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

Effect of salt stress on genes encoding translation-associated proteins in Arabidopsis thaliana

Salinity negatively affects plant growth and disturbs chloroplast integrity. Here, we aimed at identifying salt-responsive translation-related genes in Arabidopsis thaliana with an emphasis on those encoding plastid-located proteins. We used quantitative real-time PCR to test the expression of 170 genes after short-term salt stress (up to 24 h) and identified several genes affected by the stress including: PRPL11, encoding plastid ribosomal protein L11, ATAB2, encoding a chloroplast-located RNA-binding protein presumably functioning as an activator of translation, and PDF1B, encoding a peptide deformylase involved in N-formyl group removal from nascent proteins synthesized in chloroplasts. These genes were previously shown to have important functions in chloroplast biology and may therefore represent new targets for biotechnological optimization of salinity tolerance.

Proteomic analysis of salt-responsive ubiquitin-related proteins in rice roots

RATIONALE

Ubiquitination of proteins plays an important role in regulating a myriad of physiological functions in plants such as xylogenesis, senescence, cell cycle control, and stress response. However, only a limited number of proteins in plants have been identified as being ubiquitinated in response to salt stress. The relationships between ubiquitination and salt-stress responses in plants are not clear.

METHODS

Rice (Oryza sativa) seedlings from the same genetic background with various salt tolerances exposed to salt stress were studied. The proteins of roots were extracted then analyzed using western blotting against ubiquitin. Differentially expressed ubiquitinated proteins were identified by nanospray liquid chromatography/tandem mass spectrometry (nano-LC/MS/MS) and quantified by label-free methods based on the Exponentially Modified Protein Abundance Index (emPAI) and on the peak areas of XIC spectra derived from ubiquitinated peptides. In addition, we performed a gel-based shotgun proteomic analysis to detect the ubiquitinated proteome that may be involved in response to salt stress.

RESULTS

The expressions of ubiquitination on pyruvate phosphate dikinase 1, heat shock protein 81-1, probable aldehyde oxidase 3, plasma membrane ATPase, cellulose synthase A catalytic subunit 4 [UDP-forming] and cyclin-C1-1 were identified and compared before and after salt treatment. The functions of those ubiquitinated proteins were further discussed for defence against salt stress. In addition, a large number of ubiquitinated proteins were successfully identified as well in this study.

CONCLUSIONS

The ubiquitination of proteins affected the protective mechanisms in rice seedlings to resist the salt stress during the initial phase. The findings in the present study also demonstrate that the regulated mechanisms through protein ubiquitination are important for rice seedlings against salt stress.

Transcriptional profiling analysis in Populus yunnanensis provides insights into molecular mechanisms of sexual differences in salinity tolerance

Physiological responses to abiotic stress in plants exhibit sexual differences. Females usually experience greater negative effects than males; however, little is known about the molecular mechanisms of sexual differences in abiotic stress responses. In the present study, transcriptional responses to salinity treatments were compared between male and female individuals of the poplar Populus yunnanensis. It was found that several functional groups of genes involved in important pathways were differentially expressed, including photosynthesis-related genes, which were mainly up-regulated in males but down-regulated in females. This gene expression pattern is consistent with physiological observations showing that salinity inhibited photosynthetic capacity more in females than in males. Furthermore, genes located in autosomes rather than in the female-specific region of the W chromosome are the major contributors to the sexual differences in the salinity tolerance of poplars. In conclusion, this study provided molecular evidence of sexual differences in the salinity tolerance of poplars. The identified sex-related genes in salinity tolerance and their functional groups will enhance our understanding of sexual differences in salinity stress at the transcription level.

Identification of mRNA transcript and screening of amino acids in response to interaction of salinity and nitrate in aquatic fern Azolla caroliniana

The mechanisms by which Azolla caroliniana respond to salt stress in absence and presence of nitrate is investigated. Screening of amino acid and differential display is used to compare overall differences in gene expression between salinity-stressed and unstressed Azolla caroliniana by quantitative reverse transcriptase polymerase chain reaction (RT-PC R). Results showed that under saline conditions, aspartic acid, glutamic acid, alanine and leucine were the amino acids found to be abundant in Azolla caroliniana, accounting for 11.26%, 8.66%, 9.43%, and 12.36%, respectively. Following salinity stress, a decrease in free glutamate concomitant with a parallel decrease in free proline was indeed evident. Interaction between nitrate and salinity stress increased proline content significantly. By screening a cDNA library, we have identified protein products by homology with known proteins. The RNA transcripts encoding protein influencing secondary metabolites and vacuolar Na+/H+ antiporter that facilitate the transport system. The databasematched under interaction of nitrate and 50 mM NaCl were associated with wall biosynthesis, disease resistance, metabolite transport and protein regulator, other gene for metabolism of steroids and secondary transport. Results obtained from this research could represent a key step in understanding the molecular mechanism of salt tolerance of Azolla caroliniana in the presence and absence of nitrate.

Transcriptional homeostasis of a mangrove species, Ceriops tagal, in saline environments, as revealed by microarray analysis

BACKGROUND

Differential responses to the environmental stresses at the level of transcription play a critical role in adaptation. Mangrove species compose a dominant community in intertidal zones and form dense forests at the sea-land interface, and although the anatomical and physiological features associated with their salt-tolerant lifestyles have been well characterized, little is known about the impact of transcriptional phenotypes on their adaptation to these saline environments.

METHODOLOGY AND PRINCIPAL FINDINGS

We report the time-course transcript profiles in the roots of a true mangrove species, Ceriops tagal, as revealed by a series of microarray experiments. The expression of a total of 432 transcripts changed significantly in the roots of C. tagal under salt shock, of which 83 had a more than 2-fold change and were further assembled into 59 unigenes. Global transcription was stable at the early stage of salt stress and then was gradually dysregulated with the increased duration of the stress. Importantly, a pair-wise comparison of predicted homologous gene pairs revealed that the transcriptional regulations of most of the differentially expressed genes were highly divergent in C. tagal from that in salt-sensitive species, Arabidopsis thaliana.

CONCLUSIONS/SIGNIFICANCE

This work suggests that transcriptional homeostasis and specific transcriptional regulation are major events in the roots of C. tagal when subjected to salt shock, which could contribute to the establishment of adaptation to saline environments and, thus, facilitate the salt-tolerant lifestyle of this mangrove species. Furthermore, the candidate genes underlying the adaptation were identified through comparative analyses. This study provides a foundation for dissecting the genetic basis of the adaptation of mangroves to intertidal environments.

