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

Salt-responsive genes in rice revealed by cDNA microarray analysis

We used cDNA microarrays containing approximately 9,000 unigenes to identify 486 salt responsive expressed sequence tags (ESTs) (representing approximately 450 unigenes) in shoots of the highly salt-tolerant rice variety, Nona Bokra (Oryza sativa L. ssp. Indica pv. Nona). Some of the genes identified in this study had previously been associated with salt stress. However the majority were novel, indicating that there is a great number of genes that are induced by salt exposure. Analysis of the salt stress expression profile data of Nona provided clues regarding some putative cellular and molecular processes that are undertaken by this tolerant rice variety in response to salt stress. Namely, we found that multiple transcription factors were induced during the initial salt response of shoots. Many genes whose encoded proteins are implicated in detoxification, protectant and transport were rapidly induced. Genes supporting photosynthesis were repressed and those supporting carbohydrate metabolism were altered. Commonality among the genes induced by salt exposure with those induced during senescence and biotic stress responses suggests that there are shared signaling pathways among these processes. We further compared the transcriptome changes of the salt-sensitive cultivar, IR28, with that of Nona rice. Many genes that are salt responsive in Nona were found to be differentially regulated in IR28. This study identified a large number of candidate functional genes that appear to be involved in salt tolerance and further examination of these genes may enable the molecular basis of salt tolerance to be elucidated.

Early effects of salinity on water transport in Arabidopsis roots. Molecular and cellular features of aquaporin expression

Aquaporins facilitate the uptake of soil water and mediate the regulation of root hydraulic conductivity (Lp(r)) in response to a large variety of environmental stresses. Here, we use Arabidopsis (Arabidopsis thaliana) plants to dissect the effects of salt on both Lp(r) and aquaporin expression and investigate possible molecular and cellular mechanisms of aquaporin regulation in plant roots under stress. Treatment of plants by 100 mm NaCl was perceived as an osmotic stimulus and induced a rapid (half-time, 45 min) and significant (70%) decrease in Lp(r), which was maintained for at least 24 h. Macroarray experiments with gene-specific tags were performed to investigate the expression of all 35 genes of the Arabidopsis aquaporin family. Transcripts from 20 individual aquaporin genes, most of which encoded members of the plasma membrane intrinsic protein (PIP) and tonoplast intrinsic protein (TIP) subfamilies, were detected in nontreated roots. All PIP and TIP aquaporin transcripts with a strong expression signal showed a 60% to 75% decrease in their abundance between 2 and 4 h following exposure to salt. The use of antipeptide antibodies that cross-reacted with isoforms of specific aquaporin subclasses revealed that the abundance of PIP1s decreased by 40% as early as 30 min after salt exposure, whereas PIP2 and TIP1 homologs showed a 20% to 40% decrease in abundance after 6 h of treatment. Expression in transgenic plants of aquaporins fused to the green fluorescent protein revealed that the subcellular localization of TIP2;1 and PIP1 and PIP2 homologs was unchanged after 45 min of exposure to salt, whereas a TIP1;1-green fluorescent protein fusion was relocalized into intracellular spherical structures tentatively identified as intravacuolar invaginations. The appearance of intracellular structures containing PIP1 and PIP2 homologs was occasionally observed after 2 h of salt treatment. In conclusion, this work shows that exposure of roots to salt induces changes in aquaporin expression at multiple levels. These changes include a coordinated transcriptional down-regulation and subcellular relocalization of both PIPs and TIPs. These mechanisms may act in concert to regulate root water transport, mostly in the long term (> or =6 h).

The use of microarrays to study the anaerobic response in Arabidopsis

BACKGROUND AND AIMS

The use of microarrays to characterize the transcript profile of Arabidopsis under various experimental conditions is rapidly expanding. This technique provides a huge amount of expression data, requiring bioinformatics tools to allow the proposal of working hypotheses. The aim of this study was to test the usefulness of this approach to examine the anaerobic response of Arabidopsis by evaluating the reliability of microarray data sets and by interrogation of microarray databases for the expression data of a set of anoxia-inducible genes.

METHODS

User-driven software tools that display large gene expression datasets onto diagrams of metabolic pathways were used. The Genevestigator software was used to explore the expression of anoxia-inducible genes throughout the life cycle of Arabidopsis as well as relative to plant organs. T-DNA tagged mutants for selected genes identified from our microarray analysis were searched in the Arabidopsis thaliana Insertion Database, looking for insertional mutants from the Salk collection.

KEY RESULTS

The results indicate that microarray data can provide the basis for new hypotheses in the field of plant responses to anaerobiosis and also provide knowledge for a targeted screening of Arabidopsis mutants.

CONCLUSIONS

Research on plant responses to anaerobiosis can enormously benefit from the microarray technology.

Genes and salt tolerance: bringing them together

Salinity tolerance comes from genes that limit the rate of salt uptake from the soil and the transport of salt throughout the plant, adjust the ionic and osmotic balance of cells in roots and shoots, and regulate leaf development and the onset of senescence. This review lists some candidate genes for salinity tolerance, and draws together hypotheses about the functions of these genes and the specific tissues in which they might operate. Little has been revealed by gene expression studies so far, perhaps because the studies are not tissue-specific, and because the treatments are often traumatic and unnatural. Suggestions are made to increase the value of molecular studies in identifying genes that are important for salinity tolerance.

Molecular cloning and characterization of a novel soybean gene encoding a leucine-zipper-like protein induced to salt stress

To understand molecular responses to salt stress in soybean (Glycine max [L.] Merr.), we identified 106 salt-inducible soybean genes that expressed differentially at 72 h after 100 mM NaCl treatment using the cDNA-amplified fragment length polymorphism (AFLP) method. The genes were designated as G. max Transcript-Derived Fragments (GmTDFs). Among these genes, we characterized a soybean gene GmTDF-5 that encoded an unknown protein of 367 amino acids. The GmTDF-5 protein was a putative cytosolic protein with two leucine-zipper motifs at the N-terminal and was calculated as 40.7 kDa. Southern blot analysis indicated that GmTDF-5 presents as an intron-less single gene on soybean genome and possibly distributes narrowly throughout the higher plants. By 100 mM NaCl treatment, the gene expression of GmTDF-5 was induced in the stem and lower-expanded leaf, and the amount of mRNA increased 5.1- and 2.0-fold up to 72 h, respectively. Interestingly, GmTDF-5 expression in the upper-leaf appeared dramatically with 10.0-fold increase at 72 h after the salt stress, but not until 48 h. Hyperosmotic pressure (mannitol treatment) and dehydration also caused the increases similar to NaCl treatment in the levels of GmTDF-5 expression. These results suggest that GmTDF-5 might be a novel cytosolic leucine-zipper-like protein functioning in mature organs of soybean shoot against water-potential changes.

