Expressed sequence tags from a NaCl-treated Suaeda salsa cDNA library

Impact of Plant Growth-Promoting Rhizobacteria Inoculation and Grafting on Tolerance of Tomato to Combined Water and Nutrient Stress Assessed via Metabolomics Analysis

In the current study, inoculation with plant growth-promoting rhizobacteria (PGPR) and grafting were tested as possible cultural practices that may enhance resilience of tomato to stress induced by combined water and nutrient shortage. The roots of tomato grown on perlite were either inoculated or not with PGPR, applying four different treatments. These were PGPR-T1, a mix of two Enterobacter sp. strains (C1.2 and C1.5); PGPR-T2, Paenibacillus sp. strain DN1.2; PGPR-T3, Enterobacter mori strain C3.1; and PGPR-T4, Lelliottia sp. strain D2.4. PGPR-treated plants were either self-grafted or grafted onto Solanum lycopersicum cv. M82 and received either full or 50% of their standard water, nitrogen, and phosphorus needs. The vegetative biomass of plants subjected to PGPR-T1 was not reduced when plants were cultivated under combined stress, while it was reduced by stress to the rest of the PGPR treatments. However, PGPR-T3 increased considerably plant biomass of non-stressed tomato plants than did all other treatments. PGPR application had no impact on fruit biomass, while grafting onto 'M82' increased fruit production than did self-grafting. Metabolomics analysis in tomato leaves revealed that combined stress affects several metabolites, most of them already described as stress-related, including trehalose, myo-inositol, and monopalmitin. PGPR inoculation with E. mori strain C3.1 affected metabolites, which are important for plant/microbe symbiosis (myo-inositol and monopalmitin). The rootstock M82 did not affect many metabolites in plant leaves, but it clearly decreased the levels of malate and D-fructose and imposed an accumulation of oleic acid. In conclusion, PGPR are capable of increasing tomato tolerance to combined stress. However, further research is required to evaluate more strains and refine protocols for their application. Metabolites that were discovered as biomarkers could be used to accelerate the screening process for traits such as stress tolerance to abiotic and/or abiotic stresses. Finally, 'M82' is a suitable rootstock for tomato, as it is capable of increasing fruit biomass production.

Identification of salt-responsive genes from C4 halophyte Suaeda nudiflora through suppression subtractive hybridization and expression analysis under individual and combined treatment of salt and elevated carbon dioxide conditions

Salinization of soil is a prime abiotic stress that limits agriculture productivity worldwide. To Study the mechanisms that halophytes take up to survive under high salt condition is important in engineering salinity stress tolerance in sensitive species. Suaeda nudiflora is a halophyte plant that grows in the saline environment and extreme high tidal belt. The species have high capability to produce high protein biomass in salty soils due to C4 photosynthesis. The physiological and biochemical changes in S. nudiflora under salinity stress were studied by measuring chlorophyll content, electrolytic leakage, level of lipid peroxidation and total soluble sugars. Increased lipid peroxidation and electrolytic leakage was observed in salt stressed S. nudiflora compared to control plants. A suppression subtractive hybridization strategy was employed to identify differentially expressed genes under salt treatment in S. nudiflora. A total of 333 positive clones were identified and screened. Of these, 250 expressed sequence tags were identified. cDNA subtraction library resulted in 33 contigs and 138 singletons. The functional annotation and metabolic pathways identification were performed using the Blast2GO program. In addition, we analyzed the expression patterns of 18 genes associated with salt stress-responsive pathways by semi-quantitative PCR under salt and elevated carbon dioxide (CO₂) conditions. Several of the analyzed genes showed an increase in expression levels under different time points of salt treatment and at different concentrations of salt. When the same genes were studied for its expression under elevated CO₂ concentrations, most of the known salt responsive genes showed higher expression under the combined treatment of elevated CO₂ concentrations (500 ppm) and NaCl treatment (200 mM) compare to ambient condition. This implies that salt responsive genes are enhanced at elevated CO₂ concentrations.

Generation, Annotation, and Analysis of a Large-Scale Expressed Sequence Tag Library from Arabidopsis pumila to Explore Salt-Responsive Genes

Arabidopsis pumila is an ephemeral plant, and a close relative of the model plant Arabidopsis thaliana, but it possesses higher photosynthetic efficiency, higher propagation rate, and higher salinity tolerance compared to those A. thaliana, thus providing a candidate plant system for gene mining for environmental adaption and salt tolerance. However, A. pumila is an under-explored resource for understanding the genetic mechanisms underlying abiotic stress adaptation. To improve our understanding of the molecular and genetic mechanisms of salt stress adaptation, more than 19,900 clones randomly selected from a cDNA library constructed previously from leaf tissue exposed to high-salinity shock were sequenced. A total of 16,014 high-quality expressed sequence tags (ESTs) were generated, which have been deposited in the dbEST GenBank under accession numbers JZ932319 to JZ948332. Clustering and assembly of these ESTs resulted in the identification of 8,835 unique sequences, consisting of 2,469 contigs and 6,366 singletons. The blastx results revealed 8,011 unigenes with significant similarity to known genes, while only 425 unigenes remained uncharacterized. Functional classification demonstrated an abundance of unigenes involved in binding, catalytic, structural or transporter activities, and in pathways of energy, carbohydrate, amino acid, or lipid metabolism. At least seven main classes of genes were related to salt-tolerance among the 8,835 unigenes. Many previously reported salt tolerance genes were also manifested in this library, for example VP1, H⁺-ATPase, NHX1, SOS2, SOS3, NAC, MYB, ERF, LEA, P5CS1. In addition, 251 transcription factors were identified from the library, classified into 42 families. Lastly, changes in expression of the 12 most abundant unigenes, 12 transcription factor genes, and 19 stress-related genes in the first 24 h of exposure to high-salinity stress conditions were monitored by qRT-PCR. The large-scale EST library obtained in this study provides first-hand information on gene sequences expressed in young leaves of A. pumila exposed to salt shock. The rapid discovery of known or unknown genes related to salinity stress response in A. pumila will facilitate the understanding of complex adaptive mechanisms for ephemerals.