Identification of genes associated with adaptation to NaCl toxicity in perennial ryegrass (Lolium perenne L.)

Perennial ryegrass (Lolium perenne L.) is a popular turfgrass species. To understand the molecular mechanisms of salinity tolerance, a suppression subtractive cDNA library was constructed for a salinity-tolerant ryegrass accession, with NaCl-treated (255 mM) plants as the tester. Differentially expressed cDNA fragments were cloned and screened. BLAST search revealed that 268 clones exhibited significant homologies to known genes. These genes could be categorized into 11 different functional groups, including metabolism, energy transfer, detoxification, compatible solute, cellular transport, transcription, signal transduction, etc. The salinity-regulated expression of selected genes was confirmed by RT-PCR analysis. The results suggested that these putatively salinity up-regulated genes may play a vital role in the salinity tolerance of perennial ryegrass. They can be used as candidate genes for creating stress-tolerant grasses and for understanding molecular mechanisms of plant adaptation to salinity stress.

Adaptation responses in C4 photosynthesis of maize under salinity

The effect of salinity on C(4) photosynthesis was examined in leaves of maize, a NADP-malic enzyme (NADP-ME) type C(4) species. Potted plants with the fourth leaf blade fully developed were treated with 3% NaCl solution for 5d. Under salt treatment, the activities of pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxylase (PEPCase), NADP-dependent malate dehydrogenase (NADP-MDH) and NAD-dependent malate dehydrogenase (NAD-MDH), which are derived mainly from mesophyll cells, increased, whereas those of NADP-ME and ribulose-1,5-bisphosphate carboxylase, which are derived mainly from bundle sheath cells (BSCs), decreased. Immunocytochemical studies by electron microscopy revealed that PPDK protein increased, while the content of ribulose-1,5-bisphosphate carboxylase/oxygenase protein decreased under salinity. In salt-treated plants, the photosynthetic metabolites malate, pyruvate and starch decreased by 40, 89 and 81%, respectively. Gas-exchange analysis revealed that the net photosynthetic rate, the transpiration rate, stomatal conductance (g(s)) and the intercellular CO(2) concentration decreased strongly in salt-treated plants. The carbon isotope ratio (δ(13)C) in these plants was significantly lower than that in control. These findings suggest that the decrease in photosynthetic metabolites under salinity was induced by a reduction in gas-exchange. Moreover, in addition to the decrease in g(s), the decrease in enzyme activities in BSCs was responsible for the decline of C(4) photosynthesis. The increase of PPDK, PEPCase, NADP-MDH, and NAD-MDH activities and the decrease of NADP-ME activity are interpreted as adaptation responses to salinity.

Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum)

About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accreted from 51 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including abiotic stresses and pathogen challenges in common wheat (Triticum aestivum). Expressed sequence tags were assembled with stringent parameters after processing with inbuild scripts, resulting in 37,138 contigs and 215,199 singlets. In the assembled sequences, 10.6% presented no matches with existing sequences in public databases. Functional characterization of wheat unigenes by gene ontology annotation, mining transcription factors, full-length cDNA, and miRNA targeting sites were carried out. A bioinformatics strategy was developed to discover single-nucleotide polymorphisms (SNPs) within our large EST resource and reported the SNPs between and within (homoeologous) cultivars. Digital gene expression was performed to find the tissue-specific gene expression, and correspondence analysis was executed to identify common and specific gene expression by selecting four biotic stress-related libraries. The assembly and associated information cater a framework for future investigation in functional genomics.

Multiple compartmentalization of sodium conferred salt tolerance in Salicornia europaea

Euhalophyte Salicornia europaea L., one of the most salt-tolerant plant species in the world, can tolerate more than 1000 mM NaCl. To study the salt tolerance mechanism of this plant, the effects of different NaCl concentrations on plant growth, as well as Na(+) accumulation and distribution at organ, tissue, and subcellular levels, were investigated. Optimal growth and an improved photosynthetic rate were observed with the plant treated with 200-400 mM NaCl. The Na(+) content in the shoots was considerably higher than that in the roots of S. europaea. The Na(+) in S. europaea cells may act as an effective osmotic adjuster to maintain cell turgor, promoting photosynthetic competence and plant growth. The results from the SEM-X-ray and TEM-X-ray microanalyses demonstrate that Na(+) was compartmentalized predominantly into the cell vacuoles of shoot endodermis tissues. Accordingly, the transcript amounts of SeNHX1, SeVHA-A, and SeVP1 increased significantly with increased NaCl concentration, suggesting their important roles in Na(+) sequestration into the vacuoles. Therefore, a multiple sodium compartmentalization mechanism is proposed to enhance further the salt tolerance of S. europaea.

Modification of OsSUT1 gene expression modulates the salt response of rice Oryza sativa cv. Taipei 309

A metabolic depletion syndrome was discovered at early vegetative stages in roots of salt sensitive rice cultivars after prolonged exposure to 100mM NaCl. Metabolite profiling analyses demonstrate that this syndrome is part of the terminal stages of the rice salt response. The phenotype encompasses depletion of at least 30 primary metabolites including sucrose, glucose, fructose, glucose-6-P, fructose-6P, organic- and amino-acids. Based on these observations we reason that sucrose allocation to the root may modify the rice response to high salt. This hypothesis was tested using antisense lines of the salt responsive OsSUT1 gene in the salt sensitive Taipei 309 cultivar. Contrary to our expectations of a plant system impaired in one component of sucrose transport, we find improved gas exchange and photosynthetic performance as well as maintenance of sucrose levels in the root under high salinity. Two independent OsSUT1 lines with an antisense inhibition similar to the naturally occurring salt induced reduction of OsSUT1 gene expression showed these phenomena but not a more extreme antisense inhibition line. We investigated the metabolic depletion syndrome by metabolomic and physiological approaches and discuss our results with regard to the potential role of sucrose transporters and sucrose transport for rice salt acclimation.

