Molecular and genetic aspects of plant responses to osmotic stress

Structure and regulation of the Asr gene family in banana

Abscisic acid, stress, ripening proteins (ASR) are a family of plant-specific small hydrophilic proteins. Studies in various plant species have highlighted their role in increased resistance to abiotic stress, including drought, but their specific function remains unknown. As a first step toward their potential use in crop improvement, we investigated the structure and regulation of the Asr gene family in Musa species (bananas and plantains). We determined that the Musa Asr gene family contained at least four members, all of which exhibited the typical two exons, one intron structure of Asr genes and the "ABA/WDS" (abscisic acid/water deficit stress) domain characteristic of Asr genes. Phylogenetic analyses determined that the Musa Asr genes were closely related to each other, probably as the product of recent duplication events. For two of the four members, two versions corresponding to the two sub-genomes of Musa, acuminata and balbisiana were identified. Gene expression and protein analyses were performed and Asr expression could be detected in meristem cultures, root, pseudostem, leaf and cormus. In meristem cultures, mAsr1 and mAsr3 were induced by osmotic stress and wounding, while mAsr3 and mAsr4 were induced by exposure to ABA. mASR3 exhibited the most variation both in terms of amino acid sequence and expression pattern, making it the most promising candidate for further functional study and use in crop improvement.

Metallothionein-like gene from Cicer microphyllum is regulated by multiple abiotic stresses

Cicer microphyllum, a wild relative of cultivated chickpea, is a high altitude cold desert-adapted species distributed in western and trans-Himalayas. A complementary DNA (cDNA) encoding metallothionein-like protein has been identified from a cold-induced subtraction cDNA library from C. microphyllum. The sequence of the cloned metallothionein gene from C. microphyllum (GQ900702) contains 240-bp-long open reading frame and encodes predicted 79-amino acid protein of 7.9 kDa. Sequence analysis identified the motifs characteristic of type II metallothionein and designated as CmMet-2. Southern hybridization confirms a single copy of the CmMet-2 gene in C. microphyllum genome. In situ hybridization indicated spatial transcript regulation of CmMet-2 in root and aerial parts and also confirmed through real-time PCR-based quantitative transcript analysis. The data revealed a significantly low level of transcript in the aerial parts than the roots. Quantitative analysis using real-time PCR assay revealed induction of transcript in all parts of plants in response to cold stress at 4°C. The transcript abundance was found to increase exponentially with time course from 6 to 24 h after exposure. Further, regulation of transcript accumulation in response to abscisic acid application, polyethylene glycol (100 μM)-induced osmotic stress, or ZnSO(4) (1 μM) foliar spray indicated by Northern hybridization suggests the involvement of CmMet-2 in multiple stress response.

Genetic, proteomic and metabolic analysis of the regulation of energy storage in rice seedlings in response to drought

We used proteomic analysis to determine the response of rice plant seedlings to drought-induced stress. The expression of 71 protein spots was significantly altered, and 60 spots were successfully identified. The greatest down-regulated protein functional category was translation. Up-regulated proteins were mainly related to protein folding and assembly. Additionally, many proteins involved in metabolism (e.g. carbohydrate metabolism) also showed differences in expression. cDNA microarray and GC-MS analysis showed 4756 differentially expressed mRNAs and 37 differentially expressed metabolites. Once these data were integrated with the proteomic analysis, we were able to elucidate the metabolic pathways affected by drought-induced stress. These results suggest that increased energy consumption from storage substances occurred during drought. In addition, increased expression of the enzymes involved in anabolic pathways corresponded with an increase in the content of six amino acids. We speculated that energy conversion from carbohydrates and/or fatty acids to amino acids was increased. Analysis of basic metabolism networks allowed us to understand how rice plants adjust to drought conditions.

Copper-induced oxidative damage, antioxidant response and genotoxicity in Lycopersicum esculentum Mill. and Cucumis sativus L

Adequate copper (Cu(2+)) concentrations are required for plants; however, at higher concentrations it can also cause multiple toxic effects. In the present study, lipid peroxidation, hydrogen peroxide levels as well as ascorbate peroxidase (APX: EC 1/11/1/11) and catalase (CAT: EC 1.11.1.6) activities were determined in Lycopersicum esculentum Mill. and Cucumis sativus L. seedlings after 7-day exposure to copper sulfate. In addition, DNA damage in these two crops was assessed by measuring micronucleus (MN) frequency and tail moments (TM) as determined by Comet assay. Inhibitory copper concentrations (EC(50): 30 and 5.5 ppm for L. esculentum and C. sativus, respectively) were determined according to dose-dependent root inhibition curves, and EC(50) and 2×EC(50) were applied. Malondialdehyde (MDA) and H(2)O(2) levels significantly increased in all groups studied. CAT activity increased in treatment groups of C. sativus. APX activity increased in L. esculentum seedlings due to 2×EC(50) treatment. Reductions in mitotic indices (MI) represented Cu(2+)dependent root growth inhibition in all treatment groups studied. According to TMs and MN frequencies, copper exposure induced significant DNA damage (p < 0.05) in all study groups, whereas the DNA damage induced was dose dependent in C. sativus roots. In conclusion, Cu(2+)induced oxidative damage, elevations in H(2)O(2) levels and alterations in APX and CAT activities, as well as significant DNA damage in nuclei of both study groups. To our knowledge, this is the first comparative and comprehensive study demonstrating the effects of copper on two different plant species at relevant cytotoxic concentrations at both biochemical and genotoxicity levels with multiple end points.

Cloning and characterization of a maize SnRK2 protein kinase gene confers enhanced salt tolerance in transgenic Arabidopsis

SnRK2 (sucrose non-fermenting 1-related protein kinases 2) represents a unique family of protein kinase in regulating signaling transduction in plants. Although the regulatory mechanisms of SnRK2 have been well demonstrated in Arabidopsis thaliana, their functions in maize are still unknown. In our study, we cloned an SnRK2 gene from maize, ZmSAPK8, which encoded a putative homolog of the rice SAPK8 protein. ZmSAPK8 had two copies in the maize genome and harbored eight introns in its coding region. We demonstrated that ZmSAPK8 expressed differentially in various organs of maize plants and was up-regulated by high-salinity and drought treatment. A green fluorescent protein (GFP)-tagged ZmSAPK8 showed subcellular localization in the cell membrane, cytoplasm and nucleus. In vitro kinase assays indicated that ZmSAPK8 preferred Mn(2+) to Mg(2+) as cofactor for phosphorylation, and Ser-182 and Thr-183 in activation loop was important for its activity. Heterologous overexpression of ZmSAPK8 in Arabidopsis could significantly strengthen tolerance to salt stress. Under salt treatment, ZmSAPK8-overexpressed transgenic plants exhibited higher germination rate and proline content, low electrolyte leakage and higher survival rate than wild type. Further analysis indicated that transgenic plants showed increased transcription of the stress-related genes, RD29A, RD29B, RAB18, ABI1, DREB2A and P5CS1, under high-salinity conditions. The results demonstrated that ZmSAPK8 was involved in diverse stress signal transduction. Moreover, no obvious adverse effects on growth and development in the ZmSAPK8-overexpressed transgenic plants implied that ZmSAPK8 was potentially useful in transgenic breeding to improve salt tolerance in crops.

