Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles

Analyses of the oligopeptide transporter gene family in poplar and grape

Background

Oligopeptide transporters (OPTs) are a group of membrane-localized proteins that have a broad range of substrate transport capabilities and that are thought to contribute to many biological processes. The OPT proteins belong to a small gene family in plants, which includes about 25 members in Arabidopsis and rice. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, expression profiling, functional divergence and selective pressure analysis has been reported thus far for Populus and Vitis.

Results

In the present study, a comprehensive analysis of the OPT gene family in Populus (P. trichocarpa) and Vitis (V. vinifera) was performed. A total of 20 and 18 full-length OPT genes have been identified in Populus and Vitis, respectively. Phylogenetic analyses indicate that these OPT genes consist of two classes that can be further subdivided into 11 groups. Gene structures are considerably conserved among the groups. The distribution of OPT genes was found to be non-random across chromosomes. A high proportion of the genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the OPT gene family. Expression patterns based on our analyses of microarray data suggest that many OPT genes may be important in stress response and functional development of plants. Further analyses of functional divergence and adaptive evolution show that, while purifying selection may have been the main force driving the evolution of the OPTs, some of critical sites responsible for the functional divergence may have been under positive selection.

Conclusions

Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus and Vitis OPT gene family and of the function and evolution of the OPT gene family in higher plants.

The effect of scale on gene expression: commercial versus laboratory wine fermentations

Molecular and cellular processes that are responsible for industrially relevant phenotypes of fermenting microorganisms are a central focus of biotechnological research. Such research intends to generate insights and solutions for fermentation-based industries with regards to issues such as improving product yield or the quality of the final fermentation product. For logistical reasons, and to ensure data reproducibility, such research is mostly carried out in defined or synthetic media and in small-scale fermentation vessels. Two questions are frequently raised regarding the applicability of this approach to solve problems experienced in industrial fermentations: (1) Is synthetic medium a sufficiently accurate approximation of the generally more complex natural (and frequently highly variable) substrates that are employed in most fermentation-based industries, and (2) can results obtained in small-scale laboratory fermentations be extrapolated to large-scale industrial environments? Here, we address the second question through a comparative transcriptomic approach by assessing the response of an industrial wine yeast strain fermenting a natural grape juice in small-scale laboratory and large-scale industrial conditions. In yeast, transcriptome analysis is arguably the best available tool to holistically assess the physiological state of a population and its response to changing environmental conditions. The data suggest that scale does indeed impact on some environmental parameters such as oxygen availability. However, the data show that small-scale fermentations nevertheless accurately reflect general molecular processes and adaptations during large-scale fermentation and that extrapolation of laboratory datasets to real industrial processes can be justified.

Water deficit and growth. Co-ordinating processes without an orchestrator?

Water deficit affects plant growth via reduced carbon accumulation, cell number and tissue expansion. We review the ways in which these processes are co-ordinated. Tissue expansion and its sensitivity to water deficit may be the most crucial process, involving tight co-ordination between the mechanisms which govern cell wall mechanical properties and plant hydraulics. The analyses of sensitivities, time constants and genetic correlations suggest that tissue expansion is loosely co-ordinated with cell division and carbon accumulation which may have limited direct effects on growth under water deficit. We therefore argue for essentially uncoupled mechanisms with feedbacks between them, rather than for a co-ordinated re-programming of all processes. Consequences on plant modelling and plant breeding in dry environment are discussed.

Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)

BACKGROUND

Global transcriptional analysis of loblolly pine (Pinus taeda L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine.

RESULTS

Microarrays were used to interrogate root cDNA populations obtained from 12 genotype × treatment combinations (four genotypes, three watering regimes). Comparison of drought-stressed roots with roots from the control treatment identified 2445 genes displaying at least a 1.5-fold expression difference (false discovery rate = 0.01). Genes commonly associated with drought response in pine and other plant species, as well as a number of abiotic and biotic stress-related genes, were up-regulated in drought-stressed roots. Only 76 genes were identified as differentially expressed in drought-recovered roots, indicating that the transcript population can return to the pre-drought state within 48 hours. Gene correlation analysis predicts a scale-free network topology and identifies eleven co-expression modules that ranged in size from 34 to 938 members. Network topological parameters identified a number of central nodes (hubs) including those with significant homology (E-values ≤ 2 × 10-30) to 9-cis-epoxycarotenoid dioxygenase, zeatin O-glucosyltransferase, and ABA-responsive protein. Identified hubs also include genes that have been associated previously with osmotic stress, phytohormones, enzymes that detoxify reactive oxygen species, and several genes of unknown function.

CONCLUSION

PtGen2 was used to evaluate transcriptome responses in loblolly pine and was leveraged to identify 2445 differentially expressed genes responding to severe drought stress in roots. Many of the genes identified are known to be up-regulated in response to osmotic stress in pine and other plant species and encode proteins involved in both signal transduction and stress tolerance. Gene expression levels returned to control values within a 48-hour recovery period in all but 76 transcripts. Correlation network analysis indicates a scale-free network topology for the pine root transcriptome and identifies central nodes that may serve as drivers of drought-responsive transcriptome dynamics in the roots of loblolly pine.

Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis vinifera L.) based on curation and mining of large-scale EST data sets

BACKGROUND

Abiotic stresses, such as water deficit and soil salinity, result in changes in physiology, nutrient use, and vegetative growth in vines, and ultimately, yield and flavor in berries of wine grape, Vitis vinifera L. Large-scale expressed sequence tags (ESTs) were generated, curated, and analyzed to identify major genetic determinants responsible for stress-adaptive responses. Although roots serve as the first site of perception and/or injury for many types of abiotic stress, EST sequencing in root tissues of wine grape exposed to abiotic stresses has been extremely limited to date. To overcome this limitation, large-scale EST sequencing was conducted from root tissues exposed to multiple abiotic stresses.

RESULTS

A total of 62,236 expressed sequence tags (ESTs) were generated from leaf, berry, and root tissues from vines subjected to abiotic stresses and compared with 32,286 ESTs sequenced from 20 public cDNA libraries. Curation to correct annotation errors, clustering and assembly of the berry and leaf ESTs with currently available V. vinifera full-length transcripts and ESTs yielded a total of 13,278 unique sequences, with 2302 singletons and 10,976 mapped to V. vinifera gene models. Of these, 739 transcripts were found to have significant differential expression in stressed leaves and berries including 250 genes not described previously as being abiotic stress responsive. In a second analysis of 16,452 ESTs from a normalized root cDNA library derived from roots exposed to multiple, short-term, abiotic stresses, 135 genes with root-enriched expression patterns were identified on the basis of their relative EST abundance in roots relative to other tissues.

CONCLUSIONS

The large-scale analysis of relative EST frequency counts among a diverse collection of 23 different cDNA libraries from leaf, berry, and root tissues of wine grape exposed to a variety of abiotic stress conditions revealed distinct, tissue-specific expression patterns, previously unrecognized stress-induced genes, and many novel genes with root-enriched mRNA expression for improving our understanding of root biology and manipulation of rootstock traits in wine grape. mRNA abundance estimates based on EST library-enriched expression patterns showed only modest correlations between microarray and quantitative, real-time reverse transcription-polymerase chain reaction (qRT-PCR) methods highlighting the need for deep-sequencing expression profiling methods.

Integrative analysis of metabolite and transcript abundance during the short-term response to saline and oxidative stress in the brown alga Ectocarpus siliculosus

The model brown alga Ectocarpus siliculosus undergoes extensive transcriptomic changes in response to abiotic stress, many of them related to primary metabolism and particularly to amino acid biosynthesis and degradation. In this study we seek to improve our knowledge of the mechanisms underlying the stress tolerance of this alga, in particular with regard to compatible osmolytes, by examining the effects of these changes on metabolite concentrations. We performed extensive metabolic profiling (urea, amino acids, sugars, polyols, organic acids, fatty acids) of Ectocarpus samples subjected to short-term hyposaline, hypersaline and oxidative stress, and integrated the results with previously published transcriptomic data. The most pronounced changes in metabolite concentrations occurred under hypersaline stress: both mannitol and proline were accumulated, but their low final concentrations indicate that, in this stress condition, both compounds are not likely to significantly contribute to osmoregulation at the level of the entire cell. Urea and trehalose were not detected in any of our samples. We also observed a shift in fatty acid composition from n-3 to n-6 fatty acids under high salinities, and demonstrated the salt stress-induced accumulation of small amounts of γ-aminobutyric acid (GABA). GABA could be synthesized in E. siliculosus through a salt stress-induced putrescine-degradation pathway.

