Characterization of a rice gene showing organ-specific expression in response to salt stress and drought

Technical advance: transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression (SAGE)

Serial analysis of gene expression (SAGE) was applied for profiling expressed genes in rice seedlings. In the SAGE method, a 9-11 bp fragment (tag) represents each transcript, and frequency of a tag in the sample directly reflects the abundance of the respective mRNA. We studied 10 122 tags derived from 5921 expressed genes in rice (Oryza sativa L.) seedlings, among which only 1367 genes (23.1%) matched the rice cDNA or EST sequences in the DNA database. SAGE showed that most of the highly expressed genes in rice seedlings belong to the category of housekeeping genes (genes encoding ribosomal proteins or proteins responsible for metabolism and cell structure). Unexpectedly, the most highly expressed gene in rice seedlings was a metallothionein (MT) gene, and together with three other messages for MT, it accounts for 2.7% of total gene expression. To our knowledge, this is the first quantitative study of global gene expression in a higher plant. We further applied the SAGE technique to identify differentially expressed genes between anaerobically treated and untreated rice seedlings. Additionally, we show that a longer cDNA fragment can be easily recovered by PCR using the SAGE tag sequence as a primer, thereby facilitating the analysis of unknown genes identified by tag sequence in SAGE. In combination with micro-array analysis, SAGE should serve as a highly efficient tool for the identification and isolation of differentially expressed genes in plants.

Transgenic overexpression of the transcription factor alfin1 enhances expression of the endogenous MsPRP2 gene in alfalfa and improves salinity tolerance of the plants

Alfin1 cDNA encodes a putative transcription factor associated with NaCl tolerance in alfalfa (Medicago sativa L.). The recombinant protein binds DNA in a sequence-specific manner, including promoter fragments of the NaCl-inducible gene MsPRP2. Alfin1 function was tested in transgenic alfalfa under the control of the 35S promoter in the sense and antisense orientations with the endogenous MsPRP2 as a reporter gene. Calli overexpressing Alfin1 were more resistant to growth inhibition by 171 mM NaCl than vector-transformed controls, whereas calli expressing Alfin1 in the antisense orientation were more sensitive to NaCl inhibition. Transgenic plants overexpressing Alfin1 in the sense orientation grew well. In contrast, the antisense transgenic plants grew poorly in soil, demonstrating that Alfin1 expression is essential for normal plant development. Transgenic calli and plant roots overexpressing Alfin1 showed enhanced levels of endogenous MsPRP2 mRNA accumulation. However, MsPRP2 mRNA accumulation was also regulated in a tissue-specific manner, as shown in leaves of transgenic plants overexpressing Alfin1. These results suggest that Alfin1 acts as a transcriptional regulator in plants and regulates MsPRP2 expression in alfalfa. Alfin1 overexpressing transgenic plants showed salinity tolerance comparable to one of our NaCl-tolerant plants, indicating that Alfin1 also functions in gene regulation in NaCl tolerance.

Drought-induced responses in plant cells

Plants subjected to water stress undergo numerous physiological and metabolic changes. A general decrease in photosynthetic rate is among the most common responses. This is due to a programmed process involving the closure of stomata and reduction in the activity of photosynthetic enzymes. The plant hormone abscisic acid plays an important role in this process. Accumulation of compatible solutes, during water stress, is thought to be an adaptive response which has been developed by some plant species. Engineering the genes involved in the synthesis of these compounds, into nonaccumulating plants, has demonstrated promising results for genetic improvement of drought tolerance. Drought stress induces alteration of gene expression. A large number of genes which are upregulated by water stress have been isolated and characterized. Proteins encoded by some of these genes share several characteristics. The biochemical role of most of these gene products is unknown, but potential adaptive functions have been suggested. Abscisic acid is involved in the regulation of some of these genes.

Antagonistic effects of abscisic acid and jasmonates on salt stress-inducible transcripts in rice roots

Abscisic acid (ABA) and jasmonates have been implicated in responses to water deficit and wounding. We compared the molecular and physiological effects of jasmonic acid (JA) (< or = 10 microM), ABA, and salt stress in roots of rice. JA markedly induced a cationic peroxidase, two novel 32- and 28-kD proteins, acidic PR-1 and PR-10 pathogenesis-related proteins, and the salt stress-responsive SalT protein in roots. Most JA-responsive proteins (JIPs) from roots also accumulated when plants were subjected to salt stress. None of the JIPs accumulated when plants were treated with ABA. JA did not induce an ABA-responsive group 3 late-embryogenesis abundant (LEA) protein. Salt stress and ABA but not JA induced oslea3 transcript accumulation. By contrast, JA, ABA, and salt stress induced transcript accumulation of salT and osdrr, which encodes a rice PR-10 protein. However, ABA also negatively affected salT transcript accumulation, whereas JA negatively affected ABA-induced oslea3 transcript levels. Endogenous root ABA and methyl jasmonate levels showed a differential increase with the dose and the duration of salt stress. The results indicate that ABA and jasmonates antagonistically regulated the expression of salt stress-inducible proteins associated with water deficit or defense responses.

