113591
Received: 3 September 2018 / Revised: 7 November 2018 / Accepted: 7 November 2018 / Published: 14 November 2018
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Abstract
Heterotrimeric G proteins are important molecules for regulating plant architecture and transmitting external signals to intracellular target proteins in higher plants and mammals. The rice genome contains one canonical α subunit gene (RGA1), four extra-large GTP-binding protein genes (XLGs), one canonical [...] Read more.
Heterotrimeric G proteins are important molecules for regulating plant architecture and transmitting external signals to intracellular target proteins in higher plants and mammals. The rice genome contains one canonical α subunit gene (RGA1), four extra-large GTP-binding protein genes (XLGs), one canonical β subunit gene (RGB1), and five γ subunit genes (tentatively named RGG1, RGG2, RGG3/GS3/Mi/OsGGC1, RGG4/DEP1/DN1/OsGGC3, and RGG5/OsGGC2). RGG1 encodes the canonical γ subunit; RGG2 encodes the plant-specific type of γ subunit with additional amino acid residues at the N-terminus; and the remaining three γ subunit genes encode the atypical γ subunits with cysteine abundance at the C-terminus. We aimed to identify the RGG3/GS3/Mi/OsGGC1 gene product, Gγ3, in rice tissues using the anti-Gγ3 domain antibody. We also analyzed the truncated protein, Gγ3∆Cys, in the RGG3/GS3/Mi/OsGGC1 mutant, Mi, using the anti-Gγ3 domain antibody. Based on nano-liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, the immunoprecipitated Gγ3 candidates were confirmed to be Gγ3. Similar to α (Gα) and β subunits (Gβ), Gγ3 was enriched in the plasma membrane fraction, and accumulated in the flower tissues. As RGG3/GS3/Mi/OsGGC1 mutants show the characteristic phenotype in flowers and consequently in seeds, the tissues that accumulated Gγ3 corresponded to the abnormal tissues observed in RGG3/GS3/Mi/OsGGC1 mutants. Full article
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Open AccessArticle
Comparative Proteomic and Physiological Analyses of Two Divergent Maize Inbred Lines Provide More Insights into Drought-Stress Tolerance Mechanisms
Int. J. Mol. Sci. 2018, 19(10), 3225; https://doi.org/10.3390/ijms19103225
Received: 6 September 2018 / Revised: 25 September 2018 / Accepted: 15 October 2018 / Published: 18 October 2018
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Abstract
Drought stress is the major abiotic factor threatening maize (Zea mays L.) yield globally. Therefore, revealing the molecular mechanisms fundamental to drought tolerance in maize becomes imperative. Herein, we conducted a comprehensive comparative analysis of two maize inbred lines contrasting in drought [...] Read more.
Drought stress is the major abiotic factor threatening maize (Zea mays L.) yield globally. Therefore, revealing the molecular mechanisms fundamental to drought tolerance in maize becomes imperative. Herein, we conducted a comprehensive comparative analysis of two maize inbred lines contrasting in drought stress tolerance based on their physiological and proteomic responses at the seedling stage. Our observations showed that divergent stress tolerance mechanisms exist between the two inbred-lines at physiological and proteomic levels, with YE8112 being comparatively more tolerant than MO17 owing to its maintenance of higher relative leaf water and proline contents, greater increase in peroxidase (POD) activity, along with decreased level of lipid peroxidation under stressed conditions. Using an iTRAQ (isobaric tags for relative and absolute quantification)-based method, we identified a total of 721 differentially abundant proteins (DAPs). Amongst these, we fished out five essential sets of drought responsive DAPs, including 13 DAPs specific to YE8112, 107 specific DAPs shared between drought-sensitive and drought-tolerant lines after drought treatment (SD_TD), three DAPs of YE8112 also regulated in SD_TD, 84 DAPs unique to MO17, and five overlapping DAPs between the two inbred lines. The most significantly enriched DAPs in YE8112 were associated with the photosynthesis antenna proteins pathway, whilst those in MO17 were related to C5-branched dibasic acid metabolism and RNA transport pathways. The changes in protein abundance were consistent with the observed physiological characterizations of the two inbred lines. Further, quantitative real-time polymerase chain reaction (qRT-PCR) analysis results confirmed the iTRAQ sequencing data. The higher drought tolerance of YE8112 was attributed to: activation of photosynthesis proteins involved in balancing light capture and utilization; enhanced lipid-metabolism; development of abiotic and biotic cross-tolerance mechanisms; increased cellular detoxification capacity; activation of chaperones that stabilize other proteins against drought-induced denaturation; and reduced synthesis of redundant proteins to help save energy to battle drought stress. These findings provide further insights into the molecular signatures underpinning maize drought stress tolerance. Full article
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Open AccessArticle
Quantitative Proteomics Analysis of Lettuce (Lactuca sativa L.) Reveals Molecular Basis-Associated Auxin and Photosynthesis with Bolting Induced by High Temperature
Int. J. Mol. Sci. 2018, 19(10), 2967; https://doi.org/10.3390/ijms19102967
Received: 16 July 2018 / Revised: 25 September 2018 / Accepted: 26 September 2018 / Published: 28 September 2018
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Abstract
Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). A high temperature can induce early bolting, which decreases both the quality and production of lettuce. However, knowledge of underlying lettuce bolting is still lacking. To better [...] Read more.
Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). A high temperature can induce early bolting, which decreases both the quality and production of lettuce. However, knowledge of underlying lettuce bolting is still lacking. To better understand the molecular basis of bolting, a comparative proteomics analysis was conducted on lettuce stems, during the bolting period induced by a high temperature (33 °C) and a control temperature (20 °C) using iTRAQ-based proteomics, phenotypic measures, and biological verifications using qRT-PCR and Western blot. The high temperature induced lettuce bolting, while the control temperature did not. Of the 5454 identified proteins, 619 proteins presented differential abundance induced by high-temperature relative to the control group, of which 345 had an increased abundance and 274 had a decreased abundance. Proteins with an abundance level change were mainly enriched in pathways associated with photosynthesis and tryptophan metabolism involved in auxin (IAA) biosynthesis. Moreover, among the proteins with differential abundance, proteins associated with photosynthesis and tryptophan metabolism were increased. These findings indicate that a high temperature enhances the function of photosynthesis and IAA biosynthesis to promote the process of bolting, which is in line with the physiology and transcription level of IAA metabolism. Our data provide a first comprehensive dataset for gaining novel understanding of the molecular basis underlying lettuce bolting induced by high temperature. It is potentially important for further functional analysis and genetic manipulation for molecular breeding to breed new cultivars of lettuce to restrain early bolting, which is vital for improving vegetable quality. Full article
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Open AccessArticle
Protein Phosphatase (PP2C9) Induces Protein Expression Differentially to Mediate Nitrogen Utilization Efficiency in Rice under Nitrogen-Deficient Condition
Int. J. Mol. Sci. 2018, 19(9), 2827; https://doi.org/10.3390/ijms19092827
Received: 18 July 2018 / Revised: 7 September 2018 / Accepted: 10 September 2018 / Published: 19 September 2018
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Abstract
Nitrogen (N) is an essential element usually limiting in plant growth and a basic factor for increasing the input cost in agriculture. To ensure the food security and environmental sustainability it is urgently required to manage the N fertilizer. The identification or development [...] Read more.
Nitrogen (N) is an essential element usually limiting in plant growth and a basic factor for increasing the input cost in agriculture. To ensure the food security and environmental sustainability it is urgently required to manage the N fertilizer. The identification or development of genotypes with high nitrogen utilization efficiency (NUE) which can grow efficiently and sustain yield in low N conditions is a possible solution. In this study, two isogenic rice genotypes i.e., wild-type rice kitaake and its transgenic line PP2C9TL overexpressed protein phosphatase gene (PP2C9) were used for comparative proteomics analysis at control and low level of N to identify specific proteins and encoding genes related to high NUE. 2D gel electrophoresis was used to perform the differential proteome analysis. In the leaf proteome, 30 protein spots were differentially expressed between the two isogenic lines under low N level which were involved in the process of energy, photosynthesis, N metabolism, signaling, and defense mechanisms. In addition, we have found that protein phosphatase enhances nitrate reductase activation by downregulation of SnRK1 and 14-3-3 proteins. Furthermore, we showed that PP2C9TL exhibits higher NUE than WT due to higher activity of nitrate reductase. This study provides new insights on the rice proteome which would be useful in the development of new strategies to increase NUE in cereal crops. Full article
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Open AccessArticle
Proteomics Analysis Reveals Non-Controlled Activation of Photosynthesis and Protein Synthesis in a Rice npp1 Mutant under High Temperature and Elevated CO2 Conditions
Int. J. Mol. Sci. 2018, 19(9), 2655; https://doi.org/10.3390/ijms19092655
Received: 15 August 2018 / Revised: 30 August 2018 / Accepted: 3 September 2018 / Published: 7 September 2018
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Abstract
Rice nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) catalyzes the hydrolytic breakdown of the pyrophosphate and phosphodiester bonds of a number of nucleotides including ADP-glucose and ATP. Under high temperature and elevated CO2 conditions (HT + ECO2), the npp1 knockout rice mutant displayed [...] Read more.