Proteomic analysis of salt stress-responsive proteins in rice root

Salt stress is one of the major abiotic stresses in agriculture worldwide. We report here a systematic proteomic approach to investigate the salt stress-responsive proteins in rice (Oryza sativa L. cv. Nipponbare). Three-week-old seedlings were treated with 150 mM NaCl for 24, 48 and 72 h. Total proteins of roots were extracted and separated by two-dimensional gel electrophoresis. More than 1100 protein spots were reproducibly detected, including 34 that were up-regulated and 20 down-regulated. Mass spectrometry analysis and database searching helped us to identify 12 spots representing 10 different proteins. Three spots were identified as the same protein, enolase. While four of them were previously confirmed as salt stress-responsive proteins, six are novel ones, i.e. UDP-glucose pyrophosphorylase, cytochrome c oxidase subunit 6b-1, glutamine synthetase root isozyme, putative nascent polypeptide associated complex alpha chain, putative splicing factor-like protein and putative actin-binding protein. These proteins are involved in regulation of carbohydrate, nitrogen and energy metabolism, reactive oxygen species scavenging, mRNA and protein processing, and cytoskeleton stability. This study gives new insights into salt stress response in rice roots and demonstrates the power of the proteomic approach in plant biology studies.

Sorghum bicolor's transcriptome response to dehydration, high salinity and ABA

Genome wide changes in gene expression were monitored in the drought tolerant C4 cereal Sorghum bicolor, following exposure of seedlings to high salinity (150 mM NaCl), osmotic stress (20% polyethylene glycol) or abscisic acid (125 microM ABA). A sorghum cDNA microarray providing data on 12,982 unique gene clusters was used to examine gene expression in roots and shoots at 3- and 27-h post-treatment. Expression of approximately 2200 genes, including 174 genes with currently unknown functions, of which a subset appear unique to monocots and/or sorghum, was altered in response to dehydration, high salinity or ABA. The modulated sorghum genes had homology to proteins involved in regulation, growth, transport, membrane/protein turnover/repair, metabolism, dehydration protection, reactive oxygen scavenging, and plant defense. Real-time PCR was used to quantify changes in relative mRNA abundance for 333 genes that responded to ABA, NaCl or osmotic stress. Osmotic stress inducible sorghum genes identified for the first time included a beta-expansin expressed in shoots, actin depolymerization factor, inositol-3-phosphate synthase, a non-C4 NADP-malic enzyme, oleosin, and three genes homologous to 9-cis-epoxycarotenoid dioxygenase that may be involved in ABA biosynthesis. Analysis of response profiles demonstrated the existence of a complex gene regulatory network that differentially modulates gene expression in a tissue- and kinetic-specific manner in response to ABA, high salinity and water deficit. Modulation of genes involved in signal transduction, chromatin structure, transcription, translation and RNA metabolism contributes to sorghum's overlapping but nonetheless distinct responses to ABA, high salinity, and osmotic stress. Overall, this study provides a foundation of information on sorghum's osmotic stress responsive gene complement that will accelerate follow up biochemical, QTL and comparative studies.

Microarray and proteomic analysis of brassinosteroid- and gibberellin-regulated gene and protein expression in rice

Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.

Analysis of salt-stress-inducible ESTs isolated by PCR-subtraction in salt-tolerant rice

To clarify the mechanisms of stress tolerance in rice and to search for rice genes associated with these mechanisms, we analyzed genes induced by a high salinity treatment using the PCR-subtractive hybridization method (PCR-subtraction). Seedlings of the salt-tolerant rice cultivar Dee-geo-woo-gen (DGWG) were either treated with 250 mM NaCl for 5 h or left untreated, and PCR-subtraction was then performed using the untreated (control) plants as a driver and the NaCl-treated plants as a tester. We obtained 384 clones of tester-specific cDNAs as salt-inducible candidates. Northern analysis performed with the cDNA fragments showed that 65 clones had been induced by the NaCl treatment. Sequence analysis and database searching indicated that these clones have homology to proteins functional for detoxification, stress response, and signal transduction in plants. Of these clones, 22% coded for unknown proteins and 12% gave no hits. We selected eight clones from each functional category and analyzed their expression pattern in DGWG. For temporal analysis, seedlings were treated with H(2)O or 250 mM NaCl for 0, 0.5, 1, 2, 5, 10 or 24 h. Different patterns of transcript regulation were found. For the analysis of expression in response to various types of stress and abscisic acid (ABA) treatments, seedlings were treated for 5 h or 10 h with H(2)O, dehydration, cold (4 degrees C), heat (40 degrees C), mannitol, ABA, or wounding. All clones were strongly up-regulated by osmotic stress (dehydration and mannitol) and the ABA treatment.

Gene expression profiling of potato responses to cold, heat, and salt stress

In order to identify genes involved in abiotic stress responses in potato, seedlings were grown under controlled conditions and subjected to cold (4 degrees C), heat (35 degrees C), or salt (100 mM NaCl) stress for up to 27 h. Using an approximately 12,000 clone potato cDNA microarray, expression profiles were captured at three time points following initiation of the stress (3, 9, and 27 h) from two different tissues, roots and leaves. A total of 3,314 clones could be identified as significantly up- or down-regulated in response to at least one stress condition. The genes represented by these clones encode transcription factors, signal transduction factors, and heat-shock proteins which have been associated with abiotic stress responses in Arabidopsis and rice, suggesting similar response pathways function in potato. These stress-regulated clones could be separated into either stress-specific or shared-response clones, suggesting the existence of general response pathways as well as more stress-specific pathways. In addition, we identified expression profiles which are indicative for the type of stress applied to the plants.

Gene expression profiling of potato responses to cold, heat, and salt stress

In order to identify genes involved in abiotic stress responses in potato, seedlings were grown under controlled conditions and subjected to cold (4 degrees C), heat (35 degrees C), or salt (100 mM NaCl) stress for up to 27 h. Using an approximately 12,000 clone potato cDNA microarray, expression profiles were captured at three time points following initiation of the stress (3, 9, and 27 h) from two different tissues, roots and leaves. A total of 3,314 clones could be identified as significantly up- or down-regulated in response to at least one stress condition. The genes represented by these clones encode transcription factors, signal transduction factors, and heat-shock proteins which have been associated with abiotic stress responses in Arabidopsis and rice, suggesting similar response pathways function in potato. These stress-regulated clones could be separated into either stress-specific or shared-response clones, suggesting the existence of general response pathways as well as more stress-specific pathways. In addition, we identified expression profiles which are indicative for the type of stress applied to the plants.