Zrp2: a novel maize gene whose mRNA accumulates in the root cortex and mature stems

A near full-length cDNA clone (pZRP2) was isolated from a cDNA library constructed from maize root mRNAs. The predicted polypeptide has a calculated molecular mass of 66,975 Da, is largely hydrophilic, and contains 26 repeats of a motif the consensus sequence of which is RKATTSYG[S][D/E][D/E][D/E][D/E][P]. The function of the putative protein remains to be elucidated. The ZRP2 mRNA accumulates to the highest levels in young roots, and is also present in mature roots and stems of maize. Further analysis of young roots indicates that the lowest level of ZRP2 mRNA is near the root tip, with relatively high levels throughout the remainder of the root. In situ hybridization reveals that ZRP2 mRNA accumulates predominantly in the cortical parenchyma cells of the root. In vitro nuclear run-on transcription experiments indicate a dramatically higher level of zrp2 gene transcription in 3-day old roots than in 5-day old leaves. A zrp2 genomic clone, which includes the transcribed region and 4.7 kb of upstream sequence, was isolated and characterized.

Effects of Osmoprotectants upon NaCl Stress in Rice

Plants accumulate a number of osmoprotective substances in response to NaCl stress, one of them being proline (Pro). While characterizing some of the changes in solute accumulation in NaCl-stressed rice (Oryza sativa L.), we identified several other potential osmoprotectants. One such substance, trehalose, begins to accumulate in small amounts in roots after 3 d. We performed a series of experiments to compare the effects of Pro and trehalose on ion accumulation to determine whether the two chemicals protect the same physiological processes. We found that Pro either has no effect or, in some cases, exasperates the effect of NaCl on growth inhibition, chlorophyll loss, and induction of a highly sensitive marker for plant stress, the osmotically regulated salT gene. By contrast, low to moderate concentrations of trehalose reduce Na+ accumulation, salT expression, and growth inhibition. Somewhat higher concentrations (10 mM) prevent NaCl-induced loss of chlorophyll in blades, preserve root integrity, and enhance growth. The results of this study indicate that during osmotic stress trehalose or carbohydrates might be more important for rice than Pro.

Transient expression of multiple genes in salinity-stressed young seedlings of rice (Oryza sativa L.) cv. bura rata

To date only about 15 abundantly expressed osmoresponsive genes/proteins have been described in rice cultivars. Using in vivo radiolabeling followed by two-dimensional electrophoresis and autoradiography, a record number of at least 35 salinity stress-induced polypeptides (14-90 kDa) and 17 salt stress-repressed polypeptides were detected in a halotolerant Indica rice cultivar Bura Rata. These include > 20 hitherto unreported rice polypeptides that exhibited a low abundance, short-term expression during NaCl stress. Prolonged exposure to NaCl decreased their synthesis. These findings have widened the scope of further investigations into new osmoresponsive genes, especially those with possibly transient regulatory functions in rice halotolerance.

A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes

Several recent reports indicate that mobile elements are frequently found in and flanking many wild-type plant genes. To determine the extent of this association, we performed computer-based systematic searches to identify mobile elements in the genes of two "model" plants, Oryza sativa (domesticated rice) and Arabidopsis thaliana. Whereas 32 common sequences belonging to nine putative mobile element families were found in the noncoding regions of rice genes, none were found in Arabidopsis genes. Five of the nine families (Gaijin, Castaway, Ditto, Wanderer, and Explorer) are first described in this report, while the other four were described previously (Tourist, Stowaway, p-SINE1, and Amy/LTP). Sequence similarity, structural similarity, and documentation of past mobility strongly suggests that many of the rice common sequences are bona fide mobile elements. Members of four of the new rice mobile element families are similar in some respects to members of the previously identified inverted-repeat element families, Tourist and Stowaway. Together these elements are the most prevalent type of transposons found in the rice genes surveyed and form a unique collection of inverted-repeat transposons we refer to as miniature inverted-repeat transposable elements or MITEs. The sequence and structure of MITEs are clearly distinct from short or long interspersed nuclear elements (SINEs or LINEs), the most common transposable elements associated with mammalian nuclear genes. Mobile elements, therefore, are associated with both animal and plant genes, but the identity of these elements is strikingly different.

THE MOLECULAR BASIS OF DEHYDRATION TOLERANCE IN PLANTS

Molecular studies of drought stress in plants use a variety of strategies and include different species subjected to a wide range of water deficits. Initial research has by necessity been largely descriptive, and relevant genes have been identified either by reference to physiological evidence or by differential screening. A large number of genes with a potential role in drought tolerance have been described, and major themes in the molecular response have been established. Particular areas of importance are sugar metabolism and late-embryogenesis-abundant (LEA) proteins. Studies have begun to examine mechanisms that control the gene expression, and putative regulatory pathways have been established. Recent attempts to understand gene function have utilized transgenic plants. These efforts are of clear agronomic importance.

Two-dimensional electrophoresis of plant proteins and standardization of gel patterns

Proteins of two plants, Arabidopsis thaliana and rice (Oryza sativa) were subjected to two-dimensional electrophoresis analysis with two modifications: (i) comigration of external standard marker proteins with resultant horizontal and vertical stripes in the gel, and (ii) deblocking with a vapor of aqueous heptafluorobutyric acid for N-acetylserine. Approximately 5000 protein spots were separated from both the five tissues of Arabidopsis and the nine tissues of rice. Over one hundred spots were electroblotted for N-terminal sequencing. Among the newly sequenced proteins, 62 were from Arabidopsis and 51 from rice.