Elucidation of physiological and biochemical mechanisms of an endemic halophyte Centaurea tuzgoluensis under salt stress

In this study, physiological and biochemical responses of Centaurea tuzgoluensis, a Turkish endemic halophyte, to salinity were studied. Therefore, the changes in shoot growth, leaf relative water content (RWC), ion concentrations, lipid peroxidation, hydroxyl (OH·) radical scavenging activity, proline (Pro) content, and antioxidant system [superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR)] were investigated. The 60 days (d) old C. tuzgoluensis seedlings were subjected to 0, 150 and 300 mM NaCl for 7 d and 14 d. The relative shoot growth was generally did not change in the 150 mM NaCl, but reduced with 300 mM NaCl stress at 7 d and 14 d. RWC was higher in 150 mM NaCl-treated leaves than that of 300 mM NaCl. Salinity decreased K⁺/Na⁺ ratio, but increased Na⁺, Cl⁻, Ca⁺² and Na⁺/Cl⁻ ratio in the leaves. On the other hand, it did not change or increase the K⁺ content at 150 and 300 mM NaCl, respectively. MDA content in the 150 and 300 mM NaCl-treated leaves remained close to control at 7 d. This was related to enhanced activities of SOD, CAT, APX and GR enzymes, and their isoenzymes especially Fe-SOD in the leaves. On the other hand, the higher sensitivity to 300 mM NaCl at 14 d was associated with inadequate increase in antioxidant enzymes and the decreased OH radical scavenging activity. All these results suggest that C. tuzgoluensis has different antioxidant metabolisms between short- (7 d) and long-term (14 d) salt treatments and salinity tolerance of C. tuzgoluensis might be closely related to increased capacity of antioxidative system to scavenge reactive oxygen species (ROS) and accumulation of osmoprotectant proline under salinity conditions.

Overexpression of a Harpin-encoding gene hrf1 in rice enhances drought tolerance

Harpin proteins are well known as eliciters that induce multiple responses in plants, such as systemic acquired resistance, hypersensitive response, enhancement of growth, resistance to the green peach aphid, and tolerance to drought. Overexpression of Harpin-encoding genes enhances plant resistance to diseases in tobacco, rice, rape, and cotton; however, it is not yet known whether the expression of Harpin-encoding genes in vivo improves plant tolerance to abiotic stresses. The results of this study showed that overexpression of a Harpin-encoding gene hrf1 in rice increased drought tolerance through abscisic acid (ABA) signalling. hrf1- overexpression induces an increase in ABA content and promotes stomatal closure in rice. The hrf1 transgenic rice lines exhibited a significant increase in water retention ability, levels of free proline and soluble sugars, tolerance to oxidative stress, reactive oxygen species-scavenging ability, and expression levels of four stress-related genes, OsLEA3-1, OsP5CS, Mn-SOD, and NM_001074345, under drought stress. The study confirmed that hrf1 conferred enhanced tolerance to drought stress on transgenic crops. These results suggest that Harpins may offer new opportunities for generating drought resistance in other crops.

Transgenic potato overproducing L-ascorbic acid resisted an increase in methylglyoxal under salinity stress via maintaining higher reduced glutathione level and glyoxalase enzyme activity

Salt-tolerance was studied in transgenic potato. It was conferred by overexpression of ascorbate pathway enzyme (D-galacturonic acid reductase, GalUR). As genetic engineering of the GalUR gene in potato enhances its ascorbic acid content (L-AsA), and subsequently plants suffered minimal oxidative stress-induced damage, we now report on the comprehensive aptness of this engineering approach for enhanced salt tolerance in transgenic potato (Solanum tuberosum L. cv. Taedong Valley). Potatoes overexpressing GalUR grew and tuberized in continuous presence of 200 mM of NaCl. The transgenic plants maintained a higher reduced to oxidized glutathione (GSH:GSSG) ratio together with enhanced activity of glutathione dependent antioxidative and glyoxalase enzymes under salinity stress. The transgenics resisted an increase in methylglyoxal that increased radically in untransformed control plants under salinity stress. This is the first report of genetic engineering of ascorbate pathway gene in maintaining higher level of GSH homeostasis along with higher glyoxalase activity inhibiting the accumulation in methylglyoxal (a potent cytotoxic compound) under salt stress. These results suggested the engineering of ascorbate pathway enzymes as a major step towards developing salinity tolerant crop plants.

Toxic effects of chemical pesticides (trichlorfon and dimehypo) on Dunaliella salina

Dunaliella salina, a unicellular green alga of environmental tolerance, was employed as test organism to investigate the toxicity effects of trichlorfon and dimehypo widely used in agriculture and veterinary as pesticides. The influences of trichlorfon and dimehypo on cell growth, β-carotene level, cell morphology changes, and activities of superoxide dismutase (Sod) and catalase (Cat) were investigated. At the concentrations less than 0.050 g L(-1) trichlorfon or 0.0005 g L(-1) dimehypo, cell responses were similar to control. When treated with 0.075-0.100 g L(-1) trichlorfon or 0.001-0.004 g L(-1) dimehypo, cell growth and β-carotene levels declined at first and then revived. When concentrations were higher than 0.125 g L(-1) trichlorfon or 0.005 g L(-1) dimehypo, both cell growth and β-carotene levels decreased until they were undetectable. The 10-d IC50 of trichlorfon and dimehypo on D. salina were 0.179 g L(-1) and 0.032 g L(-1). Both pollutants could stimulate the increase of Cat activity at a low concentration. Tolerance of D. salina to trichlorfon was obviously higher than that of dimehypo.

Quantitative proteomic analyses of crop seedlings subjected to stress conditions; a commentary

Quantitative proteomics is one of the analytical approaches used to clarify crop responses to stress conditions. Recent remarkable advances in proteomics technologies allow for the identification of a wider range of proteins than was previously possible. Current proteomic methods fall into roughly two categories: gel-based quantification methods, including conventional two-dimensional gel electrophoresis and two-dimensional fluorescence difference gel electrophoresis, and MS-based quantification methods consists of label-based and label-free protein quantification approaches. Although MS-based quantification methods have become mainstream in recent years, gel-based quantification methods are still useful for proteomic analyses. Previous studies examining crop responses to stress conditions reveal that each method has both advantages and disadvantages in regard to protein quantification in comparative proteomic analyses. Furthermore, one proteomics approach cannot be fully substituted by another technique. In this review, we discuss and highlight the basis and applications of quantitative proteomic analysis approaches in crop seedlings in response to flooding and osmotic stress as two environmental stresses.

The genetic and physiological analysis of late-flowering phenotype of T-DNA insertion mutants of AtCAL1 and AtCAL2 in Arabidopsis

The homozygous T-DNA mutants of AtCAL1 (Rat1) and AtCAL2 (Rat2) were obtained. The double mutant of Rat2/Rat1RNAi was constructed which showed obvious late-flowering phenotype from others. The expression of various flowering-related genes was studied among mutants and wild-type plants by quantitative RT-PCR. The double mutant plants showed the shortest root length compared with T-DNA insertion mutants and wild type plants under red light, blue light, and white light. The double mutants showed hypersensitivity to NaCl and ABA. However, these mutants had no effect on stomatal closure by ABA.

Molecular cloning and characterization of an F-box family gene CarF-box1 from chickpea (Cicer arietinum L.)