Specific patterns of changes in wheat gene expression after treatment with three antifungal compounds

The two fungicides azoxystrobin and fenpropimorph are used against powdery mildew and rust diseases in wheat (Triticum aestivumL). Azoxystrobin, a strobilurin, inhibits fungal mitochondrial respiration and fenpropimorph, a morpholin, represses biosynthesis of ergosterol, the major sterol of fungal membranes. Although the fungitoxic activity of these compounds is well understood, their effects on plant metabolism remain unclear. In contrast to the fungicides which directly affect pathogen metabolism, benzo(1,2,3) thiadiazole-7-carbothioic acid S-methylester (BTH) induces resistance against wheat pathogens by the activation of systemic acquired resistance in the host plant. In this study, we monitored gene expression in spring wheat after treatment with each of these agrochemicals in a greenhouse trial using a microarray containing 600 barley cDNA clones. Defence-related genes were strongly induced after treatment with BTH, confirming the activation of a similar set of genes as in dicot plants following salicylic acid treatment. A similar gene expression pattern was observed after treatment with fenpropimorph and some defence-related genes were induced by azoxystrobin, demonstrating that these fungicides also activate a defence reaction. However, less intense responses were triggered than with BTH. The same experiments performed under field conditions gave dramatically different results. No gene showed differential expression after treatment and defence genes were already expressed at a high level before application of the agrochemicals. These differences in the expression patterns between the two environments demonstrate the importance of plant growth conditions for testing the impact of agrochemicals on plant metabolism.

Expression of ascorbate peroxidase and glutathione reductase in roots of rice seedlings in response to NaCl and H2O2

The accumulation of H2O2 by NaCl was observed in the roots of rice seedlings. Treatment with NaCl caused an increase in the activities of ascorbate peroxidase (APX) and glutathione reductase (GR) and the expression of OsAPX and OsGR in rice roots. Exogenously applied H2O2 also enhanced the activities of APX and GR and the expression of OsAPX and OsGR in rice roots. The accumulation of H2O2 in rice roots in response to NaCl was inhibited by the NADPH oxidase inhibitors, diphenyleneiodonium chloride (DPI) and imidazole (IMD). However, DPI, IMD, and dimethylthiourea, a H2O2 trap, did not reduce NaCl-enhanced activities of APX and GR and expression of OsAPX and OsGR. It appears that H2O2 is not involved in the regulation of NaCl-induced APX and GR activities and OsAPX and OsGR expression in rice roots.

Salt tolerance and salinity effects on plants: a review

Plants exposed to salt stress undergo changes in their environment. The ability of plants to tolerate salt is determined by multiple biochemical pathways that facilitate retention and/or acquisition of water, protect chloroplast functions, and maintain ion homeostasis. Essential pathways include those that lead to synthesis of osmotically active metabolites, specific proteins, and certain free radical scavenging enzymes that control ion and water flux and support scavenging of oxygen radicals or chaperones. The ability of plants to detoxify radicals under conditions of salt stress is probably the most critical requirement. Many salt-tolerant species accumulate methylated metabolites, which play crucial dual roles as osmoprotectants and as radical scavengers. Their synthesis is correlated with stress-induced enhancement of photorespiration. In this paper, plant responses to salinity stress are reviewed with emphasis on physiological, biochemical, and molecular mechanisms of salt tolerance. This review may help in interdisciplinary studies to assess the ecological significance of salt stress.

Salinity inhibits post transcriptional processing of chloroplast 16S rRNA in shoot cultures of jojoba (Simmondsia chinesis)

Chloroplast metabolism is rapidly affected by salt stress. Photosynthesis is one of the first processes known to be affected by salinity. Here, we report that salinity inhibits chloroplast post-transcriptional RNA processing. A differentially expressed 680-bp cDNA, containing the 3' sequence of 16S rRNA, transcribed intergenic spacer, exon 1 and intron of tRNA(Ile), was isolated by differential display reverse transcriptase PCR from salt-grown jojoba (Simmondsia chinesis) shoot cultures. Northern blot analysis indicated that although most rRNA appears to be fully processed, partially processed chloroplast 16S rRNA accumulates in salt-grown cultures. Thus, salinity appears to decrease the processing of the rrn transcript. The possible effect of this decreased processing on physiological processes is, as yet, unknown.

The OsLti6 genes encoding low-molecular-weight membrane proteins are differentially expressed in rice cultivars with contrasting sensitivity to low temperature

Rice (Oryza sativa L.) is sensitive to chilling particularly at early stages of seedling establishment. Two closely related genes (OsLti6a, OsLti6b), which are induced by low temperature during seedling emergence were isolated from a cold tolerant temperate japonica rice cultivar. These genes are closely related to the Arabidopsis rare cold-inducible (RCI2) and barley low-temperature-inducible (BLT101) genes. Based on direct biochemical and indirect physiological evidence and similarity with a conserved protein domain in the Cluster of Orthologous Groups (COG) database (e.g., yeast PMP3), the rice genes belong to a class of low-molecular-weight hydrophobic proteins involved in maintaining the integrity of the plasma membrane during cold, dehydration and salt stress conditions. Both genes exhibit a genotype-specific expression signature characterized by early and late stress-inducible expression in tolerant and intolerant genotypes, respectively. The differences in temporal expression profiles are consistent with cultivar differences in cold-induced membrane leakiness and seedling vigor. The presence of CRT/DRE promoter cis-elements is consistent with the synchronized expression of OsLti6 genes with the C-repeat binding factor/drought responsive element-binding protein (CBF/DREB) transcriptional activator. The present results indicate that the Oslti6 genes are part of a battery of cold stress defense-related genes regulated by a common switch.

Indications of limited altered gene expression in Pinus sylvestris trees from the Chernobyl region

To evaluate the consequences of irradiation on the vegetation of the Chernobyl region, gene expression was compared in morphologically normal and dwarf needles from the same Pinus sylvestris trees in a region where the absorbed dose was 3-5 Gy. To compare the levels of gene expression, arrays consisting of 373 Pinus taeda cDNAs were hybridized with labeled cDNA derived from normal and dwarf needles of P. sylvestris. Twelve genes were significantly (P<0.01) up- or down-regulated between normal and dwarf needles for all five trees taken together. Five of these, related to stress or development, were up- or down-regulated 1.25-1.7-fold in the dwarf needles. There were no significant differences in (137)Cs content in the normal and dwarf needles, or in elongation growth rate of seedlings raised under controlled conditions from seed derived from trees in the region that had received a radiation dose over the range 2-12 Gy.

