Gene expression profiles during the initial phase of salt stress in rice

A plastid-localized glycogen synthase kinase 3 modulates stress tolerance and carbohydrate metabolism

Glycogen synthase kinase 3 (GSK-3) was originally identified as a regulator of glycogen synthesis in mammals. Like starch in plants, glycogen is a polymer of glucose, and serves as an energy and carbon store. Starch is the main carbohydrate store in plants. Regulation of starch metabolism, in particular in response to environmental cues, is of primary importance for carbon and energy flow in plants but is still obscure. Here, we provide evidence that MsK4, a novel Medicago sativa GSK-3-like kinase, connects stress signalling with carbon metabolism. MsK4 was found to be a plastid-localized protein kinase that is associated with starch granules. High-salt stress rapidly induced the in vivo kinase activity of MsK4. Metabolic profiling of MsK4 over-expressor lines revealed changes in sugar metabolism, including increased amounts of maltose, the main degradation product of starch in leaves. Plants over-expressing MsK4 showed improved tolerance to salt stress. Moreover, under high-salinity conditions, MsK4-over-expressing plants accumulated significantly more starch and showed modified carbohydrate content compared with wild-type plants. Overall, these data indicate that MsK4 is an important regulator that adjusts carbohydrate metabolism to environmental stress.

Monitoring of gene expression profiles and identification of candidate genes involved in drought responses in Festuca mairei

To understand the molecular genetic basis underlying drought tolerance in grasses, the cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique was applied for identification of genes responding to drought stress in a xerophytic adapted plant, Festuca mairei. A total of 11,346 transcript derived fragments (TDFs) were detected, and 464 (4.1%) TDFs were identified as differentially expressed fragments (DEFs) during the drought treatment of the plant. The expression patterns of these DEFs included up-regulated ( approximately 30%), down-regulated ( approximately 54.3%), and the remainder ( approximately 16.7%) showing transient changes. The differential expression patterns of 171 DEFs were further confirmed by macroarray hybridization analysis. Sequences had been obtained for 163 DEFs, and 62 sequences had no significant hits to sequences currently in public databases. Predicted functions of remaining 101 sequences were subdivided into 17 categories. Down-regulated genes were highly represented by metabolism and cellular biogenesis. Up-regulated DEFs were enriched in genes involved in transcription, defense, cell cycle and DNA processing. Analysis of the 163 DEFs provides a first glimpse into the transcripts of F. mairei during drought stress treatment. The combination of data from studies on genetic model plants and on diverse plant species will enhance understanding of the drought tolerance mechanisms in plants.

Desiccation and zinc binding induce transition of tomato abscisic acid stress ripening 1, a water stress- and salt stress-regulated plant-specific protein, from unfolded to folded state

Abscisic acid stress ripening 1 (ASR1) is a low molecular weight plant-specific protein encoded by an abiotic stress-regulated gene. Overexpression of ASR1 in transgenic plants increases their salt tolerance. The ASR1 protein possesses a zinc-dependent DNA-binding activity. The DNA-binding site was mapped to the central part of the polypeptide using truncated forms of the protein. Two additional zinc-binding sites were shown to be localized at the amino terminus of the polypeptide. ASR1 protein is presumed to be an intrinsically unstructured protein using a number of prediction algorithms. The degree of order of ASR1 was determined experimentally using nontagged recombinant protein expressed in Escherichia coli and purified to homogeneity. Purified ASR1 was shown to be unfolded using dynamic light scattering, gel filtration, microcalorimetry, circular dichroism, and Fourier transform infrared spectrometry. The protein was shown to be monomeric by analytical ultracentrifugation. Addition of zinc ions resulted in a global change in ASR1 structure from monomer to homodimer. Upon binding of zinc ions, the protein becomes ordered as shown by Fourier transform infrared spectrometry and microcalorimetry, concomitant with dimerization. Tomato (Solanum lycopersicum) leaf soluble ASR1 is unstructured in the absence of added zinc and gains structure upon binding of the metal ion. The effect of zinc binding on ASR1 folding and dimerization is discussed.

Genome-wide identification and analyses of the rice calmodulin and related potential calcium sensor proteins

BACKGROUND

A wide range of stimuli evoke rapid and transient increases in [Ca2+]cyt in plant cells which are transmitted by protein sensors that contain EF-hand motifs. Here, a group of Oryza sativa L. genes encoding calmodulin (CaM) and CaM-like (CML) proteins that do not possess functional domains other than the Ca2+-binding EF-hand motifs was analyzed.

RESULTS

By functional analyses and BLAST searches of the TIGR rice database, a maximum number of 243 proteins that possibly have EF-hand motifs were identified in the rice genome. Using a neighbor-joining tree based on amino acid sequence similarity, five loci were defined as Cam genes and thirty two additional CML genes were identified. Extensive analyses of the gene structures, the chromosome locations, the EF-hand motif organization, expression characteristics including analysis by RT-PCR and a comparative analysis of Cam and CML genes in rice and Arabidopsis are presented.

CONCLUSION

Although many proteins have unknown functions, the complexity of this gene family indicates the importance of Ca2+-signals in regulating cellular responses to stimuli and this family of proteins likely plays a critical role as their transducers.

Genotypic variability in sequence and expression of HVA1 gene in Tibetan hulless barley, Hordeum vulgare ssp. vulgare, associated with resistance to water deficit

Late embryogenesis abundant (LEA) proteins are thought to protect against water stress in plants. Characteristics of sequence and expression of barley gene HVA1, a member of LEA group 3 protein, were investigated in hulless barley (Hordeum vulgare ssp. vulgare), associated with phenotypically diverse drought-tolerant genotypes. Sensitive and tolerant genotypes were identified from Tibetan populations of cultivated hulless barley, based on scores of water loss rate (WLR), maldondialdehyde (MDA), and proline content. The results indicated that lower MDA contents, lower scores of WLR, and higher proline contents were associated with drought-tolerant genotypes in hulless barley. Notably, differential trends of expression patterns were detected among the selected contrasting genotypes, depending on the duration of dehydration stress. The HVA1 gene tended to respond earlier in the tolerance (after 2 h) compared with sensitive genotypes (after 4 h). Results of quantitative real-time PCR indicated that the relative level of HVA1 expression was always higher in tolerant genotypes, rapidly increasing at the earlier stages (after 2–4 h of dehydration). However, HVA1 expressions of sensitive genotypes had a fast increase from 8 to 12 h of stress. Variable numbers of the 11-amino-acid-motif in LEA3 proteins were not consistent with the lines of drought resistance in hulless barley. Molecular characteristic of LEA3 protein in tolerant lines existed in the consistency of Gln32, Arg33, and Ala195 in Tibetan hulless barley. The present study may indicate that the differential HVA1 gene has a functional role in the dehydration tolerance in hulless barley. The authors suggested that the observed variability in sequence and expression of HVA1 could be related to the diverse drought-tolerant genotypes in crops.

Identification of stress-responsive genes in an indica rice (Oryza sativa L.) using ESTs generated from drought-stressed seedlings

The impacts of drought on plant growth and development limit cereal crop production worldwide. Rice (Oryza sativa) productivity and production is severely affected due to recurrent droughts in almost all agroecological zones. With the advent of molecular and genomic technologies, emphasis is now placed on understanding the mechanisms of genetic control of the drought-stress response. In order to identify genes associated with water-stress response in rice, ESTs generated from a normalized cDNA library, constructed from drought-stressed leaf tissue of an indica cultivar, Nagina 22 were used. Analysis of 7794 cDNA sequences led to the identification of 5815 rice ESTs. Of these, 334 exhibited no significant sequence homology with any rice ESTs or full-length cDNAs in public databases, indicating that these transcripts are enriched during drought stress. Analysis of these 5815 ESTs led to the identification of 1677 unique sequences. To characterize this drought transcriptome further and to identify candidate genes associated with the drought-stress response, the rice data were compared with those for abiotic stress-induced sequences obtained from expression profiling studies in Arabidopsis, barley, maize, and rice. This comparative analysis identified 589 putative stress-responsive genes (SRGs) that are shared by these diverse plant species. Further, the identified leaf SRGs were compared to expression profiles for a drought-stressed rice panicle library to identify common sequences. Significantly, 125 genes were found to be expressed under drought stress in both tissues. The functional classification of these 125 genes showed that a majority of them are associated with cellular metabolism, signal transduction, and transcriptional regulation.