Short-term control of maize cell and root water permeability through plasma membrane aquaporin isoforms

Although it is widely accepted that aquaporins are involved in the regulation of root water uptake, the role of specific isoforms in this process is poorly understood. The mRNA expression and protein level of specific plasma membrane intrinsic proteins (PIPs) were analysed in Zea mays in relation to cell and root hydraulic conductivity. Plants were analysed during the day/night period, under different growth conditions (aeroponics/hydroponics) and in response to short-term osmotic stress applied through polyethylene glycol (PEG). Higher protein levels of ZmPIP1;2, ZmPIP2;1/2;2, ZmPIP2;5 and ZmPIP2;6 during the day coincided with a higher water permeability of root cortex cells during the day compared with night period. Similarly, plants which were grown under aeroponic conditions and which developed a hypodermis ('exodermis') with Casparian bands, effectively forcing more water along a membranous uptake path across roots, showed increased levels of ZmPIP2;5 and ZmPIP1;2 in the rhizodermis and exodermis. When PEG was added to the root medium (2-8 h), expression of PIPs and cell water permeability in roots increased. These data support a role of specific PIP isoforms, in particular ZmPIP1;2 and ZmPIP2;5, in regulating root water uptake and cortex cell hydraulic conductivity in maize.

S-methylmethionine is involved in the salinity tolerance of Arabidopsis thaliana plants at germination and early growth stages

Methionine (Met) is biosynthesized by the activated methyl cycle and S-methylmethionine (SMM) cycle in one-carbon (C1) metabolism in plants. It is converted to S-adenosylmethionine (SAM) which serves as a precursor for many metabolites including glycinebetaine, methylated polyols, polyamines and ethylene which accumulate in plants in response to salinity. We have investigated how the Met biosynthetic pathway is regulated under saline conditions at the transcriptional level in Arabidopsis thaliana plants. Within Met biosynthesis-related genes, the expression of homocysteine methyltransferase (HMT) and methionine methyltransferase (MMT) genes in SMM cycle had altered toward increasing Met production by the presence of NaCl. We have determined the salinity tolerance of an Arabidopsis mmt mutant with an insertional mutation in the single copy of the AtMMT gene. Although the mmt mutant showed comparable germination and shoot growth with wild type under normal conditions, NaCl treatment caused severe repression of germination rate and shoot growth in the mmt mutant compared with in the wild type. These results indicate that the utilization of SMM is important for the salinity tolerance of Arabidopsis plants at the germination and early growth stages.

Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions

The root system is a crucial determinant of plant growth potential because of its important functions, e.g. uptake of water and nutrients, structural support and interaction with symbiotic organisms. Elucidating the molecular mechanism of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants, including rice (Oryza sativa). As an initial step towards developing a comprehensive understanding of the root system, we performed a large-scale transcriptome analysis of the rice root via a combined laser microdissection and microarray approach. The crown root was divided into eight developmental stages along the longitudinal axis and three radial tissue types at two different developmental stages, namely: epidermis, exodermis and sclerenchyma; cortex; and endodermis, pericycle and stele. We analyzed a total of 38 microarray data and identified 22,297 genes corresponding to 17,010 loci that showed sufficient signal intensity as well as developmental- and tissue type-specific transcriptome signatures. Moreover, we clarified gene networks associated with root cap function and lateral root formation, and further revealed antagonistic and synergistic interactions of phytohormones such as auxin, cytokinin, brassinosteroids and ethylene, based on the expression pattern of genes related to phytohormone biosynthesis and signaling. Expression profiling of transporter genes defined not only major sites for uptake and transport of water and nutrients, but also distinct signatures of the radial transport system from the rhizosphere to the xylem vessel for each nutrient. All data can be accessed from our gene expression profile database, RiceXPro (http://ricexpro.dna.affrc.go.jp), thereby providing useful information for understanding the molecular mechanisms involved in root system development of crop plants.

An apoplastic h-type thioredoxin is involved in the stress response through regulation of the apoplastic reactive oxygen species in rice

Thioredoxins (Trxs) are a multigenic family of proteins in plants that play a critical role in redox balance regulation through thiol-disulfide exchange reactions. There are 10 members of the h-type Trxs in rice (Oryza sativa), and none of them has been clearly characterized. Here, we demonstrate that OsTRXh1, a subgroup I h-type Trx in rice, possesses reduction activity in vitro and complements the hydrogen peroxide sensitivity of Trx-deficient yeast mutants. OsTRXh1 is ubiquitously expressed in rice, and its expression is induced by salt and abscisic acid treatments. Intriguingly, OsTRXh1 is secreted into the extracellular space, and salt stress in the apoplast of rice induces its expression at the protein level. The knockdown of OsTRXh1 results in dwarf plants with fewer tillers, whereas the overexpression of OsTRXh1 leads to a salt-sensitive phenotype in rice. In addition, both the knockdown and overexpression of OsTRXh1 decrease abscisic acid sensitivity during seed germination and seedling growth. We also analyzed the levels of hydrogen peroxide produced in transgenic plants, and the results show that more hydrogen peroxide is produced in the extracellular space of OsTRXh1 knockdown plants than in wild-type plants, whereas the OsTRXh1 overexpression plants produce less hydrogen peroxide under salt stress. These results show that OsTRXh1 regulates the redox state of the apoplast and influences plant development and stress responses.

The sprout inhibitor 1,4-dimethylnaphthalene induces the expression of the cell cycle inhibitors KRP1 and KRP2 in potatoes

The suppression of sprout growth is critical for the long-term storage of potato tubers. 1,4-Dimethylenapthlene (DMN) is a new class of sprout control agent but the metabolic mode of action for this compound has yet to be elucidated. Changes in transcriptional profiles of meristems isolated from potato tubers treated with the DMN were investigated using an Agilent 44 K 60-mer-oligo microarray. RNA was isolated from nondormant Russet Burbank meristems isolated from tubers treated with DMN for 3 days or activated charcoal as a control. RNA was used to develop probes that were hybridized against a microarray developed by the Potato Oligo Chip Initiative. Analysis of the array data was conducted in two stages: total array data was examined using a linear model and the software Limma and pathway analysis was conducted by linking the potato sequences to the Arabidopsis thaliana. DMN elicited a change in a number of transcripts associated with cold responses, water regulation, salt stress, and osmotic adjustment. DMN also resulted in a repression of cyclin or cyclin-like transcripts. DMN also resulted in a 50% decrease in thymidine incorporation suggesting a repression of the S phase of the cell cycle. Quantitative real-time polymerase chain reaction analysis demonstrated that DMN increased transcripts for the cell cycle inhibitors KRP1 and KRP2. We conclude the DMN results in alteration of genes associated with the maintenance of a G1/S phase block possibly through the induction of the cell cycle inhibitors KRP1 and KRP2.

