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Special Issue "Abiotic Stress and Gene Networks in Plants"

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 (29 May 2015).

Special Issue Editors

Guest Editor
Prof. Dr. Ann Cuypers

Centre for Environmental Sciences, Research Group Environmental Biology, Hasselt University–Campus Diepenbeek, Diepenbeek, Belgium
Website | E-Mail
Interests: cellular toxicity of abiotic stress factors; Molecular-biochemical analysis of oxidative stress and antioxidants; Oxidative damage and oxidative signalling in plant acclimation to external abiotic stress factors
Guest Editor
Dr. Tony Remans

Centre for Environmental Sciences, Research Group Environmental Biology, Hasselt University–Campus Diepenbeek, Diepenbeek, Belgium
Website | E-Mail
Interests: The influence of abiotic stress factors on root architecture and the molecular mechanisms of root development; Optimizing root architectures for biomass production and phytoremediation, using beneficial properties of plant-associated bacteria

Special Issue Information

Dear Colleagues,

Exposure of plants to abiotic stress causes the activation of perception mechanisms, triggers signaling cascades and downstream responses. Genes involved in abiotic stress responses have been identified by, e.g., transcriptomic or proteomic approaches or by genetic screens, and validated by reverse genetics and heterologous or overexpression. Many stress conditions lead to common changes in gene expression or protein abundance or activities, suggesting common pathways are affected, although stress-specific changes have also been observed.

The gene networks affected by the stress condition may act to enable acclimation of plants to the stress condition. Alternatively, normal functioning of gene networks may be disturbed such that normal plant functioning is hindered. Discovering how gene networks operate under stress conditions is further complicated by feedback loops, regulation at different levels (epigenetic, posttranscriptional) and interactions between different pathways.

To understand how and which gene networks are affected by different abiotic stresses is fundamental for molecular understanding of stress and acclimation responses, and for the applied approaches of increasing crop yield under stress conditions for either food, feed or (energy) biomass.

The scope of the special issue is to summarize and enlarge the knowledge in plant gene networks activated or affected under abiotic stress conditions. Authors are invited to submit research papers, meta-analyses, methods or reviews, related to but not limited to the following suggested topics:

  • Linking upstream perception mechanisms of stress to downstream activation or disturbance of gene networks.
  • Linking early perception and signaling responses to long-term acclimation.
  • Comparison of different stress conditions revealing general and stress specific mechanisms.
  • Resolving feedback loops and interactions in gene expression networks.
  • Gene families in gene networks: redundancy and specificity.

We are looking forward to receiving your contribution,

Prof. Dr. Ann Cuypers
Dr. Tony Remans
Guest Editors

Keywords

  • abiotic stress
  • gene expression
  • gene regulation
  • signaling
  • oxidative stress
  • stress responses
  • stress perception
  • acclimation

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Published Papers (22 papers)