Microarray analysis of Fusarium graminearum-induced wheat genes: identification of organ-specific and differentially expressed genes

A wheat cDNA microarray consisting of 5739 expressed sequence tags (ESTs) was used to investigate the transcriptome patterns of the glume, lemma, palea, anther, ovary and rachis dissected from infected wheat spikes after inoculation with the fungus Fusarium graminearum, the causal agent of fusarium head blight (FHB) disease. Stringent conditions were employed to reduce the false discovery rate. The significance analysis of microarrays (SAM) was used to identify transcripts that showed a differential response between fungal-challenged vs. control plants. To verify the microarray data, Northern blot analysis was carried out on randomly selected up-regulated clones. We observed 185 (3.2%) up-regulated and 16 (0.28%) down-regulated ESTs in the six organs constituting the wheat spike. Many up-regulated ESTs (46.67%) showed no homology with sequences of known functions, whereas others showed homology with genes involved in defence and stress responses, the oxidative burst of H(2)O(2), regulatory functions, protein synthesis and the phenylpropanoid pathway. The monitoring of genes in specific organs avoided the averaging of expression values over multiple organs that occurs when using data from the whole spike. Our data allowed us to uncover new up-regulated genes expressed in specific organs. The study revealed that each organ had a defined and distinctive transcriptome pattern in response to F. graminearum infection.

How does arbuscular mycorrhizal symbiosis regulate root hydraulic properties and plasma membrane aquaporins in Phaseolus vulgaris under drought, cold or salinity stresses?

Here, we evaluated how the arbuscular mycorrhizal (AM) symbiosis regulates root hydraulic properties and root plasma membrane aquaporins (PIP) under different stresses sharing a common osmotic component. Phaseolus vulgaris plants were inoculated or not with the AM fungus Glomus intraradices, and subjected to drought, cold or salinity. Stress effects on root hydraulic conductance (L), PIP gene expression and protein abundance were evaluated. Under control conditions, L in AM plants was about half that in nonAM plants. However, L was decreased as a result of the three stresses in nonAM plants, while it was almost unchanged in AM plants. At the same time, PIP2 protein abundance and phosphorylation state presented the same trend as L. Finally, the expression of each PIP gene responded differently to each stress and was dependent on the AM fungal presence. Differential expression of the PIP genes studied under each stress depending on the AM fungal presence may indicate a specific function and regulation by the AM symbiosis of each gene under the specific conditions of each stress tested.

Time-course metabolic profiling in Arabidopsis thaliana cell cultures after salt stress treatment

Salt stress is one of the most important factors limiting plant cultivation. Many investigations of plant response to high salinity have been performed using conventional transcriptomics and/or proteomics approaches. However, transcriptomics and proteomics techniques are not all-encompassing methods that can achieve exclusive insights into the metabolite networks contributing to biochemical reactions. Hence, the functions of the complex stress response pathways are yet to be determined, especially at the metabolic level. A time-course metabolic profiling with Arabidopsis thaliana cell cultures after the imposition of salt stress is reported in this study. Analyses of primary metabolites, especially small polar metabolites such as amino acids, sugars, sugar alcohols, organic acids, and amines, was performed by GC/MS and LC/MS at 0.5, 1, 2, 4, 12, 24, 48, and 72 h after a salt-stress treatment with 100 mM NaCl being the final concentration. The mass chromatographic data were converted into matrix data sets, which were subjected to data mining processes, including principal component analysis (PCA) and batch-learning self-organizing mapping analysis (BL-SOM). The mining results suggest that the methylation cycle for the supply of methyl groups, the phenylpropanoid pathway for lignin production, and glycinebetaine biosynthesis are synergetically induced as a short-term response against salt-stress treatment. The results also suggest the the co-induction of glycolysis and sucrose metabolism as well as co-reduction of the methylation cycle as long-term responses to salt stress.

Comparative proteomic analysis of NaCl stress-responsive proteins in Arabidopsis roots

NaCl stress is a major abiotic stress limiting the productivity and the geographical distribution of many plant species. Roots are the primary site of salinity perception. To understand better NaCl stress responses in Arabidopsis roots, a comparative proteomic analysis of roots that had been exposed to 150 mM NaCl for either 6 h or 48 h was conducted. Changes in the abundance of protein species within roots were examined using two-dimensional electrophoresis. Among the >1000 protein spots reproducibly detected on each gel, the abundance of 112 protein spots decreased and 103 increased, at one or both time points, in response to NaCl treatment. Through liquid-chromatography-tandem mass spectrometry, identity was assigned to 86 of the differentially abundant spots. The proteins identified included many previously characterized stress-responsive proteins and others related to processes including scavenging for reactive oxygen species; signal transduction; translation, cell wall biosynthesis, protein translation, processing and degradation; and metabolism of energy, amino acids, and hormones. At the resolution of individual genes and proteins, poor statistical correlation (6 h, r= -0.13; 48 h, r=0.11) of these protein expression data with previous microarray results was detected, supporting the concept that post-transcriptional regulation plays an important role in stress-responsive gene expression, and highlighting the need for combined transcriptomic and proteomic analyses.

Putative role of aquaporins in variable hydraulic conductance of leaves in response to light

Molecular and physiological studies in walnut (Juglans regia) are combined to establish the putative role of leaf plasma membrane aquaporins in the response of leaf hydraulic conductance (K(leaf)) to irradiance. The effects of light and temperature on K(leaf) are described. Under dark conditions, K(leaf) was low, but increased by 400% upon exposure to light. In contrast to dark conditions, K(leaf) values of light-exposed leaves responded to temperature and 0.1 mm cycloheximide treatments. Furthermore, K(leaf) was not related to stomatal aperture. Data of real-time reverse transcription-polymerase chain reaction showed that K(leaf) dynamics were tightly correlated with the transcript abundance of two walnut aquaporins (JrPIP2,1 and JrPIP2,2). Low K(leaf) in the dark was associated with down-regulation, whereas high K(leaf) in the light was associated with up-regulation of JrPIP2. Light responses of K(leaf) and aquaporin transcripts were reversible and inhibited by cycloheximide, indicating the importance of de novo protein biosynthesis in this process. Our results indicate that walnut leaves can rapidly change their hydraulic conductance and suggest that these changes can be explained by regulation of plasma membrane aquaporins. Model simulation suggests that variable leaf hydraulic conductance in walnut might enhance leaf gas exchanges while buffering leaf water status in response to ambient light fluctuations.

Identification of early salt stress response genes in tomato root by suppression subtractive hybridization and microarray analysis

High salinity is one of the most serious threats to crop production. To understand the molecular basis of plant responses to salt stress better, suppression subtractive hybridization (SSH) and microarray approaches were combined to identify the potential important or novel genes involved in the early stage of tomato responses to severe salt stress. First, SSH libraries were constructed for the root tissue of two cultivated tomato (Solanum lycopersicum) genotypes: LA2711, a salt-tolerant cultivar, and ZS-5, a salt-sensitive cultivar, to compare salt treatment and non-treatment plants. Then a subset of clones from these SSH libraries were used to construct a tomato cDNA array and microarray analysis was carried out to verify the expression changes of this set of clones upon a high concentration of salt treatment at various time points compared to the corresponding non-treatment controls. A total of 201 non-redundant genes that were differentially expressed upon 30 min of severe salt stress either in LA2711 or ZS-5 were identified from microarray analysis; most of these genes have not previously been reported to be associated with salt stress. The diversity of the putative functions of these genes indicated that salt stress resulted in a complex response in tomato plants.