Overexpression of S-Adenosyl-l-Methionine Synthetase 2 from Sugar Beet M14 Increased Arabidopsis Tolerance to Salt and Oxidative Stress

The sugar beet monosomic addition line M14 is a unique germplasm that contains genetic materials from Beta vulgaris L. and Beta corolliflora Zoss, and shows tolerance to salt stress. Our study focuses on exploring the molecular mechanism of the salt tolerance of the sugar beet M14. In order to identify differentially expressed genes in M14 under salt stress, a subtractive cDNA library was generated by suppression subtractive hybridization (SSH). A total of 36 unique sequences were identified in the library and their putative functions were analyzed. One of the genes, S-adenosylmethionine synthetase (SAMS), is the key enzyme involved in the biosynthesis of S-adenosylmethionine (SAM), a precursor of polyamines. To determine the potential role of SAMS in salt tolerance, we isolated BvM14-SAMS2 from the salt-tolerant sugar beet M14. The expression of BvM14-SAMS2 in leaves and roots was greatly induced by salt stress. Overexpression of BvM14-SAMS2 in Arabidopsis resulted in enhanced salt and H₂O₂ tolerance. Furthermore, we obtained a knock-down T-DNA insertion mutant of AtSAMS3, which shares the highest homology with BvM14-SAMS2. Interestingly, the mutant atsam3 showed sensitivity to salt and H₂O₂ stress. We also found that the antioxidant system and polyamine metabolism play an important role in salt and H₂O₂ tolerance in the BvM14-SAMS2-overexpressed plants. To our knowledge, the function of the sugar beet SAMS has not been reported before. Our results have provided new insights into SAMS functions in sugar beet.

The interactive effects of mercury and selenium on metabolic profiles, gene expression and antioxidant enzymes in halophyte Suaeda salsa

Suaeda salsa is the pioneer halophyte in the Yellow River Delta and was consumed as a popular vegetable. Mercury has become a highly risky contaminant in the sediment of intertidal zones of the Yellow River Delta. In this work, we investigated the interactive effects of mercury and selenium in S. salsa on the basis of metabolic profiling, antioxidant enzyme activities and gene expression quantification. Our results showed that mercury exposure (20 μg L(-1)) inhibited plant growth of S. salsa and induced significant metabolic responses and altered expression levels of INPS, CMO, and MDH in S. salsa samples, together with the increased activities of antioxidant enzymes including SOD and POD. Overall, these results indicated osmotic and oxidative stresses, disturbed protein degradation and energy metabolism change in S. salsa after mercury exposures. Additionally, the addition of selenium could induce both antagonistic and synergistic effects including alleviating protein degradation and aggravating osmotic stress caused by mercury.

A novel gene SbSI-2 encoding nuclear protein from a halophyte confers abiotic stress tolerance in E. coli and tobacco

Salicornia brachiata is an extreme halophyte that grows luxuriantly in coastal marshes. Previously, we have reported isolation and characterization of ESTs from Salicornia with large number of novel/unknown salt-responsive gene sequences. In this study, we have selected a novel salt-inducible gene SbSI-2 (Salicornia brachiata salt-inducible-2) for functional characterization. Bioinformatics analysis revealed that SbSI-2 protein has predicted nuclear localization signals and a strong protein-protein interaction domain. Transient expression of the RFP:SbSI2 fusion protein confirmed that SbSI-2 is a nuclear-localized protein. Genomic organization study showed that SbSI-2 is intronless and has a single copy in Salicornia genome. Quantitative RT-PCR analysis revealed higher SbSI-2 expression under salt stress and desiccation conditions. The SbSI-2 gene was transformed in E. coli and tobacco for functional characterization. pET28a-SbSI-2 recombinant E. coli cells showed higher tolerance to desiccation and salinity compared to vector alone. Transgenic tobacco plants overexpressing SbSI-2 have improved salt- and osmotic tolerance, accompanied by better growth parameters, higher relative water content, elevated accumulation of compatible osmolytes, lower Na+ and ROS accumulation and lesser electrolyte leakage than the wild-type. Overexpression of the SbSI-2 also enhanced transcript levels of ROS-scavenging genes and some stress-related transcription factors under salt and osmotic stresses. Taken together, these results demonstrate that SbSI-2 might play an important positive modulation role in abiotic stress tolerance. This identifies SbSI-2 as a novel determinant of salt/osmotic tolerance and suggests that it could be a potential bioresource for engineering abiotic stress tolerance in crop plants.