Metabolite and mineral analyses of cotton near-isogenic lines introgressed with QTLs for productivity and drought-related traits

Quantitative trait loci (QTLs) for yield and drought-related traits were exchanged via marker-assisted selection between elite cultivars of two cotton species, Gossypium barbadense (GB) cv. F-177 and Gossypium hirsutum (GH) cv. Siv'on. Three of the resultant near-isogenic lines (NILs), each introgressed with a different QTL region, expressed an advantage in osmotic adjustment (OA) and other drought-related traits relative to their recipient parents. These NILs and the parental genotypes were field-grown under well-watered and water-limited conditions, and characterized for their metabolic and mineral compositions. Comparisons were then made between (1) GB and GH genotypes, (2) the contrasting water regimes and (3) each NIL and its recipient parent. Hierarchical clustering analysis clearly distinguished between GB and GH genotypes based on either metabolite or mineral composition. Comparisons between well-watered and water-limited conditions in each of the genotypes showed differing trends in the various solutes. The greater concentrations of potassium, magnesium and calcium under water stress, when compared with well-watered conditions, may have enhanced OA or osmoprotection. All NILs exhibited significantly modified solute composition relative to their recipient parents. In particular, increased levels of alanine, aspartic acid, citric acid, malic acid, glycerol, myoinositol, threonic acid, potassium, magnesium and calcium were found under drought conditions in one or more of the NILs relative to their recipient parents. The increased values of these solutes could contribute to the superior capacity of these NILs to cope with drought.

Water deficits uncouple growth from photosynthesis, increase C content, and modify the relationships between C and growth in sink organs

In plants, carbon (C) molecules provide building blocks for biomass production, fuel for energy, and exert signalling roles to shape development and metabolism. Accordingly, plant growth is well correlated with light interception and energy conversion through photosynthesis. Because water deficits close stomata and thus reduce C entry, it has been hypothesised that droughted plants are under C starvation and their growth under C limitation. In this review, these points are questioned by combining literature review with experimental and modelling illustrations in various plant organs and species. First, converging evidence is gathered from the literature that water deficit generally increases C concentration in plant organs. The hypothesis is raised that this could be due to organ expansion (as a major C sink) being affected earlier and more intensively than photosynthesis (C source) and metabolism. How such an increase is likely to interact with C signalling is not known. Hence, the literature is reviewed for possible links between C and stress signalling that could take part in this interaction. Finally, the possible impact of water deficit-induced C accumulation on growth is questioned for various sink organs of several species by combining published as well as new experimental data or data generated using a modelling approach. To this aim, robust correlations between C availability and sink organ growth are reported in the absence of water deficit. Under water deficit, relationships weaken or are modified suggesting release of the influence of C availability on sink organ growth. These results are interpreted as the signature of a transition from source to sink growth limitation under water deficit.

An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

BACKGROUND

Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency.

RESULTS

Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories.

CONCLUSION

We present the first comprehensive genome-wide transcript profile study of C. arabica and C. canephora, which can be freely assessed by the scientific community at http://www.lge.ibi.unicamp.br/coffea. Our data reveal the presence of species-specific/prevalent genes in coffee that may help to explain particular characteristics of these two crops. The identification of differentially expressed transcripts offers a starting point for the correlation between gene expression profiles and Coffea spp. developmental traits, providing valuable insights for coffee breeding and biotechnology, especially concerning sugar metabolism and stress tolerance.

Water deficit increases stilbene metabolism in Cabernet Sauvignon berries

The impact of water deficit on stilbene biosynthesis in wine grape (Vitis vinifera) berries was investigated. Water deficit increased the accumulation of trans-piceid (the glycosylated form of resveratrol) by 5-fold in Cabernet Sauvignon berries but not in Chardonnay. Similarly, water deficit significantly increased the transcript abundance of genes involved in the biosynthesis of stilbene precursors in Cabernet Sauvignon. Increased expression of stilbene synthase, but not that of resveratrol-O-glycosyltransferase, resulted in increased trans-piceid concentrations. In contrast, the transcript abundance of the same genes declined in Chardonnay in response to water deficit. Twelve single nucleotide polymorphisms (SNPs) were identified in the promoters of stilbene synthase genes of Cabernet Sauvignon, Chardonnay, and Pinot Noir. These polymorphisms resulted in eight changes within the predicted cis regulatory elements in Cabernet Sauvignon and Chardonnay. These results suggest that cultivar-specific molecular mechanisms might exist that control resveratrol biosynthesis in grapes.

Rubisco activity in Mediterranean species is regulated by the chloroplastic CO2 concentration under water stress

Water stress decreases the availability of the gaseous substrate for ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) by decreasing leaf conductance to CO(2). In spite of limiting photosynthetic carbon assimilation, especially in those environments where drought is the predominant factor affecting plant growth and yield, the effects of water deprivation on the mechanisms that control Rubisco activity are unclear. In the present study, 11 Mediterranean species, representing different growth forms, were subject to increasing levels of drought stress, the most severe one followed by rewatering. The results confirmed species-specific patterns in the decrease in the initial activity and activation state of Rubisco as drought stress and leaf dehydration intensified. Nevertheless, all species followed roughly the same trend when Rubisco activity was related to stomatal conductance (g(s)) and chloroplastic CO(2) concentration (C(c)), suggesting that deactivation of Rubisco sites could be induced by low C(c), as a result of water stress. The threshold level of C(c) that triggered Rubisco deactivation was dependent on leaf characteristics and was related to the maximum attained for each species under non-stressing conditions. Those species adapted to low C(c) were more capable of maintaining active Rubisco as drought stress intensified.

Metabolomics: creating new potentials for unraveling the mechanisms in response to salt and drought stress and for the biotechnological improvement of xero-halophytes

Breeders have long been interested in understanding the biological function and mechanism of xero-halophytes and their ability for growth in drought-stricken and salinized environments. However, the mechanisms in response to stress have been difficult to unravel because their defenses require regulatory changes to the activation of multiple genes and pathways. Metabolomics is becoming a key tool in comprehensively understanding the cellular response to abiotic stress and represents an important addition to the tools currently employed in genomics-assisted selection for plant improvement. In this review, we highlight the applications of plant metabolomics in characterizing metabolic responses to salt and drought stress, and identifying metabolic quantitative trait loci (QTLs). We also discuss the potential of metabolomics as a tool to unravel stress response mechanisms, and as a viable option for the biotechnological improvement of xero-halophytes when no other genetic information such as linkage maps and QTLs are available, by combining with germplasm-regression-combined marker-trait association identification.

Isolation and expression analysis of salt induced genes from contrasting grapevine (Vitis vinifera L.) cultivars

Salt stress adversely affects the growth of grapevine plants. In order to understand the molecular basis of salt stress response in grapevine plants, suppression subtractive hybridization (SSH) and microarray based screening approaches were combined. Two leaf-specific subtractive cDNA libraries were constructed from grapevine plants subjected to a moderate, incremental salt stress treatment. SSH were performed 6h and 24h after NaCl peaked at 100mM using cDNAs prepared from leaves of a salt tolerant cultivar (Razegui) as testers and cDNAs from unstressed leaves as drivers. Then, a pre-screened subset of cDNA clones from these SSH libraries were used to construct a Vitis vinifera cDNA array, in order to verify the expression changes of the genes upon salt treatment. Expression profiles were compared between the salt tolerant and a susceptible cultivar (Syrah) under both control conditions and after salt stress treatment. Seven cDNA clones were identified which were up-regulated by salt stress in two independent growth experiments and confirmed by RNA blot analysis. The transcript expression patterns of the selected genes differed between the contrasting grapevine cultivars tested with respect to stress-regulation. The possible relationship of individual cDNAs with salinity tolerance mechanisms is discussed.

Common and divergent physiological, hormonal and metabolic responses of Arabidopsis thaliana and Thellungiella halophila to water and salt stress

To explain the higher tolerance of Thellungiella to abiotic stress in comparison to Arabidopsis, several studies have focused on differences in ion absorption and gene expression. However, little is known about hormone regulation and metabolic responses. In this work, plants of both species were subjected to desiccation and salt stress to compare common and divergent responses. In control conditions, the number of significantly upregulated mass features as well as proline levels was higher in Tellungiella than in Arabidopsis. When subjected to desiccation, both species exhibited similar rates of water loss but proline over accumulation only occurred in Thellungiella; both species accumulated ABA and JA with a similar trend although Arabidopsis showed higher concentrations of both hormones which indicated a stronger impact of desiccation on Arabidopsis. However, Arabidopsis showed a higher number of significantly altered mass features than Thellungiella. Under salt stress, Thellungiella plants accumulated lower amounts of Cl(-) ions than Arabidopsis but exhibited a similar proline response. Under these conditions, ABA and JA levels increased in Arabidopsis whereas minimal changes in both hormone concentrations were recorded in Thellungiella. Contrastingly, the impact of salt stress on metabolite profiles was higher in Thellungiella than in Arabidopsis. Overall, data indicated that physiological responses in Arabidopsis are induced after stress imposition through hormonal regulation whereas Thellungiella has a basal metabolic configuration, better prepared to endure environmental cues.

