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

Regulatory network of gene expression in the drought and cold stress responses

Molecular and genomic studies have shown that several genes with various functions are induced by drought and cold stresses, and that various transcription factors are involved in the regulation of stress-inducible genes. The products of stress-inducible genes function not only in stress tolerance but also in stress response. Genetic studies have identified many factors that modify the regulation of stress responses. Recent progress has been made in analyzing the complex cascades of gene expression in drought and cold stress responses, especially in identifying specificity and crosstalk in stress signaling.

Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis

The formation of symbiotic associations with arbuscular mycorrhizal (AM) fungi is a phenomenon common to the majority of vascular flowering plants. Here, we used cDNA arrays to examine transcript profiles in Medicago truncatula roots during the development of an AM symbiosis with Glomus versiforme and during growth under differing phosphorus nutrient regimes. Three percent of the genes examined showed significant changes in transcript levels during the development of the symbiosis. Most genes showing increased transcript levels in mycorrhizal roots showed no changes in response to high phosphorus, suggesting that alterations in transcript levels during symbiosis were a consequence of the AM fungus rather than a secondary effect of improved phosphorus nutrition. Among the mycorrhiza-induced genes, two distinct temporal expression patterns were evident. Members of one group showed an increase in transcripts during the initial period of contact between the symbionts and a subsequent decrease as the symbiosis developed. Defense- and stress-response genes were a significant component of this group. Genes in the second group showed a sustained increase in transcript levels that correlated with the colonization of the root system. The latter group contained a significant proportion of new genes similar to components of signal transduction pathways, suggesting that novel signaling pathways are activated during the development of the symbiosis. Analysis of the spatial expression patterns of two mycorrhiza-induced genes revealed distinct expression patterns consistent with the hypothesis that gene expression in mycorrhizal roots is signaled by both cell-autonomous and cell-nonautonomous signals.

Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress

Plant nutrition critically depends on the activity of membrane transporters that translocate minerals from the soil into the plant and are responsible for their intra- and intercellular distribution. Most plant membrane transporters are encoded by multigene families whose members often exhibit overlapping expression patterns and a high degree of sequence homology. Furthermore, many inorganic nutrients are transported by more than one transporter family. These considerations, coupled with a large number of so-far non-annotated putative transporter genes, hamper our progress in understanding how the activity of specific transporters is integrated into a response to fluctuating conditions. We designed an oligonucleotide microarray representing 1096 Arabidopsis transporter genes and analysed the root transporter transcriptome over a 96-h period with respect to 80 mM NaCl, K+ starvation and Ca2+ starvation. Our data show that cation stress led to changes in transcript level of many genes across most transporter gene families. Analysis of transcriptionally modulated genes across all functional groups of transporters revealed families such as V-type ATPases and aquaporins that responded to all treatments, and families - which included putative non-selective cation channels for the NaCl treatment and metal transporters for Ca2+ starvation conditions - that responded to specific ionic environments. Several gene families including primary pumps, antiporters and aquaporins were analysed in detail with respect to the mRNA levels of different isoforms during ion stress. Cluster analysis allowed identification of distinct expression profiles, and several novel putative regulatory motifs were discovered within sets of co-expressed genes.

Gene expression profiling in response to ultraviolet radiation in maize genotypes with varying flavonoid content

Microarray hybridization was used to assess acclimation responses to four UV regimes by near isogenic maize (Zea mays) lines varying in flavonoid content. We found that 355 of the 2,500 cDNAs tested were regulated by UV radiation in at least one genotype. Among these, 232 transcripts are assigned putative functions, whereas 123 encode unknown proteins. UV-B increased expression of stress response and ribosomal protein genes, whereas photosynthesis-associated genes were down-regulated; lines lacking UV-absorbing pigments had more dramatic responses than did lines with these pigments, confirming the shielding role of these compounds. Sunlight filtered to remove UV-B or UV-B plus UV-A resulted in significant expression changes in many genes not previously associated with UV responses. Some pathways regulated by UV radiation are shared with defense, salt, and oxidative stresses; however, UV-B radiation can activate additional pathways not shared with other stresses.

Gene expression profiling in response to ultraviolet radiation in maize genotypes with varying flavonoid content

Microarray hybridization was used to assess acclimation responses to four UV regimes by near isogenic maize (Zea mays) lines varying in flavonoid content. We found that 355 of the 2,500 cDNAs tested were regulated by UV radiation in at least one genotype. Among these, 232 transcripts are assigned putative functions, whereas 123 encode unknown proteins. UV-B increased expression of stress response and ribosomal protein genes, whereas photosynthesis-associated genes were down-regulated; lines lacking UV-absorbing pigments had more dramatic responses than did lines with these pigments, confirming the shielding role of these compounds. Sunlight filtered to remove UV-B or UV-B plus UV-A resulted in significant expression changes in many genes not previously associated with UV responses. Some pathways regulated by UV radiation are shared with defense, salt, and oxidative stresses; however, UV-B radiation can activate additional pathways not shared with other stresses.

Proteome analysis of cultivar-specific deregulations ofOryza sativa indicaandO. sativa japonicacellular suspensions undergoingRice yellow mottle virusinfection

We have used two-dimensional gel electrophoresis with mass spectrometry analysis to study the temporal patterns of protein expression during RYMV (Rice yellow mottle virus) infection in rice cells of two cultivars: IR64, Oryza sativa indica, susceptible, and Azucena, O. sativa japonica, partially resistant to RYMV. Proteomic analysis of nonstressed and RYMV inoculated cells showed statistically significant changes in the relative levels of 40 IR64 proteins and 24 Azucena proteins. Protein identification using mass spectrometry was attempted for all the differentially regulated proteins. This global analysis detected 32 hypothetical "new" proteins. Nineteen differentially regulated proteins were identified for IR64 cultivar, while 13 were identified for Azucena cultivar, including proteins in three functional categories: metabolism, stress-related proteins, and translation. These data revealed that a number of proteins regulated by abiotic stress response pathway were activated by RYMV in both cultivars (such as salt-induced protein, heat shock proteins (HSPs), superoxide dismutase (SOD), and others have functions consistent with the susceptibility or partially resistance trait (such as dehydrin, proteins involved in glycolysis pathway).