DNA array analyses of Arabidopsis thaliana lacking a vacuolar Na+/H+ antiporter: impact of AtNHX1 on gene expression

AtNHX1, a vacuolar cation/proton antiporter of Arabidopsis, plays an important role in salt tolerance, ion homeostasis and development. We used the T-DNA insertional mutant of AtNHX1 (nhx1 plants) and Affymetrix ATH1 DNA arrays to assess differences in transcriptional profiles and further characterize the roles of a vacuolar cation/proton antiporter. Mature, soil-grown plants were used in this study to approximate typical physiological growing conditions. A comparison of plants grown in the absence of salt stress yielded many transcripts that were affected by the absence of the AtNHX1 vacuolar antiporter. Furthermore, changes in gene expression due to a non-lethal salt stress (100 mm NaCl) in the nhx1 plants were significantly different from the changes seen in wild-type plants. The nhx1 transcriptome was differentially affected when the plants were grown in the absence or presence of salt. In conclusion, in addition to the known role(s) of AtNHX1 on ion homeostasis, the vacuolar cation/proton antiporter plays a significant role in intracellular vesicular trafficking, protein targeting, and other cellular processes.

Deciphering genetic variations of proteome responses to water deficit in maize leaves

The proteome of the basal part of growing Zea mays leaves was analyzed from 4 to 14 d after stopping watering and in well watered controls. The relative quantity of 46 proteins was found to increase in leaves of plants submitted to water deficit. Different types of responses were observed, some proteins showing a constant increase during water deficit, while others showed stabilization after a first increase or a transient increase. Isoforms encoded by the same gene showed different responses. The response to water deficit showed genetic variation. Some increased proteins were induced specifically in one of the two studied genotypes (e.g. ASR1) while others were significantly induced in both genotypes but to a different level or with different kinetics. Analyses of relations between protein quantities, relative water content (RWC) and abscisic acid (ABA) concentration allowed us to show that the quantitative variation of some proteins (e.g. ABA45 and OSR40 proteins) was linked to differences in ABA accumulation between the genotypes. Other proteins showed genetic variations that were not related to differences in water status or ABA concentration (e.g. a cystatin). Data obtained from these experiments, together with data from other experiments, contribute to the characterization of maize proteome response to drought in different conditions and in different genotypes. This characterization allows the search for candidate proteins, i.e. for protein whose genetic variation of expression could be partly responsible for the variability of plant responses to drought.

A transcriptomics resource for wheat functional genomics

Grain development, germination and plant development under abiotic stresses are areas of biology that are of considerable interest to the cereal community. Within the Investigating Gene Function programme we have produced the resources required to investigate alterations in the transcriptome of hexaploid wheat during these developmental processes. We have single pass sequenced the cDNAs of between 700 and 1300 randomly picked clones from each of 35 cDNA libraries representing highly specific stages of grain and plant development. Annotated sequencing results have been stored in a publicly accessible, online database at http://www.cerealsdb.uk.net. Each of the tissue stages used has also been photographed in detail, resulting in a collection of high-quality micrograph images detailing wheat grain development. These images have been collated and annotated in order to produce a web site focused on wheat development (http://www.wheatbp.net/). We have also produced high-density microarrays of a publicly available wheat unigene set based on the 35 cDNA libraries and have completed a number of microarray experiments which validate their quality.

Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array

Plants alter their gene expression patterns in response to drought. Sometimes these transcriptional changes are successful adaptations leading to tolerance, while in other instances the plant ultimately fails to adapt to the stress and is labeled as sensitive to that condition. We measured the expression of approximately half of the genes in rice ( approximately 21,000) in phenotypically divergent accessions and their transgressive segregants to associate stress-regulated gene expression changes with quantitative trait loci (QTLs) for osmotic adjustment (OA, a trait associated with drought tolerance). Among the parental lines, a total of 662 transcripts were differentially expressed. Only 12 genes were induced in the low OA parent, CT9993, at moderate dehydration stress levels while over 200 genes were induced in the high OA parent, IR62266. The high and low OA parents had almost entirely different transcriptional responses to dehydration stress suggesting a complete absence of an appropriate response rather than a slower response in CT9993. Sixty-nine genes were up-regulated in all the high OA lines and nine of those genes were not induced in any of the low OA lines. The annotation of four of those genes, sucrose synthase, a pore protein, a heat shock and an LEA protein, suggests a role in maintaining high OA and membrane stability. Of the 3,954-probe sets that correspond to the QTL intervals, very few had a differential expression pattern between the high OA and low OA lines that suggest a role leading to the phenotypic variation. However, several promising candidates were identified for each of the five QTL including a snRNP auxiliary factor, a LEA protein, a protein phosphatase 2C and a Sar1 homolog.

Athb-12, a homeobox-leucine zipper domain protein from Arabidopsis thaliana, increases salt tolerance in yeast by regulating sodium exclusion

An Arabidopsis cDNA clone that encodes Athb-12, a homeobox-leucine zipper domain protein (HD-Zip), was isolated by functional complementation of the NaCl-sensitive phenotype of a calcineurin (CaN)-deficient yeast mutant (cnbDelta, regulatory subunit null). CaN, a Ca2+/calmodulin-dependent protein phosphatase, regulates Na+ ion homeostasis in yeast. Expression of Athb-12 increased NaCl tolerance but not osmotic stress tolerance of these cnbDelta cells. Furthermore, expression of two other HD-Zip from Arabidopsis, Athb-1 and -7, did not suppress NaCl sensitivity of cnbDelta cells. These results suggest that Athb-12 specifically functions in Na+ ion homeostasis in yeast. Consistent with these observations, expression of Athb-12 in yeast turned on transcription of the NaCl stress-inducible PMR2A, which encodes a Na+/Li+ translocating P-type ATPase, and decreased Na+ levels in yeast cells. To investigate the biological function of Athb-12 in Arabidopsis, we performed Northern blot analysis. Expression of Athb-12 was dramatically induced by NaCl and ABA treatments, but not by KCl. In vivo targeting experiments using a green fluorescent protein reporter indicated that Athb-12 was localized to the nucleus. These results suggest that Athb-12 is a putative transcription factor that may be involved in NaCl stress responses in plants.

A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway

Arabidopsis thaliana RD26 cDNA, isolated from dehydrated plants, encodes a NAC protein. Expression of the RD26 gene was induced not only by drought but also by abscisic acid (ABA) and high salinity. The RD26 protein is localized in the nucleus and its C terminal has transcriptional activity. Transgenic plants overexpressing RD26 were highly sensitive to ABA, while RD26-repressed plants were insensitive. The results of microarray analysis showed that ABA- and stress-inducible genes are upregulated in the RD26-overexpressed plants and repressed in the RD26-repressed plants. Furthermore, RD26 activated a promoter of its target gene in Arabidopsis protoplasts. These results indicate that RD26 functions as a transcriptional activator in ABA-inducible gene expression under abiotic stress in plants.