Overexpression of a pea DNA helicase 45 in bacteria confers salinity stress tolerance

Salinity stress is one of the major factors negatively affecting growth and productivity in living organisms including plants and bacteria resulting in significant losses worldwide. Therefore, it would be fruitful to develop salinity stress tolerant useful species and also to understand the mechanism of stress tolerance. The pea DNA helicase 45 (PDH45) is a DNA and RNA helicase, homologous to eukaryotic translation initiation factor 4A (eIF-4A) and is involved in various processes including protein synthesis, maintaining the basic activities of the cell, upregulation of topoisomerase I activity and salinity stress tolerance in plant, but its role in salinity stress tolerance in bacteria has not heretofore been studied. This study provides an evidence for a novel function of the PDH45 gene in high salinity (NaCl) stress tolerance in bacteria (Eschericia coli, BL21 cells) also. Furthermore, it has been shown that the functionally active PDH45 gene is required to show the stress tolerance in bacteria because the single mutants (E183G or R363Q) and the double mutant (E183G + R363Q) of the gene could not confer the same function. The response was specific to Na+ ions as the bacteria could not grow in presence of LiCl. This study suggests that the cellular response to high salinity stress across prokaryotes and plant kingdom is conserved and also helps in our better understanding of mechanism of stress tolerance in bacteria and plants. It could also be very useful in developing high salinity stress tolerant useful bacteria of agronomic importance. Overall, this study provides an evidence for a novel function of the PDH45 gene in high salinity stress tolerance in bacteria.

Inositol polyphosphate 5-phosphatase7 regulates the production of reactive oxygen species and salt tolerance in Arabidopsis

Plants possess remarkable ability to adapt to adverse environmental conditions. The adaptation process involves the removal of many molecules from organelles, especially membranes, and replacing them with new ones. The process is mediated by an intracellular vesicle-trafficking system regulated by phosphatidylinositol (PtdIns) kinases and phosphatases. Although PtdIns comprise a fraction of membrane lipids, they function as major regulators of stress signaling. We analyzed the role of PtdIns 5-phosphatases (5PTases) in plant salt tolerance. The Arabidopsis (Arabidopsis thaliana) genome contains 15 At5PTases. We analyzed salt sensitivity in nine At5ptase mutants and identified one (At5ptase7) that showed increased sensitivity, which was improved by overexpression. At5ptase7 mutants demonstrated reduced production of reactive oxygen species (ROS). Supplementation of mutants with exogenous PtdIns dephosphorylated at the D5' position restored ROS production, while PtdIns(4,5)P(2), PtdIns(3,5)P(2), or PtdIns(3,4,5)P(3) were ineffective. Compromised salt tolerance was also observed in mutant NADPH Oxidase, in agreement with the low ROS production and salt sensitivity of PtdIns 3-kinase mutants and with the inhibition of NADPH oxidase activity in wild-type plants. Localization of green fluorescent protein-labeled At5PTase7 occurred in the plasma membrane and nucleus, places that coincided with ROS production. Analysis of salt-responsive gene expression showed that mutants failed to induce the RD29A and RD22 genes, which contain several ROS-dependent elements in their promoters. Inhibition of ROS production by diphenylene iodonium suppressed gene induction. In summary, our results show a nonredundant function of At5PTase7 in salt stress response by regulating ROS production and gene expression.

Changes in the plant proteome resulting from salt stress: toward the creation of salt-tolerant crops?

Salinity in agricultural land is a major problem worldwide, placing a severe constraint on crop growth and productivity in many regions, and increased salinization of arable land is expected to have devastating global effects. Though plants vary in their sensitivity to salt stress, high salinity causes water deficit and ion toxicity in many plant species. Considerable efforts have therefore been made to investigate how genes respond to salt stress in various plants by using several approaches, including proteomics. Proteomic approaches for identifying proteins that are regulated in response to salt stress are becoming common in the post-genomics era of crop research. In this review, we describe the physiological and biological changes in the proteomes of several important food crops under salt stress. We also provide a viewpoint into how proteomics-based research is likely to develop in this field.

Double-filter identification of vascular-expressed genes using Arabidopsis plants with vascular hypertrophy and hypotrophy

Genes expressed in vascular tissues have been identified by several strategies, usually with a focus on mature vascular cells. In this study, we explored the possibility of using two opposite types of altered tissue compositions in combination with a double-filter selection to identify genes with a high probability of vascular expression in early organ primordia. Specifically, we generated full-transcriptome microarray profiles of plants with (a) genetically strongly reduced and (b) pharmacologically vastly increased vascular tissues and identified a reproducible cohort of 158 transcripts that fulfilled the dual requirement of being underrepresented in (a) and overrepresented in (b). In order to assess the predictive value of our identification scheme for vascular gene expression, we determined the expression patterns of genes in two unbiased subsamples. First, we assessed the expression patterns of all twenty annotated transcription factor genes from the cohort of 158 genes and found that seventeen of the twenty genes were preferentially expressed in leaf vascular cells. Remarkably, fifteen of these seventeen vascular genes were clearly expressed already very early in leaf vein development. Twelve genes with published leaf expression patterns served as a second subsample to monitor the representation of vascular genes in our cohort. Of those twelve genes, eleven were preferentially expressed in leaf vascular tissues. Based on these results we propose that our compendium of 158 genes represents a sample that is highly enriched for genes expressed in vascular tissues and that our approach is particularly suited to detect genes expressed in vascular cell lineages at early stages of their inception.

Analysis of transcriptional and upstream regulatory sequence activity of two environmental stress-inducible genes, NBS-Str1 and BLEC-Str8, of rice

Two abiotic stress-inducible upstream regulatory sequences (URSs) from rice have been identified and functionally characterized in rice. NBS-Str1 and BLEC-Str8 genes have been identified, by analysing the transcriptome data of cold, salt and desiccation stress-treated 7-day-old rice (Oryza sativa L. var. IR64) seedling, to be preferentially responsive to desiccation and salt stress, respectively. NBS-Str1 and BLEC-Str8 genes code for putative NBS (nucleotide binding site)-LRR (leucine rich repeat) and β-lectin domain protein, respectively. NBS-Str1 URS is induced in root tissue, preferentially in vascular bundle, during 3 and 24 h of desiccation stress condition in transgenic 7-day-old rice seedling. In mature transgenic plants, this URS shows induction in root and shoot tissue under desiccation stress as well as under prolonged (1 and 2 day) salt stress. BLEC-Str8 URS shows basal activity under un-stressed condition, however, it is inducible under salt stress condition in both root and leaf tissues in young seedling and mature plants. Activity of BLEC-Str8 URS has been found to be vascular tissue preferential, however, under salt stress condition its activity is also found in the mesophyll tissue. NBS-Str1 and BLEC-Str8 URSs are inducible by heavy metal, copper and manganese. Interestingly, both the URSs have been found to be non responsive to ABA treatment, implying them to be part of ABA-independent abiotic stress response pathway. These URSs could prove useful for expressing a transgene in a stress responsive manner for development of stress tolerant transgenic systems.