F-box protein family has been found to play important roles in plant development and abiotic stress responses via the ubiquitin pathway. In this study, an F-box gene CarF-box1 (for Cicer arietinum F-box gene 1, Genbank accession no. GU247510) was isolated based on a cDNA library constructed with chickpea seedling leaves treated by polyethylene glycol. CarF-box1 encoded a putative protein with 345 amino acids and contained no intron within genomic DNA sequence. CarF-box1 is a KFB-type F-box protein, having a conserved F-box domain in the N-terminus and a Kelch repeat domain in the C-terminus. CarF-box1 was localized in the nucleus. CarF-box1 exhibited organ-specific expression and showed different expression patterns during seed development and germination processes, especially strongly expressed in the blooming flowers. In the leaves, CarF-box1 could be significantly induced by drought stress and slightly induced by IAA treatment, while in the roots, CarF-box1 could be strongly induced by drought, salinity and methyl jasmonate stresses. Our results suggest that CarF-box1 encodes an F-box protein and may be involved in various plant developmental processes and abiotic stress responses.

Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes

Background

Cells must respond to various perturbations using their limited available gene repertoires. In order to study how cells coordinate various responses, we conducted a comprehensive comparison of 1,186 gene expression signatures (gene lists) associated with various genetic and chemical perturbations.

Results

We identified 7,419 statistically significant overlaps between various published gene lists. Most (80%) of the overlaps can be represented by a highly connected network, a "molecular signature map," that highlights the correlation of various expression signatures. By dissecting this network, we identified sub-networks that define clusters of gene sets related to common biological processes (cell cycle, immune response, etc). Examination of these sub-networks has confirmed relationships among various pathways and also generated new hypotheses. For example, our result suggests that glutamine deficiency might suppress cellular growth by inhibiting the MYC pathway. Interestingly, we also observed 1,369 significant overlaps between a set of genes upregulated by factor X and a set of genes downregulated by factor Y, suggesting a repressive interaction between X and Y factors.

Conclusions

Our results suggest that molecular-level responses to diverse chemical and genetic perturbations are heavily interconnected in a modular fashion. Also, shared molecular pathways can be identified by comparing newly defined gene expression signatures with databases of previously published gene expression signatures.

Arabidopsis thaliana 26S proteasome subunits RPT2a and RPT5a are crucial for zinc deficiency-tolerance

RPTs (regulatory particle triple-A-ATPase) are components of 26S proteasome. We found novel roles of RPT2a and RPT5a in Zn deficiency-tolerance. Arabidopsis thaliana mutants carrying T-DNA in RPT2a and RPT5a were more sensitive to Zn deficiency than the wild-type. In the rpt mutants, the shoot Zn contents were similar to those of the wild-type. Transcripts of Zn deficiency-inducible genes were highly accumulated in the rpt mutants, suggesting that the rpt mutants suffer from various Zn deficiency symptoms, although the Zn levels are not reduced. Lipid peroxidation levels, known to be increased under Zn deficiency, were higher in the rpt mutants than in the wild-type. Poly-ubiquitinated proteins were accumulated upon exposure to Zn deficiency, especially in the rpt mutants. Overall, this study indicates that RPT2a and RPT5a are involved in Zn deficiency-tolerance, possibly through alleviation of oxidative stresses and/or processing of poly-ubiquitinated proteins.

Homeostatic control of polyamine levels under long-term salt stress in Arabidopsis: changes in putrescine content do not alleviate ionic toxicity

Salt stress has been frequently studied in its first osmotic phase. Very often, data regarding the second ionic phase is missing. It has also been suggested that Putrescine or/and Spermine could be responsible for salt resistance. In order to test this hypothesis under long-term salt stress, we obtained Arabidopsis thaliana transgenic plants harboring pRD29A::oatADC or pRD29A::GUS construction. Although Putrescine was the only polyamine significantly increased after salt acclimation in pRD29A::oatADC transgenic lines, this rendered in no advantage to this kind of stress. The higher Spermine levels found in WT and transgenic lines when compared to control conditions along with no increment on Putrescine levels in WT plants under salt acclimation, leads us to analyze Spermine effect on pADC1 and pADC2 expression. Increasing levels of this polyamine inhibits these promoters expression while enhances pRD29A expression, making Spermine the polyamine responsible for salt acclimation, and the transgenic lines developed in this work suitable for studying Putrescine roles in conditions where its biosynthesis would be inhibited in the WT genotype.

Role of the stomatal development regulators FLP/MYB88 in abiotic stress responses

Stomata are vital for the adaptation of plants to abiotic stress, and in turn stomatal density is modulated by environmental factors. Less clear, however, is whether regulators of stomatal development themselves participate in the sensing or response of stomata to abiotic stress. FOUR LIPS (FLP) and its paralog MYB88 encode MYB proteins that establish stomatal patterning by permitting only a single symmetric division before stomata differentiate. Hence, flp-1 myb88 double mutants have an excess of stomata, which are often misplaced in direct contact. Here, we investigate the consequences of loss of FLP/MYB88 function on the ability of Arabidopsis plants to respond to abiotic stress. While flp-1 myb88 double mutants are viable and display no obvious aerial phenotypes under normal greenhouse growth conditions, we show that flp-1 myb88 plants are significantly more susceptible to drought and high salt, and have increased rates of water loss. To determine whether flp-1 myb88 plants are already challenged under normal growth conditions, we compared genome-wide transcript levels between flp-1 myb88 and wild-type green tissues. Unexpectedly, uninduced flp-1 myb88 plants showed a reduced accumulation of many typical abiotic stress gene transcripts. Moreover, the induction of many of these stress genes under high-salt conditions was significantly lower in flp-1 myb88 plants. Our results provide evidence for a new function of FLP/MYB88 in sensing and/or transducing abiotic stress, which is severely compromised in flp-1 myb88 mutants.

Proteomic analysis of rice leaves shows the different regulations to osmotic stress and stress signals

Following the idea of partial root-zone drying (PRD) in crop cultivation, the morphological and physiological responses to partial root osmotic stress (PROS) and whole root osmotic stress (WROS) were investigated in rice. WROS caused stress symptoms like leaf rolling and membrane leakage. PROS stimulated stress signals, but did not cause severe leaf damage. By proteomic analysis, a total of 58 proteins showed differential expression after one or both treatments, and functional classification of these proteins suggests that stress signals regulate photosynthesis, carbohydrate and energy metabolism. Two other proteins (anthranilate synthase and submergence-induced nickel-binding protein) were upregulated only in the PROS plants, indicating their important roles in stress resistance. Additionally, more enzymes were involved in stress defense, redox homeostasis, lignin and ethylene synthesis in WROS leaves, suggesting a more comprehensive regulatory mechanism induced by osmotic stress. This study provides new insights into the complex molecular networks within plant leaves involved in the adaptation to osmotic stress and stress signals.