Generation and analysis of expressed sequence tags (ESTs) from halophyte Atriplex canescens to explore salt-responsive related genes

Little information is available on gene expression profiling of halophyte A. canescens. To elucidate the molecular mechanism for stress tolerance in A. canescens, a full-length complementary DNA library was generated from A. canescens exposed to 400 mM NaCl, and provided 343 high-quality ESTs. In an evaluation of 343 valid EST sequences in the cDNA library, 197 unigenes were assembled, among which 190 unigenes (83.1% ESTs) were identified according to their significant similarities with proteins of known functions. All the 343 EST sequences have been deposited in the dbEST GenBank under accession numbers JZ535802 to JZ536144. According to Arabidopsis MIPS functional category and GO classifications, we identified 193 unigenes of the 311 annotations EST, representing 72 non-redundant unigenes sharing similarities with genes related to the defense response. The sets of ESTs obtained provide a rich genetic resource and 17 up-regulated genes related to salt stress resistance were identified by qRT-PCR. Six of these genes may contribute crucially to earlier and later stage salt stress resistance. Additionally, among the 343 unigenes sequences, 22 simple sequence repeats (SSRs) were also identified contributing to the study of A. canescens resources.

Proteomic study of a tolerant genotype of durum wheat under salt-stress conditions

Salinity is one of the major abiotic stress conditions limiting crop growth and productivity. Duilio is a wheat genotype that shows tolerant behavior in both salt-stress and drought-stress conditions. Toward better understanding of the biochemical response to salinity in this genotype of durum wheat, a comparative label-free shotgun proteomic analysis based on normalized spectral abundance factors was conducted on wheat leaf samples subjected to increasing salt-stress levels (100 and 200 mmol L(-1) NaCl) with respect to untreated samples. We found significant changes in 71 proteins for the first stress level, in 83 proteins at the higher salinity level, and in 88 proteins when comparing salt-stress levels with each other. The major changes concerned the proteins involved in primary metabolism and production of energy, followed by those involved in protein metabolism and cellular defense mechanisms. Some indications of different specific physiological and defense mechanisms implicated in increasing tolerance were obtained. The enhanced salinity tolerance in Duilio appeared to be governed by a higher capacity for osmotic homeostasis, a more efficient defense, and an improvement of protection from mechanical stress by increased cell wall lignifications, allowing a better potential for growth recovery.

Gene expression profiling of soybean leaves and roots under salt, saline-alkali and drought stress by high-throughput Illumina sequencing

Salt, saline-alkali and drought stresses are major environmental constraints for the production and yield of soybean worldwide. To identify genes responsible for stress tolerance, the transcriptional profiles of genes in leaves and roots of seedlings (two-leaf stage) of the soybean inbred line HJ-1 were examined after 48 h under various stress conditions; salt (120 mM NaCl), saline-alkali (70 mM NaCl and 50mM NaHCO(3)) and drought (2% PEG 8000). Gene expression at the transcriptional level was investigated using high-throughput Illumina sequencing technology and bioinformatics tools. Under salt, saline-alkali and drought stress, 874, 1897, and 535 genes, respectively, were up-regulated in leaves, and 1822, 1731 and 1690 genes, respectively, were up-regulated in roots, compared with expression in the corresponding organ in control plants. Comparisons among salt, saline-alkali and drought stress yielded similar results in terms of the percentage of genes classified into each GO category. Moreover, 69 genes differentially expressed in both organs with similar expression patterns clustered together in the taxonomic tree across all conditions. Furthermore, comparison of gene expression among salt, saline-alkali and drought treated plants revealed that genes associated with calcium-signaling and nucleic acid pathways were up-regulated in the responses to all three stresses, indicating a degree of cross-talk among these pathways. These results could provide new insights into the stress tolerance mechanisms of soybean.

Toxicological effects of environmentally relevant lead and zinc in halophyte Suaeda salsa by NMR-based metabolomics

Lead (Pb) and zinc (Zn) are two typical metal contaminants with high levels in both seawater and sediment in the intertidal zones of the Bohai Sea. Suaeda salsa is the pioneer halophyte plant in the intertidal zones of the Bohai Sea. In the present work, the short (1 week) and long term (1 month) toxicological effects of environmentally relevant concentrations of Pb and Zn were characterized in S. salsa using NMR-based metabolomics combined with antioxidant enzyme activities. After metal exposure for 1 week, no significant metabolic responses were detected in root tissues of S. salsa. The significant metabolic responses included the increase of isocaproate, glucose and fructose, and decrease of malate, citrate and sucrose in root tissues of S. salsa exposed to Pb for 1 month. The increased phosphocholine and betaine, and decreased choline were uniquely found in Zn-exposed samples. The metabolic changes including decreased malate, citrate and sucrose were detected in both Pb and Zn-exposed groups. These metabolic biomarkers revealed that both Pb and Zn exposures could induce osmotic stress and disturbances in energy metabolism in S. salsa after exposures for 1 month. Overall, this work demonstrates that metabolomics can be used to elucidate toxicological effects of environmentally relevant metal contaminants using halophyte S. salsa as the bioindicator.