Phosphate starvation triggers distinct alterations of genome expression in Arabidopsis roots and leaves

Arabidopsis genome expression pattern changes in response to phosphate (Pi) starvation were examined during a 3-d period after removal of Pi from the growth medium. Available Pi concentration was decreased after the first 24 h of Pi starvation in roots by about 22%, followed by a slow recovery during the 2nd and 3rd d after Pi starvation, but no significant change was observed in leaves within the 3 d of Pi starvation. Microarray analysis revealed that more than 1,800 of the 6,172 genes present in the array were regulated by 2-fold or more within 72 h from the onset of Pi starvation. Analysis of these Pi starvation-responsive genes shows that they belong to wide range of functional categories. Many genes for photosynthesis and nitrogen assimilation were down-regulated. A complex set of metabolic adaptations appears to occur during Pi starvation. More than 100 genes each for transcription factors and cell-signaling proteins were regulated in response to Pi starvation, implying major regulatory changes in cellular growth and development. A significant fraction of those regulatory genes exhibited distinct or even contrasting expression in leaves and roots in response to Pi starvation, supporting the idea that distinct Pi starvation response strategies are used for different plant organs in response to a shortage of Pi in the growth medium.

Temporal progression of gene expression responses to salt shock in maize roots

Using a cDNA microarray containing 7943 ESTs, the behavior of the maize root transcriptome has been monitored in a time course for 72 h after imposition of salinity stress (150 mM NaCI). Under these conditions, root sodium amounts increased faster than in leaves, and root potassium decreased significantly. Although the overall free amino acid concentration was not affected, amino acid composition was changed with proline and asparagine increasing. Microarray analysis identified 916 ESTs representing genes whose steady-state RNA levels were significantly altered at various time points, corresponding to 11% of the ESTs printed. The response of the transcriptome to sub-lethal salt stress was rapid and transient, leading to a burst of changes at the three-hour time point. The salt-regulated ESTs represented 472 tentatively unique genes (TUGs), which, based on functional category analysis, are involved in a broad range of cellular and biochemical activities, prominent amongst which were transport and signal transduction pathways. Clustering of regulated transcripts based on the timing and duration of changes suggests a structured succession of induction and repression for salt responsive genes in multiple signal and response cascades. Within this framework, 16 signaling molecules, including six protein kinases, two protein phosphatases and eight transcription factors, were regulated with distinct expression patterns by high salinity.

A novel brassinolide-enhanced gene identified by cDNA microarray is involved in the growth of rice

Brassinosteroids (BRs) are growth-promoting natural substances required for normal plant growth and development. To understand the molecular mechanism of BR action, a cDNA microarray containing 1265 rice genes was analyzed for expression differences in rice lamina joint treated with brassinolide (BL). A novel BL-enhanced gene, designated OsBLE2, was identified and cloned. The full-length cDNA is 3243 bp long, encoding a predicted polypeptide of 761 amino acid residues and nine possible transmembrane regions. OsBLE2 expression was most responsive to BL in the lamina joint and leaf sheath in rice seedlings. Besides, auxin and gibberellins also increased its expression. OsBLE2 expressed more, as revealed by in situ hybridization, in vascular bundles and root primordia, where the cells are actively undergoing division, elongation, and differentiation. Transgenic rice expressing antisense OsBLE2 exhibits various degrees of repressed growth. BL could not enhance its expression in transgenic rice expressing antisense BRI1, a BR receptor, indicating that BR signaling to the enhanced expression of OsBLE2 is through BRI1 . BL effect in the d1 mutant rice was much weaker than that in its wild-type control, indicating that heterotrimeric G protein may be a component of BRs signaling. These results suggest that OsBLE2 is involved in BL-regulated growth and development processes in rice.

Gene expression profiling of plant responses to abiotic stress

Expression profiling has become an important tool to investigate how an organism responds to environmental changes. Plants, being sessile, have the ability to dramatically alter their gene expression patterns in response to environmental changes such as temperature, water availability or the presence of deleterious levels of ions. Sometimes these transcriptional changes are successful adaptations leading to tolerance while in other instances the plant ultimately fails to adapt to the new environment and is labeled as sensitive to that condition. Expression profiling can define both tolerant and sensitive responses. These profiles of plant response to environmental extremes (abiotic stresses) are expected to lead to regulators that will be useful in biotechnological approaches to improve stress tolerance as well as to new tools for studying regulatory genetic circuitry. Finally, data mining of the alterations in the plant transcriptome will lead to further insights into how abiotic stress affects plant physiology.

Na+ tolerance and Na+ transport in higher plants

Tolerance to high soil [Na(+)] involves processes in many different parts of the plant, and is manifested in a wide range of specializations at disparate levels of organization, such as gross morphology, membrane transport, biochemistry and gene transcription. Multiple adaptations to high [Na(+)] operate concurrently within a particular plant, and mechanisms of tolerance show large taxonomic variation. These mechanisms can occur in all cells within the plant, or can occur in specific cell types, reflecting adaptations at two major levels of organization: those that confer tolerance to individual cells, and those that contribute to tolerance not of cells per se, but of the whole plant. Salt-tolerant cells can contribute to salt tolerance of plants; but we suggest that equally important in a wide range of conditions are processes involving the management of Na(+) movements within the plant. These require specific cell types in specific locations within the plant catalysing transport in a coordinated manner. For further understanding of whole plant tolerance, we require more knowledge of cell-specific transport processes and the consequences of manipulation of transporters and signalling elements in specific cell types.

