Integrative analysis of the salt stress response in cyanobacteria
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PROVIDER: PRJNA729426 | ENA |
REPOSITORIES: ENA
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Project description:In many habitats, microorganisms are exposed to high or fluctuating salinities and evolved specific acclimation strategies to thrive in those environments. Euryhaline microorganisms can grow in a broad range of salinities, from low ionic strength like freshwater up to twofold seawater salinities. Here, we analyzed the salt acclimation process of the euryhaline model cyanobacterium Synechocystis sp. PCC 6803 in a multi-omics approach by combining transcriptomic, proteomic and metabolomic analyses. The Overall, the comparison of salt-induced proteome and transcriptome changes revealed a good correleation between the proteome and transcriptome that as most the majority of stably up-regulated proteins also showed elevated mRNA transcript levels. However, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably also involves the action of small regulatory RNAs acting at the post-transcriptional level. In addition to the rapid and stable steady upregulation of compatible solute biochemistry, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably involves the action of small regulatory RNAs. Moreover, the coordinated induction of several stress proteins known to be involved in iron and oxidative stress responses as well as of mechano-sensitive channels was observed. Based on these data, an extended salt stimulon can be defined comprising many proteins directly or indirectly related to compatible solute metabolism, ion and water movements as well as a defined set of small regulatory RNAs. Moreover, the massive accumulation of the compatible solute glucosylglycerol had large impact on the overall carbon and nitrogen metabolism. Our comprehensive data set provides the basis for future attempts to engineer cyanobacterial salt tolerance and to search for processes regulating this important environmental acclimation process.
2022-01-07 | GSE174316 | GEO
Project description:Microorganisms evolved specific acclimation strategies to thrive in environments of high or fluctuating salinities. Here, salt acclimation in the model cyanobacterium Synechocystis sp. PCC 6803 was analyzed by integrating transcriptomic, proteomic and metabolomic data. A dynamic reorganization of the transcriptome occurred during the first hours after salt shock, e.g. involving the upregulation of genes to activate compatible solute biochemistry balancing osmotic pressure. The massive accumulation of glucosylglycerol then had a measurable impact on the overall carbon and nitrogen metabolism. In addition, we observed the coordinated induction of putative regulatory RNAs and of several proteins known for their involvement in other stress responses. Overall, salt-induced changes in the proteome and transcriptome showed good correlations, especially among the stably up-regulated proteins and their transcripts. We define an extended salt stimulon comprising proteins directly or indirectly related to compatible solute metabolism, ion and water movements, and a distinct set of regulatory RNAs involved in post-transcriptional regulation. Our comprehensive data set provides the basis for engineering cyanobacterial salt tolerance and to further understand its regulation.
| S-EPMC8670252 | biostudies-literature
Project description:ra06-02_staygreen - drought and salt stress response - Modification of the transcriptome by the eskimo mutation and response to stress. - Individual plants were grown in Fertiss clods in a culture chamber. 3 treatments were made to the plants : control, drought and salt. Keywords: gene knock out,treated vs untreated comparison
2008-09-11 | GSE10384 | GEO
Project description:Adaptation to changes in the environment is crucial for the viability of all organisms. Although the importance of calcineurin in the stress response has been highlighted in filamentous fungi, little is known about the involvement of ion-responsive genes and pathways in conferring salt tolerance without calcium signaling. In this study, high-throughput RNA-seq was used to investigate salt stress-induced genes in the parent, ΔcnaB, and ΔcnaBΔcchA strains of Aspergillus nidulans, which differ greatly in their salt adaption under salt stress. In total, 2,884 differentially expressed genes including 1,382 up- and 1,502 down-regulated genes were identified. Secondary transporters, which were up-regulated to a greater extent in ΔcnaBΔcchA than in the parent or ΔcnaB strains, are likely to play important roles in response to salt stress. Furthermore, 36 genes were exclusively up-regulated in the ΔcnaBΔcchA mutant under salt stress. Functional analysis of differentially expressed genes revealed that genes involved in transport, heat shock protein binding, and cell division processes were exclusively activated in ΔcnaBΔcchA. Overall, our findings reveal that secondary transporters and stress-responsive genes may play crucial roles in salt tolerance to bypass the requirement for the CchA-calcineurin pathway, contributing to a deeper understanding of the mechanisms that influence fungal salt stress adaption in Aspergillus.
2017-10-04 | GSE100353 | GEO
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.
2011-08-16 | GSE16765 | GEO
Project description:Purpose:to identify the response of Frankia sp.strain CcI6 to salt and osmotic stress. Frankia sp.strain CcI6 was exposed to salt and osmotic stress for seven days. RNAseq analysis was carried out to ge an insight into the response of the bacterium under salt and osmotic stress conditons
2017-09-22 | GSE95217 | GEO
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. 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.
2011-08-15 | E-GEOD-16765 | biostudies-arrayexpress
Project description:ra06-02_staygreen - drought and salt stress response - Modification of the transcriptome by the eskimo mutation and response to stress. - Individual plants were grown in Fertiss clods in a culture chamber. 3 treatments were made to the plants : control, drought and salt. Keywords: gene knock out,treated vs untreated comparison 6 dye-swap - CATMA arrays
2008-09-10 | E-GEOD-10384 | biostudies-arrayexpress
Project description:Generally, salt stress causes both osmotic and ionic stress. To discern the effects of osmotic and ionic specific effects on Burma mangrove transcriptome, we conducted expression profiling in 500 mM NaCl or 1M solbitol treated leaves. This study will lead to a rapid and effective selection of gene that confers high salt tolerance in transgenic plants and to a comprehensive understanding of plant stress response. Keywords: Stress response
2007-03-10 | GSE7228 | GEO
Project description:rs06-07_della - della-regulation of salt stress responses - Identification of DELLA-dependent dowtream targets in response to salt stress - Aim was to determine downstream target of DELLA proteins involved in salt stress tolerance. Wt, ga1-3, penta seeds were sterilized, sown on MS agar plates then put for stratification for 3 days at 4degreeC. Plates were placed in growth cabinet for 9 days. Seedlings were transferred to 24 well-plates, with 2 seedlings per well (0.5 ml MS liquid per well). Plates were placed in the same condition for 3 days. Finally, NaCl were added (final concentration 200 mM), except for the control. The salt treatment was applied for 30 min and 1h. Treatment was stopped by freezing in liquid nitrogen. Keywords: dose response,gene knock out,time course
2008-07-01 | GSE8556 | GEO