Global transcriptional regulation of Sphingomonas melonis TY in response to hyperosmotic stress
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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:sRNA participates in hyperosmotic stress response regulation in Sphingomonas melonis TY
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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)
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Project description:Sphingomonas melonis TY strain:TY Genome sequencing and assembly
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Project description:Drought and salinity are ubiquitous environmental factors that pose hyperosmotic threats to microorganisms and impair their efficiency in performing environmental functions. However, bacteria have developed various responses and regulatory systems to cope with these abiotic challenges. Posttranscriptional regulation plays vital roles in regulating gene expression and cellular homeostasis, as hyperosmotic stress conditions can lead to the induction of specific small RNA molecules (sRNAs) that participate in stress response regulation. Here, we report a candidate functional sRNA landscape of Sphingomonas melonis TY under hyperosmotic stress, and 18 sRNAs were found with a clear response to hyperosmotic stress. These findings will help in the comprehensive analysis of sRNA regulation in Sphingomonas species. Weighted correlation network analysis revealed a 263 nucleotide sRNA, SNC251, which was transcribed from its own promoter and showed the most significant correlation with hyperosmotic response factors. Deletion of snc251 affected biofilm formation and multiple cellular processes, including ribosome-related pathways, aromatic compound degradation, and the nicotine degradation capacity of S. melonis TY, while overexpression of SNC251 facilitated biofilm formation by TY under hyperosmotic stress. Two genes involved in the TonB system were further verified to be activated by SNC251, which also indicated that SNC251 is a trans-acting sRNA. Briefly, this research reports a landscape of sRNAs participating in the hyperosmotic stress response in S. melonis and reveals a novel sRNA, SNC251, which contributes to the S. melonis TY biofilm formation and thus enhances its hyperosmotic stress response ability.IMPORTANCESphingomonas species play a vital role in plant defense and pollutant degradation and survive extensively under drought or salinity. Previous studies have focused on the transcriptional and translational responses of Sphingomonas under hyperosmotic stress, but the posttranscriptional regulation of small RNA molecules (sRNAs) is also crucial for quickly modulating cellular processes to adapt dynamically to osmotic environments. In addition, the current knowledge of sRNAs in Sphingomonas is extremely scarce. This research revealed a novel sRNA landscape of Sphingomonas melonis and will greatly enhance our understanding of sRNAs' acting mechanisms in the hyperosmotic stress response.
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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.
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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.
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