Genome structures and halophyte-specific gene expression of the extremophile Thellungiella parvula in comparison with Thellungiella salsuginea (Thellungiella halophila) and Arabidopsis

The genome of Thellungiella parvula, a halophytic relative of Arabidopsis (Arabidopsis thaliana), is being assembled using Roche-454 sequencing. Analyses of a 10-Mb scaffold revealed synteny with Arabidopsis, with recombination and inversion and an uneven distribution of repeat sequences. T. parvula genome structure and DNA sequences were compared with orthologous regions from Arabidopsis and publicly available bacterial artificial chromosome sequences from Thellungiella salsuginea (previously Thellungiella halophila). The three-way comparison of sequences, from one abiotic stress-sensitive species and two tolerant species, revealed extensive sequence conservation and microcolinearity, but grouping Thellungiella species separately from Arabidopsis. However, the T. parvula segments are distinguished from their T. salsuginea counterparts by a pronounced paucity of repeat sequences, resulting in a 30% shorter DNA segment with essentially the same gene content in T. parvula. Among the genes is SALT OVERLY SENSITIVE1 (SOS1), a sodium/proton antiporter, which represents an essential component of plant salinity stress tolerance. Although the SOS1 coding region is highly conserved among all three species, the promoter regions show conservation only between the two Thellungiella species. Comparative transcript analyses revealed higher levels of basal as well as salt-induced SOS1 expression in both Thellungiella species as compared with Arabidopsis. The Thellungiella species and other halophytes share conserved pyrimidine-rich 5' untranslated region proximal regions of SOS1 that are missing in Arabidopsis. Completion of the genome structure of T. parvula is expected to highlight distinctive genetic elements underlying the extremophile lifestyle of this species.

Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds

BACKGROUND

Jatropha curcas L. is promoted as an important non-edible biodiesel crop worldwide. Jatropha oil, which is a triacylglycerol, can be directly blended with petro-diesel or transesterified with methanol and used as biodiesel. Genetic improvement in jatropha is needed to increase the seed yield, oil content, drought and pest resistance, and to modify oil composition so that it becomes a technically and economically preferred source for biodiesel production. However, genetic improvement efforts in jatropha could not take advantage of genetic engineering methods due to lack of cloned genes from this species. To overcome this hurdle, the current gene discovery project was initiated with an objective of isolating as many functional genes as possible from J. curcas by large scale sequencing of expressed sequence tags (ESTs).

RESULTS

A normalized and full-length enriched cDNA library was constructed from developing seeds of J. curcas. The cDNA library contained about 1 × 10(6) clones and average insert size of the clones was 2.1 kb. Totally 12,084 ESTs were sequenced to average high quality read length of 576 bp. Contig analysis revealed 2258 contigs and 4751 singletons. Contig size ranged from 2-23 and there were 7333 ESTs in the contigs. This resulted in 7009 unigenes which were annotated by BLASTX. It showed 3982 unigenes with significant similarity to known genes and 2836 unigenes with significant similarity to genes of unknown, hypothetical and putative proteins. The remaining 191 unigenes which did not show similarity with any genes in the public database may encode for unique genes. Functional classification revealed unigenes related to broad range of cellular, molecular and biological functions. Among the 7009 unigenes, 6233 unigenes were identified to be potential full-length genes.

CONCLUSIONS

The high quality normalized cDNA library was constructed from developing seeds of J. curcas for the first time and 7009 unigenes coding for diverse biological functions including oil biosynthesis were identified. These genes will serve as invaluable genetic resource for crop improvement in jatropha to make it an ideal and profitable crop for biodiesel production.

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

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

Antioxidative responses of Ocimum basilicum to sodium chloride or sodium sulphate salinization

Soils and ground water in nature are dominated by chloride and sulphate salts. There have been several studies concerning NaCl salinity, however, little is known about the Na(2)SO(4) one. The effects on antioxidative activities of chloride or sodium sulphate in terms of the same Na(+) equivalents (25 mM Na(2)SO(4) and 50 mM NaCl) were studied on 30 day-old plants of Ocimum basilicum L., variety Genovese subjected to 15 and 30 days of treatment. Growth, thiobarbituric acid reactive substances (TBARS), relative ion leakage ratio (RLR), hydrogen peroxide (H(2)O(2)), ascorbate and glutathione contents as well as the activities of ascorbate peroxidase (APX, EC 1.11.1.11); glutathione reductase (GR, EC 1.6.4.2) and peroxidases (POD, EC 1.11.1.7) were determined. In leaves, growth was more depressed by 25 mM Na(2)SO(4) than 50 mM NaCl. The higher sensitivity of basil to Na(2)SO(4) was associated with an enhanced accumulation of H(2)O(2), an inhibition of APX, GR and POD activities (with the exception of POD under the 30-day-treatment) and a lower regeneration of reduced ascorbate (AsA) and reduced glutathione (GSH). However, the changes in the antioxidant metabolism were enough to limit oxidative damage, explaining the fact that RLR and TBARS levels were unchanged under both Na(2)SO(4) and NaCl treatment. Moreover, for both salts the 30-day-treatment reduced H(2)O(2) accumulation, unchanged RLR and TBARS levels, and enhanced the levels of antioxidants and antioxidative enzymes, thus achieving an adaptation mechanism against reactive oxygen species.

The pepper oxidoreductase CaOXR1 interacts with the transcription factor CaRAV1 and is required for salt and osmotic stress tolerance

RAV1 (Related to ABI3/VP1) proteins function as a transcription factor in signal transduction pathways in plants. The yeast-two-hybrid and in vivo coimmunoprecipitation assays identified the pepper (Capsicum annuum) oxidoreductase protein CaOXR1 that physically interacts with the pepper CaRAV1 transcription factor. The AP2 domain of CaRAV1 protein is essential for its direct interaction with CaOXR1. Both CaRAV1 and CaOXR1 proteins co-localize to the nuclei of plant cells. Virus-induced gene silencing of CaRAV1 and CaRAV1/CAOXR1 confers enhanced susceptibility to high salinity and osmotic stresses, which is accompanied by altered expression of the stress marker genes in pepper. Expression of CaAMP1 (pepper antimicrobial protein) and CaOSM1 (pepper osmotin) is suppressed by 1.2-6.6-fold in silenced leaves upon treatment with NaCl or mannitol. Overexpression of CaRAV1, CaOXR1 and CaOXR1/CaRAV1 in Arabidopsis also confers enhanced resistance to the biotrophic oomycete Hyaloperonospora arabidopsidis infection. In addition, CaRAV1- and CaOXR1/CaRAV1-overexpression (OX) Arabidopsis plants are highly tolerant to high salinity and osmotic stress. Together, these results suggest that CaOXR1 protein positively controls CaRAV1-mediated plant defense during biotic and abiotic stresses.

Changes in content of free, conjugated and bound polyamines and osmotic adjustment in adaptation of vetiver grass to water deficit

Osmotic adjustment and alteration of polyamines (PAs) have been suggested to play roles in plant adaptation to water deficit/drought stress. In this study, the changes in cell intactness, photosynthesis, compatible solutes and PAs [including putrescine (Put), spermidine (Spd) and spermine (Spm) each in free, conjugated and bound forms] were investigated in leaves of vetiver grass exposed to different intensity of water deficit stress and subsequent rewatering. The results showed that, when vetiver grass was exposed to the moderate (20% and 40% PEG-6000 solutions) and severe (60% PEG solution) water deficit for 6days, the plant injury degree (expressed as the parameters of plant growth, cell membrane integrity, water relations and photosynthesis) increased and contents of free and conjugated Put decreased with the rise of PEG concentration. Under the moderate water deficit, the plants could survive by the reduced osmotic potential (psi(s)), increased free and conjugated Spd and Spm in leaves. After subsequent rewatering, the osmotic balance was re-established, most of the above investigated physiological parameters were fully or partly recovered to the control levels. However, it was not the case for the severely-stressed and rewatering plants. It indicates that, vetiver grass can cope well with the moderate water deficit/drought stress by using the strategies of osmotic adjustment and maintenance of total contents of free, conjugated and bound PAs in leaves.