Early PLDalpha-mediated events in response to progressive drought stress in Arabidopsis: a transcriptome analysis

Phospholipase D (PLD) has been implicated in a variety of stresses including osmotic stress and wounding. PLDalpha1-derived phosphatidic acid interacts with ABI1 phosphatase 2C and promotes abscisic acid signalling. It has also been shown to regulate proline biosynthesis negatively. Plants with abrogated PLDalpha show insensitivity to abscisic acid (ABA) and impaired stomatal conductance. The goal in the present study was to identify early PLDalpha-mediated events in response to progressive drought stress in Arabidopsis. Water was withheld from 7-week-old Arabidopsis thaliana (Col-0) and antisense-PLDalpha1 (anti-PLDalpha) in a controlled environment chamber. Diurnal leaf water potential (LWP) and photosynthesis measurements were recorded five and three times a day, respectively. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and microarray analyses were conducted using RNA from shoots collected at the fourth LWP time point on the ninth day after stress imposition. Anti-PLDalpha experienced severe water stress (-1.28 MPa) at the same time period that Col-0 experienced less water stress (-0.31 MPa). Diurnal LWP measurements showed that anti-PLDalpha had a lower LWP than Col-0 in both control and drought-stress conditions. Photosynthesis was also more affected in anti-PLDalpha than in Col-0. Anti-PLDalpha plants recovered fully following rehydration after 10 d of stress. qRT-PCR revealed up to 18-fold lower values for PLDalpha transcripts in stressed anti-PLDalpha plants when compared with stressed Col-0. Microarray expression profiles revealed distinct gene expression patterns in Col-0 and anti-PLDalpha. No differences in gene expression were detected between the two genotypes in the absence of drought stress. ROP8, PLDdelta, and lipid transfer proteins were among the differentially expressed genes between the two genotypes.

Proteomic responses of rice young panicles to salinity

Rice (Oryza sativa) is most sensitive to salinity during the reproductive stage. We employed a proteomic approach to further understand the mechanism of plant responses to salinity at an early reproductive stage. Plants were grown in culture solution and salt stress imposed at panicle initiation. After 12 days of stress, young panicles were collected from control and salt stressed plants. The Na+ and K+ content of panicle and several yield components changed significantly in response to short-term salt stress. The collected panicles were sorted into three different sizes (7 +/- 1, 11 +/- 1, and 15 +/- 1 mm) and their proteome patterns were analyzed using 2-DE in triplicates. The expression pattern of 13 proteins significantly changed in all panicle sizes in response to stress. MS analysis of salt responsive proteins and 16 other highly abundant proteins of panicle led to the identification of proteins involved in several salt responsive mechanisms which may increase plant adaptation to salt stress including higher constitutive expression level and up-regulation of antioxidants, up-regulation of proteins involved in translation, transcription, signal transduction, and ATP generation. To the best of our knowledge, this is the first proteome analysis of plant young panicle which may enhance our understanding of plant molecular responses to salinity. Proteome reference map of rice young panicle is available at http://www.proteome.ir.

DNA Microarray Analyses in Higher Plants

DNA microarrays were originally devised and described as a convenient technology for the global analysis of plant gene expression. Over the past decade, their use has expanded enormously to cover all kingdoms of living organisms. At the same time, the scope of applications of microarrays has increased beyond expression analyses, with plant genomics playing a leadership role in the on-going development of this technology. As the field has matured, the rate-limiting step has moved from that of the technical process of data generation to that of data analysis. We currently face major problems in dealing with the accumulating datasets, not simply with respect to how to archive, access, and process the huge amounts of data that have been and are being produced, but also in determining the relative quality of the different datasets. A major recognized concern is the appropriate use of statistical design in microarray experiments, without which the datasets are rendered useless. A vigorous area of current research involves the development of novel statistical tools specifically for microarray experiments. This article describes, in a necessarily selective manner, the types of platforms currently employed in microarray research and provides an overview of recent activities using these platforms in plant biology.

Use of differential display for the identification of touch-induced genes from an ethylene-insensitive Arabidopsis mutant and partial characterization of these genes

Touch has been shown to affect plant growth and development and ethylene has been shown to have similar effects. However, the mechanisms responsible for touch-induced responses remain unclear. Differential display PCR was used to identify touch-regulated genes from 3-week-light-grown ethylene-insensitive etr1-3 Arabidopsis (Columbia ecotype) mutant plants. The differential display PCR screening process yielded 32 cDNA fragments. Subsequent screening of the 32 fragments using northern analysis yielded three touch-inducible clones (A8A, G5A and G7F). These three cDNA were then used to screen a cDNA library. A 1.2kb fragment for OPR3 was obtained from A8A screenings. This cDNA fragment encodes 12-oxophytodienoate-10, 11-reductase (OPR), an enzyme in the jasmonic acid biosynthetic pathway. OPR3 was found to be induced by touch, wounding, methyl jasmonate (MeJA), NaCl and CaCl(2) while ethylene and darkness had no effect. A 2kb cDNA encoding a calcium-dependent protein kinase (CDPK32) was obtained with G5A screenings. CDPK32 was shown to be induced by touch, wounding, NaCl and darkness while ethylene and MeJA had little or no effect. A 1.4kb cDNA encoding a novel protein was recovered from the cDNA library screenings with a G7F fragment. This cDNA had some sequence similarity to GDA1 and was designated GDL for GDA1-like cDNA. GDL was activated by touch, wounding, MeJA, NaCl and CaCl(2) while there was no induction with ethylene and darkness. Using differential display PCR we have successfully been able to identify three clones that are inducible by touch and not by ethylene.

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

Grapes are grown in semiarid environments, where drought and salinity are common problems. Microarray transcript profiling, quantitative reverse transcription-PCR, and metabolite profiling were used to define genes and metabolic pathways in Vitis vinifera cv. Cabernet Sauvignon with shared and divergent responses to a gradually applied and long-term (16 days) water-deficit stress and equivalent salinity stress. In this first-of-a-kind study, distinct differences between water deficit and salinity were revealed. Water deficit caused more rapid and greater inhibition of shoot growth than did salinity at equivalent stem water potentials. One of the earliest responses to water deficit was an increase in the transcript abundance of RuBisCo activase (day 4), but this increase occurred much later in salt-stressed plants (day 12). As water deficit progressed, a greater number of affected transcripts were involved in metabolism, transport, and the biogenesis of cellular components than did salinity. Salinity affected a higher percentage of transcripts involved in transcription, protein synthesis, and protein fate than did water deficit. Metabolite profiling revealed that there were higher concentrations of glucose, malate, and proline in water-deficit-treated plants as compared to salinized plants. The metabolite differences were linked to differences in transcript abundance of many genes involved in energy metabolism and nitrogen assimilation, particularly photosynthesis, gluconeogenesis, and photorespiration. Water-deficit-treated plants appear to have a higher demand than salinized plants to adjust osmotically, detoxify free radicals (reactive oxygen species), and cope with photoinhibition.

Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs

Despite the significant contributions of utilizing heterosis to crop productivity worldwide, the biological mechanisms of heterosis remained largely uncharacterized. In this study, we analyzed gene expression profiles of an elite rice hybrid and the parents at three stages of young panicle development, using a cDNA microarray consisting of 9198 expressed sequence tags (ESTs), with the objective to reveal patterns of gene expression that may be associated with heterosis in yield. A total of 8422 sequences showed hybridization signals in all three genotypes in at least one stage and 5771 sequences produced detectable signals in all slides. Significant differences in expression level were detected for 438 sequences among the three genotypes in at least one of the three stages, as determined by ANOVA validated with 100 permutations at P < 0.05. Significant mid-parent heterosis was detected for 141 sequences, which demonstrated the following features: a much larger number of sequences showed negative heterosis than ones showing positive heterosis; genes functioning in DNA replication and repair tended to show positive heterosis; genes functioning in carbohydrate metabolism, lipid metabolism, energy metabolism, translation, protein degradation, and cellular information processing showed negative heterosis; both positive and negative heterosis were observed for genes in amino acid metabolism, transcription, signal transduction, plant defense and transportation. The results are indicative of the biochemical and physiological activities taking place in the hybrid relative to the parents. Identification of genes showing expression polymorphisms among different genotypes and heterotic expression in the hybrid may provide new avenues for exploring the biological mechanisms underlying heterosis.

Deciphering the regulatory mechanisms of abiotic stress tolerance in plants by genomic approaches

Environmental constraints that include abiotic stress factors such as salt, drought, cold and extreme temperatures severely limit crop productivity. Improvement of crop plants with traits that confer tolerance to these stresses was practiced using traditional and modern breeding methods. Molecular breeding and genetic engineering contributed substantially to our understanding of the complexity of stress response. Mechanisms that operate signal perception, transduction and downstream regulatory factors are now being examined and an understanding of cellular pathways involved in abiotic stress responses provide valuable information on such responses. This review presents genomic-assisted methods which have helped to reveal complex regulatory networks controlling abiotic stress tolerance mechanisms by high-throughput expression profiling and gene inactivation techniques. Further, an account of stress-inducible regulatory genes which have been transferred into crop plants to enhance stress tolerance is discussed as possible modes of integrating information gained from functional genomics into knowledge-based breeding programs. In addition, we envision an integrative genomic and breeding approach to reveal developmental programs that enhance yield stability and improve grain quality under unfavorable environmental conditions of abiotic stresses.

Comprehensive transcriptional profiling of NaCl-stressed Arabidopsis roots reveals novel classes of responsive genes

BACKGROUND

Roots are an attractive system for genomic and post-genomic studies of NaCl responses, due to their primary importance to agriculture, and because of their relative structural and biochemical simplicity. Excellent genomic resources have been established for the study of Arabidopsis roots, however, a comprehensive microarray analysis of the root transcriptome following NaCl exposure is required to further understand plant responses to abiotic stress and facilitate future, systems-based analyses of the underlying regulatory networks.

RESULTS

We used microarrays of 70-mer oligonucleotide probes representing 23,686 Arabidopsis genes to identify root transcripts that changed in relative abundance following 6 h, 24 h, or 48 h of hydroponic exposure to 150 mM NaCl. Enrichment analysis identified groups of structurally or functionally related genes whose members were statistically over-represented among up- or down-regulated transcripts. Our results are consistent with generally observed stress response themes, and highlight potentially important roles for underappreciated gene families, including: several groups of transporters (e.g. MATE, LeOPT1-like); signalling molecules (e.g. PERK kinases, MLO-like receptors), carbohydrate active enzymes (e.g. XTH18), transcription factors (e.g. members of ZIM, WRKY, NAC), and other proteins (e.g. 4CL-like, COMT-like, LOB-Class 1). We verified the NaCl-inducible expression of selected transcription factors and other genes by qRT-PCR.

CONCLUSION

Microarray profiling of NaCl-treated Arabidopsis roots revealed dynamic changes in transcript abundance for at least 20% of the genome, including hundreds of transcription factors, kinases/phosphatases, hormone-related genes, and effectors of homeostasis, all of which highlight the complexity of this stress response. Our identification of these transcriptional responses, and groups of evolutionarily related genes with either similar or divergent transcriptional responses to stress, will facilitate mapping of regulatory networks and extend our ability to improve salt tolerance in plants.

Evaluation of Lolium temulentum as a model grass species for the study of salinity stress by PCR-based subtractive suppression hybridization analysis

Soil salinity is one of the major abiotic stresses responsible for reduced persistence, yield and biomass accumulation in many crops including forage grass. Forage grass species are generally polymorphic, obligate out-crossers, that are self-incompatible. Because of their high genetic diversity, the mechanisms of salt tolerance are poorly understood. Consequently, the development of a useful model grass plant for the study of abiotic stresses is of great importance. We propose the use of Lolium temulentum L. (Darnel ryegrass), a diploid self-fertile species with a short life cycle (2-3 months), as a model system for the study of forage/turf grass species. To evaluate the utility of L. temulentum as a model grass species to study salt stress, a PCR-based subtractive suppression hybridization library was generated and sequenced. A total of 528 unique sequences were identified, among which 167 corresponded to orthologs of previously identified plant stress response genes. The expression patterns in leaf, crown and root tissues of selected genes were analyzed by Northern blot analysis, demonstrating salinity depended regulation of gene expression. These preliminary studies provide proof of concept supporting the use of L. temulentum as a model forage grass for molecular genetic analyses of salinity stress.

Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode)

Changes in gene expression within roots of Glycine max (soybean), cv. Kent, susceptible to infection by Heterodera glycines (the soybean cyst nematode [SCN]), at 6, 12, and 24 h, and 2, 4, 6, and 8 days post-inoculation were monitored using microarrays containing more than 6,000 cDNA inserts. Replicate, independent biological samples were examined at each time point. Gene expression was analyzed statistically using T-tests, ANOVA, clustering algorithms, and online analytical processing (OLAP). These analyses allow the user to query the data in several ways without importing the data into third-party software. RT-PCR confirmed that WRKY6 transcription factor, trehalose phosphate synthase, EIF4a, Skp1, and CLB1 were differentially induced across most time-points. Other genes induced across most timepoints included lipoxygenase, calmodulin, phospholipase C, metallothionein-like protein, and chalcone reductase. RT-PCR demonstrated enhanced expression during the first 12 h of infection for Kunitz trypsin inhibitor and sucrose synthase. The stress-related gene, SAM-22, phospholipase D and 12-oxophytodienoate reductase were also induced at the early time-points. At 6 and 8 dpi there was an abundance of transcripts expressed that encoded genes involved in transcription and protein synthesis. Some of those genes included ribosomal proteins, and initiation and elongation factors. Several genes involved in carbon metabolism and transport were also more abundant. Those genes included glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase and sucrose synthase. These results identified specific changes in gene transcript levels triggered by infection of susceptible soybean roots by SCN.

Plant aquaporins: new perspectives on water and nutrient uptake in saline environment

The mechanisms of salt stress and tolerance have been targets for genetic engineering, focusing on ion transport and compartmentation, synthesis of compatible solutes (osmolytes and osmoprotectants) and oxidative protection. In this review, we consider the integrated response to salinity with respect to water uptake, involving aquaporin functionality. Therefore, we have concentrated on how salinity can be alleviated, in part, if a perfect knowledge of water uptake and transport for each particular crop and set of conditions is available.

An ABRE-binding factor, OSBZ8, is highly expressed in salt tolerant cultivars than in salt sensitive cultivars of indica rice

BACKGROUND

The bZIP class Abscisic acid Responsive Element (ABRE)-binding factor, OSBZ8 (38.5 kD) has been considered to regulate ABA-mediated transcription in the suspension cultured cells of japonica rice. Still, nothing is known about the expression of OSBZ8 at protein level in vegetative tissue of salt sensitive and salt tolerant rice plants. In our previous study, Electrophoretic Mobility Shift Assay (EMSA) of [32P]ABRE-DNA and nuclear extracts prepared from the lamina of Pokkali rice plants has detected the presence of an ABRE-binding factor. Northern analysis has also detected salinity stress induced accumulation of transcripts for bZIP class of factor. Therefore, OSBZ8 was considered to play an important role in the regulation of transcription in the vegetative tissue of rice. The aim of this study is to find out whether OSBZ8 has any role in regulating the NaCl-stress induced gene expression in vegetative tissue and whether the expression of OSBZ8 factor directly correlates with the stress tolerance of different varieties of indica type rice.

