Natural variation of transcriptional networks in Arabidopsis thaliana in response to salt stress
ABSTRACT: Arabidopsis ecotypes of Sha and Ler showed differences in tolerance to salinity stress. A previous study indicated that a premature stop codon resulting in a truncated Response to ABA and Salt 1 (RAS1) protein in Sha contributes to the increased salt tolerance relative to Ler ecotype. Sha exhibited higher germination rates and longer roots on MS plate, presumably due to the decreased ABA sensitivity in Sha. More Sha plants also survived in soil after salt treatment with relatively lower electrolyte leakage when compared to Ler. Transcriptome analysis revealed that expression levels of many genes were changed between Sha and Ler ecotypes and by salt treatments. About 500 transcripts were commonly changed by at least one salinity effect and one ecotype effect, and 171 of them were co-regulated by all four comparisons. Transcripts involved in redox, secondary metabolism, auxin metabolism, photosynthesis, cell wall, and protein synthesis were mainly down-regulated by salinity effects, while transposable element genes, microRNA and antisense sequences, histone superfamily genes, and biotic stress related genes were significantly changed by Sha ecotype effects and only slightly by salinity. Several metabolic pathways such as stress, TCA, hormone/lipid/secondary metabolism, redox, development, and GO terms involved in stress, oxidation, and defense response were enriched by both salinity and ecotype effects. Ninety-five highly inducible genes were identified as candidates of RAS1 target genes and the functions involved hormone metabolism, biotic stress, RNA, DNA synthesis, protein metabolism, cell, and microRNA metabolism. All these results indicated that the Sha ecotype was possibly preconditioned to abiotic stress relative to Ler through regulation of signaling pathways and stress responsive gene expression. These comparative transcriptomic and analytical results also confirm the complexity of ABA responses and salt stress tolerance mechanisms, and they suggest additional targets for improving tolerance. Ten days old seedlings of two Arabidopsis ecotypes, Sha and Ler, were treated with 100 mM NaCl on MS plate. Plant materials were collected for RNA extraction at 4th days after treatments.
Project description:Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity, have profound effects on crop performance and yeilds To analyze such responses, we initially compared transcriptome changes in ten Arabidopsis thaliana ecotypes using cold, heat, high light, salt and flagellin treatments as single stress factors or their double combinations. Arabidopsis thaliana plants of ecotypes (Col, Ler, C24, Cvi, Kas1, An1, Sha, Kyo2, Eri and Kond) were subjected to the following stress treatments: Salt, Cold, Heat, High Light (HL), Salt+Heat, Salt+HL, Cold+HL, Heat+HL, as well as FLG (Flagellin, flg22 peptide), Cold+FLG, Heat+FLG
Project description:Loss of the seed-specific WRKY transcription factor WRKY43 confers enhanced tolerance towards high salt, high osmolarity and low temperature with respect to seed germination. wrky43 loss of function lines display increased inhibition of seed germination in response to exogenous ABA, while WRKY43 overexpression lines are more tolerant towards exogenous ABA. The opposing effect of the wrky43 mutant on salt and ABA tolerance is reminiscent of fatty acid desaturase mutants. Loss of WRKY43 enhances polyunsaturated fatty acid content, particularly 18:2 and 18:3 in TAGs and Phospholipids. Gene chip arrays show that ABA-induced regulation of FUSCA3, ZAT10 and seed storage proteins are absent in the wrky43 mutant. Promoter-Luciferase studies confirm direct regulation of ZAT10 by WRKY43 and suggest indirect regulation of FUS3 and SSPs. In summary WRKY43 acts as a positive regulator of ABA-dependent gene regulation and of fatty acid desaturation that finally results in enhanced tolerance to abiotic stress. 2 biological replicates of Arabidopsis thaliana Ler-0 wildtype and wrky43 muatnt seeds were compared after incubation in liquid 0.5 MS media with 2 µM ABA for 4 days
Project description:Abiotic stresses such as salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein, 1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance. In this study, the gene expression patterns across two organs including leaves and roots at seedling stage were characterized under control, salinity, salinity+ABA treatments by using the Affymetrix rice microarray platform based on a salinity tolerant rice line derived from IR64.