Transcriptome changes in grapevine (Vitis vinifera L.) cv. Malbec leaves induced by ultraviolet-B radiation

BACKGROUND

Ultraviolet-B radiation (UV-B, 280-315 nm) is a natural component of sunlight, which has numerous regulatory effects on plant physiology. The nature of the response to UV-B is dependent on fluence rate, dose, duration and wavelength of the UV-B treatment. Some reports have analyzed the changes in gene expression caused by UV-B light on several plant species using microarray technology. However, there is no information on the transcriptome response triggered by UV-B in grapevine. In this paper we investigate the gene expression responses of leaves from in vitro cultured Vitis vinifera cv. Malbec plants subjected to the same dose of biologically effective UV-B radiation (4.75 kJ m-2 d-1) administered at two different fluence rates (16 h at ≅ 8.25 μW cm-2, 4 h at ≅ 33 μW cm-2) using a new custom made GrapeGen Affymetrix GeneChip®.

RESULTS

The number of genes modulated by high fluence rate UV-B doubled the number of genes modulated by low fluence UV-B. Their functional analyses revealed several functional categories commonly regulated by both UV-B treatments as well as categories more specifically modulated depending on UV-B fluence rate. General protective responses, namely the induction of pathways regulating synthesis of UV-B absorbing compounds such as the Phenylpropanoid pathway, the induction of different antioxidant defense systems and the activation of pathways commonly associated with pathogen defense and abiotic stress responses seem to play critical roles in grapevine responses against UV-B radiation. Furthermore, high fluence rate UV-B seemed to specifically modulate additional pathways and processes in order to protect grapevine plantlets against UV-B-induced oxidative stress, stop the cell cycle progression, and control protein degradation. On the other hand, low fluence rate UV-B regulated the expression of specific responses in the metabolism of auxin and abscisic acid as well as in the modification of cell walls that could be involved in UV-B acclimation-like processes.

CONCLUSION

Our results show the UV-B radiation effects on the leaf transcriptome of grapevine (Vitis vinifera cv. Malbec) plantlets. Functional categories commonly modulated under both UV-B treatments as well as transcripts specifically regulated in an UV-B-intensity dependent way were identified. While high fluence rate UV-B had regulatory effects mainly on defense or general multiple-stress responses pathways, low fluence rate UV-B promoted the expression of genes that could be involved in UV-B protection or the amelioration of the UV-B-induced damage. This study also provides an extensive list of genes regulating multiple metabolic pathways involved in the response of grapevine to UV-B that can be used for future researches.

Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice

Water-deficit stress is detrimental for rice growth, development, and yield. Transcriptome analysis of 1-week-old rice (Oryza sativa L. var. IR64) seedling under water-deficit stress condition using Affymetrix 57 K GeneChip® has revealed 1,563 and 1,746 genes to be up- and downregulated, respectively. In an effort to amalgamate data across laboratories, we identified 5,611 differentially expressing genes under varying extrinsic water-deficit stress conditions in six vegetative and one reproductive stage of development in rice. Transcription factors (TFs) involved in ABA-dependent and ABA-independent pathways have been found to be upregulated during water-deficit stress. Members of zinc-finger TFs namely, C₂H₂, C₂C₂, C₃H, LIM, PHD, WRKY, ZF-HD, and ZIM, along with TF families like GeBP, jumonji, MBF1 and ULT express differentially under water-deficit conditions. NAC (NAM, ATAF and CUC) TF family emerges to be a potential key regulator of multiple abiotic stresses. Among the 12 TF genes that are co-upregulated under water-deficit, salt and cold stress conditions, five belong to the NAC TF family. We identified water-deficit stress-responsive genes encoding key enzymes involved in biosynthesis of osmoprotectants like polyols and sugars; amino acid and quaternary ammonium compounds; cell wall loosening and structural components; cholesterol and very long chain fatty acid; cytokinin and secondary metabolites. Comparison of genes responsive to water-deficit stress conditions with genes preferentially expressed during panicle and seed development revealed a significant overlap of transcriptome alteration and pathways.

Changes in sulphur metabolism of grey poplar (Populus x canescens) leaves during salt stress: a metabolic link to photorespiration

The poplar hybrid Populus x canescens (syn. Populus tremula x Populus alba) was subjected to salt stress by applying 75 mM NaCl for 2 weeks in hydroponic cultures. Decreasing maximum quantum yield (Fv/Fm) indicated damage of photosystem II (PS II), which was more pronounced under nitrate compared with ammonium nutrition. In vivo staining with diaminobenzidine showed no accumulation of H(2)O(2) in the leaf lamina; moreover, staining intensity even decreased. But at the leaf margins, development of necrotic tissue was associated with a strong accumulation of H(2)O(2). Glutathione (GSH) contents increased in response to NaCl stress in leaves but not in roots, the primary site of salt exposure. The increasing leaf GSH concentrations correlated with stress-induced decreases in transpiration and net CO(2) assimilation rates at light saturation. Enhanced rates of photorespiration could also be involved in preventing reactive oxygen species formation in chloroplasts and, thus, in protecting PS II from damage. Accumulation of Gly and Ser in leaves indeed indicates increasing rates of photorespiration. Since Ser and Gly are both immediate precursors of GSH that can limit GSH synthesis, it is concluded that the salt-induced accumulation of leaf GSH results from enhanced photorespiration and is thus probably restricted to the cytosol.

Arabidopsis plants acclimate to water deficit at low cost through changes of carbon usage: an integrated perspective using growth, metabolite, enzyme, and gene expression analysis

Growth and carbon (C) fluxes are severely altered in plants exposed to soil water deficit. Correspondingly, it has been suggested that plants under water deficit suffer from C shortage. In this study, we test this hypothesis in Arabidopsis (Arabidopsis thaliana) by providing an overview of the responses of growth, C balance, metabolites, enzymes of the central metabolism, and a set of sugar-responsive genes to a sustained soil water deficit. The results show that under drought, rosette relative expansion rate is decreased more than photosynthesis, leading to a more positive C balance, while root growth is promoted. Several soluble metabolites accumulate in response to soil water deficit, with K(+) and organic acids as the main contributors to osmotic adjustment. Osmotic adjustment costs only a small percentage of the daily photosynthetic C fixation. All C metabolites measured (not only starch and sugars but also organic acids and amino acids) show a diurnal turnover that often increased under water deficit, suggesting that these metabolites are readily available for being metabolized in situ or exported to roots. On the basis of 30 enzyme activities, no in-depth reprogramming of C metabolism was observed. Water deficit induces a shift of the expression level of a set of sugar-responsive genes that is indicative of increased, rather than decreased, C availability. These results converge to show that the differential impact of soil water deficit on photosynthesis and rosette expansion results in an increased availability of C for the roots, an increased turnover of C metabolites, and a low-cost C-based osmotic adjustment, and these responses are performed without major reformatting of the primary metabolism machinery.

Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence

The recent release of the genome sequences of a number of crop and model plant species has made it possible to define the genome organisation and functional characteristics of specific genes and gene families of agronomic importance. For instance, Sorghum bicolor, maize (Zea mays) and Brachypodium distachyon genome sequences along with the model grass species rice (Oryza sativa) enable the comparative analysis of genes involved in plant defence. Germin-like proteins (GLPs) are a small, functionally and taxonomically diverse class of cupin-domain containing proteins that have recently been shown to cluster in an area of rice chromosome 8. The genomic location of this gene cluster overlaps with a disease resistance QTL that provides defence against two rice fungal pathogens (Magnaporthe oryzae and Rhizoctonia solani). Studies showing the involvement of GLPs in basal host resistance against powdery mildew (Blumeria graminis ssp.) have also been reported in barley and wheat. In this mini-review, we compare the close proximity of GLPs in publicly available cereal crop genomes and discuss the contribution that these proteins, and their genome sequence organisation, play in plant defence.

Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum

Studies of the resurrection plant Craterostigma plantagineum have revealed some of the mechanisms which these desiccation-tolerant plants use to survive environments with extreme dehydration and restricted seasonal water. Most resurrection plants are polyploid with large genomes, which has hindered efforts to obtain whole genome sequences and perform mutational analysis. However, the application of deep sequencing technologies to transcriptomics now permits large-scale analyses of gene expression patterns despite the lack of a reference genome. Here we use pyro-sequencing to characterize the transcriptomes of C. plantagineum leaves at four stages of dehydration and rehydration. This reveals that genes involved in several pathways, such as those required for vitamin K and thiamin biosynthesis, are tightly regulated at the level of gene expression. Our analysis also provides a comprehensive picture of the array of cellular responses controlled by gene expression that allow resurrection plants to survive desiccation.

Sulphate as a xylem-borne chemical signal precedes the expression of ABA biosynthetic genes in maize roots

Recent reports suggest that early sensing of soil water stress by plant roots and the concomitant reduction in stomatal conductance may not be mediated by root-sourced abscisic acid (ABA), but that other xylem-borne chemicals may be the primary stress signal(s). To gain more insight into the role of root-sourced ABA, the timing and location of the expression of genes for key enzymes involved in ABA biosynthesis in Zea mays roots was measured and a comprehensive analysis of root xylem sap constituents from the early to the later stages of water stress was conducted. Xylem sap and roots were sampled from plants at an early stage of water stress when only a reduction in leaf conductance was measured, as well as at later stages when leaf xylem pressure potential decreased. It was found that the majority of ABA biosynthetic genes examined were only significantly expressed in the elongation region of roots at a later stage of water stress. Apart from ABA, sulphate was the only xylem-borne chemical that consistently showed significantly higher concentrations from the early to the later stages of stress. Moreover, there was an interactive effect of ABA and sulphate in decreasing maize transpiration rate and Vicia faba stomatal aperture, as compared to ABA alone. The expression of a sulphate transporter gene was also analysed and it was found that it had increased in the elongation region of roots from the early to the later stages of water stress. Our results support the suggestion that in the early stage of water stress, increased levels of ABA in xylem sap may not be due to root biosynthesis, ABA glucose ester catabolism or pH-mediated redistribution, but may be due to shoot biosynthesis and translocation to the roots. The analysis of xylem sap mineral content and bioassays indicate that the anti-transpirant effect of the ABA reaching the stomata at the early stages of water stress may be enhanced by the increased concentrations of sulphate in the xylem which is also transported from the roots to the leaves.

Differential floral development and gene expression in grapevines during long and short photoperiods suggests a role for floral genes in dormancy transitioning

Daylength is an important environmental cue for synchronizing growth, flowering, and dormancy with seasonality. As many floral development genes are photoperiod regulated, it has been suggested that they could have a regulatory role in bud endodormancy. Therefore, the influence of photoperiod was studied on inflorescence primordia differentiation and floral pathway related gene expression during the development of overwintering buds in Vitis riparia and V. spp. 'Seyval'. Photoperiod treatments were imposed 35 days after budbreak, and histological and transcriptomic analyses were conducted during the subsequent 42 days of bud development. Long day (LD, 15 h) and short day (SD, 13 h) buds were floral competent by 21 days of photoperiod treatment (56 days after budbreak); however, the floral meristem developed faster in LD than in SD buds. Analysis of 132 floral pathway related genes represented on the Affymetrix Grape Genome array indicated 60 were significantly differentially expressed between photoperiod treatments. Genes predominantly related to floral transition or floral meristem development were identified by their association with distinct grape floral meristem development and an expression pattern in LD consistent with their previously identified roles in flowering literature. Genes with a potential dual role in floral development and dormancy transitioning were identified using photoperiod induced differences in floral development between LD and SD buds and uncharacteristic gene expression trends in relation to floral development. Candidate genes with the potential to play a dual role in SD dormancy induction include circadian rhythm or flowering transition related genes: AP2, BT1, COL-13, EIN3, ELF4, DDTR, GAI and HY5.

Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus

Translational genomics, the use of model species to generate knowledge about biological processes and the functions of genes, offers great promise to biotechnologists. Few studies have sought robust responses of model plants to environmental stresses, such as salinity, by altering the stress dosage or by repeating experiments in consecutive years and/or different seasons. We mined our published and unpublished data on legume salt acclimation for robust system features at the ionomic, transcriptomic and metabolomic levels. We analysed data from the model legume Lotus japonicus, obtained through six independent, long-term, non-lethal salt stress experiments which were carried out over two consecutive years. Best possible controlled greenhouse conditions were applied and two main questions asked: how reproducible are results obtained from physiologically meaningful salinity experiments, and what degree of bias may be expected if conclusions are drawn from less well-repeated sampling? A surprisingly large fraction of the transcriptional and metabolic responses to salt stress were not reproducible between experiments. A core set of robust changes was found that was shared between experiments. Many of these robust responses were qualitatively and quantitatively conserved between different accessions of the same species, indicating that the robust responses may be a sound starting point for translational genomics.

Isolation of WDR and bHLH genes related to flavonoid synthesis in grapevine (Vitis vinifera L.)

Anthocyanins and tannins are two of the most abundant flavonoids found in grapevine, and their synthesis is derived from the phenylpropanoid pathway. As described for model species such as Arabidopsis thaliana, maize and petunia, the end-point branches of this pathway are tightly regulated by the combinatorial interaction of three families of regulatory factors; MYB, bHLH (also known as MYC) and WDR proteins. Among these, only MYB genes have been previously identified in grapes. Here, we report the isolation of the first members from the WDR and bHLH families found in Vitis vinifera, named WDR1, WDR2 and MYCA1. WDR1 contributed positively to the accumulation of anthocyanins when it was overexpressed in A. thaliana, although it was not possible to determine the function of WDR2 by ectopic expression. The sub-cellular localizations of WDR1 and MYCA1 were observed by means of GFP-fusion proteins, indicating both cytoplasm and nuclear localization, in contrast to the localization of a MYB factor exclusively in the nucleus. The expression patterns of these genes were quantified in coloured reproductive organs throughout development, and correlated with anthocyanin accumulation and the expression profiles of the flavonoid-related MYBA1-2, UFGT, and ANR genes. In vitro grapevine plantlets grown under high salt concentrations showed a cultivar-dependent response for anthocyanin accumulation, which correlated with the expression of MYBA1-2, MYCA1 and WDR1 genes. These results suggest that MYCA1 may regulate ANR and UFGT and that this last control is easier to distinguish whenever MYBA genes are absent or in low abundance. Future studies should address the specific interactions of these proteins and their quantitative contribution to flavonoid synthesis in grape berries.

Identification of Fe-excess-induced genes in rice shoots reveals a WRKY transcription factor responsive to Fe, drought and senescence

Fe participates in several important reactions in plant metabolism. However, Fe homeostasis in plants is not completely understood, and molecular studies on Fe-excess stress are scarce. Rice (Oryza sativa L. ssp. indica) is largely cultivated in submerged conditions, where the extremely reductive environment can lead to severe Fe overload. In this work, we used representational difference analysis (RDA) to isolate sequences up-regulated in rice shoots after exposure to Fe-excess. We isolated 24 sequences which have putative functions in distinct cellular processes, such as transcription regulation (OsWRKY80), stress response (OsGAP1, DEAD-BOX RNA helicase), proteolysis (oryzain-α, rhomboid protein), photosynthesis (chlorophyll a/b binding protein), sugar metabolism (β glucosidase) and electron transport (NADH ubiquinone oxireductase). We show that the putative WRKY transcription factor OsWRKY80 is up-regulated in rice leaves, stems and roots after Fe-excess treatment. This up-regulation is also observed after dark-induced senescence and drought stress, indicating that OsWRKY80 could be a general stress-responsive gene. To our knowledge, this is the first report of an Fe-excess-induced transcription factor in plants.

Developmental stage specificity and the role of mitochondrial metabolism in the response of Arabidopsis leaves to prolonged mild osmotic stress

When subjected to stress, plants reprogram their growth by largely unknown mechanisms. To provide insights into this process, the growth of Arabidopsis (Arabidopsis thaliana) leaves that develop under mild osmotic stress was studied. Early during leaf development, cell number and size were reduced by stress, but growth was remarkably adaptable, as division and expansion rates were identical to controls within a few days of leaf initiation. To investigate the molecular basis of the observed adaptability, leaves with only proliferating, exclusively expanding, and mature cells were analyzed by transcriptomics and targeted metabolomics. The stress response measured in growing and mature leaves was largely distinct; several hundred transcripts and multiple metabolites responded exclusively in the proliferating and/or expanding leaves. Only a few genes were differentially expressed across the three stages. Data analysis showed that proliferation and expansion were regulated by common regulatory circuits, involving ethylene and gibberellins but not abscisic acid. The role of ethylene was supported by the analysis of ethylene-insensitive mutants. Exclusively in proliferating cells, stress induced genes of the so-called "mitochondrial dysfunction regulon," comprising alternative oxidase. Up-regulation for eight of these genes was confirmed with promoter:beta-glucuronidase reporter lines. Furthermore, mitochondria of stress-treated dividing cells were morphologically distinct from control ones, and growth of plants overexpressing the alternative oxidase gene was more tolerant to osmotic and drought stresses. Taken together, our data underline the value of analyzing stress responses in development and demonstrate the importance of mitochondrial respiration for sustaining cell proliferation under osmotic stress conditions.