Association between winter anthocyanin production and drought stress in angiosperm evergreen species

Leaves of many evergreen angiosperm species turn red under high light during winter due to the production of anthocyanin pigments, while leaves of other species remain green. There is currently no explanation for why some evergreen species exhibit winter reddening while others do not. Conditions associated with low leaf water potentials (Psi) have been shown to induce reddening in many plant species. Because evergreen species differ in susceptibility to water stress during winter, it is hypothesized that species which undergo winter colour change correspond with those that experience/tolerate the most severe daily declines in leaf Psi during winter. Six angiosperm evergreen species which synthesize anthocyanin in leaves under high light during winter and five species which do not were studied. Field Psi, pressure/volume curves, and gas exchange measurements were derived in summer (before leaf colour change had occurred) and winter. Consistent with the hypothesis, red-leafed species as a group had significantly lower midday Psi in winter than green-leafed species, but not during the summer when all the leaves were green. However, some red-leafed species showed midday declines similar to those of green-leafed species, suggesting that low Psi alone may not induce reddening. Pressure-volume curves also provided some evidence of acclimation to more negative water potentials by red-leafed species during winter (e.g. greater osmotic adjustment and cell wall hardening on average). However, much overlap in these physiological parameters was observed as well between red and green-leafed species, and some of the least drought-acclimated species were red-leafed. No difference was observed in transpiration (E) during winter between red and green-leaved species. When data were combined, only three of the six red-leafed species examined appeared physiologically acclimated to prolonged drought stress, compared to one of the five green-leafed species. This suggests that drought stress alone is not sufficient to explain winter reddening in evergreen angiosperms.

Cloning, expression and physiological analysis of broccoli catalase gene and Chinese cabbage ascorbate peroxidase gene under heat stress

The objectives of this work were to clone the catalase (CAT) gene from broccoli (Brassica oleracea) and the ascorbate peroxidase (APX) gene from Chinese cabbage and measure the regulation of CAT and APX gene expressions under heat-stress conditions. Different genotypes responded differently to heat stress according to their various antioxidant enzymes and physiological parameters. CAT and APX gene expression profiles were well matched with the data for CAT and APX enzyme activities in the broccoli and Chinese cabbage plants, respectively. Full-length of the CAT and APX cDNA were 1,768 and 1,070 bp, respectively. A phylogenetic analysis of CAT and APX indicated that plant CATs and APXs diverged into two major clusters.

Salt-induced expression of genes related to Na(+)/K(+) and ROS homeostasis in leaves of salt-resistant and salt-sensitive poplar species

Using the Affymetrix poplar genome array, we explored the leaf transcriptome of salt-tolerant Populus euphratica Oliv. and salt-sensitive P. popularis 35-44 (P. popularis) under control and saline conditions. Our objective was to clarify the genomic differences in regulating K(+)/Na(+) and reactive oxygen species (ROS) homeostasis between the two species. Compared to P. popularis, salt-tolerant P. euphratica responses to salinity involved induction of a relatively larger number of probesets after short-term (ST) exposure to 150 mM NaCl (24 h) and relatively fewer probesets after a long-term (LT) exposure to salinity (200 mM NaCl, 28 days). Compared to P. popularis, leaves of the control P. euphratica plants exhibited a higher transcript abundance of genes related to Na(+)/H(+) antiport (Na(+)/H(+) antiporters, H(+) pumps) and K(+) uptake and transport. Notably, the expression of these genes did not decrease (with a few exceptions) during salt treatment. Regarding ROS homeostasis, P. euphratica exhibited rapid up-regulation of a variety of antioxidant enzymes after exposure to ST salinity, indicating a rapid adaptive response to salt stress. However, the effect of NaCl on transcription in P. popularis leaves was more pronounced after exposure to prolonged salinity. LT-stressed P. popularis up-regulated some genes mediating K(+)/Na(+) homeostasis but decreased transcription of main scavengers of superoxide radicals and H(2)O(2) except for some isoforms of a few scavengers. Mineral and ROS analyses show that NaCl induced a marked increase of leaf Na(+) and H(2)O(2) in LT-stressed plants of the two species and the effects were even more pronounced in the salt-sensitive poplar. We place the transcription results in the context of our physiological measurements to infer some implications of NaCl-induced alterations in gene expression related to K(+)/Na(+) and ROS homeostasis.

Comparative analysis of soybean plasma membrane proteins under osmotic stress using gel-based and LC MS/MS-based proteomics approaches

To study the soybean plasma membrane proteome under osmotic stress, two methods were used: a gel-based and a LC MS/MS-based proteomics method. Two-day-old seedlings were subjected to 10% PEG for 2 days. Plasma membranes were purified from seedlings using a two-phase partitioning method and their purity was verified by measuring ATPase activity. Using the gel-based proteomics, four and eight protein spots were identified as up- and downregulated, respectively, whereas in the nanoLC MS/MS approach, 11 and 75 proteins were identified as up- and downregulated, respectively, under PEG treatment. Out of osmotic stress responsive proteins, most of the transporter proteins and all proteins with high number of transmembrane helices as well as low-abundance proteins could be identified by the LC MS/MS-based method. Three homologues of plasma membrane H(+)-ATPase, which are transporter proteins involved in ion efflux, were upregulated under osmotic stress. Gene expression of this protein was increased after 12 h of stress exposure. Among the identified proteins, seven proteins were mutual in two proteomics techniques, in which calnexin was the highly upregulated protein. Accumulation of calnexin in plasma membrane was confirmed by immunoblot analysis. These results suggest that under hyperosmotic conditions, calnexin accumulates in the plasma membrane and ion efflux accelerates by upregulation of plasma membrane H(+)-ATPase protein.

Transcriptional responses to polycyclic aromatic hydrocarbon-induced stress in Arabidopsis thaliana reveal the involvement of hormone and defense signaling pathways

BACKGROUND

Polycyclic aromatic hydrocarbons (PAHs) are toxic, widely-distributed, environmentally persistent, and carcinogenic byproducts of carbon-based fuel combustion. Previously, plant studies have shown that PAHs induce oxidative stress, reduce growth, and cause leaf deformation as well as tissue necrosis. To understand the transcriptional changes that occur during these processes, we performed microarray experiments on Arabidopsis thaliana L. under phenanthrene treatment, and compared the results to published Arabidopsis microarray data representing a variety of stress and hormone treatments. In addition, to probe hormonal aspects of PAH stress, we assayed transgenic ethylene-inducible reporter plants as well as ethylene pathway mutants under phenanthrene treatment.

RESULTS

Microarray results revealed numerous perturbations in signaling and metabolic pathways that regulate reactive oxygen species (ROS) and responses related to pathogen defense. A number of glutathione S-transferases that may tag xenobiotics for transport to the vacuole were upregulated. Comparative microarray analyses indicated that the phenanthrene response was closely related to other ROS conditions, including pathogen defense conditions. The ethylene-inducible transgenic reporters were activated by phenanthrene. Mutant experiments showed that PAH inhibits growth through an ethylene-independent pathway, as PAH-treated ethylene-insensitive etr1-4 mutants exhibited a greater growth reduction than WT. Further, phenanthrene-treated, constitutive ethylene signaling mutants had longer roots than the untreated control plants, indicating that the PAH inhibits parts of the ethylene signaling pathway.