Identification of NaCl stress-responsive apoplastic proteins in rice shoot stems by 2D-DIGE

Plants have evolved sophisticated systems to cope with adverse environmental conditions such as cold, drought, and salinity. Although a number of stress response networks have been proposed, the role of plant apoplast in plant stress response has been ignored. To investigate the role of apoplastic proteins in the salt stress response, 10-day old rice plants were treated with 200mM NaCl for 1, 6 or 12h, and the soluble apoplast proteins of rice shoot stems were extracted for differential analysis, compared with untreated controls, by 2-D DIGE saturation labeling techniques. One hundred twenty-two significantly changed spots were identified by LC-MS/MS, and 117 spots representing 69 proteins have been identified. Of these proteins, 37 are apoplastic proteins according to the bioinformatic analysis. These proteins are mainly involved in the processes of carbohydrate metabolism, oxido-reduction, and protein processing and degradation. According to their functional categories and cluster analysis, a stress response model of apoplastic proteins has been proposed. These data indicate that the apoplast is important in plant stress signal reception and response.

Genome-wide analysis of rice and Arabidopsis identifies two glyoxalase genes that are highly expressed in abiotic stresses

Glyoxalase pathway, ubiquitously found in all organisms from prokaryotes to eukaryotes, consists of glyoxalase I (GLY I) and glyoxalase II (GLY II) enzymes, which detoxify a cytotoxic molecule, methylglyoxal (MG). Increase in MG has been correlated with various diseases in humans and different abiotic stresses in plants. We have previously shown that overproduction of GLY I and/or GLY II enzymes in transgenic plants provide tolerance towards salinity and heavy metal stresses. We have identified nineteen potential GLY I and four GLY II proteins in rice and twenty two GLY I and nine GLY II proteins in Arabidopsis. An analysis of complete set of genes coding for the glyoxalase proteins in these two genomes is presented, including classification and chromosomal distribution. Expression profiling of these genes has been performed in response to multiple abiotic stresses, in different tissues and during various stages of vegetative and reproductive development using publicly available databases (massively parallel signature sequencing and microarray). AtGLYI8, OsGLYI3, and OsGLYI10 expresses constitutively high in seeds while AtGLYI4, AtGLYI7, OsGLYI6, and OsGLYI11 are highly stress inducible. To complement this analyses, qRT-PCR is performed in two contrasting rice genotypes, i.e., IR64 and Pokkali where OsGLYI6 and OsGLYI11 are found to be highly stress inducible.

Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors

Transcriptome of Glycine soja leaf tissue during a detailed time course formed a foundation for examining transcriptional processes during NaHCO(3) stress treatment. Of a total of 2,310 detected differentially expressed genes, 1,664 genes were upregulated and 1,704 genes were downregulated at various time points. The number of stress-regulated genes increased dramatically after a 6-h stress treatment. GO category gene enrichment analysis revealed that most of the differentially expressed genes were involved in cell structure, protein synthesis, energy, and secondary metabolism. Another enrichment test revealed that the response of G. soja to NaHCO(3) highlights specific transcription factors, such as the C2C2-CO-like, MYB-related, WRKY, GARP-G2-like, and ZIM families. Co-expressed genes were clustered into ten classes (P < 0.001). Intriguingly, one cluster of 188 genes displayed a unique expression pattern that increases at an early stage (0.5 and 3 h), followed by a decrease from 6 to 12 h. This group was enriched in regulation of transcription components, including AP2-EREBP, bHLH, MYB/MYB-related, C2C2-CO-like, C2C2-DOF, C2C2, C3H, and GARP-G2-like transcription factors. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified 19 conserved motifs, potential binding sites for transcription factors. The appearance of ABA-responsive elements in the upstream of co-expression genes reveals that ABA-mediated signaling participates in the signal transduction in alkaline response.

Signal transduction during cold, salt, and drought stresses in plants

Abiotic stresses, especially cold, salinity and drought, are the primary causes of crop loss worldwide. Plant adaptation to environmental stresses is dependent upon the activation of cascades of molecular networks involved in stress perception, signal transduction, and the expression of specific stress-related genes and metabolites. Plants have stress-specific adaptive responses as well as responses which protect the plants from more than one environmental stress. There are multiple stress perception and signaling pathways, some of which are specific, but others may cross-talk at various steps. In this review article, we first expound the general stress signal transduction pathways, and then highlight various aspects of biotic stresses signal transduction networks. On the genetic analysis, many cold induced pathways are activated to protect plants from deleterious effects of cold stress, but till date, most studied pathway is ICE-CBF-COR signaling pathway. The Salt-Overly-Sensitive (SOS) pathway, identified through isolation and study of the sos1, sos2, and sos3 mutants, is essential for maintaining favorable ion ratios in the cytoplasm and for tolerance of salt stress. Both ABA-dependent and -independent signaling pathways appear to be involved in osmotic stress tolerance. ROS play a dual role in the response of plants to abiotic stresses functioning as toxic by-products of stress metabolism, as well as important signal transduction molecules and the ROS signaling networks can control growth, development, and stress response. Finally, we talk about the common regulatory system and cross-talk among biotic stresses, with particular emphasis on the MAPK cascades and the cross-talk between ABA signaling and biotic signaling.

Proteomic identification of OsCYP2, a rice cyclophilin that confers salt tolerance in rice (Oryza sativa L.) seedlings when overexpressed

BACKGROUND

High Salinity is a major environmental stress influencing growth and development of rice. Comparative proteomic analysis of hybrid rice shoot proteins from Shanyou 10 seedlings, a salt-tolerant hybrid variety, and Liangyoupeijiu seedlings, a salt-sensitive hybrid variety, was performed to identify new components involved in salt-stress signaling.