VitisNet: "Omics" integration through grapevine molecular networks

Background

Genomic data release for the grapevine has increased exponentially in the last five years. The Vitis vinifera genome has been sequenced and Vitis EST, transcriptomic, proteomic, and metabolomic tools and data sets continue to be developed. The next critical challenge is to provide biological meaning to this tremendous amount of data by annotating genes and integrating them within their biological context. We have developed and validated a system of Grapevine Molecular Networks (VitisNet).

Methodology/Principal Findings

The sequences from the Vitis vinifera (cv. Pinot Noir PN40024) genome sequencing project and ESTs from the Vitis genus have been paired and the 39,424 resulting unique sequences have been manually annotated. Among these, 13,145 genes have been assigned to 219 networks. The pathway sets include 88 “Metabolic”, 15 “Genetic Information Processing”, 12 “Environmental Information Processing”, 3 “Cellular Processes”, 21 “Transport”, and 80 “Transcription Factors”. The quantitative data is loaded onto molecular networks, allowing the simultaneous visualization of changes in the transcriptome, proteome, and metabolome for a given experiment.

Conclusions/Significance

VitisNet uses manually annotated networks in SBML or XML format, enabling the integration of large datasets, streamlining biological functional processing, and improving the understanding of dynamic processes in systems biology experiments. VitisNet is grounded in the Vitis vinifera genome (currently at 8x coverage) and can be readily updated with subsequent updates of the genome or biochemical discoveries. The molecular network files can be dynamically searched by pathway name or individual genes, proteins, or metabolites through the MetNet Pathway database and web-portal at http://metnet3.vrac.iastate.edu/. All VitisNet files including the manual annotation of the grape genome encompassing pathway names, individual genes, their genome identifier, and chromosome location can be accessed and downloaded from the VitisNet tab at http://vitis-dormancy.sdstate.org.

Abscisic acid stimulated ripening and gene expression in berry skins of the Cabernet Sauvignon grape

We investigated the effect of exogenous abscisic acid (ABA) application on the transcriptome as well as the phenolic profiles in the skins of Vitis vinifera cv. Cabernet Sauvignon grape berries grown on the vine and cultured in vitro. ABA application rapidly induced the accumulation of anthocyanin and flavonol. Correlatively, the structural genes in the phenylpropanoid and flavonoid pathways, their transcriptional regulators, as well as genes considered to be involved in the acylation and transport of anthocyanin into the vacuole, were upregulated by ABA treatment. The Genechip analysis showed that the ABA treatment significantly up- or downregulated a total of 345 and 1,482 transcripts in the skins of berries grown on the vine and cultured in vitro, respectively. Exogenous ABA modulated the transcripts associated with osmotic responses, stress responses, cell wall modification, auxin and ethylene metabolism and responses, in addition to the induction of anthocyanin biosynthetic genes, and reduced those associated with photosynthesis; approximately half of these transcripts were identical to the previously reported ripening-specific genes.

Role of plant glyoxylate reductases during stress: a hypothesis

Molecular modelling suggests that a group of proteins in plants known as the β-hydroxyacid dehydrogenases, or the hydroxyisobutyrate dehydrogenase superfamily, includes enzymes that reduce succinic semialdehyde and glyoxylate to γ-hydroxybutyrate and glycolate respectively. Recent biochemical and expression studies reveal that NADPH-dependent cytosolic (termed GLYR1) and plastidial (termed GLYR2) isoforms of succinic semialdehyde/glyoxylate reductase exist in Arabidopsis. Succinic semialdehyde and glyoxylate are typically generated in leaves via two distinct metabolic pathways, γ-aminobutyrate and glycolate respectively. In the present review, it is proposed that the GLYRs function in the detoxification of both aldehydes during stress and contribute to redox balance. Outstanding questions are highlighted in a scheme for the subcellular organization of the detoxification mechanism in Arabidopsis.

Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance

Plants show varied cellular responses to salinity that are partly associated with maintaining low cytosolic Na(+) levels and a high K(+)/Na(+) ratio. Plant metabolites change with elevated Na(+), some changes are likely to help restore osmotic balance while others protect Na(+)-sensitive proteins. Metabolic responses to salt stress are described for two barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differed in salinity tolerance under the experimental conditions used. After 3 weeks of salt treatment, Clipper ceased growing whereas Sahara resumed growth similar to the control plants. Compared with Clipper, Sahara had significantly higher leaf Na(+) levels and less leaf necrosis, suggesting they are more tolerant to accumulated Na(+). Metabolite changes in response to the salt treatment also differed between the two cultivars. Clipper plants had elevated levels of amino acids, including proline and GABA, and the polyamine putrescine, consistent with earlier suggestions that such accumulation may be correlated with slower growth and/or leaf necrosis rather than being an adaptive response to salinity. It is suggested that these metabolites may be an indicator of general cellular damage in plants. By contrast, in the more tolerant Sahara plants, the levels of the hexose phosphates, TCA cycle intermediates, and metabolites involved in cellular protection increased in response to salt. These solutes remain unchanged in the more sensitive Clipper plants. It is proposed that these responses in the more tolerant Sahara are involved in cellular protection in the leaves and are involved in the tolerance of Sahara leaves to high Na(+).

Screening of genes induced by salt stress from Alfalfa

An alfalfa cDNA library induced by salt stress was constructed by suppression subtraction hybridization (SSH) technology. Total RNA from 10-day-old seedlings was used as a "driver," and total RNA from seedlings induced by salt was used as a "tester". One hundred and nineteen clones identified as positive clones by reverse Northern dot-blotting resulted in 82 uni-ESTs comprised of 16 contigs and 66 singletons. Blast analysis of deduced protein sequences revealed that 51 ESTs had identity similar to proteins with known function, while 24 could not be annotated at all. Most of the annotated sequences were homologous to genes involved in abiotic or biotic stress in plants. Among these proteins, beta-amylase, fructose-1,6-bisphosphate, aldolase, and sucrose synthase are related to osmolyte synthesis; a CCCH-type zinc finger protein, DNA binding protein, His-Asp phosphotransfer protein, and the RelA/SpoT protein partake in transcription regulation and signal transduction; and ribulose-l,5-bisphosphate carboxylase/oxygenase, chlorophyll a/b binding proteins, and an early light-inducible proteins are related to photosynthesis. In addition, several ESTs, similar to genes from other plant species, closely involved in salt stress were isolated from alfalfa, such as an aquaporin protein, a late embryogenesis-abundant protein, and glutathione peroxidase.

Regulation of malate metabolism in grape berry and other developing fruits

Organic acids are present in all plants, supporting numerous and varied facets of cellular metabolism. The type of organic acid found, and the levels to which they accumulate are extremely variable between species, developmental stages and tissue types. Acidity plays important roles in the organoleptic properties of plant tissues, where examples of both enhanced and reduced palatability can be ascribed to the presence of specific organic acids. In fruits, sourness is generally attributed to proton release from acids such as citric, malic, oxalic, quinic, succinic and tartaric, while the anion forms each contribute a distinct taste. Acidity imposes a strong influence on crop quality, and is an important factor in deciding the harvest date, particularly for fruits where acidity is important for further processing, as in wine grapes. In the grape, as for many other fruits, malate is one of the most prevalent acids, and is an important participant in numerous cellular functions. The accumulation of malate is thought to be due in large part to de novo synthesis in fruits such as the grape, through metabolism of assimilates translocated from leaf tissues, as well as photosynthetic activity within the fruit itself. During ripening, the processes through which malate is catabolised are of interest for advancing metabolic understanding, as well as for potential crop enhancement through agricultural or molecular practices. A body of literature describes research that has begun to unravel the regulatory mechanisms of enzymes involved in malate metabolism during fruit development, through exploration of protein and gene transcript levels. Datasets derived from a series of recent microarray experiments comparing transcript levels at several stages of grape berry development have been revisited, and are presented here with a focus on transcripts associated with malate metabolism. Developmental transcript patterns for enzymes potentially involved in grape malate metabolism have shown that some flux may occur through pathways that are less commonly regarded in ripening fruit, such as aerobic ethanol production. The data also suggest pyruvate as an important intermediate during malate catabolism in fruit. This review will combine an analysis of microarray data with information available on protein and enzyme activity patterns in grapes and other fruits, to explore pathways through which malate is conditionally metabolised, and how these may be controlled in response to developmental and climatic changes. Currently, an insufficient understanding of the complex pathways through which malate is degraded, and how these are regulated, prevents targeted genetic manipulation aimed at modifying fruit malate metabolism in response to environmental conditions.

Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome

Background

Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese Spring (CS), a Chinese Spring terminal deletion line (CS_5AL-10) and the durum wheat cultivar Creso were subjected to transcriptional profiling after exposure to mild and severe drought stress at the grain filling stage to find evidences of differential stress responses associated to different wheat genome regions.

Results

The transcriptome analysis of Creso, CS and its deletion line revealed 8,552 non redundant probe sets with different expression levels, mainly due to the comparisons between the two species. The drought treatments modified the expression of 3,056 probe sets. Besides a set of genes showing a similar drought response in Creso and CS, cluster analysis revealed several drought response features that can be associated to the different genomic structure of Creso, CS and CS_5AL-10. Some drought-related genes were expressed at lower level (or not expressed) in Creso (which lacks the D genome) or in the CS_5AL-10 deletion line compared to CS. The chromosome location of a set of these genes was confirmed by PCR-based mapping on the D genome (or the 5AL-10 region). Many clusters were characterized by different level of expression in Creso, CS and CS_AL-10, suggesting that the different genome organization of the three genotypes may affect plant adaptation to stress. Clusters with similar expression trend were grouped and functional classified to mine the biological mean of their activation or repression. Genes involved in ABA, proline, glycine-betaine and sorbitol pathways were found up-regulated by drought stress. Furthermore, the enhanced expression of a set of transposons and retrotransposons was detected in CS_5AL-10.

Conclusion

Bread and durum wheat genotypes were characterized by a different physiological reaction to water stress and by a substantially different molecular response. The genome organization accounted for differences in the expression level of hundreds of genes located on the D genome or controlled by regulators located on the D genome. When a genomic stress (deletion of a chromosomal region) was combined with low water availability, a molecular response based on the activation of transposons and retrotransposons was observed.

Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay

BACKGROUND

Water deficit has significant effects on grape berry composition resulting in improved wine quality by the enhancement of color, flavors, or aromas. While some pathways or enzymes affected by water deficit have been identified, little is known about the global effects of water deficit on grape berry metabolism.

RESULTS

The effects of long-term, seasonal water deficit on berries of Cabernet Sauvignon, a red-wine grape, and Chardonnay, a white-wine grape were analyzed by integrated transcript and metabolite profiling. Over the course of berry development, the steady-state transcript abundance of approximately 6,000 Unigenes differed significantly between the cultivars and the irrigation treatments. Water deficit most affected the phenylpropanoid, ABA, isoprenoid, carotenoid, amino acid and fatty acid metabolic pathways. Targeted metabolites were profiled to confirm putative changes in specific metabolic pathways. Water deficit activated the expression of numerous transcripts associated with glutamate and proline biosynthesis and some committed steps of the phenylpropanoid pathway that increased anthocyanin concentrations in Cabernet Sauvignon. In Chardonnay, water deficit activated parts of the phenylpropanoid, energy, carotenoid and isoprenoid metabolic pathways that contribute to increased concentrations of antheraxanthin, flavonols and aroma volatiles. Water deficit affected the ABA metabolic pathway in both cultivars. Berry ABA concentrations were highly correlated with 9-cis-epoxycarotenoid dioxygenase (NCED1) transcript abundance, whereas the mRNA expression of other NCED genes and ABA catabolic and glycosylation processes were largely unaffected. Water deficit nearly doubled ABA concentrations within berries of Cabernet Sauvignon, whereas it decreased ABA in Chardonnay at véraison and shortly thereafter.

CONCLUSION

The metabolic responses of grapes to water deficit varied with the cultivar and fruit pigmentation. Chardonnay berries, which lack any significant anthocyanin content, exhibited increased photoprotection mechanisms under water deficit conditions. Water deficit increased ABA, proline, sugar and anthocyanin concentrations in Cabernet Sauvignon, but not Chardonnay berries, consistent with the hypothesis that ABA enhanced accumulation of these compounds. Water deficit increased the transcript abundance of lipoxygenase and hydroperoxide lyase in fatty metabolism, a pathway known to affect berry and wine aromas. These changes in metabolism have important impacts on berry flavor and quality characteristics. Several of these metabolites are known to contribute to increased human-health benefits.

Transcriptome pathways unique to dehydration tolerant relatives of modern wheat

Among abiotic stressors, drought is a major factor responsible for dramatic yield loss in agriculture. In order to reveal differences in global expression profiles of drought tolerant and sensitive wild emmer wheat genotypes, a previously deployed shock-like dehydration process was utilized to compare transcriptomes at two time points in root and leaf tissues using the Affymetrix GeneChip(R) Wheat Genome Array hybridization. The comparison of transcriptomes reveal several unique genes or expression patterns such as differential usage of IP(3)-dependent signal transduction pathways, ethylene- and abscisic acid (ABA)-dependent signaling, and preferential or faster induction of ABA-dependent transcription factors by the tolerant genotype that distinguish contrasting genotypes indicative of distinctive stress response pathways. The data also show that wild emmer wheat is capable of engaging known drought stress responsive mechanisms. The global comparison of transcriptomes in the absence of and after dehydration underlined the gene networks especially in root tissues that may have been lost in the selection processes generating modern bread wheats.

Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocks

Salinity tolerance in Citrus is strongly related to leaf chloride accumulation. Both chloride homeostasis and specific genetic responses to Cl(-) toxicity are issues scarcely investigated in plants. To discriminate the transcriptomic network related to Cl(-) toxicity and salinity tolerance, we have used two Cl(-) salt treatments (NaCl and KCl) to perform a comparative microarray approach on two Citrus genotypes, the salt-sensitive Carrizo citrange, a poor Cl(-) excluder, and the tolerant Cleopatra mandarin, an efficient Cl(-) excluder. The data indicated that Cl(-) toxicity, rather than Na(+) toxicity and/or the concomitant osmotic perturbation, is the primary factor involved in the molecular responses of citrus plant leaves to salinity. A number of uncharacterized membrane transporter genes, like NRT1-2, were differentially regulated in the tolerant and the sensitive genotypes, suggesting its potential implication in Cl(-) homeostasis. Analyses of enriched functional categories showed that the tolerant rootstock induced wider stress responses in gene expression while repressing central metabolic processes such as photosynthesis and carbon utilization. These features were in agreement with phenotypic changes in the patterns of photosynthesis, transpiration, and stomatal conductance and support the concept that regulation of transpiration and its associated metabolic adjustments configure an adaptive response to salinity that reduces Cl(-) accumulation in the tolerant genotype.

Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell

BACKGROUND

Plants are often subjected to periods of soil and atmospheric water deficits during their life cycle as well as, in many areas of the globe, to high soil salinity. Understanding how plants respond to drought, salt and co-occurring stresses can play a major role in stabilizing crop performance under drought and saline conditions and in the protection of natural vegetation. Photosynthesis, together with cell growth, is among the primary processes to be affected by water or salt stress.

SCOPE

The effects of drought and salt stresses on photosynthesis are either direct (as the diffusion limitations through the stomata and the mesophyll and the alterations in photosynthetic metabolism) or secondary, such as the oxidative stress arising from the superimposition of multiple stresses. The carbon balance of a plant during a period of salt/water stress and recovery may depend as much on the velocity and degree of photosynthetic recovery, as it depends on the degree and velocity of photosynthesis decline during water depletion. Current knowledge about physiological limitations to photosynthetic recovery after different intensities of water and salt stress is still scarce. From the large amount of data available on transcript-profiling studies in plants subjected to drought and salt it is becoming apparent that plants perceive and respond to these stresses by quickly altering gene expression in parallel with physiological and biochemical alterations; this occurs even under mild to moderate stress conditions. From a recent comprehensive study that compared salt and drought stress it is apparent that both stresses led to down-regulation of some photosynthetic genes, with most of the changes being small (ratio threshold lower than 1) possibly reflecting the mild stress imposed. When compared with drought, salt stress affected more genes and more intensely, possibly reflecting the combined effects of dehydration and osmotic stress in salt-stressed plants.