Arabidopsis microarrays identify conserved and differentially expressed genes involved in shoot growth and development from distantly related plant species

Expressed sequence tags (EST)-based microarrays are powerful tools for gene discovery and signal transduction studies in a small number of well-characterized species. To explore the usefulness of this technique for poorly characterized species, we have hybridized the 11,522-element Arabidopsis microarrays with labeled cDNAs from mature leaf and shoot apices from several different species. Expression of 23 to 47% of the genes on the array was detected, demonstrating that a large number of genes from distantly related species can be surveyed on Arabidopsis arrays. Differential expression of genes with known functions was indicative of the physiological state of the tissues tested. Genes involved in cell division, stress responses, and development were conserved and expressed preferentially in growing shoots.

Molecular responses to drought, salinity and frost: common and different paths for plant protection

Drought, high salinity and low temperature are major environmental factors that limit plant productivity. Plants respond and adapt to these stresses in order to survive. Signaling pathways are induced in response to environmental stress and recent molecular and genetic studies have revealed that these pathways involve many components. In this review, we highlight recent findings on the gene expression associated with stress responses and the signaling pathways that are either common or specific to the response.

Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles

With the availability of microarray technology, the expression profiles of thousands of genes can be monitored simultaneously to help determine the mechanisms of these biological processes. We conducted Affymetrix GeneChip microarray analyses of the Arabidopsis-cyst nematode interaction and employed a statistical procedure to analyze the resultant data, which allowed us to identify significant gene expression changes. Quantitative real-time RT-PCR assays were used to confirm the microarray analyses. The results of the expression profiling revealed 128 genes with altered steady-state mRNA levels following infection by the sugar beet cyst nematode (Heterodera schachtii; BCN), in contrast to only 12 genes that had altered expression following infection by the soybean cyst nematode (H. glycines; SCN). The expression of these 12 genes also changed following infection by BCN, i.e. we did not identify any genes regulated exclusively by SCN. The identification of 116 genes whose expression changes during successful cyst nematode parasitism by BCN suggests a potential involvement of these genes in the infection events starting with successful syncytium induction. Further characterization of these genes will permit the formulation of testable hypotheses to explain successful cyst nematode parasitism.

Nylon filter arrays reveal differential gene expression in proteoid roots of white lupin in response to phosphorus deficiency

White lupin (Lupinus albus) adapts to phosphorus deficiency (-P) by the development of short, densely clustered lateral roots called proteoid (or cluster) roots. In an effort to better understand the molecular events mediating these adaptive responses, we have isolated and sequenced 2,102 expressed sequence tags (ESTs) from cDNA libraries prepared with RNA isolated at different stages of proteoid root development. Determination of overlapping regions revealed 322 contigs (redundant copy transcripts) and 1,126 singletons (single-copy transcripts) that compile to a total of 1,448 unique genes (unigenes). Nylon filter arrays with these 2,102 ESTs from proteoid roots were performed to evaluate global aspects of gene expression in response to -P stress. ESTs differentially expressed in P-deficient proteoid roots compared with +P and -P normal roots include genes involved in carbon metabolism, secondary metabolism, P scavenging and remobilization, plant hormone metabolism, and signal transduction.

Comparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water deficit

The early post-pollination phase of maize (Zea mays) development is particularly sensitive to water deficit stress. Using cDNA microarray, we studied transcriptional profiles of endosperm and placenta/pedicel tissues in developing maize kernels under water stress. At 9 d after pollination (DAP), placenta/pedicel and endosperm differed considerably in their transcriptional responses. In placenta/pedicel, 79 genes were significantly affected by stress and of these 89% were up-regulated, whereas in endosperm, 56 genes were significantly affected and 82% of these were down-regulated. Only nine of the stress-regulated genes were in common between these tissues. Hierarchical cluster analysis indicated that different sets of genes were regulated in the two tissues. After rewatering at 9 DAP, profiles at 12 DAP suggested that two regulons exist, one for genes responding specifically to concurrent imposition of stress, and another for genes remaining affected after transient stress. In placenta, genes encoding recognized stress tolerance proteins, including heat shock proteins, chaperonins, and major intrinsic proteins, were the largest class of genes regulated, all of which were up-regulated. In contrast, in endosperm, genes in the cell division and growth category represented a large class of down-regulated genes. Several cell wall-degrading enzymes were expressed at lower levels than in controls, suggesting that stress delayed normal advance to programmed cell death in the central endosperm. We suggest that the responsiveness of placenta to whole-plant stress factors (water potential, abscisic acid, and sugar flux) and of endosperm to indirect factors may play key roles in determining the threshold for kernel abortion.

Transcriptome analysis of sulfur depletion in Arabidopsis thaliana: interlacing of biosynthetic pathways provides response specificity

Higher plants assimilate inorganic sulfate into cysteine, which is subsequently converted to methionine, and into a variety of other sulfur-containing organic compounds. To resist sulfur deficiency, plants must demonstrate physiological flexibility: the expression of an extensive set of genes and gene regulators that act in the affected pathways or signalling cascades must be delicately tuned in response to environmental challenges. To elucidate this network of interactions, we have applied an array hybridisation/transcript profiling method to Arabidopsis plants subjected to 6, 10 and 13 days of constitutive and induced sulfur starvation. The temporal expression behaviour of approximately 7200 non-redundant genes was analysed simultaneously. The experiment was designed in a way to identify statistically significant changes of gene expression based on sufficient numbers of repeated hybridisations performed with five uniform pools of plant material. The expression profiles were processed to select differentially expressed genes. Among the 1507 sulfur-responsive clones implicated in this way, 632 genes responded specifically to sulfur deficiency by significant over-expression. The sulfur-responsive genes were grouped according to functional categories or biosynthetic pathways. As expected, genes of the sulfur assimilation pathway were altered in expression. Furthermore, genes involved in flavonoid, auxin, and jasmonate biosynthesis pathways were upregulated in conditions of sulfur deficiency. Based on the correlative analysis of gene expression patterns, we suggest that a complex co-ordination of systematic responses to sulfur depletion is provided via integration of flavonoid, auxin and jasmonate pathway elements. Plait concept for transduction of specificity via the main non-specific signalling stream is proposed.