Exploration for the salt stress tolerance genes from a salt-treated halophyte, Suaeda asparagoides

Salinity stress severely affects plant growth and development causing crop loss worldwide. Suaeda asparagoides is a salt-marsh euhalophyte widely distributed in southwestern foreshore of Korea. To isolate salt tolerance genes from S. asparagoides, we constructed a cDNA library from leaf tissues of S. asparagoides that was treated with 200 mM NaCl. A total of 1,056 clones were randomly selected for EST sequencing, and 932 of them produced readable sequence. By sequence analysis, we identified 538 unigenes and registered each in National Center for Biotechnology Information. The 80 salt stress related genes were selected to study their differential expression. Reverse transcription-PCR and Northern blot analysis revealed that 23 genes were differentially expressed under the high salinity stress conditions in S. asparagoides. They are functionally diverse including transport, signal transduction, transcription factor, metabolism and stress associated protein, and unknown function. Among them dehydrin (SaDhn) and RNA binding protein (SaRBP1) were examined for their abiotic stress tolerance in yeast (Saccharomyces cerevisiae). Yeast overexpressing SaDhn and SaRBP1 showed enhanced tolerance to osmotic, freezing and heat shock stresses. This study provides the evidence that SaRBP1 and SaDhn from S. asparagoides exert abiotic stress tolerance in yeast. Information of salt stress related genes from S. asparagoides would contribute for the accumulating genetic resources to improve osmotic tolerance in plants.

Mechanisms of plant salt response: insights from proteomics

Soil salinity is a major abiotic stress that limits plant growth and agriculture productivity. To cope with salt stress, plants have evolved complex salt-responsive signaling and metabolic processes at the cellular, organ, and whole-plant levels. Investigation of the physiological and molecular mechanisms underlying plant salinity tolerance will provide valuable information for effective engineering strategies. Current proteomics provides a high-throughput approach to study sophisticated molecular networks in plants. In this review, we describe a salt-responsive protein database by an integrated analysis of proteomics-based studies. The database contains 2171 salt-responsive protein identities representing 561 unique proteins. These proteins have been identified from leaves, roots, shoots, seedlings, unicells, grains, hypocotyls, radicles, and panicles from 34 plant species. The identified proteins provide invaluable information toward understanding the complex and fine-tuned plant salt-tolerance mechanisms in photosynthesis, reactive oxygen species (ROS) scavenging, ion homeostasis, osmotic modulation, signaling transduction, transcription, protein synthesis/turnover, cytoskeleton dynamics, and cross-tolerance to different stress conditions.

Physiological and proteomic analysis of salinity tolerance in Puccinellia tenuiflora

Soil salinity poses a serious threat to agriculture productivity throughout the world. Studying mechanisms of salinity tolerance in halophytic plants will provide valuable information for engineering plants for enhanced salt tolerance. Monocotyledonous Puccinellia tenuiflora is a halophytic species that widely distributed in the saline-alkali soil of the Songnen plain in northeastern China. Here we investigate the molecular mechanisms underlying moderate salt tolerance of P. tenuiflora using a combined physiological and proteomic approach. The changes in biomass, inorganic ion content, osmolytes, photosynthesis, defense-related enzyme activities, and metabolites in the course of salt treatment were analyzed in the leaves. Comparative proteomic analysis revealed 107 identities (representing 93 unique proteins) differentially expressed in P. tenuiflora leaves under saline conditions. These proteins were mainly involved in photosynthesis, stress and defense, carbohydrate and energy metabolism, protein metabolism, signaling, membrane, and transport. Our results showed that reduction of photosynthesis under salt treatment was attributed to the down-regulation of the light-harvesting complex (LHC) and Calvin cycle enzymes. Selective uptake of inorganic ions, high K(+)/Na(+) ratio, Ca(2+) concentration changes, and an accumulation of osmolytes contributed to ion balance and osmotic adjustment in leaf cells. Importantly, P. tenuiflora plants developed diverse reactive oxygen species (ROS) scavenging mechanisms in their leaves to cope with moderate salinity, including enhancement of the photorespiration pathway and thermal dissipation, synthesis of the low-molecular-weight antioxidant α-tocopherol, and an accumulation of compatible solutes. This study provides important information toward improving salt tolerance of cereals.

Metabolic profiling of cadmium-induced effects in one pioneer intertidal halophyte Suaeda salsa by NMR-based metabolomics

Cadmium is a non-essential element to living organisms and has become the severe contaminant in both seawater and sediment in the intertidal zones of the Bohai Sea. The halophyte, Suaeda salsa is the pioneer plant in the intertidal zones of Bohai Sea and has been widely applied in environmental sciences. In this study, the dose- and time-dependent effects induced by environmentally relevant concentrations (2, 10 and 50 μg l(-1)) of cadmium were characterized in S. salsa using NMR-based metabolomics. The levels of amino acids (valine, leucine, glutamate, tyrosine, etc.), carbohydrates (glucose, sucrose and fructose), intermediates of tricarboxylic acid cycle (succinate, citrate, etc.) and osmolyte (betaine) were altered in the S. salsa samples after cadmium exposures. These metabolic biomarkers indicated the elevated protein degradation and disturbances in the osmotic regulation and energy metabolism caused by cadmium in S. salsa. Overall, our results demonstrated the applicability of NMR-based metabolomics for the detection of metabolic biomarkers that could be used for the interpretation of toxicological effects induced by contaminants in the pioneer plant S. salsa in the intertidal zones. In addition, the metabolic biomarkers could be potentially useful for the bio-monitoring of contaminants in the intertidal zones.