Photosynthesis limitations during water stress acclimation and recovery in the drought-adapted Vitis hybrid Richter-110 (V. berlandierixV. rupestris)

The hybrid Richter-110 (Vitis berlandierixVitis rupestris) has the reputation of being a genotype strongly adapted to drought. A study was performed with plants of R-110 subjected to sustained water-withholding to induce acclimation to two different levels of water stress, followed by rewatering to induce recovery. The goal was to analyse how photosynthesis is regulated during acclimation to water stress and recovery. In particular, the regulation of stomatal conductance (g(s)), mesophyll conductance to CO(2) (g(m)), leaf photochemistry (chlorophyll fluorescence and thermoluminescence), and biochemistry (V(c,max)) were assessed. During water stress, g(s) declined to 0.1 and less than 0.05 mol CO(2) m(-2) s(-1) in moderately and severely water-stressed plants, respectively, and was kept quite constant during an acclimation period of 1-week. Leaf photochemistry proved to be very resistant to the applied water-stress conditions. By contrast, g(m) and V(c,max) were affected by water stress, but they were not kept constant during the acclimation period. g(m) was initially unaffected by water stress, and V(c,max) even increased above control values. However, after several days of acclimation to water stress, both parameters declined below (g(m)) or at (V(c,max)) control values. For the latter two parameters there seemed to be an interaction between water stress and cumulative irradiance, since both recovered to control values after several cloudy days despite water stress. A photosynthesis limitation analysis revealed that diffusional limitations and not biochemical limitations accounted for the observed decline in photosynthesis during water stress and slow recovery after rewatering, both in moderately and severely stressed plants. However, the relative contribution of stomatal (SL) and mesophyll conductance (MCL) limitations changes during acclimation to water stress, from predominant SL early during water stress to similar SL and MCL after acclimation. Finally, photosynthesis recovery after rewatering was mostly limited by SL, since stomatal closure recovered much more slowly than g(m).

Indian mustard aquaporin improves drought and heavy-metal resistance in tobacco

An aquaporin cDNA BjPIP1 isolated from heavy-metal accumulator Indian mustard (Brassica juncea L.) encodes a 286-residue protein. The deduced amino acid sequence of BjPIP1 with six putative transmembrane domains showed highest identity (85-99%) to PIP1 subfamily members. Semi-quantitative RT-PCR analysis revealed that BjPIP1 transcripts were more abundantly expressed in roots compared to aerial parts of Indian mustard. However, the expression of BjPIP1 in leaves was up-regulated by drought, salt, low temperature, and heavy metal stress, suggesting that BjPIP1 was involved in resistance to abiotic stresses. BjPIP1 under the control of 35S promoter was introduced into tobacco mediated with Agrobacterium tumefaciens, the transgenic tobacco exhibited a lower water loss rate, a decreased transpiration rate, and stomatal conductance compared to the wild-type plants under osmotic stress, indicating that BjPIP1 might enhance plant drought resistance by decreasing transpiration via reducing stomatal conductance. Furthermore, overexpression of BjPIP1 in tobacco enhanced Cd resistance of root growth, and lowered transpiration rate and stomatal conductance upon Cd exposure, suggesting that BjPIP1 might increase heavy-metal resistance by maintaining reasonable water status in tobacco. Moreover, the BjPIP1-overexpressing plants showed higher activities of antioxidative enzymes, and lower level of electrolyte leakage and malondialdehyde content under Cd stress, indicating BjPIP1 might enhance the antioxidative activity and membrane integrity in transgenic plants. Taken together, these results suggested that BjPIP1 might improve plant heavy-metal resistance through alleviating water deficit and oxidative damage induced by metal ions.

Plant metabolomics reveals conserved and divergent metabolic responses to salinity

New metabolic profiling technologies provide data on a wider range of metabolites than traditional targeted approaches. Metabolomic technologies currently facilitate acquisition of multivariate metabolic data using diverse, mostly hyphenated, chromatographic detection systems, such as GC-MS or liquid chromatography coupled to mass spectrometry, Fourier-transformed infrared spectroscopy or NMR-based methods. Analysis of the resulting data can be performed through a combination of non-supervised and supervised statistical methods, such as independent component analysis and analysis of variance, respectively. These methods reduce the complex data sets to information, which is relevant for the discovery of metabolic markers or for hypothesis-driven, pathway-based analysis. Plant responses to salinity involve changes in the activity of genes and proteins, which invariably lead to changes in plant metabolism. Here, we highlight a selection of recent publications in the salt stress field, and use gas chromatography time-of-flight mass spectrometry profiles of polar fractions from the plant models, Arabidopsis thaliana, Lotus japonicus and Oryza sativa to demonstrate the power of metabolite profiling. We present evidence for conserved and divergent metabolic responses among these three species and conclude that a change in the balance between amino acids and organic acids may be a conserved metabolic response of plants to salt stress.

Metabolomics for plant stress response

Stress in plants could be defined as any change in growth condition(s) that disrupts metabolic homeostasis and requires an adjustment of metabolic pathways in a process that is usually referred to as acclimation. Metabolomics could contribute significantly to the study of stress biology in plants and other organisms by identifying different compounds, such as by-products of stress metabolism, stress signal transduction molecules or molecules that are part of the acclimation response of plants. These could be further tested by direct measurements, correlated with changes in transcriptome and proteome expression and confirmed by mutant analysis. In this review, we will discuss recent application of metabolomics and system biology to the area of plant stress response. We will describe approaches such as metabolic profiling and metabolic fingerprinting as well as combination of different 'omics' platforms to achieve a holistic view of the plant response stress and conduct detailed pathway analysis.

Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis

BACKGROUND

Considering that sunflower production is expanding to arid regions, tolerance to abiotic stresses as drought, low temperatures and salinity arises as one of the main constrains nowadays. Differential organ-specific sunflower ESTs (expressed sequence tags) were previously generated by a subtractive hybridization method that included a considerable number of putative abiotic stress associated sequences. The objective of this work is to analyze concerted gene expression profiles of organ-specific ESTs by fluorescence microarray assay, in response to high sodium chloride concentration and chilling treatments with the aim to identify and follow up candidate genes for early responses to abiotic stress in sunflower.

RESULTS

Abiotic-related expressed genes were the target of this characterization through a gene expression analysis using an organ-specific cDNA fluorescence microarray approach in response to high salinity and low temperatures. The experiment included three independent replicates from leaf samples. We analyzed 317 unigenes previously isolated from differential organ-specific cDNA libraries from leaf, stem and flower at R1 and R4 developmental stage. A statistical analysis based on mean comparison by ANOVA and ordination by Principal Component Analysis allowed the detection of 80 candidate genes for either salinity and/or chilling stresses. Out of them, 50 genes were up or down regulated under both stresses, supporting common regulatory mechanisms and general responses to chilling and salinity. Interestingly 15 and 12 sequences were up regulated or down regulated specifically in one stress but not in the other, respectively. These genes are potentially involved in different regulatory mechanisms including transcription/translation/protein degradation/protein folding/ROS production or ROS-scavenging. Differential gene expression patterns were confirmed by qRT-PCR for 12.5% of the microarray candidate sequences.

CONCLUSION

Eighty genes isolated from organ-specific cDNA libraries were identified as candidate genes for sunflower early response to low temperatures and salinity. Microarray profiling of chilling and NaCl-treated sunflower leaves revealed dynamic changes in transcript abundance, including transcription factors, defense/stress related proteins, and effectors of homeostasis, all of which highlight the complexity of both stress responses. This study not only allowed the identification of common transcriptional changes to both stress conditions but also lead to the detection of stress-specific genes not previously reported in sunflower. This is the first organ-specific cDNA fluorescence microarray study addressing a simultaneous evaluation of concerted transcriptional changes in response to chilling and salinity stress in cultivated sunflower.

Transcriptional and metabolic profiling of grape (Vitis vinifera L.) leaves unravel possible innate resistance against pathogenic fungi

Grapevine species (Vitis sp.) are prone to several diseases, fungi being the major pathogens compromising its cultivation and economic profit around the world. Knowledge of the complexity of mechanisms responsible for resistance to fungus infection of cultivars, such as Regent, is necessary for strategies to be defined which will improve resistance in highly susceptible crop species. Transcript and metabolic profiles of the Vitis vinifera cultivars Regent and Trincadeira (resistant and susceptible to fungi, respectively) were analysed by cDNA microarray, quantitative real-time PCR, and nuclear magnetic resonance spectroscopy. The integration of datasets obtained through transcriptome and metabolome analysis revealed differences in transcripts and metabolites between both cultivars. These differences are probably associated with the innate resistance of Regent towards the mildews. Several transcripts related to stress and defence, namely a subtilisin-like protease, phenylalanine ammonia lyase, S-adenosylmethionine synthase, WD-repeat protein like, and J2P, were up-regulated in Regent suggesting an intrinsic resistance capability of this cultivar. A metabolic profile revealed an accumulation of compounds such as inositol and caffeic acid, which are known to confer resistance to fungi. The differences in transcripts and metabolites detected are discussed in terms of the metabolic pathways and their possible role in plant defence against pathogen attack, as well as their potential interest to discriminate among resistant and susceptible grapevine cultivars.