Overexpression of a plasma membrane aquaporin in transgenic tobacco improves plant vigor under favorable growth conditions but not under drought or salt stress

Most of the symplastic water transport in plants occurs via aquaporins, but the extent to which aquaporins contribute to plant water status under favorable growth conditions and abiotic stress is not clear. To address this issue, we constitutively overexpressed the Arabidopsis plasma membrane aquaporin, PIP1b, in transgenic tobacco plants. Under favorable growth conditions, PIP1b overexpression significantly increased plant growth rate, transpiration rate, stomatal density, and photosynthetic efficiency. By contrast, PIP1b overexpression had no beneficial effect under salt stress, whereas during drought stress it had a negative effect, causing faster wilting. Our results suggest that symplastic water transport via plasma membrane aquaporins represents a limiting factor for plant growth and vigor under favorable conditions and that even fully irrigated plants face limited water transportation. By contrast, enhanced symplastic water transport via plasma membrane aquaporins may not have any beneficial effect under salt stress, and it has a deleterious effect during drought stress.

Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress

To identify genes of potential importance to cold, salt, and drought tolerance, global expression profiling was performed on Arabidopsis plants subjected to stress treatments of 4 degrees C, 100 mM NaCl, or 200 mM mannitol, respectively. RNA samples were collected separately from leaves and roots after 3- and 27-h stress treatments. Profiling was conducted with a GeneChip microarray with probe sets for approximately 8,100 genes. Combined results from all three stresses identified 2,409 genes with a greater than 2-fold change over control. This suggests that about 30% of the transcriptome is sensitive to regulation by common stress conditions. The majority of changes were stimulus specific. At the 3-h time point, less than 5% (118 genes) of the changes were observed as shared by all three stress responses. By 27 h, the number of shared responses was reduced more than 10-fold (< 0.5%), consistent with a progression toward more stimulus-specific responses. Roots and leaves displayed very different changes. For example, less than 14% of the cold-specific changes were shared between root and leaves at both 3 and 27 h. The gene with the largest induction under all three stress treatments was At5g52310 (LTI/COR78), with induction levels in roots greater than 250-fold for cold, 40-fold for mannitol, and 57-fold for NaCl. A stress response was observed for 306 (68%) of the known circadian controlled genes, supporting the hypothesis that an important function of the circadian clock is to "anticipate" predictable stresses such as cold nights. Although these results identify hundreds of potentially important transcriptome changes, the biochemical functions of many stress-regulated genes remain unknown.

OSM1/SYP61: a syntaxin protein in Arabidopsis controls abscisic acid-mediated and non-abscisic acid-mediated responses to abiotic stress

To identify the genetic loci that control salt tolerance in higher plants, a large-scale screen was conducted with a bialaphos marker-based T-DNA insertional collection of Arabidopsis ecotype C24 mutants. One line, osm1 (for osmotic stress-sensitive mutant), exhibited increased sensitivity to both ionic (NaCl) and nonionic (mannitol) osmotic stress in a root-bending assay. The osm1 mutant displayed a more branched root pattern with or without stress and was hypersensitive to inhibition by Na(+), K(+), and Li(+) but not Cs(+). Plants of the osm1 mutant also were more prone to wilting when grown with limited soil moisture compared with wild-type plants. The stomata of osm1 plants were insensitive to both ABA-induced closing and inhibition of opening compared with wild-type plants. The T-DNA insertion appeared in the first exon of an open reading frame on chromosome 1 (F3M18.7, which is the same as AtSYP61). This insertion mutation cosegregated closely with the osm1 phenotype and was the only functional T-DNA in the mutant genome. Expression of the OSM1 gene was disrupted in mutant plants, and abnormal transcripts accumulated. Gene complementation with the native gene from the wild-type genome completely restored the mutant phenotype to the wild type. Analysis of the deduced amino acid sequence of the affected gene revealed that OSM1 is related most closely to mammalian syntaxins 6 and 10, which are members of the SNARE superfamily of proteins required for vesicular/target membrane fusions. Expression of the OSM1 promoter::beta-glucuronidase gene in transformants indicated that OSM1 is expressed in all tissues except hypocotyls and young leaves and is hyperexpressed in epidermal guard cells. Together, our results demonstrate important roles of OSM1/SYP61 in osmotic stress tolerance and in the ABA regulation of stomatal responses.

Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress

To identify genes of potential importance to cold, salt, and drought tolerance, global expression profiling was performed on Arabidopsis plants subjected to stress treatments of 4 degrees C, 100 mM NaCl, or 200 mM mannitol, respectively. RNA samples were collected separately from leaves and roots after 3- and 27-h stress treatments. Profiling was conducted with a GeneChip microarray with probe sets for approximately 8,100 genes. Combined results from all three stresses identified 2,409 genes with a greater than 2-fold change over control. This suggests that about 30% of the transcriptome is sensitive to regulation by common stress conditions. The majority of changes were stimulus specific. At the 3-h time point, less than 5% (118 genes) of the changes were observed as shared by all three stress responses. By 27 h, the number of shared responses was reduced more than 10-fold (< 0.5%), consistent with a progression toward more stimulus-specific responses. Roots and leaves displayed very different changes. For example, less than 14% of the cold-specific changes were shared between root and leaves at both 3 and 27 h. The gene with the largest induction under all three stress treatments was At5g52310 (LTI/COR78), with induction levels in roots greater than 250-fold for cold, 40-fold for mannitol, and 57-fold for NaCl. A stress response was observed for 306 (68%) of the known circadian controlled genes, supporting the hypothesis that an important function of the circadian clock is to "anticipate" predictable stresses such as cold nights. Although these results identify hundreds of potentially important transcriptome changes, the biochemical functions of many stress-regulated genes remain unknown.