Transcriptomic analysis of grain amaranth (Amaranthus hypochondriacus) using 454 pyrosequencing: comparison with A. tuberculatus, expression profiling in stems and in response to biotic and abiotic stress

BACKGROUND

Amaranthus hypochondriacus, a grain amaranth, is a C4 plant noted by its ability to tolerate stressful conditions and produce highly nutritious seeds. These possess an optimal amino acid balance and constitute a rich source of health-promoting peptides. Although several recent studies, mostly involving subtractive hybridization strategies, have contributed to increase the relatively low number of grain amaranth expressed sequence tags (ESTs), transcriptomic information of this species remains limited, particularly regarding tissue-specific and biotic stress-related genes. Thus, a large scale transcriptome analysis was performed to generate stem- and (a)biotic stress-responsive gene expression profiles in grain amaranth.

RESULTS

A total of 2,700,168 raw reads were obtained from six 454 pyrosequencing runs, which were assembled into 21,207 high quality sequences (20,408 isotigs + 799 contigs). The average sequence length was 1,064 bp and 930 bp for isotigs and contigs, respectively. Only 5,113 singletons were recovered after quality control. Contigs/isotigs were further incorporated into 15,667 isogroups. All unique sequences were queried against the nr, TAIR, UniRef100, UniRef50 and Amaranthaceae EST databases for annotation. Functional GO annotation was performed with all contigs/isotigs that produced significant hits with the TAIR database. Only 8,260 sequences were found to be homologous when the transcriptomes of A. tuberculatus and A. hypochondriacus were compared, most of which were associated with basic house-keeping processes. Digital expression analysis identified 1,971 differentially expressed genes in response to at least one of four stress treatments tested. These included several multiple-stress-inducible genes that could represent potential candidates for use in the engineering of stress-resistant plants. The transcriptomic data generated from pigmented stems shared similarity with findings reported in developing stems of Arabidopsis and black cottonwood (Populus trichocarpa).

CONCLUSIONS

This study represents the first large-scale transcriptomic analysis of A. hypochondriacus, considered to be a highly nutritious and stress-tolerant crop. Numerous genes were found to be induced in response to (a)biotic stress, many of which could further the understanding of the mechanisms that contribute to multiple stress-resistance in plants, a trait that has potential biotechnological applications in agriculture.

A novel salt-inducible gene SbSI-1 from Salicornia brachiata confers salt and desiccation tolerance in E. coli

Salicornia brachiata is one of the extreme salt tolerant plants and grows luxuriantly in coastal areas. Previously we have reported isolation and characterization of ESTs from S. brachiata with large number of unknown gene sequences. Reverse Northern analysis showed upregulation and downregulation of few unknown genes in response to salinity. Some of these unknown genes were made full length and their functional analysis is being tested. In this study, we have selected a novel unknown salt inducible gene SbSI-1 (Salicornia brachiata salt inducible-1) for the functional validation. The SbSI-1 (Gen-Bank accession number JF 965339) was made full length and characterized in detail for its functional validation under desiccation and salinity. The SbSI-1 gene is 917 bp long, and contained 437 bp 3' UTR, and 480 bp ORF region encoding 159 amino acids protein with estimated molecular mass of 18.39 kDa and pI 8.58. The real time PCR analysis revealed high transcript expression in salt, desiccation, cold and heat stresses. However, the maximum expression was obtained by desiccation. The ORF region of SbSI-1 was cloned in pET28a vector and transformed in BL21 (DE3) E. coli cells. The SbSI-1 recombinant E. coli cells showed tolerance to desiccation and salinity stress compared to only vector in the presence of stress.

Identification of salt-induced genes from Salicornia brachiata, an extreme halophyte through expressed sequence tags analysis

Salinity severely affects plant growth and development causing crop loss worldwide. We have isolated a large number of salt-induced genes as well as unknown and hypothetical genes from Salicornia brachiata Roxb. (Amaranthaceae). This is the first description of identification of genes in response to salinity stress in this extreme halophyte plant. Salicornia accumulates salt in its pith and survives even at 2 M NaCl under field conditions. For isolating salt responsive genes, cDNA subtractive hybridization was performed between control and 500 mM NaCl treated plants. Out of the 1200 recombinant clones, 930 sequences were submitted to the NCBI database (GenBank accession: EB484528 to EB485289 and EC906125 to EC906292). 789 ESTs showed matching with different genes in NCBI database. 4.8% ESTs belonged to stress-tolerant gene category and approximately 29% ESTs showed no homology with known functional gene sequences, thus classified as unknown or hypothetical. The detection of a large number of ESTs with unknown putative function in this species makes it an interesting contribution. The 90 unknown and hypothetical genes were selected to study their differential regulation by reverse Northern analysis for identifying their role in salinity tolerance. Interestingly, both up and down regulation at 500 mM NaCl were observed (21 and 10 genes, respectively). Northern analysis of two important salt tolerant genes, ASR1 (Abscisic acid stress ripening gene) and plasma membrane H+ATPase, showed the basal level of transcripts in control condition and an increase with NaCl treatment. ASR1 gene is made full length using 5' RACE and its potential role in imparting salt tolerance is being studied.

Comparison analysis of transcripts from the halophyte Thellungiella halophila

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

Primary responses to salt stress in a halophyte, smooth cordgrass (Spartina alterniflora Loisel.)