Benzothiadiazole, a novel class of inducers of systemic acquired resistance, activates gene expression and disease resistance in wheat

Systemic acquired resistance is an important component of the disease resistance repertoire of plants. In this study, a novel synthetic chemical, benzo(1,2,3)thiadiazole-7-carbothioic acid S-methyl ester (BTH), was shown to induce acquired resistance in wheat. BTH protected wheat systemically against powdery mildew infection by affecting multiple steps in the life cycle of the pathogen. The onset of resistance was accompanied by the induction of a number of newly described wheat chemically induced (WCI) genes, including genes encoding a lipoxygenase and a sulfur-rich protein. With respect to both timing and effectiveness, a tight correlation existed between the onset of resistance and the induction of the WCI genes. Compared with other plant activators, such as 2,6-dichloroisonicotinic acid and salicylic acid, BTH was the most potent inducer of both resistance and gene induction. BTH is being developed commercially as a novel type of plant protection compound that works by inducing the plant's inherent disease resistance mechanisms.

The SAL1 gene of Arabidopsis, encoding an enzyme with 3'(2'),5'-bisphosphate nucleotidase and inositol polyphosphate 1-phosphatase activities, increases salt tolerance in yeast

A cDNA library in a yeast expression vector was prepared from roots of Arabidopsis exposed to salt and was used to select Li(+)-tolerant yeast transformants. The cDNA SAL1 isolated from one of these transformants encodes a polypeptide of 353 amino acid residues. This protein is homologous to the HAL2 and CysQ phosphatases of yeast and Escherichia coli, respectively. Partial cDNA sequences in the data bases indicate that rice produces a phosphatase highly homologous to SAL1 and that a second gene homologous to SAL1 exists in Arabidopsis. The SAL1 protein expressed in E. coli showed 3'(2'),5'-bisphosphate nucleotidase and inositol polyphosphate 1-phosphatase activities. In yeast, SAL1 restored the ability of a hal2/met22 mutant to grow on sulfate as a sole sulfur source, increased the intracellular Li+ tolerance, and modified Na+ and Li+ effluxes. We propose that the product of SAL1 participates in the sulfur assimilation pathway as well as in the phosphoinositide signaling pathway and that changes in the latter may affect Na+ and Li+ fluxes.

The SAL1 gene of Arabidopsis, encoding an enzyme with 3'(2'),5'-bisphosphate nucleotidase and inositol polyphosphate 1-phosphatase activities, increases salt tolerance in yeast

A cDNA library in a yeast expression vector was prepared from roots of Arabidopsis exposed to salt and was used to select Li(+)-tolerant yeast transformants. The cDNA SAL1 isolated from one of these transformants encodes a polypeptide of 353 amino acid residues. This protein is homologous to the HAL2 and CysQ phosphatases of yeast and Escherichia coli, respectively. Partial cDNA sequences in the data bases indicate that rice produces a phosphatase highly homologous to SAL1 and that a second gene homologous to SAL1 exists in Arabidopsis. The SAL1 protein expressed in E. coli showed 3'(2'),5'-bisphosphate nucleotidase and inositol polyphosphate 1-phosphatase activities. In yeast, SAL1 restored the ability of a hal2/met22 mutant to grow on sulfate as a sole sulfur source, increased the intracellular Li+ tolerance, and modified Na+ and Li+ effluxes. We propose that the product of SAL1 participates in the sulfur assimilation pathway as well as in the phosphoinositide signaling pathway and that changes in the latter may affect Na+ and Li+ fluxes.

The expression of mRNAs for light-stress proteins in barley: inverse relationship of mRNA levels of individual genes within the leaf gradient

Two cDNAs coding for putative light-stress proteins of barley (Hordeum vulgare L.) were cloned and the expression of the corresponding mRNAs analyzed in the barley leaf and compared to that of the well-studied ELIP (early-inducible protein) mRNA. During greening the mRNA for clone HL No. 2, which shows homology to two rice proteins of as yet unknown function, was transiently induced; its level rose more slowly and remained elevated for a longer time than was described for ELIP mRNAs. The mRNA corresponding to clone HL No. 13 was recognized as homologous to subunit P of pea glycine decarboxylase, a nuclear-encoded mitochondrial protein involved in photorespiration. Its mRNA level rose more slowly with cellular development than that of the mRNA for LHC II, the apoprotein of the chlorophyll-a/b-binding protein of PSII. The mRNAs of both novel proteins were induced by high light up to an irradiance of 2000 W.m-2. Their levels remained elevated under high light for up to 9 h, the longest time span examined, while after return to culture light conditions the mRNAs rapidly decayed, each with an individual time course. In green barley leaves the mRNA for clone HL No. 2 was expressed to the highest level in the most basal segment, similar to that of ELIPs, while in contrast the mRNA for subunit P of glycine decarboxylase accumulated to the highest level in the leaf apex where the fully developed cells and mitochondria reside. The latter finding strongly indicates that photorespiration is regulated by high light also at the level of mRNA transcription or mRNA accumulation. In addition, we show that perception of light stress is under the control of cellular development and differentiation.

Jasmonate signalling can be uncoupled from abscisic acid signalling in barley: identification of jasmonate-regulated transcripts which are not induced by abscisic acid

Jasmonate and abscisic acid induce several identical mRNAs and proteins in barley. In order to study whether both hormones act through the same signalling pathway, we identified four transcripts induced by jasmonic acid methylester (JM) in leaf segments of barley (Hordeum vulgare L. cv. Salome). These newly identified transcripts were not induced by abscisic acid within the tested times of 2-72 h. This finding supports the conclusion that jasmonate signalling in barley is independent of abscisic acid, in contrast to the wound-induction signal cascade of proteinase-inhibitor II in tomato and potato. Of the four isolated cDNAs, the putative translation frame of one was homologous to caffeic acid methyltransferase, another was homologous to chalcone synthase, and the C-terminus of the third showed homology to two proteins from rice (a salt-induced protein and a root-specific protein); the last cDNA was not homologous to any sequences in the databases. The new cDNAs will be valuable tools for studying jasmonate signal transduction in barley.