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Research

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Open AccessArticle
Evaluation of Appropriate Reference Genes for Reverse Transcription-Quantitative PCR Studies in Different Tissues of a Desert Poplar via Comparision of Different Algorithms
Int. J. Mol. Sci. 2015, 16(9), 20468-20491; https://doi.org/10.3390/ijms160920468
Received: 23 April 2015 / Accepted: 7 August 2015 / Published: 28 August 2015
Cited by 8 | PDF Full-text (1226 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
Involvement of Ethylene in the Latex Metabolism and Tapping Panel Dryness of Hevea brasiliensis
Int. J. Mol. Sci. 2015, 16(8), 17885-17908; https://doi.org/10.3390/ijms160817885
Received: 23 April 2015 / Revised: 3 July 2015 / Accepted: 6 July 2015 / Published: 4 August 2015
Cited by 20 | PDF Full-text (2421 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
Stress-Responsive Expression, Subcellular Localization and Protein–Protein Interactions of the Rice Metacaspase Family
Int. J. Mol. Sci. 2015, 16(7), 16216-16241; https://doi.org/10.3390/ijms160716216
Received: 26 April 2015 / Revised: 17 June 2015 / Accepted: 3 July 2015 / Published: 17 July 2015
Cited by 14 | PDF Full-text (2964 KB) | HTML Full-text | XML Full-text
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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Open AccessArticle
Analysis of Cell Wall-Related Genes in Organs of Medicago sativa L. under Different Abiotic Stresses
Int. J. Mol. Sci. 2015, 16(7), 16104-16124; https://doi.org/10.3390/ijms160716104
Received: 28 May 2015 / Revised: 7 July 2015 / Accepted: 9 July 2015 / Published: 16 July 2015
Cited by 20 | PDF Full-text (2239 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
β-Radiation Stress Responses on Growth and Antioxidative Defense System in Plants: A Study with Strontium-90 in Lemna minor
Int. J. Mol. Sci. 2015, 16(7), 15309-15327; https://doi.org/10.3390/ijms160715309
Received: 28 May 2015 / Revised: 23 June 2015 / Accepted: 26 June 2015 / Published: 7 July 2015
Cited by 10 | PDF Full-text (1121 KB) | HTML Full-text | XML Full-text
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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Open AccessArticle
Global Reprogramming of Transcription in Chinese Fir (Cunninghamia lanceolata) during Progressive Drought Stress and after Rewatering
Int. J. Mol. Sci. 2015, 16(7), 15194-15219; https://doi.org/10.3390/ijms160715194
Received: 6 April 2015 / Revised: 21 June 2015 / Accepted: 30 June 2015 / Published: 6 July 2015
Cited by 6 | PDF Full-text (1554 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing
Int. J. Mol. Sci. 2015, 16(6), 13937-13958; https://doi.org/10.3390/ijms160613937
Received: 17 April 2015 / Revised: 21 May 2015 / Accepted: 1 June 2015 / Published: 18 June 2015
Cited by 15 | PDF Full-text (1112 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
Induction of Oxidative Stress and Antioxidative Mechanisms in Arabidopsis thaliana after Uranium Exposure at pH 7.5
Int. J. Mol. Sci. 2015, 16(6), 12405-12423; https://doi.org/10.3390/ijms160612405
Received: 16 March 2015 / Revised: 6 May 2015 / Accepted: 21 May 2015 / Published: 2 June 2015
Cited by 3 | PDF Full-text (945 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
Functional Analysis of the Maize C-Repeat/DRE Motif-Binding Transcription Factor CBF3 Promoter in Response to Abiotic Stress
Int. J. Mol. Sci. 2015, 16(6), 12131-12146; https://doi.org/10.3390/ijms160612131
Received: 4 March 2015 / Revised: 16 April 2015 / Accepted: 20 May 2015 / Published: 28 May 2015
Cited by 12 | PDF Full-text (1743 KB) | HTML Full-text | XML Full-text
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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Open AccessArticle
Comparative Analysis of Anther Transcriptome Profiles of Two Different Rice Male Sterile Lines Genotypes under Cold Stress
Int. J. Mol. Sci. 2015, 16(5), 11398-11416; https://doi.org/10.3390/ijms160511398
Received: 3 March 2015 / Revised: 29 April 2015 / Accepted: 13 May 2015 / Published: 18 May 2015
Cited by 29 | PDF Full-text (1132 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
De Novo Transcriptome Sequencing of Low Temperature-Treated Phlox subulata and Analysis of the Genes Involved in Cold Stress
Int. J. Mol. Sci. 2015, 16(5), 9732-9748; https://doi.org/10.3390/ijms16059732
Received: 15 March 2015 / Revised: 21 April 2015 / Accepted: 22 April 2015 / Published: 29 April 2015
Cited by 11 | PDF Full-text (2647 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
Genome-Wide Identification and Analysis of Drought-Responsive Genes and MicroRNAs in Tobacco
Int. J. Mol. Sci. 2015, 16(3), 5714-5740; https://doi.org/10.3390/ijms16035714
Received: 7 December 2014 / Revised: 19 January 2015 / Accepted: 29 January 2015 / Published: 12 March 2015
Cited by 12 | PDF Full-text (1359 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
A Ribosomal Protein AgRPS3aE from Halophilic Aspergillus glaucus Confers Salt Tolerance in Heterologous Organisms
Int. J. Mol. Sci. 2015, 16(2), 3058-3070; https://doi.org/10.3390/ijms16023058
Received: 17 December 2014 / Revised: 30 December 2014 / Accepted: 21 January 2015 / Published: 29 January 2015
Cited by 11 | PDF Full-text (2634 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessArticle
Reactive Oxygen and Nitrogen Species in Defense/Stress Responses Activated by Chitosan in Sycamore Cultured Cells
Int. J. Mol. Sci. 2015, 16(2), 3019-3034; https://doi.org/10.3390/ijms16023019
Received: 22 December 2014 / Revised: 12 January 2015 / Accepted: 23 January 2015 / Published: 29 January 2015
Cited by 11 | PDF Full-text (434 KB) | HTML Full-text | XML Full-text
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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Review