Project description:Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity. RNA from roots from Control and salt treated hydroponically grown seedlings were extracted and subjected to microarray analysis
Project description:We have used a strain of Tobacco etch potyvirus (TEV) experimentally adapted to Arabidopsis thaliana ecotype Ler-0 to infect a set of seven A. thaliana plant ecotypes(Col-0, Ei-2, Wt-1, ler-0, Oy-0, St-0). Each ecotype was inoculated with the same amount of the virus. Using commercial microarrays containing probes Arabidopsis thaliana ssp. Col-0 plant transcripts, we explored the effect of viral infection in the plant transcriptome This microarray can be useful to study gene activity of Arabidopsis thaliana associated with response to virus infection. For ecotypes ST-0, Wt-1, Ler-0, Di-2 there are five biological replicates and for ecotype Oy-0 there are three. As control we used four technical replicates of each ecotype, but five for Ler-0. Rows and columns are numbered as scanned by a GenePix Scanner (barcode on the bottom, DNA on the front surface).
Project description:Gene expression patterns in roots of Camelina sativa with enhanced salinity tolerance arising from growth in soil treated with plant growth promoting bacteria producing 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase) or from expression of the corresponding acdS gene in transgenic lines. Salinity stress negatively affects crop production. However in camelina, grown in soils treated with PGPB producing 1-aminocyclopropane-1-carboxylate deaminase (acdS ) or transgenic lines expressing acdS exhibited increased salinity tolerance. AcdS reducing the level of stress ethylene to below the point where it is inhibitory to growth. Gene expression patterns in roots responding to salt stress was affected by the expression of acdS under the control of CaMV 35S or root-specific (rolD) promoters in transgenic lines, or by growth in soils treated with endophytic PGPB producing acdS indicate that the number of the genes were differentially expressed were more assigned to genome III in transgenic plants however in PGPB treated plants the number of the genes were differentially expressed were almost equally assigned to all three genomes. Different promoter may induce different set or even different homeologues genes in camelina with probably the same function in response to salt stress. Though root is not a photosynthetic tissue reduction of the ethylene in root cells has positive effect on plant photosynthetic machinery. The expression of the genes involved in minor CHO metabolism was up-regulated mainly in roots of acdS contain plants during salt stress. Moderate reduction in ethylene production has positive effect on root growth during salt stress but reduction of the ethylene higher than a certain level has negative effect on root growth due to reduction of the expression of the genes involved in root cell elongation. AcdS gene modulating the level of ROS in cells in the level that induce ROS signaling but preventing cellular damage by make a balance on up and down-regulation of the genes involved in oxidation-reduction process in root cells under salinity stress. The acdS containing PGPB (8R6) were mostly effected the ethylene signaling and ABA biosynthesis and signaling in positive way but transgenic line depends to the promoter affecting Auxin, JA and BR signaling or biosynthesis. Overall design: Four experimental conditions were tested: the parental Camelina (DH55), a transgenic with acdS contitutively expressed (35S::acdS), a transgenic with acdS most highly expressed in roots (rolD::acdS), and DH55 exposed to a plant growth promoting bacteria expressing acdS (8R6). Camelina roots (DH55, 35S::acdS, rolD::acdS, PGPB (8R6)) with salt treatment were analyzed. 3 replicates of each were compared.
Project description:Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control and salt-stressed seedlings. De novo assembly of 184 million high-quality paired-end reads yielded 42,327 unique transcripts longer than 300 bp with RPKM ≥1. When compared with non-redundant proteins, we could annotate 67% unigenes obtained in our study. Based on the mapping to expressed sequence tags (ESTs), 52.6% unigenes are novel compared to EST data available for B. juncea and constituent genomes. Differential expression analysis revealed altered expression of 1469 unigenes in response to salinity stress. Of these, 587, mainly associated with ROS detoxification, sulfur assimilation and calcium signaling pathways, are up regulated. Notable of these is RSA1 (SHORT ROOT IN SALT MEDIUM 1) INTERACTING TRANSCRIPTION FACTOR 1 (RITF1) homolog up regulated by >100 folds in response to stress. RITF1, encoding a bHLH transcription factor, is a positive regulator of SOS1 and several key genes involved in scavenging of salt stress-induced reactive oxygen species (ROS). Further, we performed comparative expression profiling of key genes implicated in ion homeostasis and sequestration (SOS1, SOS2, SOS3, ENH1, NHX1), calcium sensing pathway (RITF1) and ROS detoxification in contrasting cultivars, B. juncea and B. nigra, for salinity tolerance. The results revealed higher transcript accumulation of most of these genes in B. juncea var. CS52 compared to salt-sensitive cultivar even under normal growth conditions. Together, these findings reveal key pathways and signaling components that contribute to salinity tolerance in B. juncea var. CS52. We report transcriptome sequencing of two-weeks-old seedlings of B. juncea var. CS52 under normal growth conditions (CTRL) and in response to salinity stress (SS) using Illumina paired-end sequencing