RESULTS

Phenotypic analysis of one protein that was upregulated during salt-induced stress, cyclophilin 2 (OsCYP2), indicated that OsCYP2 transgenic rice seedlings had better tolerance to salt stress than did wild-type seedlings. Interestingly, wild-type seedlings exhibited a marked reduction in maximal photochemical efficiency under salt stress, whereas no such change was observed for OsCYP2-transgenic seedlings. OsCYP2-transgenic seedlings had lower levels of lipid peroxidation products and higher activities of antioxidant enzymes than wild-type seedlings. Spatiotemporal expression analysis of OsCYP2 showed that it could be induced by salt stress in both Shanyou 10 and Liangyoupeijiu seedlings, but Shanyou 10 seedlings showed higher OsCYP2 expression levels. Moreover, circadian rhythm expression of OsCYP2 in Shanyou 10 seedlings occurred earlier than in Liangyoupeijiu seedlings. Treatment with PEG, heat, or ABA induced OsCYP2 expression in Shanyou 10 seedlings but inhibited its expression in Liangyoupeijiu seedlings. Cold stress inhibited OsCYP2 expression in Shanyou 10 and Liangyoupeijiu seedlings. In addition, OsCYP2 was strongly expressed in shoots but rarely in roots in two rice hybrid varieties.

CONCLUSIONS

Together, these data suggest that OsCYP2 may act as a key regulator that controls ROS level by modulating activities of antioxidant enzymes at translation level. OsCYP2 expression is not only induced by salt stress, but also regulated by circadian rhythm. Moreover, OsCYP2 is also likely to act as a key component that is involved in signal pathways of other types of stresses-PEG, heat, cold, or ABA.

Comparative transcriptome analysis of contrasting foxtail millet cultivars in response to short-term salinity stress

Soil salinity represents a major abiotic stress that adversely affects crop growth and productivity. In this study, 21-day-old seedlings of two foxtail millet (Setaria italica) cultivars differing in salt tolerance were found to also differ in lipid peroxidation, ion balance and activity of antioxidative enzymes (glutathione reductase and catalase) under short-term salinity stress (250 mM NaCl for 1-48 h). With the aim of better understanding the molecular mechanisms underlying plant responses to short-term salinity stress, two suppression subtractive hybridization cDNA libraries (forward and reverse) were constructed of these cultivars. A total of 249 non-redundant ESTs was identified by random EST sequencing and grouped into 11 functional categories. Macroarray analysis of these clones showed that 159 (63.9%) were differentially expressed (≥ 2-fold) in response to salinity stress, with 115 (72.3%) up and 44 (27.7%) down-regulated. A data search of transcriptional profiling under salinity stress in other species revealed that 81 (51%) of the 159 differentially expressed transcripts found in foxtail millet have not been reported in previous studies. Hence, these new transcripts may represent untapped gene sources allowing specific responses to short-term salt-stress in an orphan crop known to possess a natural adaptation capacity to abiotic stress. Quantitative real-time PCR of 21 highly up-regulated (≥ 2.5-fold) transcripts showed temporal variation in expression in both cultivars under salinity. Among them, several transcription factors and signalling genes were preferentially expressed in the tolerant cultivar. These results suggest that the tolerant cultivar possesses more effective signal-perception mechanisms for metabolic adjustments in plants under harsh saline conditions. Our findings provide evidence that the unknown genes identified in this study, in addition to several known genes, may play important roles in stress tolerance mechanisms present in foxtail millet.

The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE

BACKGROUND

The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level.

RESULTS

We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress.Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available.

CONCLUSIONS

This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.

Genome-wide analysis of rice and Arabidopsis identifies two glyoxalase genes that are highly expressed in abiotic stresses

Glyoxalase pathway, ubiquitously found in all organisms from prokaryotes to eukaryotes, consists of glyoxalase I (GLY I) and glyoxalase II (GLY II) enzymes, which detoxify a cytotoxic molecule, methylglyoxal (MG). Increase in MG has been correlated with various diseases in humans and different abiotic stresses in plants. We have previously shown that overproduction of GLY I and/or GLY II enzymes in transgenic plants provide tolerance towards salinity and heavy metal stresses. We have identified nineteen potential GLY I and four GLY II proteins in rice and twenty two GLY I and nine GLY II proteins in Arabidopsis. An analysis of complete set of genes coding for the glyoxalase proteins in these two genomes is presented, including classification and chromosomal distribution. Expression profiling of these genes has been performed in response to multiple abiotic stresses, in different tissues and during various stages of vegetative and reproductive development using publicly available databases (massively parallel signature sequencing and microarray). AtGLYI8, OsGLYI3, and OsGLYI10 expresses constitutively high in seeds while AtGLYI4, AtGLYI7, OsGLYI6, and OsGLYI11 are highly stress inducible. To complement this analyses, qRT-PCR is performed in two contrasting rice genotypes, i.e., IR64 and Pokkali where OsGLYI6 and OsGLYI11 are found to be highly stress inducible.

Functional characterisation of OsCPK21, a calcium-dependent protein kinase that confers salt tolerance in rice

Calcium acts as a messenger in various signal transduction pathways in plants. Calcium-dependent protein kinases (CDPKs) play important roles in regulating downstream components in calcium signaling pathways. In rice, the CDPKs constitute a large multigene family consisting of 29 genes, but the biological functions and functional divergence or redundancy of most of these genes remain unclear. Using a mini-scale full-length cDNA overexpressor (FOX) gene hunting system, we generated 250 independent transgenic rice plants overexpressing individual rice CDPKs (CDPK FOX-rice lines). These CDPK FOX-rice lines were screened for salt stress tolerance. The survival rate of the OsCPK21-FOX plants was higher than that of wild-type (WT) plants grown under high salinity conditions. The inhibition of seedling growth by abscisic acid (ABA) treatment was greater in the OsCPK21-FOX plants than in WT plants. Several ABA- and high salinity-inducible genes were more highly expressed in the OsCPK21-FOX plants than in WT plants. These results suggest that OsCPK21 is involved in the positive regulation of the signaling pathways that are involved in the response to ABA and salt stress.

Transcriptome analysis of grain-filling caryopses reveals involvement of multiple regulatory pathways in chalky grain formation in rice

BACKGROUND

Grain endosperm chalkiness of rice is a varietal characteristic that negatively affects not only the appearance and milling properties but also the cooking texture and palatability of cooked rice. However, grain chalkiness is a complex quantitative genetic trait and the molecular mechanisms underlying its formation are poorly understood.