RESULTS

Northern analysis of total RNA from roots and lamina of salt-sensitive M-I-48 and salt-tolerant Nonabokra, when probed with the N-terminal unique region of OSBZ8 (OSBZ8p, without the highly conserved basic region), a transcript of 1.3 kb hybridized and its level was much higher in tolerant cultivar. EMSA with Em1a, the strongest ABA Responsive Element till reported from the upstream of EmBP1, and the nuclear extracts from laminar tissue of untreated and salt-treated seedlings of three salt sensitive, one moderately sensitive and two salt tolerant indica rice cultivars showed specific binding of nuclear factor to ABRE element. Intensity of binding was low and inducible in salt sensitive rice cultivars while high and constitutive in salt tolerant cultivars. EMSA with 300 bp 5'upstream region of Rab16A gene, a well known salt stress and ABA-inducible gene of rice, showed formation of two complexes, again very weak in salt sensitive and strong in salt tolerant rice cultivar.

CONCLUSION

The bZIP factor OSBZ8 was found to be present in the ABRE-DNA: protein complex as shown by the supershift of the complex by the purified antiserum raised against OSBZ8p. Treatment of the seedlings with NaCl was found to enhance the complex formation, suggesting the regulation of OSBZ8 gene at both transcriptional and post-translational steps. Comparative EMSA with different varieties of rice suggests a positive correlation with the expression pattern of OSBZ8 and salt tolerance in rice cultivars.

Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by downregulation of miR398 and important for oxidative stress tolerance

MicroRNAs (miRNAs) are a class of regulatory RNAs of approximately 21 nucleotides that posttranscriptionally regulate gene expression by directing mRNA cleavage or translational inhibition. Increasing evidence points to a potential role of miRNAs in diverse physiological processes. miR398 targets two closely related Cu/Zn superoxide dismutases (cytosolic CSD1 and chloroplastic CSD2) that can detoxify superoxide radicals. CSD1 and CSD2 transcripts are induced in response to oxidative stress, but the regulatory mechanism of the induction is unknown. Here, we show that miR398 expression is downregulated transcriptionally by oxidative stresses, and this downregulation is important for posttranscriptional CSD1 and CSD2 mRNA accumulation and oxidative stress tolerance. We also provide evidence for an important role of miR398 in specifying the spatial and temporal expression patterns of CSD1 and CSD2 mRNAs. Our results suggest that CSD1 and CSD2 expression is fine-tuned by miR398-directed mRNA cleavage. Additionally, we show that transgenic Arabidopsis thaliana plants overexpressing a miR398-resistant form of CSD2 accumulate more CSD2 mRNA than plants overexpressing a regular CSD2 and are consequently much more tolerant to high light, heavy metals, and other oxidative stresses. Thus, relieving miR398-guided suppression of CSD2 in transgenic plants is an effective new approach to improving plant productivity under oxidative stress conditions.

Salt stress response in rice: genetics, molecular biology, and comparative genomics

Significant progress has been made in unraveling the molecular biology of rice in the past two decades. Today, rice stands as a forerunner amongst the cereals in terms of details known on its genetics. Evidence show that salt tolerance in plants is a quantitative trait. Several traditional cultivars, landraces, and wild types of rice like Pokkali, CSR types, and Porteresia coarctata appear as promising materials for donation of requisite salt tolerance genes. A large number of quantitative trait loci (QTL) have been identified for salt tolerance in rice through generation of recombinant inbred lines and are being mapped using different types of DNA markers. Salt-tolerant transgenic rice plants have been produced using a host of different genes and transcript profiling by micro- and macroarray-based methods has opened the gates for the discovery of novel salt stress mechanisms in rice, and comparative genomics is turning out to be a critical input in this respect. In this paper, we present a comprehensive review of the genetic, molecular biology, and comparative genomics effort towards the generation of salt-tolerant rice. From the data on comprehensive transcript expression profiling of clones representing salt-stress-associated genes of rice, it is shown that transcriptional and translational machineries are important determinants in controlling salt stress response, and gene expression response in tolerant and susceptible rice plants differs mainly in quantitative terms.

Effects of chronic ozone exposure on gene expression in Arabidopsis thaliana ecotypes and in Thellungiella halophila

Arabidopsis thaliana (At) ecotypes Columbia-0 (Col-0), Wassilewskija (WS), Cape Verde Islands (Cvi-0) and a relative, Thellungiella halophila (Th), were exposed to 20-25% over ambient ozone [O3] in a free air concentration enrichment (FACE) experiment (http://www.soyFACE. uiuc.edu), mirroring increases expected in the near future. Col-0 and WS accelerated development and developed lesions within 10 d under increased ozone, while Cvi-0 and Th grew slowly. RNAs were used in microarray hybridizations (Col-0-based 26 000 elements, 70-mer oligonucleotides). A two-step analysis of variance (ANOVA) model, including comparison with values obtained under [O3], was used for analyses. WS showed the greatest number of changes in gene expression in response to ozone. Th showed the least changes, suggesting that its expression state at [O3] was sufficient for resistance at increased ozone. Patterns observed in ambient air controls for Cvi-0 and Col-0 were most similar, while Th showed the greatest number of differences compared with the other controls. Compared with Col-0, however, Cvi-0 showed higher levels of expression of chaperones, receptor kinase-like and photosynthesis-related genes in ambient air. Cvi-0 exhibited ozone-mediated changes in a pathway involving AtSR, a homologue of the mammalian NF kappa B family of redox-sensitive transcription factors, changes in chaperones, WRKY and C2H2 proteins and antioxidants. WS displayed ozone-mediated decreases in the expression of two AtSR/NF kappa B family members, C2-domain proteins and genes associated with cell wall growth and changes in the expression of marker genes for programmed cell death (PCD), among them RCD1, a key regulator in this pathway. Microarray data were verified by reverse transcriptase (RT)-PCR. We relate O3-response diversity across the four lines to different responses among signaling and transcriptional response networks and differences in gene expression at [O3] levels.

Comparative transcriptome analyses of barley and rice under salt stress

Although barley and rice belong to the same family Poaceae, they differ in their ability to tolerate salt stress. In an attempt to understand the molecular bases of such differences, we compared changes in transcriptome between barley and rice in response to salt stress using barley cDNA microarrays. At 1 and 24 h after salt stress, many genes were up-regulated in barley, but not in rice. Leaf water potential declined in the first 10 h of stress in both species, but recovered in the period 24-48 h only in barley. In addition, we found that barley partitioned Na+ to the roots and away from the shoots more efficiently than rice. These differences in physiological responses were correlated with the differences in the steady-state abundance of transcripts for the genes related to adaptive functions. Transcripts for plasma membrane protein 3 and inorganic pyrophosphatase were up-regulated in both species, but only transiently in rice. This indicates that adaptive mechanisms for regulating ion homeostasis are partly conserved in the two species, but it seems that rice cannot sustain cellular ion homeostasis for a long time like barley. These results imply that genetic modification of regulatory controls of early salt-responsive genes might lead to development of the salt tolerance trait in rice.

Modulating the expression of aquaporin genes in planta: A key to understand their physiological functions?

Aquaporins (AQPs) are believed to act as "cellular plumbers", allowing plants to rapidly alter their membrane water permeability in response to environmental cues. This study of AQP regulation at both the RNA and protein levels has revealed a large number of possible mechanisms. Currently, modulation of AQP expression in planta is considered the strategy of choice for elucidating the role of AQPs in plant physiology. This review highlights the fact that this strategy is complicated by many factors, such as the incomplete characterization of transport selectivity of the targeted AQP, the fact that AQPs might act as multifunctional channels with multiple physiological roles, and the number of post-translational regulation mechanisms. The classification of AQPs as constitutive or stress-responsive isoforms is also proposed.

Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray

Development of crop varieties with high nitrogen use efficiency (NUE) is imperative for sustainable agriculture. Understanding how plant genes respond to low N stress is essential for formulating approaches to manipulating genes for improving NUE. In this study we analyzed the expression profiles of an indica rice cultivar Minghui 63 at seedling stage at 20 min, 1 and 2 h after low N stress with the normal N as the control, using a microarray of 11,494 rice ESTs representing 10,422 unique genes. While no significant difference was detected in the leaf tissue, a total of 471 ESTs were detected as responsive to low N stress in the root tissue with 115 ESTs showing up-regulation and 358 ESTs showing down-regulation. The analysis of expression profiles after low N stress identified following patterns: (1) the genes involved in photosynthesis and energy metabolism were down-regulated rapidly; (2) many of the genes involved in early responses to biotic and abiotic stresses were up-regulated while many other stress responsive genes were down-regulated; (3) regulatory genes including transcription factors and ones involved in signal transduction were both up- and down-regulated; and (4) the genes known to be involved in N uptake and assimilation showed little response to the low N stress. The challenges for future studies are to characterize the functional roles of the low N stress responsive genes in N metabolisms, including the large number of genes presently with unknown functions.

A global assembly of cotton ESTs

Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; A(T) and D(T) genomes) as well as its two diploid progenitors, Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to recognition of 33,665 exemplar sequences that represent a nonredundant set of putative Gossypium genes containing partial or full-length coding regions and usually one or two UTRs. The assembly, along with their UniProt BLASTX hits, GO annotation, and Pfam analysis results, are freely accessible as a public resource for cotton genomics. Because ESTs from diploid and allotetraploid Gossypium were combined in a single assembly, we were in many cases able to bioinformatically distinguish duplicated genes in allotetraploid cotton and assign them to either the A or D genome. The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics.

Global patterns of gene expression in the aleurone of wild-type and dwarf1 mutant rice

The cereal aleurone layer is a model system for studying the regulation of transcription by gibberellin (GA) and abscisic acid (ABA). GA stimulates and ABA prevents the transcription of genes for alpha-amylases and other secreted hydrolytic enzymes, but how GA and ABA affect the transcription of other genes is largely unknown. We characterized gene expression in rice (Oryza sativa) aleurone using a half-genome rice microarray. Of the 23,000 probe sets on the chip, approximately 11,000 hybridized with RNA from rice aleurone treated with ABA, GA, or no hormone. As expected, GA regulated the expression of many genes, and 3 times as many genes were up-regulated by GA at 8 h than were down-regulated. Changes in gene expression resulting from ABA treatment were not consistent with the hypothesis that the role of ABA in this tissue is primarily to repress gene expression, and 10 times more genes were up-regulated by ABA at 8 h than were down-regulated by ABA. We also measured transcript abundance in aleurone of dwarf1 (d1) mutant rice. The d1 protein is the sole alpha-subunit of heterotrimeric G-proteins in rice. Genes up-regulated by GA or ABA had higher expression in wild type than in d1 aleurone, and genes down-regulated by GA had lower expression in wild type relative to d1 aleurone. The d1 mutation did not result in a decrease in sensitivity to GA at the level of transcription. Rather, changes in transcript abundance were smaller in the d1 mutant than in wild type.

New evidence about the relationship between water channel activity and calcium in salinity-stressed pepper plants

This study, of how Ca2+ availability (intracellular, extracellular or linked to the membrane) influences the functionality of aquaporins of pepper (Capsicum annuum L.) plants grown under salinity stress, was carried out in plants treated with NaCl (50 mM), CaCl2 (10 mM), and CaCl2 (10 mM) + NaCl (50 mM). For this, water transport through the plasma membrane of isolated protoplasts, and the involvement of aquaporins and calcium (extracellular, intracellular and linked to the membrane) has been determined. After these treatments, it could be seen that the calcium concentration was reduced in the apoplast, in the cells and on the plasma membrane of roots of pepper plants grown under saline conditions; these concentrations were increased or restored when extra calcium was added to the nutrient solution. Protoplasts extracted from plants grown under Ca2+ starvation showed no aquaporin functionality. However, for the protoplasts to which calcium was added, an increase of aquaporin functionality of the plasma membrane was observed [osmotic water permeability (Pf) inhibition after Hg addition]. Interestingly, when verapamil (a Ca2+ channel blocker) was added, no functionality was observed, even when Ca2+ was added with verapamil. Therefore, calcium seems to be involved in plasma membrane aquaporin regulation via a chain of processes within the cell but not by alteration of the stability of the plasma membrane.

Changes in gene expression in maize kernel in response to water and salt stress

Increasing pressure on limited water resources for agriculture, together with the global temperature increase, highlight the importance of breeding for drought-tolerant cultivars. A better understanding of the molecular nature of drought stress can be expected through the use of genomics approaches. Here, a macroarray of approximately 2500 maize cDNAs was used for determining transcript changes during water- and salt-stress treatments of developing kernels at 15 days after pollination. Normalization of relative transcript abundances was carried out using a human nebulin control sequence. The proportions of transcripts that changed significantly in abundance upon treatment (>2-fold compared to the control) were determined; 1.5% of the sequences examined were up-regulated by high salinity and 1% by water stress. Both stresses induced 0.8% of the sequences. These include genes involved in various stress responses: abiotic, wounding and pathogen attack (abscisic acid response binding factor, glycine and proline-rich proteins, pathogenesis-related proteins, etc.). The proportion of down-regulated genes was higher than that for up-regulated genes for water stress (3.2%) and lower for salt stress (0.7%), although only eight genes, predominantly involved in energy generation, were down-regulated in both stress conditions. Co-expression of genes of unknown function under defined conditions may help in elucidating their roles in coordinating stress responses.

Expression analysis of barley (Hordeum vulgare L.) during salinity stress

Barley (Hordeum vulgare L.) is a salt-tolerant crop species with considerable economic importance in salinity-affected arid and semiarid regions of the world. In this work, barley cultivar Morex was used for transcriptional profiling during salinity stress using a microarray containing approximately 22,750 probe sets. The experiment was designed to target the early responses of genes to a salinity stress at seedling stage. We found a comparable number of probe sets up-regulated and down-regulated in response to salinity. The differentially expressed genes were broadly characterized using gene ontology and through expression-based hierarchical clustering to identify interesting features in the data. A prominent feature of the response to salinity was the induction of genes involved in jasmonic acid biosynthesis and genes known to respond to jasmonic acid treatment. A large number of abiotic stress (heat, drought, and low temperature) related genes were also found to be responsive to salinity stress. Our results also indicate osmoprotection to be an early response of barley under salinity stress. Additionally, we compared the results of our studies with two other reports characterizing gene expression of barley under salinity stress and found very few genes in common.

Increasing salt tolerance in the tomato

In this paper, a number of strategies to overcome the deleterious effects of salinity on plants will be reviewed; these strategies include using molecular markers and genetic transformation as tools to develop salinity-tolerant genotypes, and some cultural techniques. For more than 12 years, QTL analysis has been attempted in order to understand the genetics of salt tolerance and to deal with component traits in breeding programmes. Despite innovations like better marker systems and improved genetic mapping strategies, the success of marker-assisted selection has been very limited because, in part, of inadequate experimental design. Since salinity is variable in time and space, experimental design must allow the study of genotype x environment interaction. Genetic transformation could become a powerful tool in plant breeding, but the growing knowledge from plant physiology must be integrated with molecular breeding techniques. It has been shown that the expression of several transgenes promotes a higher level of salt tolerance in some species. Despite this promising result, the development of a salt-tolerant cultivar by way of transgenesis has still not been achieved. Future directions in order to overcome the present limitations are proposed. Three cultural techniques have proved useful in tomato to overcome, in part, the effects of salinity: treatment of seedlings with drought or NaCl ameliorates the adaptation of adult plants to salinity; mist applied to tomato plants grown in Mediterranean conditions improves vegetative growth and yield in saline conditions; and grafting tomato cultivars onto appropriate rootstocks could reduce the effects of salinity.