Project description:Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects. In these studies we sought to examine differential gene expression in response to salinity for two widely used Arabidopsis thaliana ecotypes, Wassilewskija (Ws) and Columbia (Col), and a single gene mutation (glabrous, gl1-1) in the Col background (Col(gl)), in relation to genetic, phenotypic, and fitness differences. Growth analyses were performed with seedlings germinated on culture media and growth chamber-grown plants carried through the full life cycle. Transcriptome analyses were performed with salt treated and control growth-chamber grown plants six days post initiation of salt stress. Ws plants had the least salt injury and highest dry matter accumulation and seed production in salt stressed conditions. ELPs among genoytypes and in response to 100 mM NaCl were enriched for genes associated with response to stress, including stress-associated transcription factors, heat shock and redox metabolism genes, and R genes. Application of salt resulted in many more transcripts up- or down-regulated in Col and Ws than in Col(gl). Many of the transcripts influenced by salt in Col were already altered in gl1-1 plants in the absence of salt, although Col(gl) plants did not show any detectable signs of stress, or effects on fecundity in the absence of salt treatment. The majority of salt-induced transcriptional changes that occurred in Ws also occurred in Col, suggesting common salt stress responses in these two ecotypes. Many more genes were affected by salt in Col than Ws, however, possibly reflecting the greater salt injury observed for Col. There was minimal overlap between the transcripts that differed for Ws and Col prior to salt treatment and those that were subsequently affected by salt stress. Thus, many genes conferring comparative salt stress tolerance in Ws likely differ from those whose expression levels are modified in response to salt stress. These studies demonstrate transcriptional variation among Arabidopsis genotypes in response to salt stress. Greater transcriptome differences did not necessarily correspond with greater genetic difference or phenotypic differences in morphology, fecundity, and resistance to salt stress. These results suggest that depending on circumstance, transcriptional changes can reflect response to injury, facilitate adaptive expression of fitness-associated traits, or allow for phenotypic buffering to minimize the impact of genetic changes. Overall design: Three Arabidopsis genotypes were grown in the growth chamber in the absence and presence of salt stress. Plants from 20 days after sowing (6 days after salt treatment) were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and salt treatment combination.
Project description:High salinity is one of the major environmental factors, which hampers plant growth, development and productivity. To better understand the regulatory mechanisms by which plants cope with salt stress, we used genetic approaches to identify salt hypersensitive mutant 9 (sahy9), a new allele of apum23, in Arabidopsis thaliana. The sahy9/apum23 mutant seedlings display postgemination developmental arrest and later become bleached under agar plates supplemented with various salt stressors. Transcriptomic and proteomic analyses of the salt-treated sahy9/apum23 and wild-type seedlings revealed differential expression of genes with similar functional categories, primarily including cellular and metabolic processes, and abiotic and biotic stress responses. However, the consistency of gene expression at both transcript and protein levels is low (), suggesting the involvement of posttranscriptional processing in salt response. Furthermore, the altered gene/protein expression mediated by SAHY9/APUM23 in salt sensitivity is involved in several functional groups, particularly in ABA biosynthesis and signaling, abiotic stress response, LEA proteins, and ribosome biogenesis-related genes. Importantly, NCED3, a key gene involved in ABA biosynthesis, and major ABA responsive marker genes, such as RD20 and RD29B, are down-regulated at both transcript and protein levels in sahy9/apum23 under salt stress. Consistently, lower contents of ABA and proline, and expression changes of a subset of LEA proteins also support the nature of sahy9/apum23 showing salt hypersensitivity. Collectively, these data suggest that SAHY9/APUM23-mediated salt response is associated with ABA signaling pathway and its downstream stress responsive or tolerant genes. Overall design: 150 mM NaCl treatment 1 day for Col-0 and sahy9-1 after 10 days germination. Two independent experiments were performed.
Project description:The molecular response to salt exposure was studied in the leaves of a S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed. On the other hand, we observed the induction of various kinds of transcription factors implicated in osmotic stress response via ABA-dependent or ABA-independent pathways but also in plant defense pathways. This revealed a crosstalk between abiotic and biotic stress responses during salt exposure, which activated several adaptation mechanisms including HSP, LEA, dehydrins and PR proteins. Gene expression changes related to carbohydrate and amino acid metabolism were also observed, pointing at putative modifications at the metabolic level. Overall design: Gene expression has been followed at two different time-points (one and three day after salinity treatment) and conditions: salt-treatment (150 mM NaCl) and control conditions. For each time-point and conditions 3 independent biological replicates were sampled.