Monitoring the expression profiles of genes induced by hyperosmotic, high salinity, and oxidative stress and abscisic acid treatment in Arabidopsis cell culture using a full-length cDNA microarray

Transcriptional regulation in response to hyperosmotic, high-salinity and oxidative stress, and abscisic acid (ABA) treatment in Arabidopsis suspension-cultured cell line T87 was investigated with a cDNA microarray containing 7000 independent full-length Arabidopsis cDNAs. The transcripts of 102, 11, 84 and 73 genes were increased more than 5-fold within 5h after treatment with 0.5M mannitol, 0.1M NaCl, 50 microM ABA and 10mM H2O2, respectively. On the other hand, the transcripts of 44, 57, 25 and 34 genes were down-regulated to less than one-third within 5h after treatment with 0.5M mannitol, 0.1M NaCl, 50 microM ABA and 10mM H2O2, respectively. Venn diagram analysis revealed 11 genes were induced significantly by mannitol, NaCl, and ABA, indicating crosstalk among these signaling pathways. Comparison of the genes induced by each stress revealed that 32%, 17% and 33% of mannitol-, NaCl- and ABA-inducible genes were also induced by H2O2, indicating the crosstalk between the signaling pathways for osmotic stress and oxidative stress. Although the expression profiles revealed that the T87 cells had most of the regulatory systems seen in Arabidopsis seedlings, the T87 cells did not have one of ABA-dependent signaling pathways.

Enhanced photosynthesis and redox energy production contribute to salinity tolerance in Dunaliella as revealed by homology-based proteomics

Salinity is a major limiting factor for the proliferation of plants and inhibits central metabolic activities such as photosynthesis. The halotolerant green alga Dunaliella can adapt to hypersaline environments and is considered a model photosynthetic organism for salinity tolerance. To clarify the molecular basis for salinity tolerance, a proteomic approach has been applied for identification of salt-induced proteins in Dunaliella. Seventy-six salt-induced proteins were selected from two-dimensional gel separations of different subcellular fractions and analyzed by mass spectrometry (MS). Application of nanoelectrospray mass spectrometry, combined with sequence-similarity database-searching algorithms, MS BLAST and MultiTag, enabled identification of 80% of the salt-induced proteins. Salinity stress up-regulated key enzymes in the Calvin cycle, starch mobilization, and redox energy production; regulatory factors in protein biosynthesis and degradation; and a homolog of a bacterial Na(+)-redox transporters. The results indicate that Dunaliella responds to high salinity by enhancement of photosynthetic CO(2) assimilation and by diversion of carbon and energy resources for synthesis of glycerol, the osmotic element in Dunaliella. The ability of Dunaliella to enhance photosynthetic activity at high salinity is remarkable because, in most plants and cyanobacteria, salt stress inhibits photosynthesis. The results demonstrated the power of MS BLAST searches for the identification of proteins in organisms whose genomes are not known and paved the way for dissecting molecular mechanisms of salinity tolerance in algae and higher plants.

Rice cDNA microarray-based gene expression profiling of the response to flagellin perception in cultured rice cells

Incompatible strains of Acidovorax avenae elicit an immune response in cultured rice cells, with immunity specifically induced by the flagellin of the incompatible strain. To identify genes regulated by flagellin perception signaling in cultured rice cells, gene expression patterns were analyzed with rice cDNA microarrays, including 3,353 independent rice cDNA clones. In all, 131 genes were differentially expressed between incompatible and compatible interactions. K-means clustering showed that 94 genes were upregulated and 32 genes were downregulated during incompatible interactions, whereas only 5 genes were upregulated during compatible interactions. Among the 126 genes that were up- or downregulated during incompatible interactions, expression of 46 genes was decreased when cultured rice cells were inoculated with a flagellin-deficient incompatible strain (delta fla1141-2), indicating that approximately 37% of the 126 genes were directly controlled by flagellin perception. Real-time reverse-transcription polymerase chain reaction analysis using flagellins purified from incompatible or compatible strains was performed to confirm flagellin-regulated expression of candidate genes selected by microarray analysis. Results showed that induction of some genes involved in the immune response is regulated not only by the flagellin perception pathway, but also by another recognition molecule-perception pathway.

Isolation and analysis of water stress induced genes in maize seedlings by subtractive PCR and cDNA macroarray

In order to identify genes induced during the water stress response in maize (Zea mays) seedlings, suppression subtractive hybridization (SSH) was performed using mixed cDNAs prepared from maize seedlings treated with 20% PEG as testers and cDNAs from unstressed maize seedlings as drivers. A forward subtractive cDNA library was constructed, from which 960 recombinant colonies were picked and amplified. Through differential screening of the subtractive cDNA library, 533 clones were identified as water stress induced. After sequencing, 190 unique expressed sequence tags (ESTs) were obtained by clustering and blast analysis, which included transcripts that had previously been reported as responsive to stress as well as some functionally unknown transcripts. The ESTs with significant protein homology were sorted into 13 functional categories. A cDNA marcoarray containing the 190 unique ESTs was used to analyze their expression profiles in maize seedling during both PEG treatment and natural drought. The results indicated that 67 ESTs in leaves and 113 ESTs in roots were significantly up-regulated by PEG-stress. 123 ESTs were found to be up-regulated for at least one time-course point in either maize leaves or roots. Correspondingly, 163 ESTs were significantly up-regulated by drought stress. Results from the hierarchical cluster analysis suggest that the leaves and roots of maize seedlings had different expression profiles after PEG treatment and that there was a lot of overlap between PEG- and drought-stress induced up-regulated transcripts. A set of transcripts has been identified, which have significantly increased expression and probably involved in water stress signaling pathway based on data analysis.

Ovule abortion in Arabidopsis triggered by stress

Environmental stresses frequently decrease plant fertility. In Arabidopsis, the effect of salt stress on reproduction was examined using plants grown in hydroponic medium. Salt stress inhibited microsporogenesis and stamen filament elongation. Because plants grown in hydroponic media can be rapidly and transiently stressed, the minimum inductive treatment to cause ovule abortion could be determined. Nearly 90% of the ovules aborted when roots were incubated for 12 h in a hydroponic medium supplemented with 200 mm NaCl. The anatomical effects of salt stress on maternal organs were distinct from those in the gametophyte. A fraction of cells in the chalaza and integuments underwent DNA fragmentation and programmed cell death. While three-fourths of the gametophytes aborted prior to fertilization, DNA fragmentation was not detected in these cells. Those gametophytes that survived were fertilized and formed embryos. However, very few of these developing embryos formed seeds; most senesced during seed development. Thus, during seed formation, there were multiple points where stress could prematurely terminate plant reproduction. These decreases in fecundity are discussed with respect to the hypothesis of serial adjustment of maternal investment.