Isolation of differentially expressed cDNA clones from salt-adapted Aspergillus nidulans

Differentially expressed cDNA clones were isolated from salt-adapted Aspergillus nidulans (FGSC #359). Poly (A)+ RNA from adapted mycelia was used to construct a lambda Uni-ZAP cDNA library. The library was screened with mixed subtracted cDNA probes. Three-hundred and fifty-seven positive plaques were isolated in the primary screening. Sixty-two randomly selected plaques were purified and placed into eight different cross-hybridization groups. A representative cDNA from each group was used to study expression under unadapted, salt-adapted and salt-shock conditions. These clones, representing eight different genes, displayed enhanced expression under salt stress. Exploratory nucleotide sequencing was performed, and the predicted amino-acid sequence was compared with known gene sequences in the data-bank. Five of the cDNA clones were identified as a mitochondrial (mt) ATPase beta subunit, a mt ATPase subunit 9, a mt transport protein, a ubiquitin-extension protein and a ribosomal protein. Three cDNA clones could not be identified due to lack of adequate homology with known sequences. These results suggest that at least five genes with known function in cellular processes like ATP generation and protein synthesis, and three other genes of unknown identity, are greatly induced in salt-adapted conditions.

Detection of a highly heterozygous locus in recombinant inbred lines of rice and its possible involvement in heterosis

Forty-seven recombinant inbred (RI) lines derived from a cross between two indica rices, cv 'Phalguna' and the Assam land race ARC 6650, were subjected to restriction fragment length polymorphism (RFLP) analysis using cloned probes defining 150 single-copy loci uniformly dispersed on the 12 chromosomes of rice. Of the probes tested, 47 detected polymorphism between the parents. Heterozygosity was calculated for each line and for each of the polymorphic loci. Average heterozygosity per line was 9.6% but was excessive (>20%) in the 5 lines that seemed to have undergone outcrossing immediately prior to harvest. Average heterozygosity detected by each probe across the 47 RI lines was 9.7%. The majority of probes revealed the low level of heterozygosity (<8%) expected for F5-F6 lines in a species showing about 5% outbreeding. On the other hand, 7 probes exhibited heterozygosity in excess of 15%, while with a eighth probe (RG2 from chromosome 11) heterozygosity varied according to the restriction enzyme employed, ranging from 2% with SaII to 72% with EcoRV. The presence of 34 recombination sites in a segment of the genome as short as 24 kb indicates a strong selection for recombination between two neighbouring loci, one required as homozygous for the 'Phalguna' allele, and the other heterozygous. Since selection was principally for yield advantage over that of the high-yielding parent, 'Phalguna', one or both of these loci may be important for heterosis in this cross. The results also indicate that heterozygosity as measured by RFLP can depend on the particular restriction endonuclease employed.

Identification of sucrose-regulated genes in cultured rice cells using mRNA differential display

In order to get more information about carbon metabolite regulation pathways, cloning and sequence analysis of sucrose-regulated genes from rice-suspension-cultured cells were performed. We used a new method, mRNA differential display, to screen differentially expressed genes under conditions of 3% and no sucrose in the cultured medium. Six candidate clones were identified and sequenced. Clones SI1 and SI2 were repressed by sucrose starvation, while clones SR1, SR2, SR3 and SR4 were induced by sucrose starvation. Nucleotide sequence analysis showed that clone SR2 has 94.8% homology to the salT gene, and clones SI1 and SR3 show 88.3 and 96.9% identity, respectively, to partial cDNA sequences in the GenBank database. The results suggest that mRNA differential display provides an easy and quick way to clone genes involved in the carbon metabolite regulation pathway.

A gene encoding a truncated large subunit of Rubisco is transcribed and salt-inducible in rice

Using the rice salt-tolerant mutant 20 as material, a cDNA library was constructed and two salt-inducible clones, SIR5.5 and SIR8.1, were isolated by differential screening. Homology analysis revealed that the two clones together constituted a chimeric rbcL which encoded a truncated large subunit of Rubisco with 337 amino-acids, plus 64 amino-acids of unknown origin. The expressions of both the normal and the chimeric locus appeared to be developmentally regulated and salt-inducible in shoots of the salt-tolerant mutant 20 and its original variety 77-170. In roots, their expressions were salt-inducible in the salt-tolerant mutant 20 whereas no, or only premature, forms were present in the salt-treated original variety 77-170. Higher concentrations of salt reduced the expressions of both normal rbcL and the chimeric locus. ABA showed no effect on their expression.

Characterization of a rice gene family encoding root-specific proteins

Two cDNA clones (RCc2 and RCc3) corresponding to mRNAs highly expressed only in root tissues of rice (Oryza sativa L.) seedlings were characterized. Respectively, they encode polypeptides of 146 (14.5 kDa) and 133 amino acids (13.4 kDa) that share high (> 70%) sequence similarity with a polypeptide encoded by a cDNA (ZRP3) encoding an mRNA preferentially expressed in young maize roots. Genomic DNA blot analysis revealed that they are members of a small gene family and RCg2, the gene corresponding to RCc2, was isolated. A 1656 bp 5'-upstream sequence of RCg2 was translationally fused to a beta-glucuronidase (GUS) reporter gene and stable introduction of the chimeric construct into rice was confirmed by PCR and genomic DNA blot analyses. Histochemical analysis of transgenic rice plants containing the full-length chimeric gene showed high levels of GUS activity in mature cells and the elongation and maturation zones of primary and secondary roots, and in the root caps, but no GUS activity was detected in root meristematic regions. Surprisingly, high GUS activity was also detected in leaves of the same plants. This raises the possibility that the RCg2 5'-upstream element may not be sufficient for the proper spatial control of root specificity in transgenic rice.