Gene expression profiling of Arabidopsis thaliana in compatible plant-aphid interactions

Phloem feeding involves unique biological interactions between the herbivore and its host plant. The economic importance of aphids, whiteflies, and other phloem-feeding insects as pests has prompted research to isolate sources of resistance to piercing-sucking insects in crops. However, little information exists about the molecular nature of plant sensitivity to phloem feeding. Recent discoveries involving elicitation by plant pathogens and chewing insects and limited studies on phloem feeders suggest that aphids are capable of inducing responses in plants broadly similar to those associated with pathogen infection and wounding. Our past work showed that compatible aphid feeding on leaves of Arabidopsis thaliana induces localized changes in levels of transcripts of genes that are also associated with infection, mechanical damage, chewing herbivory, or resource allocation shifts. We used microarray and macroarray gene expression analyses of infested plants to better define the response profile of A. thaliana to M. persicae feeding. The results suggest that genes involved in oxidative stress, calcium-dependent signaling, pathogenesis-related responses, and signaling are key components of this profile in plants infested for 72 or 96 h. The use of plant resistance to aphids in crops will benefit from a better understanding of induced responses. The establishment of links between insect elicitation, plant signaling associated with phloem feeding, and proximal resistance mechanisms is critical to further research progress in this area.

Improvement of drought tolerance in maize: towards the functional validation of the Zm-Asr1 gene and increase of water use efficiency by over-expressing C4-PEPC

Water availability is one of the major limiting factors for plant growth. Maize is particularly sensitive to water stress at reproductive stages with a strong impairment of photosynthesis and grain filling. Here, we describe the use of genetic transformation first to assess the role of a candidate gene Asr1-a putative transcription factor-as an explanation for genetically linked drought tolerance Quantitative Trait Loci (QTLs), and second to modify CO(2) fixation rates in leaves through changes of C(4) phosphoenolpyruvate carboxylase (C(4)-PEPC) activity. Transgenic Asr1 over-expressing lines show an increase in foliar senescence under drought conditions. The highest C(4)-PEPC overexpressing line exhibited an increase (+30%) in intrinsic water use efficiency (WUE) accompanied by a dry weight increase (+20%) under moderate drought conditions. Opposite effects were observed for transgenic plants under-expressing the corresponding proteins. The data presented here indicate the feasibility to increase the level of endogenous biochemical activities related to water economy and/or drought tolerance, and opens a way to develop maize varieties more tolerant to dry growing conditions.

Salt tolerance

Studying salt stress is an important means to the understanding of plant ion homeostasis and osmo-balance. Salt stress research also benefits agriculture because soil salinity significantly limits plant productivity on agricultural lands. Decades of physiological and molecular studies have generated a large body of literature regarding potential salt tolerance determinants. Recent advances in applying molecular genetic analysis and genomics tools in the model plant Arabidopsis thaliana are shading light on the molecular nature of salt tolerance effectors and regulatory pathways.

Does proline accumulation play an active role in stress-induced growth reduction?

An interesting observation, reported for transgenic plants that have been engineered to overproduce osmolytes, is that they often exhibit impaired growth in the absence of stress. As growth reduction and accumulation of osmolytes both typically result from adaptation, we hypothesized that growth reduction may actually result from osmolyte accumulation. To examine this possibility more closely, intracellular proline level was manipulated by expressing mutated derivatives of tomPRO2 (a Delta(1)-pyrroline-5-carboxylate synthetase, P5CS, from tomato) in Saccharomyces cerevisiae. This was done in the presence and absence of a functional proline oxidase, followed by selection and screening for increased accumulation of proline in the absence of any stress. Here we show, in support of our hypothesis, that the level of proline accumulation and the amount of growth are inversely correlated in cells grown under normal osmotic conditions. In addition, the intracellular concentration of proline also resulted in increases in ploidy level, vacuolation and altered accumulation of several different transcripts related to cell division and gene expression control. Because these cellular modifications are common responses to salt stress in both yeast and plants, we propose that proline and other osmolytes may act as a signaling/regulatory molecule able to activate multiple responses that are part of the adaptation process. As in previous studies with transgenic plants that overaccumulate osmolytes, we observed some increase in relative growth of proline-overaccumulating cells in mild hyperosmotic stress.

The role of aquaporins in root water uptake

The capacity of roots to take up water is determined in part by the resistance of living tissues to radial water flow. Both the apoplastic and cell-to-cell paths mediate water transport in these tissues but the contribution of cell membranes to the latter path has long been difficult to estimate. Aquaporins are water channel proteins that are expressed in various membrane compartments of plant cells, including the plasma and vacuolar membranes. Plant aquaporins are encoded by a large multigene family, with 35 members in Arabidopsis thaliana, and many of these aquaporins show a cell-specific expression pattern in the root. Mercury acts as an efficient blocker of most aquaporins and has been used to demonstrate the significant contribution of water channels to overall root water transport. Aquaporin-rich membranes may be needed to facilitate intense water flow across root tissues and may represent critical points where an efficient and spatially restricted control of water uptake can be exerted. Roots, in particular, show a remarkable capacity to alter their water permeability over the short term (i.e. in a few hours to less than 2-3 d) in response to many stimuli, such as day/night cycles, nutrient deficiency or stress. Recent data suggest that these rapid changes can be mostly accounted for by changes in cell membrane permeability and are mediated by aquaporins. Although the processes that allow perception of environmental changes by root cells and subsequent aquaporin regulation are nearly unknown, the study of root aquaporins provides an interesting model to understand the regulation of water transport in plants and sheds light on the basic mechanisms of water uptake by roots.