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Open AccessReview
Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective
Int. J. Mol. Sci. 2015, 16(9), 20913-20942; https://doi.org/10.3390/ijms160920913
Received: 20 May 2015 / Revised: 16 July 2015 / Accepted: 10 August 2015 / Published: 1 September 2015
Cited by 38 | PDF Full-text (956 KB) | HTML Full-text | XML Full-text | Supplementary Files
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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Open AccessReview
Gene Networks Involved in Hormonal Control of Root Development in Arabidopsis thaliana: A Framework for Studying Its Disturbance by Metal Stress
Int. J. Mol. Sci. 2015, 16(8), 19195-19224; https://doi.org/10.3390/ijms160819195
Received: 30 May 2015 / Accepted: 1 August 2015 / Published: 14 August 2015
Cited by 20 | PDF Full-text (1071 KB) | HTML Full-text | XML Full-text
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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Open AccessReview
Physiological and Molecular Aspects of Tolerance to Environmental Constraints in Grain and Forage Legumes
Int. J. Mol. Sci. 2015, 16(8), 18976-19008; https://doi.org/10.3390/ijms160818976
Received: 24 May 2015 / Revised: 9 July 2015 / Accepted: 5 August 2015 / Published: 13 August 2015
Cited by 12 | PDF Full-text (2270 KB) | HTML Full-text | XML Full-text
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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Open AccessReview
Effect of Heavy Metals in Plants of the Genus Brassica
Int. J. Mol. Sci. 2015, 16(8), 17975-17998; https://doi.org/10.3390/ijms160817975
Received: 3 June 2015 / Revised: 13 July 2015 / Accepted: 27 July 2015 / Published: 4 August 2015
Cited by 49 | PDF Full-text (727 KB) | HTML Full-text | XML Full-text | Supplementary Files
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)
Open AccessReview
Network Candidate Genes in Breeding for Drought Tolerant Crops
Int. J. Mol. Sci. 2015, 16(7), 16378-16400; https://doi.org/10.3390/ijms160716378
Received: 30 May 2015 / Revised: 9 July 2015 / Accepted: 13 July 2015 / Published: 17 July 2015
Cited by 25 | PDF Full-text (714 KB) | HTML Full-text | XML Full-text
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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Open AccessReview
Plant MYB Transcription Factors: Their Role in Drought Response Mechanisms
Int. J. Mol. Sci. 2015, 16(7), 15811-15851; https://doi.org/10.3390/ijms160715811
Received: 20 May 2015 / Revised: 18 June 2015 / Accepted: 25 June 2015 / Published: 13 July 2015
Cited by 94 | PDF Full-text (1488 KB) | HTML Full-text | XML Full-text
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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Open AccessReview
Function of ABA in Stomatal Defense against Biotic and Drought Stresses
Int. J. Mol. Sci. 2015, 16(7), 15251-15270; https://doi.org/10.3390/ijms160715251
Received: 28 May 2015 / Revised: 30 June 2015 / Accepted: 2 July 2015 / Published: 6 July 2015
Cited by 80 | PDF Full-text (1188 KB) | HTML Full-text | XML Full-text
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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Open AccessReview
Ascorbate Peroxidase and Catalase Activities and Their Genetic Regulation in Plants Subjected to Drought and Salinity Stresses
Int. J. Mol. Sci. 2015, 16(6), 13561-13578; https://doi.org/10.3390/ijms160613561
Received: 19 May 2015 / Revised: 5 June 2015 / Accepted: 8 June 2015 / Published: 12 June 2015
Cited by 113 | PDF Full-text (1550 KB) | HTML Full-text | XML Full-text
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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