A pea chloroplast translation elongation factor that is regulated by abiotic factors

We report the cloning and characterization of both the cDNA (tufA) and genomic clones encoding for a chloroplast translation elongation factor (EF-Tu) from pea. The analysis of the deduced amino acids of the cDNA clone reveals the presence of putative transit peptide sequence and four GTP binding domains and two EF-Tu signature motifs in the mature polypeptide region. Using in vivo immunostaining followed by confocal microscopy pea EF-Tu was localized to chloroplast. The steady state transcript level of pea tufA was high in leaves and not detectable in roots. The expression of this gene is stimulated by light. The differential expression of this gene in response to various abiotic stresses showed that it is down-regulated in response to salinity and ABA and up-regulated in response to low temperature and salicylic acid treatment. These results indicate that regulation of pea tufA may have an important role in plant adaptation to environmental stresses.

Long term transcript accumulation during the development of dehydration adaptation in Cicer arietinum

Cool season crops face intermittent drought. Exposure to drought and other abiotic stresses is known to increase tolerance of the plants against subsequent exposure to such stresses. Storage of environmental signals is also proposed. Preexposure to a dehydration shock improved adaptive response during subsequent dehydration treatment in a cool season crop chickpea (Cicer arietinum). We have identified 101 dehydration-inducible transcripts of chickpea by repetitive rounds of cDNA subtraction; differential DNA-array hybridization followed by northern-blot analysis and analyzed their responses to exogenous application of abscisic acid (ABA). Steady-state expression levels of the dehydration-induced transcripts were monitored during the recovery period between 2 consecutive dehydration stresses. Seven of them maintained more than 3-fold of expression after 24 h and more than 2-fold of expression level even at 72 h after the removal of stress. Noticeably, all of them were inducible by exogenous ABA treatment. When the seedlings were subjected to recover similarly after an exposure to exogenous ABA, the steady-state abundances of 6 of them followed totally different kinetics returning to basal level expression within 24 h. This observation indicated a correlation between the longer period of abundance of those transcripts in the recovery period and improved adaptation of the plants to subsequent dehydration stress and suggested that both ABA-dependent and -independent mechanisms are involved in the maintenance of the messages from the previous stress experience.

An evolutionary approach for gene expression patterns

This study presents an evolutionary algorithm, called a heterogeneous selection genetic algorithm (HeSGA), for analyzing the patterns of gene expression on microarray data. Microarray technologies have provided the means to monitor the expression levels of a large number of genes simultaneously. Gene clustering and gene ordering are important in analyzing a large body of microarray expression data. The proposed method simultaneously solves gene clustering and gene-ordering problems by integrating global and local search mechanisms. Clustering and ordering information is used to identify functionally related genes and to infer genetic networks from immense microarray expression data. HeSGA was tested on eight test microarray datasets, ranging in size from 147 to 6221 genes. The experimental clustering and visual results indicate that HeSGA not only ordered genes smoothly but also grouped genes with similar gene expressions. Visualized results and a new scoring function that references predefined functional categories were employed to confirm the biological interpretations of results yielded using HeSGA and other methods. These results indicate that HeSGA has potential in analyzing gene expression patterns.

Overexpression of a zinc-finger protein gene from rice confers tolerance to cold, dehydration, and salt stress in transgenic tobacco

Stress perception and signal transduction leading to tolerance involve a complex interplay of different gene products. We describe here the isolation and characterization of an intronless gene (OSISAP1) from rice encoding a zinc-finger protein that is induced after different types of stresses, namely cold, desiccation, salt, submergence, and heavy metals as well as injury. The gene is also induced by stress hormone abscisic acid. Overexpression of the gene in transgenic tobacco conferred tolerance to cold, dehydration, and salt stress at the seed-germination/seedling stage as reflected by the percentage of germination/green seedlings, the fresh weight of seedlings, and their developmental pattern. Thus, OSISAP1 seems to be an important determinant of stress response in plants.

Structural and functional analysis of rice genome

Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (>10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macro- and micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.

Transcriptome changes in foxtail millet genotypes at high salinity: identification and characterization of a PHGPX gene specifically upregulated by NaCl in a salt-tolerant line

Using a macro array filter with 711 cDNA inserts representing 620 unigenes selected from a barley EST collection, we identified transcripts differentially expressed in salt (NaCl)-treated tolerant (cv. Prasad) and sensitive (cv. Lepakshi) seedlings of foxtail millet (Setaria italica L.). Transcripts of hydrogen peroxide scavenging enzymes such as phospholipid hydroperoxide glutathione peroxidase (PHGPX), ascorbate peroxidase (APX) and catalase 1 (CAT1) in addition to some genes of cellular metabolism were found to be especially up-regulated at high salinity in the tolerant line. To analyse this process at the protein level we examined protein expression patterns under various stress conditions. A 25 kD protein with a pI of 4.8 was found to be induced prominently under high salt concentrations (250 mmol/L). This salt-induced 25 kD protein has been purified and identified by peptide sequencing as PHGPX protein. The increase of the PHGPX protein level under salt stress in the tolerant line parallels the PHGPX mRNA results of array analysis but was more pronounced. We cloned and characterized the foxtail millet PHGPX cDNA, which shows 85% and 95% homology at the DNA and protein level, respectively, to one stress-induced member of the small barley PHGPX gene family encoding non-selenium glutathione peroxidases. As shown by Southern blot analysis, a small family of PHGPX genes exists in foxtail millet, too. The specific expression pattern of the PHGPX gene in salt-induced tolerant millet seedlings suggests that its product plays an important role in the defense reaction against salt-induced oxidative damage and that the characterized glutathione peroxidase is one of the components conferring resistance against salt to the tolerant foxtail millet cultivar.

Monitoring of gene expression profiles and isolation of candidate genes involved in pollination and fertilization in rice ( Oryza sativa L.) with a 10K cDNA microarray

To monitor gene expression profiles during pollination and fertilization in rice at a genome scale, we generated 73,424 high-quality expressed sequence tags (ESTs) derived from the green/etiolated shoot and pistil (0-5 h after pollination, 5hP) of rice, which were subsequently used to construct a cDNA microarray containing ca. 10 000 unique rice genes. This microarray was used to analyze gene expression in pistil unpollinated (UP), 5hP and 5DAP(5 days after pollination), anther, shoot, root, 10-day-old embryo (10EM) and 10-day-old endosperm (10EN). Clustering analysis revealed that the anther has a gene-expression profile more similar to root than to pistil and most pistil-preferentially expressed genes respond to pollination and/or fertilization. There are 253 ESTs exhibiting differential expression (e +/- 2-fold changes) during pollination and fertilization, and about 70% of them can be assigned a putative function. We also recovered 20 genes similar to pollination-related and/or fertility-related genes previously identified as well as genes that were not implicated previously. Microarray and real-time PCR analyses showed that the array sensitivity was estimated at 1-5 copies of mRNA per cell, and the differentially expressed genes showed a high correlation between the two methods. Our results indicated that this cDNA microarray constructed here is reliable and can be used for monitoring gene expression profiles in rice. In addition, the genes that differentially expressed during pollination represent candidate genes for dissecting molecular mechanism of this important biological process in rice.