CONCLUSIONS

This study identified major physiological systems that participate in the PAH-induced stress response in Arabidopsis. At the transcriptional level, the results identify specific gene targets that will be valuable in finding lead compounds and engineering increased tolerance. Collectively, the results open a number of new avenues for researching and improving plant resilience and PAH phytoremediation.

Acceleration of germination and early growth of wheat and bean seedlings grown under various magnetic field and osmotic conditions

Magnetic field (MF) can have different effects on plant metabolism depending on its application style, intensity, and environmental conditions. This study reports the effects of different intensities of static MF (4 or 7 mT) on seed germination and seedling growth of bean or wheat seeds in different media having 0, 2, 6, and 10 atmosphere (atm) osmotic pressure prepared with sucrose or salt. The germination percentages of the treated seeds were compared with untreated seeds germinated in different osmotic pressure during 7 days of incubation. The application of both MFs promoted the germination ratios of bean and wheat seeds, regardless of increasing osmotic pressure of sucrose or salt. Growth data measured on the 7th day showed that the treated plants grew faster than control. After 7 days of incubation, the mean length of treated seedlings was statistically higher than control plants in all the media. The greatest germination and growth rates in both plants were from the test groups exposed to 7 mT MF. Strikingly, effects of static MF on germination and growth increased positively with increasing osmotic pressure or salt stress compared to their respective controls. On the other hand, MF application caused an increase in dry biomass accumulation of root and shoots of both seedlings; however, this effect was found statistically important in all the conditions for wheat but not for bean, in general.

Genome-wide transcriptome analysis of two maize inbred lines under drought stress

Drought stress greatly affects plant growth and crop yield. To understand the transcriptome dynamics during drought stress in maize seedlings, genome-wide gene expression profiling was compared between the drought-tolerant line Han21 and drought-sensitive line Ye478 using Affymetrix Maize Genome Array containing 17,555 probe sets. The results showed that in response to drought, the Han21 line had fewer probe sets with significant expression change than the Ye478 line and both lines had a common set of ~2,600 regulated probe sets under drought stress. The potential components of the abscisic acid signaling pathway were significantly identified from the common probe sets. A total of 827 probe sets with significantly differential expression between the two lines under drought stress were identified. The differential expression levels of cell wall-related and transporter genes may contribute to the different tolerances of the two lines. Additionally, we found that, compared to the sensitive line Ye478, the transcriptional levels of drought-responsive probe sets in the tolerant line Han21 recovered more quickly after re-watering, and more probe sets in the tolerant line Han21 were exclusively up-regulated at the re-watering stage. Our study provides a global gene expression dynamics of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize.

A large insert Thellungiella halophila BIBAC library for genomics and identification of stress tolerance genes

Salt cress (Thellungiella halophila), a salt-tolerant relative of Arabidopsis, has turned to be an important model plant for studying abiotic stress tolerance. One binary bacterial artificial chromosome (BIBAC) library was constructed which represents the first plant-transformation-competent large-insert DNA library generated for Thellungiella halophila. The BIBAC library was constructed in BamHI site of binary vector pBIBAC2 by ligation of partial digested nuclear DNA of Thellungiella halophila. This library consists of 23,040 clones with an average insert size of 75 kb, and covers 4x Thellungiella halophila haploid genomes. BIBAC clones which contain inserts over 50 kb were selected and transformed into Arabidopsis for salt tolerant plant screening. One transgenic line was found to be more salt tolerant than wild type plants from the screen of 200 lines. It was demonstrated that the library contains candidates of stress tolerance genes and the approach is suitable for the transformation of stress susceptible plants for genetic improvement.

Ectopic over-expression of BhHsf1, a heat shock factor from the resurrection plant Boea hygrometrica, leads to increased thermotolerance and retarded growth in transgenic Arabidopsis and tobacco

Plant heat shock transcription factors (Hsfs) are commonly found to be involved in various stress responses. Several Hsfs displayed dwarf phenotype while conferred stress tolerance when over-expressed. However, the underlying mechanisms were not fully understood. Here we report the cloning and characterization of an Hsf (BhHsf1) from the resurrection plant Boea hygrometrica. Drought, heat and wound can induce BhHsf1 expression. The over-expression of BhHsf1 conferred growth retardation and stress tolerance in both Arabidopsis and tobacco. Evidence was presented to show that the growth retardation of aerial organs in the transgenic plants was resulted from the reduction of cell proliferation. Gene expression profiling using microarray hybridization and pathway analysis showed that Hsps and stress-associated genes were induced whereas the genes related to DNA replication and mitotic cell cycle were down-regulated in BhHsf1 over-expression Arabidopsis, which was in consistence with the observation of the impaired nuclear endoreduplication. Taking together, our results suggest that BhHsf1 may play dual roles in mediating the processes in heat stress tolerance and growth retardation via regulation of target genes related to stress protection and mitotic cell cycle.

Overexpression of TaSTRG gene improves salt and drought tolerance in rice

High salt and drought are the main factors affecting agricultural production. Thus, cloning stress-tolerance-related genes and identifying their functions are essential to enhancing crop tolerance to stresses. In this study, a salt-induced unknown wheat (Triticum aestivum L.) gene was identified and cloned according to microarray analysis of salt-tolerant wheat mutant RH8706-49 under salt stress. The gene was named Triticum aestivum salt tolerance-related gene (TaSTRG) and submitted to Genbank (Accession number: EF599631). TaSTRG expression in wheat is induced by multiple stresses including salt, polyethylene glycol (PEG), abscisic acid (ABA), and cold. Transgenic rice plants overexpressing TaSTRG gene showed higher salt and drought tolerance than the control. Under salt stress, the transgenic rice had a lower intracellular Na(+)/K(+) ratio than the control. Under salt and PEG treatments, these TaSTRG overexpressing rice plants had higher survival rate, fresh weight and chlorophyll content, accumulated higher proline and soluble sugar contents, and had significantly higher expression levels of putative proline synthetase and transporter genes than the control plants. These results indicate that the wheat TaSTRG gene could enhance plant tolerance to multiple types of stresses.

Glycinebetaine-induced water-stress tolerance in codA-expressing transgenic indica rice is associated with up-regulation of several stress responsive genes

Rice (Oryza sativa L.), a non-accumulator of glycinebetaine (GB), is highly susceptible to abiotic stress. Transgenic rice with chloroplast-targeted choline oxidase encoded by the codA gene from Arthrobacter globiformis has been evaluated for inheritance of transgene up to R5 generation and water-stress tolerance. During seedling, vegetative and reproductive stages, transgenic plants could maintain higher activity of photosystem II and they show better physiological performance, for example, enhanced detoxification of reactive oxygen species compared to wild-type plants under water-stress. Survival rate and agronomic performance of transgenic plants is also better than wild-type following prolonged water-stress. Choline oxidase converts choline into GB and H2O2 in a single step. It is possible that H2O2/GB might activate stress response pathways and prepare transgenic plants to mitigate stress. To check this possibility, microarray-based transcriptome analysis of transgenic rice has been done. It unravelled altered expression of many genes involved in stress responses, signal transduction, gene regulation, hormone signalling and cellular metabolism. Overall, 165 genes show more than two-fold up-regulation at P-value < 0.01 in transgenic rice. Out of these, at least 50 genes are known to be involved in plant stress response. Exogenous application of H2O2 or GB to wild-type plants also induces such genes. Our data show that metabolic engineering for GB is a promising strategy for introducing stress tolerance in crop plants and which could be imparted, in part, by H2O2- and/or GB-induced stress response genes.