The response of a grass halophyte Spartina alterniflora at early stages of salt stress was investigated through generation and systematic analysis of expressed sequence tags (ESTs) from both leaf and root tissues. Random EST sequencing produced 1,227 quality ESTs, which were clustered into 127 contigs, and 368 were singletons. Of the 495 unigenes, 27% represented genes for stress response. Comparison of the 368 singletons against the Oryza sativa gene index showed that >85% of these genes had similarity with the rice unigenes. Moreover, the phylogenetic analysis of an EST similar to myo-inositol 1-phosphate synthase of Spartina and some selected grasses and halophytes showed closeness of Spartina with maize and rice. Transcript abundance analysis involving eight known genes of various metabolic pathways and nine transcription factor genes showed temporal and tissue-dependent variation in expression under salinity. Reverse northern analysis of a few selected unknown and ribosomal genes exhibited much higher abundance of transcripts in response to salt stress. The results provide evidence that, in addition to several unknown genes discovered in this study, genes involved in ion transport, osmolyte production, and house-keeping functions may play an important role in the primary responses to salt stress in this grass halophyte.

Expression profiling of salinity-alkali stress responses by large-scale expressed sequence tag analysis in Tamarix hispid

Tamarix hispida, a woody halophyte, thrives in saline and saline-alkali soil. To better understand the gene expression profiles that manifest in response to saline-alkali stress, three cDNA libraries were constructed from leaf tissue of T. hispida plants that were well watered and exposed to NaHCO3 for 24 and 52 h. A total of 9,447 high quality expressed sequence tags (ESTs) were obtained from the three libraries. These ESTs represent 3,945 unigenes, including 986 contigs and 2,959 singlets. The numbers of unigenes obtained from the three libraries were 1,752, 1,558 and 1,675, respectively. The EST analysis was performed to compare gene expression in the three cDNA libraries; the transcripts responsive to NaHCO3 were identified. The differentially expressed transcripts were identified. The up-regulation genes were involved in a variety function areas, such as stress-related proteins, hormone signaling transduction, antioxidative response, transcriptional regulators, protein synthesis and destination, ion homeostasis, photosynthesis and metabolism. The results indicated that the response to NaHCO3 in T. hispida is a complex one, involving multiple physiological and metabolic pathways. Nine gene expression patterns were compared in response to NaHCO3 and NaCl using real time reverse transcription-polymerase chain reaction (RT-PCR). Gene expression trends were similar after a 24-h exposure to either NaCl or NaHCO3, however, great variability was found after a 52-h exposure, indicating that short-term responses to either salt may not be obviously different.

Expression levels of 63 p53-related genes add up to similar values in 24 different tissues and are unified in cancer

The expression patterns of 62 genes interacting with p53 have been investigated in 24 normal and cancerous tissues using NIH's dbEST library. The expression levels of individual genes, such as the TTP53 gene itself, but also other genes, vary up to 33-fold among the 24 different tissues and no consistent pattern can be recognized. However, when expression levels for all 63 genes are summed, these "cumulated levels" are surprisingly constant over the 24 investigated normal tissues. In cancers, the variation is further reduced. Essentially, the cumulated expression levels in cancer are independent of those in normal tissue. We furthermore constructed a linear statistical classifier, i.e., a weighted sum of gene expression levels, which robustly distinguishes normal from cancer tissue independent of the particular kind of tissue. Thus, despite very large differences for individual genes and considerable changes during carcinogenesis, the cumulated expressions have narrowly defined levels.

Identification and sequencing of ESTs from the halophyte grass Aeluropus littoralis

Aeluropus littoralis (Gouan) Parl. is a C4 perennial halophyte monocotyledonous plant belonging to the same family as wheat. Growing as weed in dry salty areas or marshes, it is salt-secreting, rhizomatous and is used as forage. It is diploid (2n=2X=14) and has a relative small genome of around 342 Mb. A. littoralis is highly salt-tolerant since this plant has the ability to secrete salt. Thus, A. littoralis has the potential to become an important genetic resource for biotechnological strategies to improve salt and drought tolerance in economically important crops such as wheat. We have constructed SSH (Suppression Subtractive Hybridization) cDNA libraries from root (RSD45) and leaf (LSD45) tissues of 45 days old plants grown in the presence of 300 mM NaCl. We have also constructed full-length cDNA library from 15 days old salt stressed (300 mM NaCl) roots (RSTL15). Sequencing revealed 25 and 42 independent transcripts from the RSD45 and LSD45 cDNA libraries respectively, in both cases this was less than 25% of the clones sequenced. In contrast, 425 (60%) of the clones from the RSTL15 library revealed independent transcripts. After comparison with protein databases using BlastX, 335 (68%) ESTs (Expressed Sequence Tag) were classified into putative known functions and unclassified proteins, 59 (12%) have homology only to unidentified homologous sequences. A total of 98 (20%) of the ESTs have no homologies to known sequences in the protein databases which can be considered as novel.

Expressed sequence tags from the halophyte Limonium sinense

Halophytes can grow under a high salinity condition. Similar to glycophytes, their salt-tolerance possesses a high genetic complexity. There are many morphological and physiological studies on halophytes but very little information is at molecular level why they are salt-tolerant. Limonium sinense is a salt-secreting halophyte and can excretes salts by multi-cellular glands. Here, we report the library construction and sequence analysis of a cDNA library made from leaf tissue of L. sinenes. Among those 1082 expressed sequence tag (EST) obtained, 684 unique genes were identified: 429 showed homology to previously identified genes, 255 matched to uncharacterized genes. Compared with other EST databases, some characteristic features such as abundance genes in related to cytoskeleton and intracellular traffic, membrane transporting were observed, which may be specific to halophytes.