Transcriptional regulatory networks in cellular responses and tolerance to dehydration and cold stresses

Plant growth and productivity are greatly affected by environmental stresses such as drought, high salinity, and low temperature. Expression of a variety of genes is induced by these stresses in various plants. The products of these genes function not only in stress tolerance but also in stress response. In the signal transduction network from perception of stress signals to stress-responsive gene expression, various transcription factors and cis-acting elements in the stress-responsive promoters function for plant adaptation to environmental stresses. Recent progress has been made in analyzing the complex cascades of gene expression in drought and cold stress responses, especially in identifying specificity and cross talk in stress signaling. In this review article, we highlight transcriptional regulation of gene expression in response to drought and cold stresses, with particular emphasis on the role of transcription factors and cis-acting elements in stress-inducible promoters.

The role of monovalent cation transporters in plant responses to salinity

Exposure to high ambient levels of NaCl affects plant water relations and creates ionic stress in the form of the cellular accumulation of Cl- and, in particular, Na+ ions. However, salt stress also impacts heavily on the homeostasis of other ions such as Ca2+, K+, and NO(3)(-) and therefore requires insights into how transport and compartmentation of these nutrients is altered during salinity stress. A genomics approach can greatly help with the identification of genes, and therefore potentially gene products, that are involved in plant salinity. Both the literature and public databases contain the results of many genomics studies and, in this report, those data are collated in the context of cation membrane transport and salinity. The efficacy of genomics approaches in isolation is low due to large inherent variability and the exclusion of gene products that are predominantly regulated post-transcriptionally. In conjunction with complementary approaches, however, transcriptomics can help identify important transcripts and relevant associations between physiological processes. This analysis identified (i) vascular K+ circulation, (ii) root shoot translocation of Ca2+, and (iii) transition metal homeostasis as potentially important aspects of the plant response to salt stress.

Mapping the DNA- and zinc-binding domains of ASR1 (abscisic acid stress ripening), an abiotic-stress regulated plant specific protein

Abscisic acid stress ripening (ASR1) is a highly charged low molecular weight plant specific protein that is regulated by salt- and water-stresses. The protein possesses a zinc-dependent DNA-binding activity (Kalifa et al., Biochem. J. 381 (2004) 373) and overexpression in transgenic plants results in an increased salt-tolerance (Kalifa et al., Plant Cell Environ. 27 (2004) 1459). There are no structure homologs of ASR1, thus the structural and functional domains of the protein cannot be predicted. Here, we map the protein domains involved in the binding of Zn(2+) and DNA. Using mild acid hydrolysis, and a series of ASR1 carboxy-terminal truncations we show that the zinc-dependent DNA-binding could be mapped to the central/carboxy-terminal domain. In addition, using MALDI-TOF-MS with a non-acidic matrix, we show that two zinc ions are bound to the amino-terminal domain. Other zinc ion(s) bind the DNA-binding domain. Binding of zinc to ASR1 induces conformational changes resulting in a decreased sensitivity to proteases.

Novel markers of xylogenesis in zinnia are differentially regulated by auxin and cytokinin

The characterization of in vitro xylogenic cultures of zinnia (Zinnia elegans) has led to major discoveries in the understanding of xylem formation in plants. We have constructed and characterized a subtractive library from zinnia cultures enriched in genes that are specifically expressed at the onset of secondary wall deposition and tracheary element (TE) programmed cell death. This Late Xylogenesis Library (LXL) consisted of 236 nonredundant cDNAs, 77% of which encoded novel sequences in comparison with the 17,622 expressed sequence tag sequences publicly available. cDNA arrays were constructed to examine dynamic global gene expression during the course of TE formation. As a first step in dissecting auxin and cytokinin signaling during TE differentiation, macroarrays were probed with cDNAs from cells cultured in different hormonal conditions. Fifty-one percent of the LXL genes were induced by either auxin or cytokinin individually, the large majority by auxin. To determine the potential involvement of these categories of genes in TE differentiation, multiplex in situ-reverse transcription-PCR was performed on cells for two genes encoding putative cell wall proteins: Gibberellin stimulated transcript-1, induced by auxin alone, and expansin 5, induced by cytokinin alone. All transcriptionally active TEs expressed both genes, indicating that, although these genes may not be considered as specific markers for TE differentiation per se, they are nevertheless an integral part of TE differentiation program. Among the non-TE population, four different gene expression-based cell types could be distinguished. Together, these results demonstrate the underlying complexity of hormonal perception and the existence of several different cell types in in vitro TE cell cultures.

Calcium signaling-mediated and differential induction of calmodulin gene expression by stress in Oryza sativa L

Ca(2+)/calmodulin transduction pathways have been implicated in mediating stress response and tolerance in plants. Here, three genes encoding calmodulin (Cam) members of the EF-hand family of Ca(2+)-binding proteins were identified from Oryza sativa L. databases. Complementary DNA for each of the calmodulin genes, OsCam1, OsCam2, and OsCam3 were sequenced. OsCam1 and OsCam2 encode a conventional 148-amino acid calmodulin protein that contains four characteristic Ca(2+)-binding motifs. OsCam3 encode a similar protein with a 38-amino-acid extension containing a putative prenylation site (CVIL) at the carboxyl terminus. RT-PCR showed that each of the genes is expressed in leaves and roots of 2-week old rice seedlings. By RNA gel blot analysis, OsCam1 mRNA levels strongly increased in response to NaCl, mannitol and wounding treatments. In contrast, OsCam2 mRNA levels were relatively unchanged under all conditions investigated. NaCl treatment and wounding also increased the OsCam3 mRNA level, but in a more transient manner. Our results indicate that although the expression of genes encoding different calmodulin isoforms is ubiquitous, they are differentially regulated by various stress signals. In addition, we have demonstrated that the calcium-channel blocker lanthanum chloride inhibited the induction of OsCam1 gene expression by both NaCl and mannitol treatments. These results suggest that osmotic stressinduced expression of OsCam1 gene requires the [Ca(2+)]cyt elevation that is known to occur in response to these stimuli.

Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray

In this study, we constructed a 22k wheat oligo-DNA microarray. A total of 148,676 expressed sequence tags of common wheat were collected from the database of the Wheat Genomics Consortium of Japan. These were grouped into 34,064 contigs, which were then used to design an oligonucleotide DNA microarray. Following a multistep selection of the sense strand, 21,939 60-mer oligo-DNA probes were selected for attachment on the microarray slide. This 22k oligo-DNA microarray was used to examine the transcriptional response of wheat to salt stress. More than 95% of the probes gave reproducible hybridization signals when targeted with RNAs extracted from salt-treated wheat shoots and roots. With the microarray, we identified 1,811 genes whose expressions changed more than 2-fold in response to salt. These included genes known to mediate response to salt, as well as unknown genes, and they were classified into 12 major groups by hierarchical clustering. These gene expression patterns were also confirmed by real-time reverse transcription-PCR. Many of the genes with unknown function were clustered together with genes known to be involved in response to salt stress. Thus, analysis of gene expression patterns combined with gene ontology should help identify the function of the unknown genes. Also, functional analysis of these wheat genes should provide new insight into the response to salt stress. Finally, these results indicate that the 22k oligo-DNA microarray is a reliable method for monitoring global gene expression patterns in wheat.

