ROS and redox signalling in the response of plants to abiotic stress

Nontargeted metabolite profiling in compatible pathogen-inoculated tobacco (Nicotiana tabacum L. cv. Wisconsin 38) using UPLC-Q-TOF/MS

A biphasic reactive oxygen species (ROS) production has previously been observed in tobacco at 1 and 48 h after inoculation with the hemibiotrophic compatible pathogen, Phytophthora parasitica var. nicotianae (Ppn). To characterize the response of tobacco to biphasically produced ROS concerning the propagation of Ppn, ultraperformance liquid chromatography-quadrupole-time of flight/ mass spectrometry (UPLC-Q-TOF/MS) based metabolic profiling combined with multivariate statistical analysis was performed. Among the nonredundant 355 mass ions in ESI+ mode and 345 mass ions in ESI- mode that were selected as significantly changed by Ppn inoculation (|p(corr)| > 0.6 on S-plot of orthogonal partial least-squares discriminant analysis (OPLS-DA), fold-change > 2, and p < 0.05 in the independent two-sample t test), 76 mass ions were identified on the basis of their accurate mass ions and MS/MS spectra. Phenolic amino acids, phenylpropanoids, hydroxycinnamic acid amides, linoleic acid, linolenic acid, lysophospholipids, glycoglycerolipids, and trioxidized phospholipids were identified as having changed after Ppn inoculation. On the basis of their quantitative changes, the metabolic responses occurring at each phase of ROS production after Ppn inoculation were investigated in this study.

Ectopic expression of Arabidopsis glutaredoxin AtGRXS17 enhances thermotolerance in tomato

While various signalling networks regulate plant responses to heat stress, the mechanisms regulating and unifying these diverse biological processes are largely unknown. Our previous studies indicate that the Arabidopsis monothiol glutaredoxin, AtGRXS17, is crucial for temperature-dependent postembryonic growth in Arabidopsis. In the present study, we further demonstrate that AtGRXS17 has conserved functions in anti-oxidative stress and thermotolerance in both yeast and plants. In yeast, AtGRXS17 co-localized with yeast ScGrx3 in the nucleus and suppressed the sensitivity of yeast grx3grx4 double-mutant cells to oxidative stress and heat shock. In plants, GFP-AtGRXS17 fusion proteins initially localized in the cytoplasm and the nuclear envelope but migrated to the nucleus during heat stress. Ectopic expression of AtGRXS17 in tomato plants minimized photo-oxidation of chlorophyll and reduced oxidative damage of cell membrane systems under heat stress. This enhanced thermotolerance correlated with increased catalase (CAT) enzyme activity and reduced H₂O₂ accumulation in AtGRXS17-expressing tomatoes. Furthermore, during heat stress, expression of the heat shock transcription factor (HSF) and heat shock protein (HSP) genes was up-regulated in AtGRXS17-expressing transgenic plants compared with wild-type controls. Thus, these findings suggest a specific protective role of a redox protein against temperature stress and provide a genetic engineering strategy to improve crop thermotolerance.

Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq

Drought stress affects cereals especially during the reproductive stage. The maize (Zea mays) drought transcriptome was studied using RNA-Seq analysis to compare drought-treated and well-watered fertilized ovary and basal leaf meristem tissue. More drought-responsive genes responded in the ovary compared with the leaf meristem. Gene Ontology enrichment analysis revealed a massive decrease in transcript abundance of cell division and cell cycle genes in the drought-stressed ovary only. Among Gene Ontology categories related to carbohydrate metabolism, changes in starch and Suc metabolism-related genes occurred in the ovary, consistent with a decrease in starch levels, and in Suc transporter function, with no comparable changes occurring in the leaf meristem. Abscisic acid (ABA)-related processes responded positively, but only in the ovaries. Related responses suggested the operation of low glucose sensing in drought-stressed ovaries. The data are discussed in the context of the susceptibility of maize kernel to drought stress leading to embryo abortion and the relative robustness of dividing vegetative tissue taken at the same time from the same plant subjected to the same conditions. Our working hypothesis involves signaling events associated with increased ABA levels, decreased glucose levels, disruption of ABA/sugar signaling, activation of programmed cell death/senescence through repression of a phospholipase C-mediated signaling pathway, and arrest of the cell cycle in the stressed ovary at 1 d after pollination. Increased invertase levels in the stressed leaf meristem, on the other hand, resulted in that tissue maintaining hexose levels at an "unstressed" level, and at lower ABA levels, which was correlated with successful resistance to drought stress.