Rice nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) catalyzes the hydrolytic breakdown of the pyrophosphate and phosphodiester bonds of a number of nucleotides including ADP-glucose and ATP. Under high temperature and elevated CO2 conditions (HT + ECO2), the npp1 knockout rice mutant displayed rapid growth and high starch content phenotypes, indicating that NPP1 exerts a negative effect on starch accumulation and growth. To gain further insight into the mechanisms involved in the NPP1 downregulation induced starch overaccumulation, in this study we conducted photosynthesis, leaf proteomic, and chloroplast phosphoproteomic analyses of wild-type (WT) and npp1 plants cultured under HT + ECO2. Photosynthesis in npp1 leaves was significantly higher than in WT. Additionally, npp1 leaves accumulated higher levels of sucrose than WT. The proteomic analyses revealed upregulation of proteins related to carbohydrate metabolism and the protein synthesis system in npp1 plants. Further, our data indicate the induction of 14-3-3 proteins in npp1 plants. Our finding demonstrates a higher level of protein phosphorylation in npp1 chloroplasts, which may play an important role in carbohydrate accumulation. Together, these results offer novel targets and provide additional insights into carbohydrate metabolism regulation under ambient and adverse conditions. Full article
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Open AccessArticle
Changes in the Proteome of Medicago sativa Leaves in Response to Long-Term Cadmium Exposure Using a Cell-Wall Targeted Approach
Int. J. Mol. Sci. 2018, 19(9), 2498; https://doi.org/10.3390/ijms19092498
Received: 4 August 2018 / Revised: 20 August 2018 / Accepted: 21 August 2018 / Published: 24 August 2018
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Abstract
Accumulation of cadmium (Cd) shows a serious problem for the environment and poses a threat to plants. Plants employing various cellular and molecular mechanisms to limit Cd toxicity and alterations of the cell wall structure were observed upon Cd exposure. This study focuses [...] Read more.
Accumulation of cadmium (Cd) shows a serious problem for the environment and poses a threat to plants. Plants employing various cellular and molecular mechanisms to limit Cd toxicity and alterations of the cell wall structure were observed upon Cd exposure. This study focuses on changes in the cell wall protein-enriched subproteome of alfalfa (Medicago sativa) leaves during long-term Cd exposure. Plants grew on Cd-contaminated soil (10 mg/kg dry weight (DW)) for an entire season. A targeted approach was used to sequentially extract cell wall protein-enriched fractions from the leaves and quantitative analyses were conducted with two-dimensional difference gel electrophoresis (2D DIGE) followed by protein identification with matrix-assisted laser desorption/ionization (MALDI) time-of-flight/time of flight (TOF/TOF) mass spectrometry. In 212 spots that showed a significant change in intensity upon Cd exposure a single protein was identified. Of these, 163 proteins are predicted to be secreted and involved in various physiological processes. Proteins of other subcellular localization were mainly chloroplastic and decreased in response to Cd, which confirms the Cd-induced disturbance of the photosynthesis. The observed changes indicate an active defence response against a Cd-induced oxidative burst and a restructuring of the cell wall, which is, however, different to what is observed in M. sativa stems and will be discussed. Full article
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Open AccessArticle
Proteomic and Biochemical Changes during Senescence of Phalaenopsis ‘Red Dragon’ Petals
Int. J. Mol. Sci. 2018, 19(5), 1317; https://doi.org/10.3390/ijms19051317
Received: 30 March 2018 / Revised: 24 April 2018 / Accepted: 26 April 2018 / Published: 28 April 2018
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Abstract
Phalaenopsis flowers are some of the most popular ornamental flowers in the world. For most ornamental plants, petal longevity determines postharvest quality and garden performance. Therefore, it is important to have insight into the senescence mechanism of Phalaenopsis. In the present study, [...] Read more.
Phalaenopsis flowers are some of the most popular ornamental flowers in the world. For most ornamental plants, petal longevity determines postharvest quality and garden performance. Therefore, it is important to have insight into the senescence mechanism of Phalaenopsis. In the present study, a proteomic approach combined with ultrastructural observation and activity analysis of antioxidant enzymes was used to profile the molecular and biochemical changes during pollination-induced petal senescence in Phalaenopsis “Red Dragon”. Petals appeared to be visibly wilting at 24 h after pollination, accompanied by the mass degradation of macromolecules and organelles during senescence. In addition, 48 protein spots with significant differences in abundance were found by two-dimensional electrophoresis (2-DE) and subjected to matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/TOF-MS). There were 42 protein spots successfully identified and homologous to known functional protein species involved in key biological processes, including antioxidant pathways, stress response, protein metabolism, cell wall component metabolism, energy metabolism, cell structure, and signal transduction. The activity of all reactive oxygen species (ROS)-scavenging enzymes was increased, keeping the content of ROS at a low level at the early stage of senescence. These results suggest that two processes, a counteraction against increased levels of ROS and the degradation of cellular constituents for maintaining nutrient recycling, are activated during pollination-induced petal senescence in Phalaenopsis. The information provides a basis for understanding the mechanism regulating petal senescence and prolonging the florescence of Phalaenopsis. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Proteomics, Holm Oak (Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other?
Int. J. Mol. Sci. 2019, 20(3), 692; https://doi.org/10.3390/ijms20030692
Received: 10 January 2019 / Revised: 28 January 2019 / Accepted: 30 January 2019 / Published: 6 February 2019
Cited by 1 | PDF Full-text (1552 KB) | HTML Full-text | XML Full-text
Abstract
Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused [...] Read more.
Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes. Full article
(This article belongs to the Special Issue Plant Proteomic Research 2.0) Printed Edition available
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Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
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