Global transcriptional regulation of Sphingomonas melonis TY in response to hyperosmotic stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Sphingomonas melonis TY
PROVIDER: GSE212614 | GEO | 2022/09/06
REPOSITORIES: GEO
Similar Datasets
Project description:Drought and salinity are most ubiquitous environmental factors that causing hyperosmotic threats to Sphingomonas and impairs their efficiency of performing environmental functions. However, bacteria have developed various responses and regulation systems to coping with these abiotic challenges. Among which post-transcriptional regulation plays vital roles in regulating gene expression and cellular homeostasis, as hyperosmotic stress conditions could lead to induction of specific small RNA (sRNA) that participates in stress response regulation. Here, we report a candidate functional sRNAs landscape of S. melonis which could help for comprehensive analyses of sRNA regulation in Sphingomonas species. WGCNA analysis revealed a 263 nt sRNA SNC251 which transcribed from its own promoter and shew the most dramatic correlation coefficient with hyperosmotic factors was characterized. An in vivo translation-reporter system constructed in this study revealed positive regulation and feedback mechanisms between the SNC251 and nicotine degradation genes. Deletion of snc251 affected multiple cellular processes and nicotine degradation capacity of S. melonis TY, while overexpression of SNC251 facilitated the biofilm formation capability of TY under hyperosmotic stress. Two genes of TonB system were further verified could be activated by SNC251, which also means SNC251 is a trans-acting small RNA. Briefly, this research reported a summary of sRNAs which participate in hyperosmotic stress response in S. melonis TY and revealed a novel sRNA SNC251 which is necessary for hyperosmotic stress response.
2023-02-07 | GSE224545 | GEO
Project description:Sphingomonas melonis TY strain:TY Genome sequencing and assembly
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Project description:Transcriptome of the wild type (WT) of S. melonis TY and snc137 deleted cells carrying either a plasmid overexpressing SNC137 (Δsnc137 comp.), or an empty control vector (Δsnc137)
2023-02-24 | GSE224594 | GEO
Project description:Sphingomonas melonis TY Genome sequencing and assembly
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Project description:Oral streptococci metabolize carbohydrate to produce organic acids, not only decrease the environmental pH, but also increase osmolality of dental plaque fluid due to tooth demineralization and consequent calcium and phosphate accumulation. Thus, to persevere in the dental plaque, acidogenic bacteria should evolve sophisticated molecular machineries to counter the detrimental effect of elevated osmolality. This study was aimed to obtain a global view on strategies taken by streptococcus mutans to deal with physiologically relevant elevated osmolality, and preserves within a cariogenic dental plaque. We investigated phenotypic change of S. mutans biofilm upon sub-lethal level of hyperosmotic challenge. We found that hyperosmotic condition was able to initiate S. mutans biofilm dispersal by reducing both microbial content and extracellular polysaccharides matrix. We then used DNA microarray with qPCR validation to systemically investigate the underlying molecular machinery of this bacteria in response to hyperosmotic stimuli. Among those identified 50 differentially regulated genes, down-regulation of gtfB and comC were believed to be responsible for the observed biofilm dispersal. Further analysis of microarray data showed significant up-regulation of genes and pathways involved in carbohydrates metabolism. Specific genes involved in heat shock response and acid tolerance were also upregulated, indicating potential cross-talk between hyperosmotic and other environmental stress. Based on the data obtained in this study, we believe that although hyperosmotic condition may induce significant stress response on S. mutans, this cariogenic bacterium has evolved sophisticated molecular machineries to counter those elicited detrimental effects. In the meantime, it will take full advantage of these environmental stimuli to better fit the fluctuating environments within oral cavity, and thus emerge as numeric-predominant bacteria under cariogenic conditions. A six-chip study using total RNA recovered from mid-logarithmic phase of S. mutans UA159 from three separate cultures of strains submitted for 15 minutes to hyperosmotic stimuli (0.4M NaCl) and three separate cultures of strains kept under no stress condition.