ROS signaling as common element in low oxygen and heat stresses

The activation of the oxidative metabolism in plants under low oxygen conditions has prompted controversial views. The presence of a ROS component in the transcriptome in response to low oxygen has been observed and an overlap with heat stress has been proved. It has been also demonstrated that ROS are produced during both anoxia and heat, but the site of their production remain contentious. Membrane NADPH oxidase and mitochondrial electron transport flow have been indicated as possible ROS generation systems. Both anoxia and heat have been shown to induce the transcription of Heat Shock Factors (HSFs) and Heat Shock Proteins (HSPs), among which HSFA2 and some of its targets. HSFA2 over-expressing plant has been shown to be more tolerant to anoxia, while the knockout hsfa2 lose the capability of wild type plants to cross-acclimate to anoxia through mild heat pre-treatment. The production of ROS seems to be an integral part of the anoxia and heat response, where HSFs likely play a central role in activating the HSP pathway. This mechanism is suggested to result in enhanced plant tolerance to both anoxia and heat.

Proteomic analysis of chloroplast-to-chromoplast transition in tomato reveals metabolic shifts coupled with disrupted thylakoid biogenesis machinery and elevated energy-production components

A comparative proteomic approach was performed to identify differentially expressed proteins in plastids at three stages of tomato (Solanum lycopersicum) fruit ripening (mature-green, breaker, red). Stringent curation and processing of the data from three independent replicates identified 1,932 proteins among which 1,529 were quantified by spectral counting. The quantification procedures have been subsequently validated by immunoblot analysis of six proteins representative of distinct metabolic or regulatory pathways. Among the main features of the chloroplast-to-chromoplast transition revealed by the study, chromoplastogenesis appears to be associated with major metabolic shifts: (1) strong decrease in abundance of proteins of light reactions (photosynthesis, Calvin cycle, photorespiration) and carbohydrate metabolism (starch synthesis/degradation), mostly between breaker and red stages and (2) increase in terpenoid biosynthesis (including carotenoids) and stress-response proteins (ascorbate-glutathione cycle, abiotic stress, redox, heat shock). These metabolic shifts are preceded by the accumulation of plastid-encoded acetyl Coenzyme A carboxylase D proteins accounting for the generation of a storage matrix that will accumulate carotenoids. Of particular note is the high abundance of proteins involved in providing energy and in metabolites import. Structural differentiation of the chromoplast is characterized by a sharp and continuous decrease of thylakoid proteins whereas envelope and stroma proteins remain remarkably stable. This is coincident with the disruption of the machinery for thylakoids and photosystem biogenesis (vesicular trafficking, provision of material for thylakoid biosynthesis, photosystems assembly) and the loss of the plastid division machinery. Altogether, the data provide new insights on the chromoplast differentiation process while enriching our knowledge of the plant plastid proteome.

New insights into an old story: pollen ROS also play a role in hay fever

Reactive oxygen species (ROS) can exhibit negative and benign traits. In plants, ROS levels increase markedly during periods of environmental stress, and defense against pathogen attack. ROS form naturally as a by-product of normal oxygen metabolism, and evenly play an essential role in cell growth. The short ROS lifespan makes them ideal molecules to act in cell signaling, a role they share in both plants and animals. A particular plant organism, the pollen grain, may closely interact with human mucosa and an allergic inflammatory response often results. Pollen grain ROS represent a first, crucial signal which primes and magnifies a cascade of events in the allergic response.

Genome-wide transcriptional profiles during temperature and oxidative stress reveal coordinated expression patterns and overlapping regulons in rice

Genome wide transcriptional changes by cold stress, heat stress and oxidative stress in rice seedlings were analyzed. Heat stress resulted in predominant changes in transcripts of heat shock protein and heat shock transcription factor genes, as well as genes associated with synthesis of scavengers of reactive oxygen species and genes that control the level of sugars, metabolites and auxins. Cold stress treatment caused differential expression of transcripts of various transcription factors including desiccation response element binding proteins and different kinases. Transcripts of genes that are part of calcium signaling, reactive oxygen scavenging and diverse metabolic reactions were differentially expressed during cold stress. Oxidative stress induced by hydrogen peroxide treatment, resulted in significant up-regulation in transcript levels of genes related to redox homeostasis and down-regulation of transporter proteins. ROS homeostasis appeared to play central role in response to temperature extremes. The key transcription factors that may underlie the concerted transcriptional changes of specific components in various signal transduction networks involved are highlighted. Co-ordinated expression pattern and promoter architectures based analysis (promoter models and overrepresented transcription factor binding sites) suggested potential regulons involved in stress responses. A considerable overlap was noted at the level of transcription as well as in regulatory modules of differentially expressed genes.