RESULTS

A near-isogenic line CSSL50-1 with high chalkiness was compared with its normal parental line Asominori for grain endosperm chalkiness. Physico-biochemical analyses of ripened grains showed that, compared with Asominori, CSSL50-1 contains higher levels of amylose and 8 DP (degree of polymerization) short-chain amylopectin, but lower medium length 12 DP amylopectin. Transcriptome analysis of 15 DAF (day after flowering) caryopses of the isogenic lines identified 623 differential expressed genes (P < 0.01), among which 324 genes are up-regulated and 299 down-regulated. These genes were classified into 18 major categories, with 65.3% of them belong to six major functional groups: signal transduction, cell rescue/defense, transcription, protein degradation, carbohydrate metabolism and redox homeostasis. Detailed pathway dissection demonstrated that genes involved in sucrose and starch synthesis are up-regulated, whereas those involved in non-starch polysaccharides are down regulated. Several genes involved in oxidoreductive homeostasis were found to have higher expression levels in CSSL50-1 as well, suggesting potential roles of ROS in grain chalkiness formation.

CONCLUSION

Extensive gene expression changes were detected during rice grain chalkiness formation. Over half of these differentially expressed genes are implicated in several important categories of genes, including signal transduction, transcription, carbohydrate metabolism and redox homeostasis, suggesting that chalkiness formation involves multiple metabolic and regulatory pathways.

Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa

In addition to regulating growth and development, the most important function of microRNAs (miRNAs) in plants is the regulation of a variety of cellular processes underlying plant adaptation to environmental stresses. To gain a deep understanding of the mechanism of drought tolerance in rice, genome-wide profiling and analysis of miRNAs was carried out in drought-challenged rice across a wide range of developmental stages, from tillering to inflorescence formation, using a microarray platform. Among the 30 miRNAs identified as significantly down- or up-regulated under the drought stress, 11 down-regulated miRNAs (miR170, miR172, miR397, miR408, miR529, miR896, miR1030, miR1035, miR1050, miR1088, and miR1126) and eight up-regulated miRNAs (miR395, miR474, miR845, miR851, miR854, miR901, miR903, and miR1125) were revealed for the first time to be induced by drought stress in plants, and nine (miR156, miR168, miR170, miR171, miR172, miR319, miR396, miR397, and miR408) showed opposite expression to that observed in drought-stressed Arabidopsis. The most conserved down-regulated miRNAs were ath-miR170, the miR171 family, and ath-miR396, and the most conserved up-regulated miRNAs were ptc-miR474 and ath-miR854a. The identification of differentially expressed novel plant miRNAs and their target genes, and the analysis of cis-elements provides molecular evidence for the possible involvement of miRNAs in the process of drought response and/or tolerance in rice.

β-Glucosidases

β-Glucosidases (3.2.1.21) are found in all domains of living organisms, where they play essential roles in the removal of nonreducing terminal glucosyl residues from saccharides and glycosides. β-Glucosidases function in glycolipid and exogenous glycoside metabolism in animals, defense, cell wall lignification, cell wall β-glucan turnover, phytohormone activation, and release of aromatic compounds in plants, and biomass conversion in microorganisms. These functions lead to many agricultural and industrial applications. β-Glucosidases have been classified into glycoside hydrolase (GH) families GH1, GH3, GH5, GH9, and GH30, based on their amino acid sequences, while other β-glucosidases remain to be classified. The GH1, GH5, and GH30 β-glucosidases fall in GH Clan A, which consists of proteins with (β/α)(8)-barrel structures. In contrast, the active site of GH3 enzymes comprises two domains, while GH9 enzymes have (α/α)(6) barrel structures. The mechanism by which GH1 enzymes recognize and hydrolyze substrates with different specificities remains an area of intense study.

Transcriptional profile of maize roots under acid soil growth

BACKGROUND

Aluminum (Al) toxicity is one of the most important yield-limiting factors of many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth leading to poor water and nutrient absorption. Al tolerance has been extensively studied using hydroponic experiments. However, unlike soil conditions, this method does not address all of the components that are necessary for proper root growth and development. In the present study, we grew two maize genotypes with contrasting tolerance to Al in soil containing toxic levels of Al and then compared their transcriptomic responses.

RESULTS

When grown in acid soil containing toxic levels of Al, the Al-sensitive genotype (S1587-17) showed greater root growth inhibition, more Al accumulation and more callose deposition in root tips than did the tolerant genotype (Cat100-6). Transcriptome profiling showed a higher number of genes differentially expressed in S1587-17 grown in acid soil, probably due to secondary effects of Al toxicity. Genes involved in the biosynthesis of organic acids, which are frequently associated with an Al tolerance response, were not differentially regulated in both genotypes after acid soil exposure. However, genes related to the biosynthesis of auxin, ethylene and lignin were up-regulated in the Al-sensitive genotype, indicating that these pathways might be associated with root growth inhibition. By comparing the two maize lines, we were able to discover genes up-regulated only in the Al-tolerant line that also presented higher absolute levels than those observed in the Al-sensitive line. These genes encoded a lipase hydrolase, a retinol dehydrogenase, a glycine-rich protein, a member of the WRKY transcriptional family and two unknown proteins.

CONCLUSIONS

This work provides the first characterization of the physiological and transcriptional responses of maize roots when grown in acid soil containing toxic levels of Al. The transcriptome profiles highlighted several pathways that are related to Al toxicity and tolerance during growth in acid soil. We found several genes that were not found in previous studies using hydroponic experiments, increasing our understanding of plant responses to acid soil. The use of two germplasms with markedly different Al tolerances allowed the identification of genes that are a valuable tool for assessing the mechanisms of Al tolerance in maize in acid soil.

Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment

BACKGROUND

Plant roots are the primary site of perception and injury for saline-alkaline stress. The current knowledge of saline-alkaline stress transcriptome is mostly focused on saline (NaCl) stress and only limited information on alkaline (NaHCO3) stress is available.

RESULTS

Using Affymetrix Soybean GeneChip, we conducted transcriptional profiling on Glycine soja roots subjected to 50 mmol/L NaHCO3 treatment. In a total of 7088 probe sets, 3307 were up-regulated and 5720 were down-regulated at various time points. The number of significantly stress regulated genes increased dramatically after 3 h stress treatment and peaked at 6 h. GO enrichment test revealed that most of the differentially expressed genes were involved in signal transduction, energy, transcription, secondary metabolism, transporter, disease and defence response. We also detected 11 microRNAs regulated by NaHCO3 stress.

CONCLUSIONS

This is the first comprehensive wild soybean root transcriptome analysis under alkaline stress. These analyses have identified an inventory of genes with altered expression regulated by alkaline stress. The data extend the current understanding of wild soybean alkali stress response by providing a set of robustly selected, differentially expressed genes for further investigation.

Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.)