An expression analysis of a gene family encoding plasma membrane aquaporins in response to abiotic stresses in Arabidopsis thaliana

Aquaporin belongs to a highly conserved group of membrane proteins called major intrinsic proteins that facilitate water transport across biological membranes. The genome of Arabidopsis encodes 35 aquaporin genes with 13 homologs in the plasma membrane intrinsic protein (PIP) subgroup. However, the function of each individual aquaporin isoform and the integrated function of plant aquaporins under various physiological conditions remain unclear. As a step toward understanding the aquaporin function in plants under various environmental stimuli, the expressions of a gene family encoding 13 PIPs in Arabidopsis thaliana under various abiotic stress conditions including drought, cold, and high salinity, or abscisic acid (ABA) treatment were investigated by a quantitative real-time reverse transcription-PCR analysis. Several PIP genes were predominantly expressed either in the roots or in the flowers. The expressions of both the highly expressed aquaporins including PIP1;1, PIP1;2, and PIP2;7 and the weakly expressed aquaporins such as PIP1;4, PIP2;1, PIP2;4, and PIP2;5 were modulated by external stimuli. The analyses of our data revealed that only the PIP2;5 was up-regulated by cold treatment, and most of the PIP genes were down-regulated by cold stress. Marked up- or down-regulation in PIP expression was observed by drought stress, whereas PIP genes were less-severely modulated by high salinity. The responsiveness of each aquaporin to ABA were different, implying that the regulation of aquaporin expression involves both ABA-dependent and ABA-independent signaling pathways. Together, our comprehensive expression profile of the 13 members of the PIP gene family provides novel basis to allocate the stress-related biological function to each PIP gene.

Improving crop salt tolerance

Salinity is an ever-present threat to crop yields, especially in countries where irrigation is an essential aid to agriculture. Although the tolerance of saline conditions by plants is variable, crop species are generally intolerant of one-third of the concentration of salts found in seawater. Attempts to improve the salt tolerance of crops through conventional breeding programmes have met with very limited success, due to the complexity of the trait: salt tolerance is complex genetically and physiologically. Tolerance often shows the characteristics of a multigenic trait, with quantitative trait loci (QTLs) associated with tolerance identified in barley, citrus, rice, and tomato and with ion transport under saline conditions in barley, citrus and rice. Physiologically salt tolerance is also complex, with halophytes and less tolerant plants showing a wide range of adaptations. Attempts to enhance tolerance have involved conventional breeding programmes, the use of in vitro selection, pooling physiological traits, interspecific hybridization, using halophytes as alternative crops, the use of marker-aided selection, and the use of transgenic plants. It is surprising that, in spite of the complexity of salt tolerance, there are commonly claims in the literature that the transfer of a single or a few genes can increase the tolerance of plants to saline conditions. Evaluation of such claims reveals that, of the 68 papers produced between 1993 and early 2003, only 19 report quantitative estimates of plant growth. Of these, four papers contain quantitative data on the response of transformants and wild-type of six species without and with salinity applied in an appropriate manner. About half of all the papers report data on experiments conducted under conditions where there is little or no transpiration: such experiments may provide insights into components of tolerance, but are not grounds for claims of enhanced tolerance at the whole plant level. Whether enhanced tolerance, where properly established, is due to the chance alteration of a factor that is limiting in a complex chain or an effect on signalling remains to be elucidated. After ten years of research using transgenic plants to alter salt tolerance, the value of this approach has yet to be established in the field.

Identification of a novel gene, HAABRC5, from Helianthus annuus (Asteraceae) that is upregulated in response to drought, salinity, and abscisic acid

Using differential display of mRNA transcripts, we obtained a partial cDNA clone, RSC5-U, that is upregulated by exposure to high salinity. A longer cDNA of 812 nucleotides, designated HaABRC5, was then cloned by rapid amplification of cDNA ends. This full-length cDNA contains an open reading frame of 423 nucleotides encoding 141 amino acids, including a "bipartite nuclear targeting sequence." The deduced amino acid sequence had no similarity to known genes in the database. The expression of HaABRC5 was investigated in more detail using quantitative reverse transcriptase-polymerase chain reaction. HaABRC5 is upregulated by drought, high salinity, and exogenous application of abscisic acid (ABA). The promoter sequence of 229 nucleotides, upstream of HaABRC5, was cloned using rapid amplification of genomic ends. Three ABA-responsive elements were found within the HaABRC5 promoter region. Therefore, HaABRC5 is probably an ABA-responsive nuclear protein playing a role in plant stress response.

Spermine accumulation under salt stress

Polyamines have long been recognized to be linked to stress situations, and it is generally accepted that they have protective characteristics. However, little is known about their physiological relevance in plants subjected to long-term salt stress. In order to precise their importance, two rice (Oryza sativa) cultivars differing in their salt tolerance were salinized for 7, 14 and 21 days. The activities of some of the enzymes involved in polyamine metabolism, free polyamines and proline contents were evaluated. Arginine decarboxylase and S-adenosyl-L-methionine decarboxylase activities were reduced in both cultivars as a consequence of salt treatment. However, spermidine synthase activity was reduced in the salt tolerant cultivar (var Giza) but not in the salt sensitive (var El Paso), while no polyamine oxidase activity was detected. During the salinization period, putrescine and spermidine levels decreased in both cultivars, although less dramatically in Giza. Simultaneously, spermine accumulations occur in both varieties, while proline accumulation was major in the sensitive one. However, spermine accumulation induced by treatment with spermidine synthase inhibitor cyclohexylamine, determined no reduction in leaf injury associated with salt stress in both cultivars. The data presented suggest that spermine accumulation is not a salt tolerance trait.

Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses

To identify cold-, drought-, high-salinity-, and/or abscisic acid (ABA)-inducible genes in rice (Oryza sativa), we prepared a rice cDNA microarray including about 1700 independent cDNAs derived from cDNA libraries prepared from drought-, cold-, and high-salinity-treated rice plants. We confirmed stress-inducible expression of the candidate genes selected by microarray analysis using RNA gel-blot analysis and finally identified a total of 73 genes as stress inducible including 58 novel unreported genes in rice. Among them, 36, 62, 57, and 43 genes were induced by cold, drought, high salinity, and ABA, respectively. We observed a strong association in the expression of stress-responsive genes and found 15 genes that responded to all four treatments. Venn diagram analysis revealed greater cross talk between signaling pathways for drought, ABA, and high-salinity stresses than between signaling pathways for cold and ABA stresses or cold and high-salinity stresses in rice. The rice genome database search enabled us not only to identify possible known cis-acting elements in the promoter regions of several stress-inducible genes but also to expect the existence of novel cis-acting elements involved in stress-responsive gene expression in rice stress-inducible promoters. Comparative analysis of Arabidopsis and rice showed that among the 73 stress-inducible rice genes, 51 already have been reported in Arabidopsis with similar function or gene name. Transcriptome analysis revealed novel stress-inducible genes, suggesting some differences between Arabidopsis and rice in their response to stress.

Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses

To identify cold-, drought-, high-salinity-, and/or abscisic acid (ABA)-inducible genes in rice (Oryza sativa), we prepared a rice cDNA microarray including about 1700 independent cDNAs derived from cDNA libraries prepared from drought-, cold-, and high-salinity-treated rice plants. We confirmed stress-inducible expression of the candidate genes selected by microarray analysis using RNA gel-blot analysis and finally identified a total of 73 genes as stress inducible including 58 novel unreported genes in rice. Among them, 36, 62, 57, and 43 genes were induced by cold, drought, high salinity, and ABA, respectively. We observed a strong association in the expression of stress-responsive genes and found 15 genes that responded to all four treatments. Venn diagram analysis revealed greater cross talk between signaling pathways for drought, ABA, and high-salinity stresses than between signaling pathways for cold and ABA stresses or cold and high-salinity stresses in rice. The rice genome database search enabled us not only to identify possible known cis-acting elements in the promoter regions of several stress-inducible genes but also to expect the existence of novel cis-acting elements involved in stress-responsive gene expression in rice stress-inducible promoters. Comparative analysis of Arabidopsis and rice showed that among the 73 stress-inducible rice genes, 51 already have been reported in Arabidopsis with similar function or gene name. Transcriptome analysis revealed novel stress-inducible genes, suggesting some differences between Arabidopsis and rice in their response to stress.

Photosynthetic acclimation is reflected in specific patterns of gene expression in drought-stressed loblolly pine

Because the product of a single gene can influence many aspects of plant growth and development, it is necessary to understand how gene products act in concert and upon each other to effect adaptive changes to stressful conditions. We conducted experiments to improve our understanding of the responses of loblolly pine (Pinus taeda) to drought stress. Water was withheld from rooted plantlets of to a measured water potential of -1 MPa for mild stress and -1.5 MPa for severe stress. Net photosynthesis was measured for each level of stress. RNA was isolated from needles and used in hybridizations against a microarray consisting of 2173 cDNA clones from five pine expressed sequence tag libraries. Gene expression was estimated using a two-stage mixed linear model. Subsequently, data mining via inductive logic programming identified rules (relationships) among gene expression, treatments, and functional categories. Changes in RNA transcript profiles of loblolly pine due to drought stress were correlated with physiological data reflecting photosynthetic acclimation to mild stress or photosynthetic failure during severe stress. Analysis of transcript profiles indicated that there are distinct patterns of expression related to the two levels of stress. Genes encoding heat shock proteins, late embryogenic-abundant proteins, enzymes from the aromatic acid and flavonoid biosynthetic pathways, and from carbon metabolism showed distinctive responses associated with acclimation. Five genes shown to have different transcript levels in response to either mild or severe stress were chosen for further analysis using real-time polymerase chain reaction. The real-time polymerase chain reaction results were in good agreement with those obtained on microarrays.

Accumulation of LEA proteins in salt (NaCl) stressed young seedlings of rice (Oryza sativa L.) cultivar Bura Rata and their degradation during recovery from salinity stress

Germination and subsequent hydroponic growth under salt stress (100 mmol/L NaCl) triggered an accumulation of six major stress proteins and resulted in a growth arrest of young seedlings of rice (Oryza sativa L.) cv. Bura Rata. Based on two-dimensional electrophoretic resolution, partial amino acid sequencing and immunodetection techniques, four of the salt stress-induced polypeptides were identified as LEA proteins. Under all experimental conditions wherein seedlings exhibited superior halotolerance, salt stress-induced LEA proteins were expressed at low levels. In contrast, accumulation of LEA proteins was found associated with growth arrest. When returned to non-saline media, seedlings stressed with salt for four days recovered immediately. Longer exposure to 100 mmol/L NaCl, however, progressively delayed recovery and reduced the number of seedlings which could recover from salt stress. Recovery from salt stress was consistently accompanied by degradation of the salt stress-induced LEA proteins. The results of this study show that LEA proteins accumulate during the salinity-triggered growth arrest of young Bura Rata seedlings and are mobilised during the recovery of seedlings from salinity stress.

Global analysis of gene expression using GeneChip microarrays

DNA microarray technology, especially the use of GeneChip microarrays, has become a standard tool for parallel gene expression analysis. Recent improvements in GeneChip microarrays enable whole-genome expression analysis, and thus open a new avenue for studies of the composition, dynamics, and regulation of the transcriptome in plants.

A snapshot of the low temperature stress transcriptome of developing rice seedlings (Oryza sativa L.) via ESTs from subtracted cDNA library

Rice (Oryza sativa L.) is sensitive to chilling particularly during early seedling development. Given the biochemical complexity of tolerance mechanisms, genetic potential for this trait depends on highly coordinated expression of many genes. We used a simple cDNA subtraction strategy to develop Expressed Sequence Tags (ESTs) that represent an important subset of cold stress-upregulated genes. The 3,084 subtracted cDNA clones represent a total of 1,967 unigenes from 1,354 singletons and 613 contigs. As expected in the developing seedlings, genes involved in basic cellular processes, i.e., metabolism, growth and development, protein synthesis, folding and destination, cellular transport, cell division and DNA replication were widely represented. Genes with stress-related and regulatory functions comprised 23.17% of the total ESTs. These categories included proteins with known function in cellular defenses against abiotic (drought, cold and salinity) and biotic (pathogen) stresses, and proteins involved in developmental and stress response signalling and transcription. Based on the types of genes represented, tolerance mechanisms rely on precise integration of developmental processes with stress-related responses. A large fraction of the ESTs (38.7%) represents unknown proteins. This EST library is a rich source of cold stress-related genes, and supplements for other publicly available libraries for comprehensive analysis of the stress-response transcriptome.