Physiological and molecular changes in plants grown at low temperatures

Apart from water availability, low temperature is the most important environmental factor limiting the productivity and geographical distribution of plants across the world. To cope with cold stress, plant species have evolved several physiological and molecular adaptations to maximize cold tolerance by adjusting their metabolism. The regulation of some gene products represents an additional mechanism of cold tolerance. A consequence of these mechanisms is that plants are able to survive exposure to low temperature via a process known as cold acclimation. In this review, we briefly summarize recent progress in research and hypotheses on how sensitive plants perceive cold. We also explore how this perception is translated into changes within plants following exposure to low temperatures. Particular emphasis is placed on physiological parameters as well as transcriptional, post-transcriptional and post-translational regulation of cold-induced gene products that occur after exposure to low temperatures, leading to cold acclimation.

Why we should stop inferring simple correlations between antioxidants and plant stress resistance: towards the antioxidomic era

A large number of studies have investigated the relationship between different forms of abiotic stress and antioxidants. However, misconceptions and technical flaws often affect studies on this important topic. Reactive oxygen species (ROS) generated under stress conditions should not be considered just as potential threats, because they are essential components of the signaling mechanism inducing plant defenses. Similarly, the complexity of the antioxidant system should be considered, to avoid misleading oversimplifications. Recent literature is discussed, highlighting the importance of accurate experimental setups for obtaining reliable results in this delicate field of research. A tentative "troubleshooting guide" is provided to help researchers interested in improving the quality of their work on the role of antioxidants in plant stress resistance. Significant advancements in the field could be reached with the development of antioxidomics, defined here as a new branch of research at the crossroads of other disciplines including metabolomics and proteomics, studying the complex relationship among antioxidants and their functions.

Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets

BACKGROUND

Plants respond to external stimuli through fine regulation of gene expression partially ensured by small RNAs. Of these, microRNAs (miRNAs) play a crucial role. They negatively regulate gene expression by targeting the cleavage or translational inhibition of target messenger RNAs (mRNAs). In Hevea brasiliensis, environmental and harvesting stresses are known to affect natural rubber production. This study set out to identify abiotic stress-related miRNAs in Hevea using next-generation sequencing and bioinformatic analysis.

RESULTS

Deep sequencing of small RNAs was carried out on plantlets subjected to severe abiotic stress using the Solexa technique. By combining the LeARN pipeline, data from the Plant microRNA database (PMRD) and Hevea EST sequences, we identified 48 conserved miRNA families already characterized in other plant species, and 10 putatively novel miRNA families. The results showed the most abundant size for miRNAs to be 24 nucleotides, except for seven families. Several MIR genes produced both 20-22 nucleotides and 23-27 nucleotides. The two miRNA class sizes were detected for both conserved and putative novel miRNA families, suggesting their functional duality. The EST databases were scanned with conserved and novel miRNA sequences. MiRNA targets were computationally predicted and analysed. The predicted targets involved in "responses to stimuli" and to "antioxidant" and "transcription activities" are presented.

CONCLUSIONS

Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs when the complete genome is not yet available. Our study provided additional information for evolutionary studies and revealed potentially specific regulation of the control of redox status in Hevea.

Reconsidering the nature and mode of action of metabolite retrograde signals from the chloroplast

Plant organelles produce retrograde signals to alter nuclear gene expression in order to coordinate their biogenesis, maintain homeostasis, or optimize their performance under adverse conditions. Many signals of different chemical nature have been described in the past decades, including chlorophyll intermediates, reactive oxygen species (ROS), and adenosine derivatives. While the effects of retrograde signaling on gene expression are well understood, the initiation and transport of the signals and their mode of action have either not been resolved, or are a matter of speculation. Moreover, retrograde signaling should be considered as part of a broader cellular network, instead of as separate pathways, required to adjust to changing physiologically relevant conditions. Here we summarize current plastid retrograde signaling models in plants, with a focus on new signaling pathways, SAL1-PAP, methylerythritol cyclodiphosphate (MEcPP), and β-cyclocitral (β-CC), and outline missing links or future areas of research that we believe need to be addressed to have a better understanding of plant intracellular signaling networks.

Heritable Effect of Plant Water Availability Conditions on Restoration of Male Fertility in the "9E" CMS-Inducing Cytoplasm of Sorghum