Environmental stress alters genes expression and induces ovule abortion: reactive oxygen species appear as ovules commit to abort

Environmental stress dramatically reduces plant reproduction. Previous results showed that placing roots in 200 mM NaCl for 12 h caused 90% of the developing Arabidopsis ovules to abort (Sun et al. in Plant Physiol 135:2358-2367, 2004). To discover the molecular responses that occur during ovule abortion, gene expression was monitored using Affymetrix 24k genome arrays. Transcript levels were measured in pistils that were stressed for 6, 12, 18, and 24 h, then compared with the levels in healthy pistils. Over the course of this experiment, a total of 535 salt-responsive genes were identified. Cluster analysis showed that differentially expressed genes exhibited reproducible changes in expression. The expression of 65 transcription factors, some of which are known to be involved in stress responses, were modulated during ovule abortion. In flowers, salt stress led to a 30-fold increase in Na+ ions and modest, but significant, decreases in the accumulation of other ions. The expression of cation exchangers and ion transporters were induced, presumably to reestablish ion homeostasis following salt stress. Genes that encode enzymes that detoxify reactive oxygen species (ROS), including ascorbate peroxidase and peroxidase, were downregulated after ovules committed to abort. These changes in gene expression coincided with the synthesis of ROS in female gametophytes. One day after salt stress, ROS spread from the gametophytes to the maternal chalaza and integuments. In addition, genes encoding proteins that regulate ethylene responses, including ethylene biosynthesis, ethylene signal transduction and ethylene-responsive transcription factors, were upregulated after stress. Hypotheses are proposed on the basis of this expression analysis, which will be evaluated further in future experiments.

Differential responses of maize MIP genes to salt stress and ABA

Salt stress is known to reduce root hydraulic conductivity and growth. To examine a concomitant regulation of aquaporins, the expression of the maize MIP gene family in response to NaCl was analysed by DNA array hybridization. Plants responded differentially to 100 versus 200 mM NaCl treatments. Leaf water content was reduced rapidly and persistently after the application of 200 mM NaCl in contrast to 100 mM NaCl. Endogenous ABA strongly accumulated in roots after 2 h; it remained at a highly elevated level for 48 h after the addition of 200 mM NaCl, but rapidly declined in plants treated with 100 mM NaCl, indicating an early recovery from water deficit. Interestingly, 2 h after the addition of 100 mM NaCl, when maize regained the osmotic potential allowing water uptake, three highly expressed, specific isoforms ZmPIP1;1, ZmPIP1;5, and ZmPIP2;4 were transiently induced. They were preferentially transcribed in the outer root tissue suggesting a role in cellular water transport. None of the ZmTIP genes was altered. By contrast, after the addition of 200 mM NaCl these responses were missing. Instead, multiple ZmPIP and ZmTIP genes were repressed by 200 mM NaCl after 24 h. After 48 h, deregulations were overridden in both cases indicating homeostasis. ABA (1 muM) exogenously applied to the roots transiently induced ZmPIP2;4 similar to 100 mM NaCl as well as ZmPIP1;2. Thus, the early induction of ZmPIP2;4 by NaCl may be mediated by ABA. Previously, an increase in root hydraulic conductivity had been observed upon ABA application. By contrast, 100 muM ABA led to a complete, possibly non-specific repression of all detected ZmPIP and ZmTIP genes after 24 h.

Comparative expression of five Lea Genes during wheat seed development and in response to abiotic stresses by real-time quantitative RT-PCR

Gene expression profiles of group 2 (dehydrins) and group 4 Late embryogenesis abundant (Lea) genes in developing seeds of Triticum durum and T. aestivum and in coleoptiles and coleorhizae of T. durum seedlings were monitored by real-time quantitative RT-PCR. The five genes exhibited clear differences in their accumulation pattern in wheat seed and in response to dehydration, low temperature, salinity and ABA. Td29b, Td16 and Td27e gene transcripts accumulate late in embryogenesis as expected for Lea genes, Td11 gene transcripts were present throughout seed development whereas no Td25a gene transcripts were detected in seeds. Drastic changes in the relative levels of Td29b, Td16, Td27e and Td11 transcripts occurred at the shift between the cell expansion and desiccation phases. All genes except the Td11 gene are more highly induced by dehydration in coleorhizae than in coleoptiles. In contrast, response to low temperature, salinity or ABA is higher in coleoptiles than in coleorhizae. Depending on both the gene and on the type of stress, a wide range of induction levels (8- to 100,000-fold) was observed.

Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage

Rice (Oryza sativa), a salt-sensitive species, has considerable genetic variation for salt tolerance within the cultivated gene pool. Two indica rice genotypes, FL478, a recombinant inbred line derived from a population developed for salinity tolerance studies, and IR29, the sensitive parent of the population, were selected for this study. We used the Affymetrix rice genome array containing 55,515 probe sets to explore the transcriptome of the salt-tolerant and salt-sensitive genotypes under control and salinity-stressed conditions during vegetative growth. Response of the sensitive genotype IR29 is characterized by induction of a relatively large number of probe sets compared to tolerant FL478. Salinity stress induced a number of genes involved in the flavonoid biosynthesis pathway in IR29 but not in FL478. Cell wall-related genes were responsive in both genotypes, suggesting cell wall restructuring is a general adaptive mechanism during salinity stress, although the two genotypes also had some differences. Additionally, the expression of genes mapping to the Saltol region of chromosome 1 were examined in both genotypes. Single-feature polymorphism analysis of expression data revealed that IR29 was the source of the Saltol region in FL478, contrary to expectation. This study provides a genome-wide transcriptional analysis of two well-characterized, genetically related rice genotypes differing in salinity tolerance during a gradually imposed salinity stress under greenhouse conditions.

Transcriptome comparison of winter and spring wheat responding to low temperature

Freezing tolerance in plants is a complex trait that occurs in many plant species during growth at low, nonfreezing temperatures, a process known as cold acclimation. This process is regulated by a multigenic system expressing broad variation in the degree of freezing tolerance among wheat cultivars. Microarray analysis is a powerful and rapid approach to gene discovery. In species such as wheat, for which large scale mutant screening and transgenic studies are not currently practical, genotype comparison by this methodology represents an essential approach to identifying key genes in the acquisition of freezing tolerance. A microarray was constructed with PCR amplified cDNA inserts from 1184 wheat expressed sequence tags (ESTs) that represent 947 genes. Gene expression during cold acclimation was compared in 2 cultivars with marked differences in freezing tolerance. Transcript levels of more than 300 genes were altered by cold. Among these, 65 genes were regulated differently between the 2 cultivars for at least 1 time point. These include genes that encode potential regulatory proteins and proteins that act in plant metabolism, including protein kinases, putative transcription factors, Ca2+ binding proteins, a Golgi localized protein, an inorganic pyrophosphatase, a cell wall associated hydrolase, and proteins involved in photosynthesis.Key words: wheat microarray, expression profile, plant transcription, cold-regulated genes, freezing tolerance, cold acclimation, winter hardiness, stress genes, gene regulation, wheat transcriptome.

Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage

Rice (Oryza sativa), a salt-sensitive species, has considerable genetic variation for salt tolerance within the cultivated gene pool. Two indica rice genotypes, FL478, a recombinant inbred line derived from a population developed for salinity tolerance studies, and IR29, the sensitive parent of the population, were selected for this study. We used the Affymetrix rice genome array containing 55,515 probe sets to explore the transcriptome of the salt-tolerant and salt-sensitive genotypes under control and salinity-stressed conditions during vegetative growth. Response of the sensitive genotype IR29 is characterized by induction of a relatively large number of probe sets compared to tolerant FL478. Salinity stress induced a number of genes involved in the flavonoid biosynthesis pathway in IR29 but not in FL478. Cell wall-related genes were responsive in both genotypes, suggesting cell wall restructuring is a general adaptive mechanism during salinity stress, although the two genotypes also had some differences. Additionally, the expression of genes mapping to the Saltol region of chromosome 1 were examined in both genotypes. Single-feature polymorphism analysis of expression data revealed that IR29 was the source of the Saltol region in FL478, contrary to expectation. This study provides a genome-wide transcriptional analysis of two well-characterized, genetically related rice genotypes differing in salinity tolerance during a gradually imposed salinity stress under greenhouse conditions.