Molecular and physiological responses to abscisic acid and salts in roots of salt-sensitive and salt-tolerant Indica rice varieties

The Indica rice (Oryza sativa L.) varieties Pokkali and Nona Bokra are well-known salt tolerance donors in classical breeding. In an attempt to understand the molecular basis of their tolerance, physiological and gene expression studies were initiated. The effect of abscisic acid (ABA) on total proteins in roots from 12-d-old seedlings of Pokkali, Nona Bokra, and the salt-sensitive cultivar Taichung N1 were analyzed on two-dimensional gels. The abundance of ABA-induced proteins was highest in the most tolerant variety, Pokkali. Three ABA-responsive proteins, present at different levels in roots from tolerant and sensitive varieties, were further characterized by partial amino acid analysis. A novel histidine-rich protein and two types of late embryogenesis abundant (LEA) proteins were identified. Protein immunoblotting revealed that the levels of dehydrins and group 3 LEA proteins were significantly higher in roots from tolerant compared with sensitive varieties. Endogenous ABA levels showed a transient increase in roots exposed to osmotic shock (150 mM NaCl). Peak ABA concentrations were 30-fold higher for Nona Bokra and 6-fold higher for Pokkali compared with Taichung N1. Both the salt-induced endogenous ABA levels and a greater molecular response of root tissue to ABA were associated with the varietal differences in tolerance.

A Salt-Induced 60-Kilodalton Plasma Membrane Protein Plays a Potential Role in the Extreme Halotolerance of the Alga Dunaliella

The halotolerant alga Dunaliella salina grows in saline conditions as varied as 0.5 and 5 M NaCl, maintaining throughout this range a low intracellular ion concentration. To discover factors potentially involved in ionic homeostasis, we grew cells in media with different salinities or osmolarities and compared their protein profiles. The comparisons indicated that the amount of a 60-kD protein, p60, greatly increased with an increase in salinity and was moderately enhanced when NaCl was substituted with iso-osmotic glycerol. Cells transferred from low to high NaCl or from high glycerol to iso-osmotic NaCl media transiently ceased to grow, and resumption of growth coincided approximately with an increase in p60. The protein, extracted from a plasma membrane fraction, was purified to homogeneity. Anti-p60 antibodies cross-reacted with a 60-kD protein in Dunaliella bardawil. Immunoelectron microscopy of D. salina cell sections indicated that p60 was exclusively located in the plasma membrane. Its induction by salt, the correlation between its accumulation and growth resumption in high concentrations of salt, and its plasma membrane localization suggest the possibility that p60 could play a role in ionic homeostasis in conditions of high salinity, although different types of function could also be considered.

Separation and characterization of rice proteins

Rice proteins from nine tissues and one organelle (leaf, chloroplast, stem, root, germ, dark germinated seedling, seed, bran, chaff and callus) were isolated and then separated by two-dimensional gel electrophoresis (2-DE). The protein spots were characterized according to molecular weight, isoelectric point and partial amino-terminal sequence. Electrophoresis was carried out by isoelectric focusing (IEF), nonequilibrium pH gradient electrophoresis (NEPHGE) and immobilized pH gradient (IPG) in the first dimension, and by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the second dimension. With the aid of nine marker proteins, the patterns of IEF, NEPHGE and IPG 2-DE gels were graphically combined by computer into a single synthetic image for each tissue, respectively, and these images for the nine tissues and one organelle were again combined into a single 2-DE image for the integrated rice protein spots. The rice 2-DE gel image resolved 4892 proteins. About 3% of the spots are characterized by amino-terminal sequencing.

Characterization of the Early Stages of Genetic Salt-Stress Responses in Salt-Tolerant Lophopyrum elongatum, Salt-Sensitive Wheat, and Their Amphiploid

Eleven unique cDNA clones corresponding to genes showing enhanced mRNA accumulation in the early stages of salt stress (early salt stress induced, ESI) were previously isolated. The accumulation of these mRNAs in Lophopyrum elongatum (Host) A. Love, salt-sensitive wheat (Triticum aestivum L.), and their amphiploid is compared. The accumulation of ESI mRNAs was much greater in the L. elongatum roots than in the shoots. Additionally, mRNA accumulation in the roots of the three genotypes showed a biphasic response. The first phase occurred within a few hours after the onset of stress and had a large osmotic shock component, as indicated by induction of the accumulation of these mRNAs by a nonsaline osmoticum. The ion-specific component, however, also played a role. External Ca2+ reduced this response. The second phase was characterized by either constantly elevated mRNA levels or gradually increasing mRNA levels. The same biphasic response was elicited by exogenous abscisic acid (ABA). The response of all mRNAs to ABA closely approximated the response to 250 mM NaCl treatment in all three genotypes. The differences among the three genotypes in response to NaCl and ABA treatments were largely confined to the first phase of the response, in which mRNA levels were highest in L. elongatum and lowest in wheat. The levels of ESI mRNAs in the amphiploid closely approximated levels calculated on the basis of the doses of wheat and L. elongatum genomes in the amphiploid, which indicated an additive contribution of the genomes to early salt stress response in the amphiploid. The inducer of the ESI mRNA accumulation in response to NaCl and other osmotica is produced in the stressed roots and shows only minor, if any, translocation. A putative candidate for this inducer is root ABA.