CBF4 is a unique member of the CBF transcription factor family of Vitis vinifera and Vitis riparia

The CBF/DREB1 transcription factors control an important pathway for increased freezing and drought tolerance in plants. We report here the isolation of one CBF/DREB1-like gene, CBF4, from both freezing-tolerant wild grape (Vitis riparia) and freezing-sensitive cultivated grape (Vitis vinifera). The deduced protein in V. riparia is 99% identical to the corresponding protein in V. vinifera; 45-48% to three other Vitis CBF proteins reported earlier and 57% to AtCBF1, and contains CBF-specific amino acid motifs. Agroinfiltration experiments in tobacco leaves revealed that VrCBF4 activates expression from reporter genes driven by a CRT-containing promoter. Expression of the endogenous Vitis CBF4 genes was low at ambient temperature, but enhanced upon exposure to low temperature (4 degrees C). Uncommon for CBF genes, this expression was maintained for several days. No significant difference in expression pattern was observed between V. riparia and V. vinifera. Vitis CBF4 was expressed in both young and mature tissue, in contrast to the previously described Vitis CBF1, 2 and 3. Together, these results suggest that CBF4 represents a second type of CBF in grape that might be more important for the over-wintering of grape plants.

Systemic and intracellular responses to photooxidative stress in Arabidopsis

As the sun tracks daily through the sky from east to west, different parts of the canopy are exposed to high light (HL). The extent of and mechanisms by which a systemic acquired acclimation (SAA) response might preacclimate shaded leaves that will be subsequently exposed to full sunlight is largely undefined. We investigated the role of an Arabidopsis thaliana zinc finger transcription factor, ZAT10, in SAA. ZAT10 overexpression resulted in enhanced tolerance to photoinhibitory light and exogenous H2O2, increased expression of antioxidative genes whose products are targeted to multiple subcellular compartments. Partial HL exposure of a leaf or leaves rapidly induced ZAT10 mRNA in distal, shaded photosynthetic tissues, including the floral stem, cauline leaves, and rosette, but not in roots. Fully 86% of fivefold HL-upregulated and 71% of HL-downregulated genes were induced and repressed, respectively, in distal, shaded leaves. Between 15 and 23% of genes whose expression changed in the HL and/or distal tissues were coexpressed in the ZAT10 overexpression plants, implicating ZAT10 in modulating the expression of SAA-regulated genes. The SAA response was detectable in plants with mutations in abscisic acid, methyl jasmonate, or salicylic acid synthesis or perception, and systemic H2O2 diffusion was not detected. Hence, SAA is distinct from pathogen-stimulated systemic acquired resistance and apparently involves a novel signal or combination of signals that preacclimate photosynthetic tissues to HL.

Tissue-specific mRNA expression profiling in grape berry tissues

Background

Berries of grape (Vitis vinifera) contain three major tissue types (skin, pulp and seed) all of which contribute to the aroma, color, and flavor characters of wine. The pericarp, which is composed of the exocarp (skin) and mesocarp (pulp), not only functions to protect and feed the developing seed, but also to assist in the dispersal of the mature seed by avian and mammalian vectors. The skin provides volatile and nonvolatile aroma and color compounds, the pulp contributes organic acids and sugars, and the seeds provide condensed tannins, all of which are important to the formation of organoleptic characteristics of wine. In order to understand the transcriptional network responsible for controlling tissue-specific mRNA expression patterns, mRNA expression profiling was conducted on each tissue of mature berries of V. vinifera Cabernet Sauvignon using the Affymetrix GeneChip^® Vitis oligonucleotide microarray ver. 1.0. In order to monitor the influence of water-deficit stress on tissue-specific expression patterns, mRNA expression profiles were also compared from mature berries harvested from vines subjected to well-watered or water-deficit conditions.

Results

Overall, berry tissues were found to express approximately 76% of genes represented on the Vitis microarray. Approximately 60% of these genes exhibited significant differential expression in one or more of the three major tissue types with more than 28% of genes showing pronounced (2-fold or greater) differences in mRNA expression. The largest difference in tissue-specific expression was observed between the seed and pulp/skin. Exocarp tissue, which is involved in pathogen defense and pigment production, showed higher mRNA abundance relative to other berry tissues for genes involved with flavonoid biosynthesis, pathogen resistance, and cell wall modification. Mesocarp tissue, which is considered a nutritive tissue, exhibited a higher mRNA abundance of genes involved in cell wall function and transport processes. Seeds, which supply essential resources for embryo development, showed higher mRNA abundance of genes encoding phenylpropanoid biosynthetic enzymes, seed storage proteins, and late embryogenesis abundant proteins. Water-deficit stress affected the mRNA abundance of 13% of the genes with differential expression patterns occurring mainly in the pulp and skin. In pulp and seed tissues transcript abundance in most functional categories declined in water-deficit stressed vines relative to well-watered vines with transcripts for storage proteins and novel (no-hit) functional assignments being over represented. In the skin of berries from water-deficit stressed vines, however, transcripts from several functional categories including general phenypropanoid and ethylene metabolism, pathogenesis-related responses, energy, and interaction with the environment were significantly over-represented.

Conclusion

These results revealed novel insights into the tissue-specific expression mRNA expression patterns of an extensive repertoire of genes expressed in berry tissues. This work also establishes an extensive catalogue of gene expression patterns for future investigations aimed at the dissection of the transcriptional regulatory hierarchies that govern tissue-specific expression patterns associated with tissue differentiation within berries. These results also confirmed that water-deficit stress has a profound effect on mRNA expression patterns particularly associated with the biosynthesis of aroma and color metabolites within skin and pulp tissues that ultimately impact wine quality.

Transcript abundance profiles reveal larger and more complex responses of grapevine to chilling compared to osmotic and salinity stress

Cabernet Sauvignon grapevines were exposed to sudden chilling (5 degrees C), water deficit (PEG), and an iso-osmotic salinity (120 mM NaCl and 12 mM CaCl(2)) for 1, 4, 8, and 24 h. Stomatal conductance and stem water potentials were significantly reduced after stress application. Microarray analysis of transcript abundance in shoot tips detected no significant differences in transcript abundance between salinity and PEG before 24 h. Chilling stress relates to changes in membrane structure, and transcript abundance patterns were predicted to reflect this. Forty-three percent of transcripts affected by stress vs control for 1 through 8 h were affected only by chilling. The functional categories most affected by stress included metabolism, protein metabolism, and signal transduction. Osmotic stress affected more protein synthesis and cell cycle transcripts, whereas chilling affected more calcium signaling transcripts, indicating that chilling has more complex calcium signaling. Stress affected many hormone (ABA, ethylene, and jasmonate) and transcription factor transcripts. The concentrations and transporter transcripts of several anions increased with time, including nitrate, sulfate, and phosphate. The transcript abundance changes in this short-term study were largely the same as a gradually applied long-term salinity and water-deficit study (Cramer et al. Funct Integr Genomics 7:111-134, 2007), but the reverse was not true, indicating a larger and more complex response in the acclimation process of a gradual long-term stress.

Transcript abundance profiles reveal larger and more complex responses of grapevine to chilling compared to osmotic and salinity stress

Cabernet Sauvignon grapevines were exposed to sudden chilling (5 degrees C), water deficit (PEG), and an iso-osmotic salinity (120 mM NaCl and 12 mM CaCl(2)) for 1, 4, 8, and 24 h. Stomatal conductance and stem water potentials were significantly reduced after stress application. Microarray analysis of transcript abundance in shoot tips detected no significant differences in transcript abundance between salinity and PEG before 24 h. Chilling stress relates to changes in membrane structure, and transcript abundance patterns were predicted to reflect this. Forty-three percent of transcripts affected by stress vs control for 1 through 8 h were affected only by chilling. The functional categories most affected by stress included metabolism, protein metabolism, and signal transduction. Osmotic stress affected more protein synthesis and cell cycle transcripts, whereas chilling affected more calcium signaling transcripts, indicating that chilling has more complex calcium signaling. Stress affected many hormone (ABA, ethylene, and jasmonate) and transcription factor transcripts. The concentrations and transporter transcripts of several anions increased with time, including nitrate, sulfate, and phosphate. The transcript abundance changes in this short-term study were largely the same as a gradually applied long-term salinity and water-deficit study (Cramer et al. Funct Integr Genomics 7:111-134, 2007), but the reverse was not true, indicating a larger and more complex response in the acclimation process of a gradual long-term stress.