Expression of mangrove allene oxide cyclase enhances salt tolerance in Escherichia coli, yeast, and tobacco cells

To analyze the mechanisms of salt tolerance in the mangrove plant, Bruguiera sexangula, functional screening for cDNAs encoding proteins essential for salt tolerance was performed using Escherichia coli as the host organism. A transformant expressing a protein homologous to Lycopersicon (tomato) allene oxide cyclase (AOC) displayed enhanced salt tolerance. However, this unusual trait is not conferred by Lycopersicon AOC or its Arabidopsis homolog. Analysis of the functional region revealed a sequence of only 70 amino acids, which contains an unusual sequence that is essential for the salt-tolerant phenotype. On the basis of its unusual function, the mangrove AOC homolog is designated "mangrin". Furthermore, expression of mangrin driven by the GAL1 promoter and the 35S cauliflower mosaic virus (CaMV) promoter in Saccharomyces cerevisiae and tobacco cell lines, respectively, also gave rise to enhanced salt tolerance. Mangrin transcripts increased in cultured B. sexangula cells in response to salt stress. We propose that mangrin plays an important role in the salt-tolerance mechanism of B. sexangula, and that the biosynthesis of mangrin might be an effective means of enhancing salt tolerance in higher plants.

Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray

Full-length cDNAs are essential for functional analysis of plant genes in the post-sequencing era of the Arabidopsis genome. Recently, cDNA microarray analysis has been developed for quantitative analysis of global and simultaneous analysis of expression profiles. We have prepared a full-length cDNA microarray containing approximately 7000 independent, full-length cDNA groups to analyse the expression profiles of genes under drought, cold (low temperature) and high-salinity stress conditions over time. The transcripts of 53, 277 and 194 genes increased after cold, drought and high-salinity treatments, respectively, more than fivefold compared with the control genes. We also identified many highly drought-, cold- or high-salinity- stress-inducible genes. However, we observed strong relationships in the expression of these stress-responsive genes based on Venn diagram analysis, and found 22 stress-inducible genes that responded to all three stresses. Several gene groups showing different expression profiles were identified by analysis of their expression patterns during stress-responsive gene induction. The cold-inducible genes were classified into at least two gene groups from their expression profiles. DREB1A was included in a group whose expression peaked at 2 h after cold treatment. Among the drought, cold or high-salinity stress-inducible genes identified, we found 40 transcription factor genes (corresponding to approximately 11% of all stress-inducible genes identified), suggesting that various transcriptional regulatory mechanisms function in the drought, cold or high-salinity stress signal transduction pathways.

A custom microarray analysis of gene expression during programmed cell death in Arabidopsis thaliana

Programmed cell death (PCD) is a form of cellular suicide requiring active gene expression, and occurs in both animals and plants. While the cascade of events and the genes that control PCD have been extensively studied in animals, we remain largely ignorant about the similar process in plant cells. Many of the key proteins of animal cell death such as the Bcl-2 family and the caspase family of proteases do not appear to be conserved in plants, suggesting that plants may employ unique mechanisms to execute PCD. To identify genetic elements of PCD in plants, we monitored changes in transcript levels of approximately 100 selected genes during cell death in an Arabidopsis cell suspension culture using a cDNA microarray. PCD was induced in the cell cultures by two independent means (heat treatment or by allowing the cultures to senesce) to allow the distinction to be drawn between changes in gene expression that are related to PCD and those that are specific to a particular treatment. We argue that genes whose expression is altered during PCD induced by two different means may be generally involved in all types of PCD. We show that certain oxidative stress-related genes, including CSD1, CSD3, and GPX, in addition to cysteine proteinases, some transcription factors, and HR-related genes may serve as markers of a core plant cell death programme. Additionally we observe a down-regulation of the mitochondrial adenine nucleotide transporter and suggest that this may be an early event in the execution of plant PCD.

Annotation and BAC/PAC localization of nonredundant ESTs from drought-stressed seedlings of an indica rice

To decipher the genes associated with drought stress response and to identify novel genes in rice, we utilized 1540 high-quality expressed sequence tags (ESTs) for functional annotation and mapping to rice genomic sequences. These ESTs were generated earlier by 3'-end single-pass sequencing of 2000 cDNA clones from normalized cDNA libraries constructed form drought-stressed seedlings of an indica rice. A rice UniGene set of 1025 transcripts was constructed from this collection through the BLASTN algorithm. Putative functions of 559 nonredundant ESTs were identified by BLAST similarity search against public databases. Putative functions were assigned at a stringency E value of 10(-6) in BLASTN and BLASTX algorithms. To understand the gene structure and function further, we have utilized the publicly available finished and unfinished rice BAC/PAC (BAC, bacterial artificial chromosome; PAC, P1 artificial chromosome) sequences for similarity search using the BLASTN algorithm. Further, 603 nonredundant ESTs have been mapped to BAC/PAC clones. BAC clones were assigned by a homology of above 95% identity along 90% of EST sequence length in the aligned region. In all, 700 ESTs showed rice EST hits in GenBank. Of the 325 novel ESTs, 128 were localized to BAC clones. In addition, 127 ESTs with identified putative functions but with no homology in IRGSP (International Rice Genome Sequencing Program) BAC/PAC sequences were mapped to the Chinese WGS (whole genome shotgun contigs) draft sequence of the rice genome. Functional annotation uncovered about a hundred candidate ESTs associated with abiotic stress in rice and Arabidopsis that were previously reported based on microarray analysis and other studies. This study is a major effort in identifying genes associated with drought stress response and will serve as a resource to rice geneticists and molecular biologists.

The advantages of cDNA microarray as an effective tool for identification of reproductive organ-specific genes in a model legume, Lotus japonicus

To understand the molecular mechanisms intrinsic to reproductive organ development a cDNA microarray, fabricated from flower bud cDNA clones, was used to isolate genes, which are specifically expressed during the development of the anther and pistil in Lotus japonicus. Cluster analysis of the microarray data revealed 21 and 111 independent cDNA groups, which were specifically expressed in immature and mature anthers, respectively. RT-PCR was performed to provide a direct assessment of the accuracy and reproducibility of our approach. Confirmation of our results suggests that cDNA microarray technology is an effective tool for identification of novel reproductive organ-specific genes.

Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barley

Responses to drought and salinity in barley (Hordeum vulgare L. cv. Tokak) were monitored by microarray hybridization of 1463 DNA elements derived from cDNA libraries of 6 and 10 h drought-stressed plants. Functional identities indicated that many cDNAs in these libraries were associated with drought stress. About 38% of the transcripts were novel and functionally unknown. Hybridization experiments were analyzed for drought- and salinity-regulated sequences, with significant changes defined as a deviation from the control exceeding 2.5-fold. Responses of transcripts showed stress-dependent expression patterns and time courses. Nearly 15% of all transcripts were either up- or down-regulated under drought stress, while NaCl led to a change in 5% of the transcripts (24 h, 150 mM NaCl). Transcripts that showed significant up-regulation under drought stress are exemplified by jasmonate-responsive, metallothionein-like, late-embryogenesis-abundant (LEA) and ABA-responsive proteins. Most drastic down-regulation in a category was observed for photosynthesis-related functions. Up-regulation under both drought and salt stress was restricted to ESTs for metallothionein-like and LEA proteins, while increases in ubiquitin-related transcripts characterized salt stress. A number of functionally unknown transcripts from cDNA libraries of drought-stressed plants showed up-regulation by drought but down-regulation by salt stress, documenting how precisely transcript profiles report different growth conditions and environments.

Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization

Assembly of 73,000 expressed sequence tags (ESTs) representing multiple organs and developmental stages of maize (Zea mays) identified approximately 22,000 tentative unique genes (TUGs) at the criterion of 95% identity. Based on sequence similarity, overlap between any two of nine libraries with more than 3,000 ESTs ranged from 4% to 20% of the constituent TUGs. The most abundant ESTs were recovered from only one or a minority of the libraries, and only 26 EST contigs had members from all nine EST sets (presumably representing ubiquitously expressed genes). For several examples, ESTs for different members of gene families were detected in distinct organs. To study this further, two types of micro-array slides were fabricated, one containing 5,534 ESTs from 10- to 14-d-old endosperm, and the other 4,844 ESTs from immature ear, estimated to represent about 2,800 and 2,500 unique genes, respectively. Each array type was hybridized with fluorescent cDNA targets prepared from endosperm and immature ear poly(A(+)) RNA. Although the 10- to 14-d-old postpollination endosperm TUGs showed only 12% overlap with immature ear TUGs, endosperm target hybridized with 94% of the ear TUGs, and ear target hybridized with 57% of the endosperm TUGs. Incomplete EST sampling of low-abundance transcripts contributes to an underestimate of shared gene expression profiles. Reassembly of ESTs at the criterion of 90% identity suggests how cross hybridization among gene family members can overestimate the overlap in genes expressed in micro-array hybridization experiments.

Novel genes are enriched in normalized cDNA libraries from drought-stressed seedlings of rice (Oryza sativa L. subsp. indica cv. Nagina 22)

We have utilized an efficient method to enrich cDNA libraries for novel genes and genes responsive to drought stress in rice (Oryza sativa L. subsp. indica). We separately constructed standard and normalized cDNA libraries from leaf tissue of rice seedlings grown under controlled drought stress. Sequencing from the 3' end was performed on 1000 clones from the normalized leaf cDNA library and 200 clones from the standard leaf cDNA library. For the first 200 clones, the clone redundancy in the non-normalized library was about 10%, compared with 3.5% in the normalized cDNA library. Comparison of these cDNAs with the sequences in public databases revealed that 28.2% of the expressed sequence tags (ESTs) from the normalized library were novel. Clones from the standard and normalized leaf libraries and a root library uncovered numerous cDNAs that are highly homologous to known drought-responsive genes including those that encode metallothioneins, late embroyonic abundant (LEA) proteins, heat-shock proteins, cytochrome P450 enzymes, catalases, peroxidases, kinases, phosphatases, and transcription factors.

Comparative physiology of salt and water stress

Plant responses to salt and water stress have much in common. Salinity reduces the ability of plants to take up water, and this quickly causes reductions in growth rate, along with a suite of metabolic changes identical to those caused by water stress. The initial reduction in shoot growth is probably due to hormonal signals generated by the roots. There may be salt-specific effects that later have an impact on growth; if excessive amounts of salt enter the plant, salt will eventually rise to toxic levels in the older transpiring leaves, causing premature senescence, and reduce the photosynthetic leaf area of the plant to a level that cannot sustain growth. These effects take time to develop. Salt-tolerant plants differ from salt-sensitive ones in having a low rate of Na+ and Cl-- transport to leaves, and the ability to compartmentalize these ions in vacuoles to prevent their build-up in cytoplasm or cell walls and thus avoid salt toxicity. In order to understand the processes that give rise to tolerance of salt, as distinct from tolerance of osmotic stress, and to identify genes that control the transport of salt across membranes, it is important to avoid treatments that induce cell plasmolysis, and to design experiments that distinguish between tolerance of salt and tolerance of water stress.

Salt and drought stress signal transduction in plants

Salt and drought stress signal transduction consists of ionic and osmotic homeostasis signaling pathways, detoxification (i.e., damage control and repair) response pathways, and pathways for growth regulation. The ionic aspect of salt stress is signaled via the SOS pathway where a calcium-responsive SOS3-SOS2 protein kinase complex controls the expression and activity of ion transporters such as SOS1. Osmotic stress activates several protein kinases including mitogen-activated kinases, which may mediate osmotic homeostasis and/or detoxification responses. A number of phospholipid systems are activated by osmotic stress, generating a diverse array of messenger molecules, some of which may function upstream of the osmotic stress-activated protein kinases. Abscisic acid biosynthesis is regulated by osmotic stress at multiple steps. Both ABA-dependent and -independent osmotic stress signaling first modify constitutively expressed transcription factors, leading to the expression of early response transcriptional activators, which then activate downstream stress tolerance effector genes.