Identification of expressed sequence tags in an alkali grass (Puccinellia tenuiflora) cDNA library

Alkali grass (Puccinellia tenuiflora), a monocotyledonous halophyte, can serve as a model of salt tolerance in monocotyledon crops. To elucidate the molecular events associated with salt tolerance in alkali grass, we generated a directional cDNA library from leaves treated with the alkali salt, NaHCO3. Large-scale sequencing of the cDNA library identified 2942 ESTs representing 2366 non-redundant transcripts. These have been deposited in the dbEST division of GenBank. BLASTX evaluation indicated that 1274 of the ESTs were homologous to various known genes/proteins in a broad range of organisms, especially gramineae species. The other 1092 ESTs, which showed little if any homology to known sequences, were considered novel. Based on the encoded proteins, the 1274 identified ESTs fell into 12 functional categories, of which four were abundant, namely metabolism (18.84%), transcription (12.48%), unclassified (11.22%) and cell rescue/defense (9.66%). The 162 unique transcripts corresponding to possible salt-related genes were also identified. This study provides an overview of gene expression in NaHCO3-stressed alkali grass, as well as useful information for further investigation of salt resistance in plants.

Antioxidative response mechanisms in halophytes: Their role in stress defence

Normal growth and development of plants is greatly dependent on the capacity to overcome environmental stresses. Environmental stress conditions like high salinity, drought, high incident light and low or high temperature cause major crop losses worldwide. A common denominator in all these adverse conditions is the production of reactive oxygen species (ROS) within different cellular compartments of the plant cell. Plants have developed robust mechanisms including enzymatic or nonenzymatic scavenging pathways to counter the deleterious effects of ROS production. There are a number of general reviews on oxidative stress in plants and few on the role of ROS scavengers during stress conditions. Here we review the regulation of antioxidant enzymes during salt stress in halophytes, especially mangroves. We conclude that (i) antioxidant enzymes protect halophytes from deleterious ROS production during salt stress, and (ii) genetic information from mangroves and other halophytes would be helpful in defining the roles of individual isoforms. This information would be critical in using the appropriate genes for oxidative stress defence for genetic engineering of enhanced stress tolerance in crop systems.

Ubiquitous cancer genes: Multipurpose molecules for protein micro-arrays

Multipurpose genes in the human genome which are over-expressed in a large variety of different cancers have been identified. Forty-two of the 19,016 human genes annotated to date (0.2%) are ubiquitously over-expressed in half or more of the 36 investigated human cancers. Of these genes, 15 are involved in protein biosynthesis and folding, six of them in glycolysis. A group of 13 solid tumours over-express almost all (39-42 of 42) ubiquitous cancer genes, suggesting a common mechanism underlying these cancers. Others, such as endocrine cancers, have only a few over-expressed ubiquitous cancer genes. The proteins for which these genes code or the corresponding antibodies are candidates for small protein microarrays aiming at maximum information with only a limited number of proteins. Since the over-expression pattern varies from cancer to cancer, distinction between different cancer classes is possible using one single set of protein or antibody molecules.

Genes of glycolysis are ubiquitously overexpressed in 24 cancer classes

Using NIH's public database dbEST for expression of genes and ESTs, genes of the glycolysis pathway have been found to be overexpressed in a set of 24 cancers representing more than 70% of human cancer cases worldwide. Genes can be classified as those that are almost ubiquitously overexpressed, particularly glyceraldehyde-3-phosphate dehydrogenase, enolase 1, and also pyruvate kinase, and those that are overexpressed in less than 50% of the investigated cancers. Cancers can be classified as those with overexpression of the majority of the glycolysis genes, particularly lymph node, prostate, and brain cancer, in which essentially all glycolysis genes are overexpressed, and those with only sporadic overexpression, particularly cancers of the cartilage or bone marrow. This classification may be useful when cancer therapies aimed at the Warburg effect are designed.

ESTs from the fibre-bearing stem tissues of flax (Linum usitatissimum L.): expression analyses of sequences related to cell wall development

In order to learn more about the diversity of genes expressed during flax fibre cell wall formation, expressed sequence tags (ESTs) were obtained from a cDNA library derived from the outer fibre-bearing tissues of flax (Linum usitatissimum) stems (cv Hermes) harvested at the mid-flowering stage. After elimination of vector and unreadable sequences, 927 ESTs were grouped into 67 clusters and 754 singletons. The flax ESTs have been submitted to the dbEST and GenBank databases with the accession numbers 25939634 - 25940560 (dbEST) and CV478070 - CV478996 (GenBank). Functional analysis allowed the grouping of ESTs into 13 functional categories and revealed that 62 % of ESTs were similar to known sequences, while 12.4 % of ESTs presented no similarity to any known sequences and 25.6 % of ESTs corresponded to proteins of unknown function. The most highly expressed transcripts belonged to four functional categories: protein maturation and metabolism (31 ESTs), signalling (22 ESTs), the cell wall (21 ESTs) and photosynthesis (19 ESTs). 4.4 % (41) of the total ESTs were potentially related to cell wall formation and maturation. The most highly expressed cell wall EST (15 ESTs) corresponded to a beta-xylosidase gene--potentially involved in cell wall remodelling during growth and development. Other cell wall-related ESTs corresponded to cellulose synthase, xyloglucan endotranglucosylase/hydrolase (XTH), beta-galactosidases, and peroxidases. The expression patterns of different cell wall-related ESTs were determined at different developmental stages in flax plants grown under different field conditions. The potential roles of gene products associated with cell wall related ESTs in fibre cell wall development is discussed.