The cis-regulatory element CCACGTGG is involved in ABA and water-stress responses of the maize gene rab28

The maize gene rab28 has been identified as ABA-inducible in embryos and vegetative tissues. It is also induced by water stress in young leaves. The proximal promoter region contains the conserved cis-acting element CCACGTGG (ABRE) reported for ABA induction in other plant genes. Transient expression assays in rice protoplasts indicate that a 134 bp fragment (-194 to -60 containing the ABRE) fused to a truncated cauliflower mosaic virus promoter (35S) is sufficient to confer ABA-responsiveness upon the GUS reporter gene. Gel retardation experiments indicate that nuclear proteins from tissues in which the rab28 gene is expressed can interact specifically with this 134 bp DNA fragment. Nuclear protein extracts from embryo and water-stressed leaves generate specific complexes of different electrophoretic mobility which are stable in the presence of detergent and high salt. However, by DMS footprinting the same guanine-specific contacts with the ABRE in both the embryo and leaf binding activities were detected. These results indicate that the rab28 promoter sequence CCACGTGG is a functional ABA-responsive element, and suggest that distinct regulatory factors with apparent similar affinity for the ABRE sequence may be involved in the hormone action during embryo development and in vegetative tissues subjected to osmotic stress.

Coordinate Gene Response to Salt Stress in Lophopyrum elongatum

Lophopyrum elongatum is a highly salt-tolerant relative of wheat. A previous study showed that the abundance of a number of mRNA species is enhanced or reduced in the roots of the L. elongatum x Triticum aestivum amphiploid by salt stress. Eleven genes with enhanced expression in the roots of salt-stressed L. elongatum plants have been cloned as cDNAs. The clones were used as probes to characterize temporal expression of these genes in roots after initiation of salt (250 mm NaCl) stress. All 11 genes are induced within 2 h after exposure to 250 mm NaCl and reached peak expression after 6 h. The decline of gene expression distinguished two groups, one in which mRNA concentrations returned to basal levels by 24 h and the other in which this occurred between 3 and 7 d. One of the 11 clones was found to be homologous to a multigene family of abscisic acid-induced genes, rab and dhn, identified in other species. We suggest that the coordinate expression of this large number of genes reflects the existence of a highly specific early response to salt stress. We refer to this response as the "early salt stress response."

Characterization of a Novel Protein Induced by Progressive or Rapid Drought and Salinity in Brassica napus Leaves

Under progressive drought stress, Brassica napus displays differential leaf modifications. The oldest leaves, developed before the onset of water deficit, wilt gradually, whereas the youngest leaves harden. Hardening was distinguished by leaf turgor and bluish wax bloom when the shoot water potential was below -3 MPa and the leaf water saturation deficit was about 60%. This adaptive change was accompanied by modifications in two-dimensional protein profiles. Ten percent of the polypeptides had altered abundance or were unique to drought-stressed plants. Two-dimensional analysis of in vitro translation products did not reveal a general decrease in mRNA population. A 22-kD double polypeptide was increased by progressive or rapid water stress and salinity and disappeared upon rehydration. These polypeptides have a common N-terminal sequence, which does not reveal homology with any known water-stress protein but which contains the signature motif of soybean Künitz trypsin inhibitors. Immunoprecipitation allowed these polypeptides to be identified on two-dimensional gels of in vitro translation products. They appeared to be synthesized as a 24-kD precursor, and their transcript was present in the control well-watered leaves, where the polypeptides were never detected, indicating a possible translational regulation. A putative function of this protein, named BnD22, in the retardation of drought-induced leaf senescence is discussed.

Molecular cloning and characterization of gravity specific cDNA in rice (Oryza sativa L.) suspension callus

Rice (Oryza sativa L. var. Nipponbare) suspension callus was exposed to gravity stress at 450,000 g for 2 hours, after which poly(A)+RNA was isolated and a cDNA library was constructed. Three different gravity specific cDNAs, namely, GSC 128, GSC 233 and GSC 381 of 0.67, 0.60 and 0.68 kilobase pairs and transcripts of 1.9, 1.6 and 2.0 kb, respectively, were isolated by differential screening and Northern hybridization. The maximum level of transcript was achieved after 4 hours of exposure to gravity at 450,000 g for GSC 128, 2 hours for GSC 233 and 8 hours for GSC 381 followed by a gradual decrease to undetectable levels with the extension of gravitation time. Callus (GSC 128), shoot and callus (GSC 381) and root and callus (GSC 233) specific expression of transcripts was identified. Although the protection of callus by treatment with ABA, kinetin and sucrose extended the period of expression of mRNA in suspension callus after gravity exposure, the expression of gravity-inducible mRNA was exclusively regulated by the degree of callus viability or survival after the stress. In addition, we demonstrated that the level of GSC 381 transcript was markedly increased by exposing the cell to periodical gravity stress, suggesting that this mRNA is expressed and translated into special proteins which are closely related to the survival of the cell against gravity stress. The sequence of GSC 233 and GSC 381, consisting of 417 and 531 base pairs of the longest open reading frames, encode polypeptides with calculated molecular weights of 15.29 and 19.47 kDa, respectively. A sequence homology search against a data bank revealed that GSC 233 and GSC 381 differed from other stress inducible genes in terms of the coding sequence and expression characteristics.