Salt and drought stress signal transduction in plants

Salt and drought stress signal transduction consists of ionic and osmotic homeostasis signaling pathways, detoxification (i.e., damage control and repair) response pathways, and pathways for growth regulation. The ionic aspect of salt stress is signaled via the SOS pathway where a calcium-responsive SOS3-SOS2 protein kinase complex controls the expression and activity of ion transporters such as SOS1. Osmotic stress activates several protein kinases including mitogen-activated kinases, which may mediate osmotic homeostasis and/or detoxification responses. A number of phospholipid systems are activated by osmotic stress, generating a diverse array of messenger molecules, some of which may function upstream of the osmotic stress-activated protein kinases. Abscisic acid biosynthesis is regulated by osmotic stress at multiple steps. Both ABA-dependent and -independent osmotic stress signaling first modify constitutively expressed transcription factors, leading to the expression of early response transcriptional activators, which then activate downstream stress tolerance effector genes.

Comprehensive gene expression analysis by transcript profiling

After the completion of the genomic sequence of Arabidopsis thaliana, it is now a priority to identify all the genes, their patterns of expression and functions. Transcript profiling is playing a substantial role in annotating and determining gene functions, having advanced from one-gene-at-a-time methods to technologies that provide a holistic view of the genome. In this review, comprehensive transcript profiling methodologies are described, including two that are used extensively by the authors, cDNA-AFLP and cDNA microarraying. Both these technologies illustrate the requirement to integrate molecular biology, automation, LIMS and data analysis. With so much uncharted territory in the Arabidopsis genome, and the desire to tackle complex biological traits, such integrated systems will provide a rich source of data for the correlative, functional annotation of genes.

DNA microarrays for functional plant genomics

DNA microarray technology is a key element in today's functional genomics toolbox. The power of the method lies in miniaturization, automation and parallelism permitting large-scale and genome-wide acquisition of quantitative biological information from multiple samples. DNA microarrays are currently fabricated and assayed by two main approaches involving either in situ synthesis of oligonucleotides ('oligonucleotide microarrays') or deposition of pre-synthesized DNA fragments ('cDNA microarrays') on solid surfaces. To date, the main applications of microarrays are in comprehensive, simultaneous gene expression monitoring and in DNA variation analyses for the identification and genotyping of mutations and polymorphisms. Already at a relatively early stage of its application in plant science, microarrays are being utilized to examine a range of biological issues including the circadian clock, plant defence, environmental stress responses, fruit ripening, phytochrome A signalling, seed development and nitrate assimilation. Novel insights are obtained into the molecular mechanisms co-ordinating metabolic pathways, regulatory and signalling networks. Exciting new information will be gained in the years to come not only from genome-wide expression analyses on a few model plant species, but also from extensive studies of less thoroughly studied species on a more limited scale. The value of microarray technology to our understanding of living processes will depend both on the amount of data to be generated and on its clever exploration and integration with other biological knowledge arising from complementary functional genomics tools for 'profiling' the genome, proteome, metabolome and phenome.

Transcript expression in Saccharomyces cerevisiae at high salinity

Transcript expression of Saccharomyces cerevisiae at high salinity was determined by microarray analysis of 6144 open reading frames (ORFs). From cells grown in 1 m NaCl for 10, 30, and 90 min, changes in transcript abundance >2-fold were classified. Salinity-induced ORFs increased over time: 107 (10 min), 243 (30 min), and 354 (90 min). Up-regulated, functionally unknown ORFs increased from 17 to 149 over this period. Expression patterns were similar early, with 67% of up-regulated transcripts after 10 min identical to those at 30 min. The expression profile after 90 min revealed different up-regulated transcripts (identities of 13% and 22%, respectively). Nucleotide and amino acid metabolism exemplified the earliest responses to salinity, followed by ORFs related to intracellular transport, protein synthesis, and destination. Transcripts related to energy production were up-regulated throughout the time course with respiration-associated transcripts strongly induced at 30 min. Highly expressed at 90 min were known salinity stress-induced genes, detoxification-related responses, transporters of the major facilitator superfamily, metabolism of energy reserves, nitrogen and sulfur compounds, and lipid, fatty acid/isoprenoid biosynthesis. We chose severe stress conditions to monitor responses in essential biochemical mechanisms. In the mutant, Deltagpd1/gpd2, lacking glycerol biosynthesis, the stress response was magnified with a partially different set of up-regulated ORFs.

Expression of a Late Embryogenesis Abundant Protein Gene, HVA1, from Barley Confers Tolerance to Water Deficit and Salt Stress in Transgenic Rice

A late embryogenesis abundant (LEA) protein gene, HVA1, from barley (Hordeum vulgare L.) was introduced into rice suspension cells using the Biolistic-mediated transformation method, and a large number of independent transgenic rice (Oryza sativa L.) plants were generated. Expression of the barley HVA1 gene regulated by the rice actin 1 gene promoter led to high-level, constitutive accumulation of the HVA1 protein in both leaves and roots of transgenic rice plants. Second-generation transgenic rice plants showed significantly increased tolerance to water deficit and salinity. Transgenic rice plants maintained higher growth rates than nontransformed control plants under stress conditions. The increased tolerance was also reflected by delayed development of damage symptoms caused by stress and by improved recovery upon the removal of stress conditions. We also found that the extent of increased stress tolerance correlated with the level of the HVA1 protein accumulated in the transgenic rice plants. Using a transgenic approach, this study provides direct evidence supporting the hypothesis that LEA proteins play an important role in the protection of plants under water-or salt-stress conditions. Thus, LEA genes hold considerable potential for use as molecular tools for genetic crop improvement toward stress tolerance.