Transcript profiling of salinity stress responses by large-scale expressed sequence tag analysis in Mesembryanthemum crystallinum

The common ice plant, Mesembryanthemum crystallinum, is a halophytic (salt-loving) member of the Aizoaceae, which switches from C3 photosynthesis to Crassulacean acid metabolism (CAM) when exposed to salinity or water-deficit stress. CAM is a metabolic adaptation of photosynthetic carbon fixation that improves water use efficiency by shifting net CO2 uptake to the night, thereby reducing transpirational water loss. To improve our understanding of the molecular genetic underpinnings and control mechanisms for Crassulacean acid metabolism (CAM) and other salinity stress response adaptations, a total of 9733 expressed sequence tags (ESTs) from cDNAs derived from leaf tissues of well-watered and salinity-stressed (0.5 M NaCl for 30 and 48 h) were characterized. Clustering and assembly of these ESTs resulted in the identification of a total of 3676 tentative unique gene sequences (1249 tentative consensus sequences and 2427 singleton ESTs) expressed in leaves of ice plant under unstressed and salinity stressed conditions. The same number (2782) of ESTs from each library (total=8346 ESTs) were randomly selected and analyzed to compare expression profiles among the control and salt stressed leaf tissues. EST frequencies for transcripts encoding CAM-related enzymes, pathogenesis-related, senescence-associated, cell death-related, and stress-related proteins such as heat shock proteins (HSPs), chaperones, early light-inducible proteins, ion homeostasis, antioxidative stress, detoxification, and biosynthetic enzymes for osmoprotectants increased 2-12-fold in cDNA libraries constructed from salt stressed plants. In contrast, the frequency of ESTs encoding light-harvesting and photosystem complexes and C3 photosynthetic enzymes decreased 4-fold overall following salinity stress with transcripts for ribulose bisphosphate carboxylase/oxygenase (RuBisCO) subunits decreasing 7-fold. Moreover, stressed plants contained a higher percentage of ESTs encoding novel and/or functionally unknown proteins. The rapid discovery of both known and unknown genes related to stress responses in M. crystallinum demonstrates the great utility of EST analysis in unraveling the complex set of adaptive mechanisms contributing to water use efficiency (CAM) and salinity tolerance.

Gene expression and EST analyses of Ustilago maydis germinating teliospores

Ustilago maydis grows in its host Zea mays eliciting the formation of obvious tumors that are full of black teliospores. Teliospores are thick-walled, dormant, diploid cells that have evolved for dispersal and survival of the pathogen. Their germination leads to new rounds of infection and is temporally linked to meiosis. We are investigating gene expression during teliospore germination to gain insight into the control of this process. Here we identify genes expressed through creation of an expressed sequence tag (EST) library. We generated 2871 ESTs that are assembled into 1293 contiguous sequences. Based upon a blast search similarity cutoff of E < or =10(-5) 38% of all contigs were orphans while 62% showed similarity to sequences in the protein database. Analyses of blast searches were used to functionally classify genes. Northern hybridizations using specific cDNA clones reveal a relative level of expression consistent with the number of sequences per contig. Identified genes and expression information provide a base for genome annotation of U. maydis and further investigation of teliospore germination and pathogenesis.

Identification of genes possibly related to storage root induction in sweet potato

To identify genes related to initiation of storage root development in sweet potato, a cDNA library was constructed with early stage storage roots (0.3-1 cm in diameter). Single-pass sequences of the 5' ends of 2859 sweet potato cDNA clones were assembled into 483 clusters and 442 singletons. Comparison of sweet potato expressed sequence tags (ESTs) to nodulation/tumorigenesis-related sequence databases (nodule-, tumor-, potato tuber- and development-related sequences) revealed that homologs of 39 sweet potato EST sequences potentially involved in gene regulation, signal transduction and development were present in at least one of the nodulation/tumorigenesis-related sequence databases. Northern blot analyses of these 39 sequences identified 22 differentially expressed genes in early stage storage root and fibrous root. These differentially expressed genes will be potential candidates for research to elucidate the molecular processes related to sweet potato storage root induction.

Immune gene discovery by expressed sequence tags generated from hemocytes of the bacteria-challenged oyster, Crassostrea gigas

An expressed sequence tag program was undertaken to isolate genes involved in defense mechanisms of the Pacific oyster, Crassostrea gigas. Putative function could be assigned to 54% of the 1142 sequenced cDNAs. We built a public database where all EST information are accessible through numerous search profiles (http://www.ifremer.fr/GigasBase). Based on sequence similarities we identified 20 genes that may be implicated in immune function. We investigated the expression of four of these genes during bacterial challenge of oysters. Three of them were induced in response to challenge lending support to their involvement in oyster immunity. Moreover, four other genes were highly homologous to components of the NF-kappa B signaling pathway which is involved in innate immune response in Drosophila and mammals. Altogether, our results open a new way to investigate the immune response in mollusks.