Identification of genes for quantitative traits is difficult using any single approach due to complex inheritance of the traits and limited resolving power of the individual techniques. Here a combination of genetic mapping and bulked transcriptome profiling was used to narrow down the number of differentially expressed salt-responsive genes in rice in order to identify functional polymorphism of genes underlying the quantitative trait loci (QTL). A population of recombinant inbred lines (RILs) derived from cross between salt-tolerant variety CSR 27 and salt-sensitive variety MI 48 was used to map QTL for salt ion concentrations in different tissues and salt stress susceptibility index (SSI) for spikelet fertility, grain weight, and grain yield. Eight significant QTL intervals were mapped on chromosomes 1, 8, and 12 for the salt ion concentrations and a QTL controlling SSI for spikelet fertility was co-located in one of these intervals on chromosome 8. However, there were total 2,681 genes in these QTL intervals, making it difficult to pinpoint the genes responsible for the functional differences for the traits. Similarly, transcriptome profiling of the seedlings of tolerant and sensitive parents grown under control and salt-stress conditions showed 798 and 2,407 differentially expressed gene probes, respectively. By analyzing pools of RNA extracted from ten each of extremely tolerant and extremely sensitive RILs to normalize the background noise, the number of differentially expressed genes under salt stress was drastically reduced to 30 only. Two of these genes, an integral transmembrane protein DUF6 and a cation chloride cotransporter, were not only co-located in the QTL intervals but also showed the expected distortion of allele frequencies in the extreme tolerant and sensitive RILs, and therefore are suitable for future validation studies and development of functional markers for salt tolerance in rice to facilitate marker-assisted breeding.

Regulation of plasma membrane aquaporins by inoculation with a Bacillus megaterium strain in maize (Zea mays L.) plants under unstressed and salt-stressed conditions

It is documented that some plant-growth-promoting rhizobacteria (PGPR) enhance plant salt tolerance. However, as to how PGPR may influence two crucial components of plant salt tolerance such as, root hydraulic characteristics and aquaporin regulation has been almost unexplored. Here, maize (Zea mays L.) plants were inoculated with a Bacillus megaterium strain previously isolated from a degraded soil and characterized as PGPR. Inoculated plants were found to exhibit higher root hydraulic conductance (L) values under both unstressed and salt-stressed conditions. These higher L values in inoculated plants correlated with higher plasma membrane type two (PIP2) aquaporin amount in their roots under salt-stressed conditions. Also, ZmPIP1;1 protein amount under salt-stressed conditions was higher in inoculated leaves than in non-inoculated ones. Hence, the different regulation of PIP aquaporin expression and abundance by the inoculation with the B. megaterium strain could be one of the causes of the different salt response in terms of root growth, necrotic leaf area, leaf relative water content and L by the inoculation treatment.

Studying the functional genomics of stress responses in loblolly pine with the Expresso microarray experiment management system

Conception, design, and implementation of cDNA microarray experiments present a variety of bioinformatics challenges for biologists and computational scientists. The multiple stages of data acquisition and analysis have motivated the design of Expresso, a system for microarray experiment management. Salient aspects of Expresso include support for clone replication and randomized placement; automatic gridding, extraction of expression data from each spot, and quality monitoring; flexible methods of combining data from individual spots into information about clones and functional categories; and the use of inductive logic programming for higher-level data analysis and mining. The development of Expresso is occurring in parallel with several generations of microarray experiments aimed at elucidating genomic responses to drought stress in loblolly pine seedlings. The current experimental design incorporates 384 pine cDNAs replicated and randomly placed in two specific microarray layouts. We describe the design of Expresso as well as results of analysis with Expresso that suggest the importance of molecular chaperones and membrane transport proteins in mechanisms conferring successful adaptation to long-term drought stress.

Cloning and expression analysis of the Ccrboh gene encoding respiratory burst oxidase in Citrullus colocynthis and grafting onto Citrullus lanatus (watermelon)

A full-length drought-responsive gene Ccrboh, encoding the respiratory burst oxidase homologue (rboh), was cloned in Citrullus colocynthis, a very drought-tolerant cucurbit species. The robh protein, also named NADPH oxidase, is conserved in plants and animals, and functions in the production of reactive oxygen species (ROS). The Ccrboh gene accumulated in a tissue-specific pattern when C. colocynthis was treated with PEG, abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA), or NaCl, while the homologous rboh gene did not show any change in C. lanatus var. lanatus, cultivated watermelon, during drought. Grafting experiments were conducted using C. colocynthis or C. lanatus as the rootstock or scion. Results showed that the rootstock significantly affects gene expression in the scion, and some signals might be transported from the root to the shoot. Ccrboh in C. colocynthis was found to function early during plant development, reaching high mRNA transcript levels 3 d after germination. The subcellular location of Ccrboh was investigated by transient expression of the 35S::Ccrboh::GFP fusion construct in protoplasts. The result confirmed that Ccrboh is a transmembrane protein. Our data suggest that Ccrboh might be functionally important during the acclimation of plants to stress and also in plant development. It holds great promise for improving drought tolerance of other cucurbit species.

A tomato bZIP transcription factor, SlAREB, is involved in water deficit and salt stress response

Abiotic stresses such as cold, water deficit, and salt stresses severely reduce crop productivity. Tomato (Solanum lycopersicum) is an important economic crop; however, not much is known about its stress responses. To gain insight into stress-responsive gene regulation in tomato plants, we identified transcription factors from a tomato cDNA microarray. An ABA-responsive element binding protein (AREB) was identified and named SlAREB. In tomato protoplasts, SlAREB transiently transactivated luciferase reporter gene expression driven by AtRD29A (responsive to dehydration) and SlLAP (leucine aminopeptidase) promoters with exogenous ABA application, which was suppressed by the kinase inhibitor staurosporine, indicating that an ABA-dependent post-translational modification is required for the transactivation ability of SlAREB protein. Electrophoretic mobility shift assays showed that the recombinant DNA-binding domain of SlAREB protein is able to bind AtRD29A and SlLAP promoter regions. Constitutively expressed SlAREB increased tolerance to water deficit and high salinity stresses in both Arabidopsis and tomato plants, which maintained PSII and membrane integrities as well as water content in plant bodies. Overproduction of SlAREB in Arabidopsis thaliana and tomato plants regulated stress-related genes AtRD29A, AtCOR47, and SlCI7-like dehydrin under ABA and abiotic stress treatments. Taken together, these results show that SlAREB functions to regulate some stress-responsive genes and that its overproduction improves plant tolerance to water deficit and salt stress.