Effects of salinity changes on the growth of Dunaliella salina and its isozyme activities of glycerol-3-phosphate dehydrogenase

Dunaliella salina could survive in media containing a wide range of NaCl concentrations ranging from about 0.05 M to saturation (around 5.5 M). Glycerol is an important osmolyte when Dunaliella survive in various salt environments, and G3pdh is a key enzyme in glycerol metabolism. The osmotic response of D. salina was investigated by studying its cell growth, glycerol content change, and isozyme activity of glycerol-3-phosphate dehydrogenase (G3pdh) in different salinities. Results showed that 2.0 M NaCl was the optimal salinity for the growth of D. salina, in which condition the highest glycerol content of 64.02 +/- 3.21 (mean +/- SD) microg/mL was detected. D. salina could rapidly increase or decrease glycerol contents to adapt to hypoosmotic or hyperosmotic environments. The glycerol content declined 52.05% when salinity was changed from 2.0 to 0.5 M NaCl, and the glycerol content increased 43.61% when salinity was increased from 2.0 to 5.0 M NaCl. In the isozyme electrophoresis assay two kinds of isozymes, G3pdh and superoxide dismutase (Sod), were detected synchronously. Interestingly, it was first found that there are five isozymes of G3pdh in D. salina. G3pdh-2 mainly takes effect in moderate to high salinities, whereas the other four isozymes take effect in low salinities, which may provide an important clue for future research on osmoregulation mechanisms.

Cloning and molecular characterization of fructose-1,6-bisphosphate aldolase gene regulated by high-salinity and drought in Sesuvium portulacastrum

Sesuvium portulacastrum, a mangrove plant from seashore, is a halophyte species well adapted to salinity and drought. Some efforts have been made to describe its physiological and structural characteristics on salt and drought-tolerance, but the underlying molecular mechanism and key components have not yet been identified. Here, a fructose-1,6-bisphosphate aldolase gene, designated SpFBA, was isolated and characterized from S. portulacastrum roots in response to seawater. The SpFBA cDNA has a total length of 1452 bp with an open reading frame of 1071 bp, and is predicted to encode a precursor protein of 357 amino acid residues sharing high degree of homology with class I FBAs from other plants. Semi-quantitative RT-PCR analysis indicated that the SpFBA was more strongly expressed in roots than in leaves and stems, and the abiotic stimuli such as Seawater, NaCl, ABA, and PEG, could trigger a significant induction of SpFBA in S. portulacastrum roots within 2-12 h. Overproduction of Recombinant SpFBA resulted in an increased tolerance to salinity in transgenic Escherichia coli. All these results suggest that the SpFBA plays very important roles in responding to salt stress and related abiotic stimuli, and in improving the survival ability of S. portulacastrum under high salinity and drought.

A nuclear-localized HSP70 confers thermoprotective activity and drought-stress tolerance on plants

To investigate the function of nuclear-localized plant HSP70, we used NtHSP70-1 isolated from Nicotiana tabacum. The subcellular localization of NtHSP70-1 was identified by fluorescence microscopy for NtHSP70-1/GFP or smGFP fusion proteins in onion epidermal cells, obtained using particle gun bombardment. To analyze the drought-stress tolerance and thermoprotective role of NtHSP70-1, we obtained transgenic tobacco plants that constitutively expressed elevated levels of NtHSP70-1 as well as transgenic plants containing either the vector alone or else having NtHSP70-1 in the antisense orientation. From analysis for genomic DNA in transgenic seedlings after heat stress, NtHSP70-1 helps to prevent the fragmentation and degradation of nuclear DNA during heat stress. In addition, seedlings constitutively overexpressing NtHSP70-1 grew to be healthy plants, whereas transgenic vector or antisense seedlings resulted in death after heat-/drought-stress.

Chymotrypsin protease inhibitor gene family in rice: Genomic organization and evidence for the presence of a bidirectional promoter shared between two chymotrypsin protease inhibitor genes

Protease inhibitors play important roles in stress and developmental responses of plants. Rice genome contains 17 putative members in chymotrypsin protease inhibitor (ranging in size from 7.21 to 11.9 kDa) gene family with different predicted localization sites. Full-length cDNA encoding for a putative subtilisin-chymotrypsin protease inhibitor (OCPI2) was obtained from Pusa basmati 1 (indica) rice seedlings. 620 bp-long OCPI2 cDNA contained 219 bp-long ORF, coding for 72 amino acid-long 7.7 kDa subtilisin-chymotrypsin protease inhibitor (CPI) cytoplasmic protein. Expression analysis by semi-quantitative RT-PCR analysis showed that OCPI2 transcript is induced by varied stresses including salt, ABA, low temperature and mechanical injury in both root and shoot tissues of the seedlings. Transgenic rice plants produced with OCPI2 promoter-gus reporter gene showed that this promoter directs high salt- and ABA-regulated expression of the GUS gene. Another CPI gene (OCPI1) upstream to OCPI2 (with 1126 bp distance between the transcription initiation sites of the two genes; transcription in the reverse orientation) was noted in genome sequence of rice genome. A vector that had GFP and GUS reporter genes in opposite orientations driven by 1881 bp intergenic sequence between the OCPI2 and OCPI1 (encompassing the region between the translation initiation sites of the two genes) was constructed and shot in onion epidermal cells by particle bombardment. Expression of both GFP and GUS from the same epidermal cell showed that this sequence represents a bidirectional promoter. Examples illustrating gene pairs showing co-expression of two divergent neighboring genes sharing a bidirectional promoter have recently been extensively worked out in yeast and human systems. We provide an example of a gene pair constituted of two homologous genes showing co-expression governed by a bidirectional promoter in rice.

Genome-wide identification of osmotic stress response gene in Arabidopsis thaliana

In this paper, we present a cis-regulatory element based computational approach to genome-wide identification of genes putatively responding to various osmotic stresses in Arabidopsis thaliana. The rationale of our method is that gene expression is largely controlled at the transcriptional level through the interactions between transcription factors and cis-regulatory elements. Using cis-regulatory motifs known to regulate osmotic stress response, we therefore built an artificial neural network model to identify other functionally relevant genes involved in the same process. We performed Gene Ontology enrichment analysis on the 500 top-scoring predictions and found that, except for un-annotated ORFs ( approximately 40%), 91.3% of the enriched GO classification was related to stress response and ABA response. Publicly available gene expression profiling data of Arabidopsis under various stresses were used for cross validation. We also conducted RT-PCR analysis to experimentally verify selected predictions. According to our results, transcript levels of 27 out of 41 top-ranked genes (65.8%) altered under various osmotic stress treatments. We believe that a similar approach could be extensively adopted elsewhere to infer gene function in various cellular processes from different species.