Molecular cloning and characterization of genes related to chilling tolerance in rice

Polyadenylated RNA was isolated and a cDNA library constructed from seedlings of a chilling-tolerant rice cultivar (Oryza sativa L. subsp. Japonica cv Nipponbare). Four clones were isolated by differential screening. Northern blot hybridization using RNAs from chilling-tolerant (Nipponbare) and -sensitive (IR36) cultivars revealed higher steady-state levels of transcripts for the four genes in Nipponbare than in IR36 maintained at the same low temperatures. The accumulation of transcripts homologous to selected cDNA sequences during chilling were tissue-specific. The nucleotide and deduced amino acid sequences of three clones, pBC121, pBC442, and pBC591, were determined, and no homology was identified by comparison with the latest version of EMBL and LASL gene data bases. The deduced protein sequences from the longest open reading frame of the clones pBC121 and pBC442 are rich in leucine and serine, whereas that of the clone pBC591 contains arginine-rich basic domains.

Expression of Osmotin-Like Genes in the Halophyte Atriplex nummularia L

A peptide (molecular mass 50 kilodaltons) that is immunologically related to tobacco osmotin was detected in cells of the halophyte Atriplex nummularia. This protein was constitutively expressed in both unadapted and NaCl-adapted cells. A predominant osmotin-like peptide (molecular mass 24 kilodaltons) was also found in culture media after cell growth. Two unique A. nummularia cDNA clones, pA8 and pA9, encoding osmotin-like proteins have been isolated. The pA8 and pA9 inserts are 952 and 792 base pairs and encode peptides of 222 and 224 amino acids, respectively. The peptide deduced from pA8 has a molecular mass of 23,808 daltons and theoretical isoelectric point of 8.31, whereas the peptide derived from pA9 has a molecular mass of 23,827 daltons and an isoelectric point of 6.88. Unique transcripts were detected by the inserts of the cDNA clones, two (1.2 and 1.0 kilobases) by pA8 and one (0.9 kilobase) by pA9. The pA8 transcripts were constitutively accumulated in unadapted and NaCl-adapted cells, whereas the mRNA levels were up-regulated by abscisic acid treatment. The level of pA9 mRNA was induced by NaCl treatment and increased in cells as a function of NaCl adaptation. Southern analysis of the genomic DNA indicated the presence of osmotin-like multigene families in A. nummularia.

Regulation of the abscisic acid-responsive gene rab28 in maize viviparous mutants

We have isolated a new maize gene, rab28, that responds to abscisic acid (ABA) treatment. This gene has been characterized by determining the sequence of the cDNA and corresponding genomic copy, and by mapping the start site of its transcript. The rab 28 gene encodes a protein of predicted molecular weight 27713 Da which shows strong homology with the Lea D-34 protein identified in cotton. The proximal promoter region contains the conserved ABA-response element, CACGTGG, reported in other plant genes to be responsible for ABA induction. rab 28 mRNA has been identified as ABA-inducible in embryos and young leaves. It is also induced by water-stress in leaves of wild-type plants. Regulation of the rab 28 gene was studied in maize viviparous mutants. The results obtained with the ABA-insensitive vp1 mutant show that rab 28 transcripts do not accumulate to a significant level during embryogenesis. Surprisingly, induction of rab 28 mRNA can be achieved in young embryos by exogenous ABA treatment. Moreover, water-stressed or ABA-treated seedlings of vp1 contain significant levels of rab 28 mRNA which is not detectable in well-watered seedlings. Regulation of the rab 28 gene in excised young embryos of ABA-deficient vp2 mutants, in which influences of the maternal environment are absent, closely resembles that found in non-mutant excised young embryos. The significance of these results is discussed.

Organ-Specific and Environmentally Regulated Expression of Two Abscisic Acid-Induced Genes of Tomato : Nucleotide Sequence and Analysis of the Corresponding cDNAs

The cDNAs, pLE4 and pLE25, represent mRNAs that accumulate in response to water deficit and elevated levels of endogenous abscisic acid in detached leaves of drought-stressed tomato (Lycopersicon esculentum Mill., cv Ailsa Craig) (A Cohen, EA Bray [1990] Planta 182: 27-33). DNA sequence analysis of pLE4 and pLE25 showed that the deduced polypeptides were 13.9 and 9.3 kilodaltons, respectively. Each polypeptide was hydrophilic, cysteine- and tryptophan-free, and found to be similar to previously identified proteins that accumulate during the late stages of embryogenesis. pLE4 and pLE25 mRNA accumulated in a similar organ-specific pattern in response to specific abiotic stresses. Yet, expression patterns of the corresponding genes in response to developmental cues were not similar. pLE25 mRNA accumulated to much higher levels in developing seeds than in drought-stressed vegetative organs. pLE4 mRNA accumulated predominantly in drought-stressed leaves. The similarities and differences in the accumulation characteristics of these two mRNAs indicates that more than one mechanism exists for the regulation of their corresponding genes.

Nucleotide sequence and spatial expression pattern of a drought- and abscisic Acid-induced gene of tomato

The nucleotide sequence of le16, a tomato (Lycopersicon esculentum Mill.) gene induced by drought stress and regulated by abscisic acid specifically in aerial vegetative tissue, is presented. The single open reading frame contained within the gene has the capacity to encode a polypeptide of 12.7 kilodaltons and is interrupted by a small intron. The predicted polypeptide is rich in leucine, glycine, and alanine and has an isoelectric point of 8.7. The amino terminus is hydrophobic and characteristic of signal sequences that target polypeptides for export from the cytoplasm. There is homology (47.2% identity) between the amino terminus of the LE 16 polypeptide and the corresponding amino terminal domain of the maize phospholipid transfer protein. le16 was expressed in drought-stressed leaf, petiole, and stem tissue and to a much lower extent in the pericarp of mature green tomato fruit and developing seeds. No expression was detected in the pericarp of red fruit or in drought-stressed roots. Expression of le16 was also induced in leaf tissue by a variety of other abiotic stresses including polyethylene glycol-mediated water deficit, salinity, cold stress, and heat stress. None of these stresses or direct applications of abscisic acid induced the expression of le16 in the roots of the same plants. The unique expression characteristics of this gene indicates that novel regulatory mechanisms, in addition to endogenous abscisic acid, are involved in controlling gene expression.