Heritable changes of phenotype arising in plant ontogenesis by the influence of environmental factors belong to the most intriguing genetic phenomena. An unusual inheritance pattern was detected during examination of male fertility restoration in the CMS-inducing "9E" type cytoplasm of sorghum: Rf-genes were functional in self-pollinated progeny of F(1) hybrids yet were either not expressed or poorly expressed in backcrosses of these hybrids to CMS-lines with the same cytoplasm type. In experiments on parallel growing of the same F(1) hybrid combinations in the "dry plot" and in the "irrigated plot," it was found that high level of plant water availability during panicle and pollen developmental stages significantly increased male fertility of F(1) and test-cross hybrid populations, in which fertility-restoring genes were in heterozygote state, whereas in F(2) populations the influences of water availability conditions cause less pronounce effects. Similarly, male-sterile F(1) plants, being transferred from the "dry plot" to greenhouse, produced male-fertile panicles. In addition, male-sterile plants from F(2) families, which segregated-out as recessives, being transferred to greenhouse also produced male-fertile panicles. In the progenies of these revertants that were grown in field conditions and in the "dry plot," stable inheritance of male fertility for three cycles of self-pollination was observed, and a number of stable fertile lines in the "9E" cytoplasm were obtained. However, in test-crosses of these fertile lines to CMS-lines with the "9E" cytoplasm restoration of male fertility was not observed, except the progeny of one revertant that behaved as fertility-restorer line. These data suggest that the functional state of fertility-restoring genes for the "9E" sorghum cytoplasm is epigenetically regulated trait established by the influence of environmental factors and is transmitted to sexual generations.

Transient MPK6 activation in response to oxygen deprivation and reoxygenation is mediated by mitochondria and aids seedling survival in Arabidopsis

Mitogen-activated protein kinases (MPKs) are regulated by diverse stresses with a reactive oxygen species (ROS) component. Here, we report the rapid and transient activation of MPK3, MPK4 and MPK6 upon oxygen deprivation as well as reoxygenation in seedlings of Arabidopsis thaliana. MPK activation peaked within 2 h of oxygen deprivation and again at a higher magnitude within 5 min of reoxygenation. MPK6 was the predominant kinase regulated by oxygen availability in both aerial and root tissue, except in mpk6 mutants, which displayed compensatory activation of MPK3. A universal consequence of oxygen deprivation in eukaryotes is inhibition of the terminal step of the mitochondrial electron transport chain (mETC). We demonstrate that treatment of seedlings with the mETC inhibitors antimycin A and potassium cyanide under normoxia promotes transient MPK6 and MPK3 activation. Confocal imaging of seedlings provided evidence that both oxygen deprivation and mETC inhibitors stimulate mitochondria-associated ROS production. We found that seedling survival of prolonged oxygen deprivation was improved in transgenics that ectopically overexpress MPK3, MPK4 and MPK6, but the induction of mRNAs associated with low oxygen acclimation responses were not markedly altered in MPK6 overexpression lines or mpk6 loss-of-function mutants. However, distinctions in MPK6 activation potential were correlated with other differences in mRNAs accumulation. Our findings suggest that oxygen deprivation and reoxygenation trigger mitochondrial ROS production to activate MPK signaling, which in turn regulate reversible processes that aid survival of transient oxygen deprivation.

Respiratory burst oxidases: the engines of ROS signaling

Reactive oxygen species (ROS) play a key signal transduction role in cells. They are involved in the regulation of growth, development, responses to environmental stimuli and cell death. The level of ROS in cells is determined by interplay between ROS producing pathways and ROS scavenging mechanisms, part of the ROS gene network of plants. Recent studies identified respiratory burst oxidase homologues (RBOHs) as key signaling nodes in the ROS gene network of plants integrating a multitude of signal transduction pathways with ROS signaling. The ability of RBOHs to integrate calcium signaling and protein phosphorylation with ROS production, coupled with genetic studies demonstrating their involvement in many different biological processes in cells, places RBOHs at the center of the ROS network of cells and demonstrate their important function in plants.

Metal-induced oxidative stress and plant mitochondria

A general status of oxidative stress in plants caused by exposure to elevated metal concentrations in the environment coincides with a constraint on mitochondrial electron transport, which enhances ROS accumulation at the mitochondrial level. As mitochondria are suggested to be involved in redox signaling under environmental stress conditions, mitochondrial ROS can initiate a signaling cascade mediating the overall stress response, i.e., damage versus adaptation. This review highlights our current understanding of metal-induced responses in plants, with focus on the production and detoxification of mitochondrial ROS. In addition, the potential involvement of retrograde signaling in these processes will be discussed.

Targeting metabolic pathways for genetic engineering abiotic stress-tolerance in crops

Abiotic stress conditions are the major limitations in modern agriculture. Although many genes associated with plant response(s) to abiotic stresses have been indentified and used to generate stress tolerant plants, the success in producing stress-tolerant crops is limited. New technologies are providing opportunities to generate stress tolerant crops. Biotechnological approaches that emphasize the development of transgenic crops under conditions that mimic the field situation and focus on the plant reproductive stage will significantly improve the opportunities of producing stress tolerant crops. Here, we highlight recent advances and discuss the limitations that hinder the fast integration of transgenic crops into agriculture and suggest possible research directions. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.