Comparison analysis of transcripts from the halophyte Thellungiella halophila

The Brassicaceae family halophyte Thellungiella halophila has a high salinity tolerance and serves as a valuable halophytic genetic model plant with experimental convenience similar to Arabidopsis thaliana. A cDNA library of Thellungiella was generated from salt-treated seedlings including rosettes and roots. More than 1 000 randomly selected clones were sequenced and 946 expressed sequence tags (ESTs) were generated. The accession numbers of our EST data are available online in the GenBank database from EC598928 to EC599965. In total 679 unique clusters were assembled, and 632 (93%) had BLASTX hits in the nr databases and 7% are Thellungiella unique. According to the Gene Ontology (GO) hierarchy, 385 of 679 unigenes were categorized. Compared with public Arabidopsis microarray data, our results provide more potential salt tolerance genes in Thellungiella. These results will provide a broader coverage into Thellungiella transcriptome and benefit the discovery of salt tolerance related genes.

Genetic approaches towards overcoming water deficit in plants - special emphasis on LEAs

Water deficit arises as a result of low temperature, salinity and dehydration, thereby affecting plant growth adversely and making it imperative for plants to surmount such situations by acclimatizing/adapting at various levels. Water deficit stress results in significant changes in gene expression, mediated by interconnected signal transduction pathways that may be triggered by calcium, and regulated via ABA dependent and/or independent pathways. Hence, adaptation of plants to such stresses involves maintaining cellular homeostasis, detoxification of harmful elements and also growth alterations. Stress in general cause excess production of reactive oxygen species (ROS) and the plants overcome the same by either preventing the accumulation of ROS or by eliminating the ROS formed. Ion homeostasis includes processes such as cellular uptake, sequestration and export in conjunction with long distance transport. Requisite amounts of osmolytes are hence synthesized under stress to maintain turgor along with maintaining the macromolecular structures and also for scavenging ROS. Another noteworthy response is the accumulation of novel proteins, including enzymes involved in the biosynthesis of osmoprotectants, heat-shock proteins (HSPs), late embryogenesis abundant (LEA) proteins, antifreeze proteins, chaperones, detoxification enzymes, transcription factors, kinases and phosphatases. The LEAs belong to a redundant protein family and are highly hydrophilic, boiling-soluble, non-globular and therefore have been defined and classified accordingly. The precise function of LEAs is still unknown, but substantial evidence indicates their involvement in dessication tolerance as the expression of LEAs confers increased resistance to stress in heterologous yeast system and also significantly improves water deficit tolerance in transgenic plants. Genetic manipulation of plants towards conferring abiotic stress tolerance is a daunting task, as the abiotic stress tolerance mechanism is highly complex and various strategies have been exploited to address and evaluate the stress tolerance mechanism, and the molecular responses to water deficit via complex signaling networks. Genomic technologies have recently been useful in integrating the multigenicity of the plant stress responses through, transcriptomics, proteomics and metabolite profilling and their interactions. This review deals with the recent developments on genetic approaches for water stress tolerance in plants, with special emphasis on LEAs.

Regulation of salt and ABA responses by CIPK14, a calcium sensor interacting protein kinase in Arabidopsis

Calcium and protein kinase serve as the common mediators to regulate plant responses to multiple stresses including salt and ABA stimulus. Here we reported a novel protein kinase (CIPK14) that regulated the responses to ABA treatment and salt stress in Arabidopsis. CIPK14 transcripts, capable been checked in roots, stems, leaves and flowers, were highly expressed in flowers and roots. CIPK14 was induced by ABA and salt treatments. The disruption of CIPK14 altered the transcriptional pattern of a gene marker line related to ABA and salt responses, and the results suggested that CIPK14 probably was responsible to the control of the salt and ABA responses. Comparing with wild types, the lines inserted with the T-DNA in which CIPK14 gene expression was knocked out were also more sensitive to ABA and salt stimulus, showing low germination rate and the less root elongation. While, when these conditioned seeds were treated with norflurazon, their germination percentages could recover to a certain extent. We also found that exogenous calcium could have an effect on the transcription of CIPK14 under ABA and salt treatments, and it seemed that calcium ion might work upstream CIPK14 to regulate the plant response to ABA and salt response.

Systematic analysis of NPK1-like genes in rice reveals a stress-inducible gene cluster co-localized with a quantitative trait locus of drought resistance

Phosphorylation by protein kinase is a ubiquitous key mechanism in translating external stimuli such as drought stress. NPK1 is a mitogen-activated protein kinase kinase kinase identified in Nicotiana tabacum and plays important roles in cytokinesis and auxin signaling transduction and responses to multiple stresses. Here we report the evolution, structure, and comprehensive expression profile of 21 NPK1-like genes in rice (Oryza sativa L.). Phylogenetic analysis of NPK1-like sequences in rice (OsNPKL), Arabidopsis, and other plants reveals that NPK1-like genes could be classified into three subgroups. Three OsNPKL gene clusters, located on chromosome 1 (OsNPKL1, 2, 3, and 4), 5 (OsNPKL14 and 15), and 10 (OsNPKL19 and 20), respectively, were identified in the rice genome. These clustered genes, which most likely evolved by tandem gene duplication, belong to the same phylogenetic subgroup, with similar genomic structures and conserved motifs in the kinase domain, which is unique to this subgroup. Expression analysis of OsNPKL genes under abiotic stresses suggests that the stress-responsive genes are mainly from the same subgroup. Especially interesting is that all the clustered genes are induced by drought, salt, or cold stress, and a few members are very strongly induced by drought. Some of the clustered genes are also induced by abscisic acid. The gene cluster on chromosome 1 is co-located with a quantitative trait locus (QTL) related to drought resistance. Although the drought-induced expression levels of the four genes in the cluster show no difference between the two parents used for QTL mapping, sequence variation in coding regions of the genes between the parents has provided some clues for further functional characterization of this gene cluster in abiotic stress tolerance in rice.

Virus-induced gene silencing and its application in characterizing genes involved in water-deficit-stress tolerance

Understanding post-transcriptional gene silencing (PTGS) phenomena in plants has provided breakthroughs in advancing plant functional genomics. A recently developed approach based on one of the strategies adopted by plants to defend against viruses, called virus-induced gene silencing (VIGS), is being widely used to enumerate the function of plant genes. Since its discovery, VIGS has been widely used to characterize plant genes involved in metabolic pathways, homeostasis, basic cellular functions, plant-microbe, plant-nematode and plant-herbivore interaction. Recently, the application of this technique has been extended to characterize the genes and cellular processes involved in abiotic-stress tolerance, and in particular drought and oxidative stress. Because abiotic-stress tolerance is multigenic, identification and characterization of genes involved in this process is challenging. VIGS could become one among the several potential tools in understanding the relevance of these stress-responsive genes. Development of VIGS protocols for the use of heterologous gene sequences as VIGS-inducers has extended its applicability to analyze genes of VIGS recalcitrant plant species. This article describes the methodology of VIGS for characterizing the water-deficit-stress-responsive genes, precautions to be taken during the experimentation, and future application of this technology as a fast forwarded as well as a reverse genetics tool to identify and characterize plant genes involved in drought tolerance. We also describe the importance of accurate water-deficit-stress imposition and quantification of stress-induced changes in the silenced plants during the process of screening to identify genes responsible for tolerance. Further, limitations of VIGS in characterizing the abiotic-stress-responsive genes are noted, with suggestions to overcome these limitations.