Germin-Like Polypeptides Increase in Barley Roots during Salt Stress

The 26 kilodalton, isoelectric point 6.3 and 6.5 (Gs1 and Gs2) polypeptides that increase in barley (Hordeum vulgare L.) roots during salt stress were isolated and identified. Both Gs1 and Gs2 had high sequence similarity to germin, a protein that increases significantly in germinating wheat seeds. Like germin, Gs1 and Gs2 were resistant to proteases and were glycosylated. Immunoblots were probed with antibodies to Gs1 and Gs2 to determine the distribution of these polypeptides among organs and cell-free fractions. Gs1 and Gs2 were present in roots and coleoptiles, but absent from leaves. In roots, Gs1 and Gs2 were present in the mature region, but not the tip. Gs1 and Gs2 increased in roots, but decreased in coleoptiles in response to salt stress. Gs1 and Gs2 were distributed among the soluble, microsomal, and cell wall fractions of roots, but the majority of Gs1 and Gs2 was present in the soluble fraction. Although Gs1 and Gs2 were heat stable, their synthesis was not affected by abscisic acid treatment. Gs2 accumulated during abscisic acid treatment, whereas Gs1 did not. However, a 25.5 kilodalton, isoelectric point 6.1 polypeptide that was immunologically related to Gs1 did accumulate with abscisic acid treatment.

A 150 Kilodalton Cell Surface Protein Is Induced by Salt in the Halotolerant Green Alga Dunaliella salina

Dunaliella salina is an extremely halotolerant, unicellular, green alga lacking a rigid cell wall. Osmotic adaptation to high salinities is based on the accumulation of glycerol. To uncover other functions responsible for halotolerance, protein profiles of algae continuously grown in different salinities were compared. A 150 kilodalton protein (p 150) increased in amount with salt concentration. Furthermore, when the cells were subjected to drastic hyperosmotic shocks, p150 started to rise long after completion of the osmotic response but coincident with reinitiation of cell proliferation. Cells with an initially higher level of p150 resumed growth faster than cells with a lower level of the protein. Addition of cycloheximide early after hyperosmotic shock prevented the rise in p150, indicating this rise was due to de novo synthesis of the protein. These observations suggest that p150 is a saltinduced protein required for proliferation of the cells in saline media. p150 was purified to homogeneity and found to be a detergent-soluble glycoprotein. Polyclonal antibodies against p150 recognized a single protein component in D. salina crude extracts. A high M(r) cross-reacting protein was also observed in another Dunaliella strain, D. bardawil. Immunoelectron microscopy localized p150 to the cell surface.

Selection of a mutation conferring high NaCl tolerance to gametophytes of Ceratopteris

Spores from a weakly salt tolerant strain of Ceratopteris richardii containing the mutation stl1 were irradiated and sown on nutrient medium supplemented with 200 mM NaCl. A single highly salt tolerant gametophyte was recovered and selfed to generate a homozygous sporophyte. Spores from this strain, 10α23, were used to document the sexual transmission of the trait and to monitor the inheritance of tolerance in crosses to both the wild type and to the parental salt tolerant strain. Genetic analysis showed the 10α23 strain to possess both the original stl1 mutation and an additional semi-dominant nuclear mutation, stl2, that individually conferred a high level of tolerance to gametophytes. In combination, both mutations had additive effects. Tolerance was also evident in sporophytes, but at a lower level than in gametophytes.

Characterization of Five Abscisic Acid-Responsive cDNA Clones Isolated from the Desiccation-Tolerant Plant Craterostigma plantagineum and Their Relationship to Other Water-Stress Genes

Leaves of resurrection plants tolerate desiccation as do embryos of many higher plants. From the resurrection plant Craterostigma plantagineum a number of desiccation-related transcripts have recently been cloned; they are abundantly expressed in dried leaves and abscisic acid-treated dried callus (D Bartels, K Schneider, G Terstappen, D Piatkowski, F Salamini [1990] Planta 18: 27-34). Five distinct cDNA clones representing low copy number genes were selected for further characterization. Their nucleotide sequences were determined and proteins were predicted with a molecular mass between 16 and 34 kilodaltons. Three of these proteins have unusual amino acid compositions and extreme hydrophilic characters. Two of them contain a cluster of contiguous serine residues and lysine-rich repeats. These sequence motifs display homologies to desiccation-related genes expressed in embryos or dehydrated seedlings of several plants. A third cDNA clone contains tracts of sequences which are related to a cotton Lea (late embryogenesis abundant) gene (JC Baker, C Steele, L Dure III [1988] Plant Mol Biol II: 277-291). Secondary structure predictions are discussed and suggest that the deduced proteins could play a role in protecting core cell structures in a dehydrated cell. It is concluded that at least in part the gene products involved in the desiccation-induced pathways are common to leaves of resurrection plants and embryos. Two cDNA clones appear to code for Craterostigma-specific mRNAs. The expression patterns of all five transcripts were studied in comparison to desiccated leaves in dehydrated roots, in wound-stressed leaves and in salt-stressed callus. The data obtained point to the possibility that not only specificity of induction but also the expression level of specific gene products may be of importance for osmoprotection.