2013-08-31 | E-GEOD-47170 | biostudies-arrayexpress
Project description:We examined the possible effect of hyperosmotic stress on Arabidopsis transcriptome using mRNA-seq. We found that the transcriptome is reprogrammed in response to hyperosmotic stress, in a DCP5-dependent.
2022-10-01 | GSE214366 | GEO
Project description:The wild type (WT) of S. melonis TY and snc251 deleted cells carrying either a plasmid overexpressing SNC251 (Δsnc251 comp.), or an empty control vector (Δsnc251) were grown in Luria-Bertani (LB) culture to an OD600 of 0.6.
2023-02-11 | PXD040071 | iProX
Project description:A screening process was used to determine hyperosmotic as well as cold stress tolerance of a diverse set of Listeria monocytogenes strains and was based on the capacity to grow at sub lethal levels of NaCl and 4°C. Analysis of gene expression in cells adapted to cold and hyperosmotic stress revealed significant strain specificity in terms of individual gene expression profiles though general patterns of expression within functional gene subsets were largely similar. . Strain ATCC19115 revealed 150 significantly up- and 146 down-regulated genes in cells adapted to both hyperosmotic and cold stress, 82 up- and 56 down-regulated genes were matching in response to both stresses in strain 70-1700, whereas ScottA, a relatively stress-tolerant strain, showed up-regulation of 77 genes whilst 106 genes were significantly down-regulated. Among these homologously expressed genes only 22 were found to be significantly up-regulated and only 7 were down-regulated in all three strains adapted to hyperosmotic stress and cold temperature, suggesting a dominating strain specific response. Overall adaptation to hyperosmotic and low temperature growth conditions in three L. monocytogenes strains were found to have many parallels, especially when examined using a statistically-based ontological approach. Evidence was presented for strong activation of genes associated with protein synthesis, in particular those coding proteins of the ribosome and involved directly in transcription. Genes associated with DNA maintenance; modification to cell envelope, and cell division were also up-regulated. On the other hand strong suppression of genes associated with carbohydrate metabolism and transport as well as flagella assembly was evident in stress adapted cells most likely due to energy preservation via CodY regulon. This suggests that adaptation to these adverse conditions engages similar mechanisms to cope with the induced stressful environments. The microarray component of the experiments had the aim of determining: i) To examine the gene expression responses of three L. monocytogenes strains that had different intrinsic salt resistances following adaptation to hyperosmotic stress. ii) To examine the gene expression responses of three L. monocytogenes strains that had different intrinsic cold tolerances following adaptation to cold stress. iii) To evaluate common pathways of adaptation to hyperosmotic and cold stresses
2013-05-04 | GSE46612 | GEO
Project description:Mouse embryonic stem cells (ESCs) display pluripotency features characteristic of the inner cell mass of the blastocyst. ESC cultures are highly heterogeneous and include a rare population of cells, which recapitulate characteristics of the 2-cell embryo, referred to as 2-cell-like cells (2CLCs). Whether and how ESC and 2CLC respond to environmental cues has not been fully elucidated. Here, we investigate the impact of mechanical stress on the reprogramming of ESC to 2CLC. We show that hyperosmotic stress induces 2CLC and that this induction can occur even after a recovery time from hyperosmotic stress, suggesting a memory response. Hyperosmotic stress in ESCs leads to accumulation of reactive-oxygen species (ROS) as well as ATR checkpoint activation. Importantly, preventing either elevated ROS levels or ATR activation impairs hyperosmotic-mediated 2CLC induction. We further show that ROS generation and the ATR checkpoint act within the same molecular pathway in response to hyperosmotic stress to induce 2CLCs. Altogether, these results shed light on the response of ESC to mechanical stress and on our understanding of 2CLC reprogramming.
2023-08-15 | GSE231475 | GEO
Project description:Analysis of mRNA stability in S. cerevisiae in connection to hyperosmotic stress at different time points following mild hyperosmotic shock in Saccharomyces cerevisiae cells.
2009-01-22 | E-TABM-622 | biostudies-arrayexpress