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Transcriptome of a malO deletion mutant of Clostridium perfringens during stationary phase growth.

ABSTRACT: The MalNO is a putative two-component signal transduction system, previously known as the VirJI sytem. MalO is the putative cognate response regulator of the MalN sensor histidine kinase. Based on previous evidence that suggested the plc gene, encoding α-toxin, was upregulated during stationary phase in the malO mutant, microarrays were used to analyse the transcriptome of a malO mutant during stationary phase growth.

ORGANISM(S): Clostridium perfringens str. 13

PROVIDER: GSE28699 | GEO | 2014/12/22

SECONDARY ACCESSION(S): PRJNA138913

REPOSITORIES: GEO

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Transcriptome of a malO deletion mutant of Clostridium perfringens during stationary phase growth.

Project description:The MalNO is a putative two-component signal transduction system, previously known as the VirJI sytem. MalO is the putative cognate response regulator of the MalN sensor histidine kinase. Based on previous evidence that suggested the plc gene, encoding ?-toxin, was upregulated during stationary phase in the malO mutant, microarrays were used to analyse the transcriptome of a malO mutant during stationary phase growth. Total RNA was isolated from stationary phase cells of the malO mutant and the wild-type control. Gene expression levels were compared between the malO mutant and wild-type strain 13

2014-12-22 | E-GEOD-28699 | biostudies-arrayexpress

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Clostridium perfringens str. 13

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Project description:The cold shock proteins belong to a family of RNA binding proteins presenting a highly conserved domain, called cold shock domain (CSD). They are involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. Here we investigate the role of CspC in C. crescentus stationary phase and the molecular mechanisms underlying gene regulation by this protein. A global transcriptional profiling experiment comparing cspC and the wild type strain both at exponential and stationary phases was carried out. The results showed that the absence of cspC affected the transcription of 20 genes at exponential phase and 65 genes at stationary phase. Genes encoding enzymes of the glyoxylate cycle were severely downregulated in the mutant at stationary phase. The stationary phase-induced RNA binding protein CspC has an important role in gene expression at this phase. It is required for the expression of the essential gene sciP, the ECF sigma factor sigU, as well as of the genes for the glyoxylate cycle enzymes and for oxidative stress response.

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Defining the impact of exoribonucleases in the shift between exponential and stationary phases

Project description:The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.

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Oxidative stress in stationary-phase cultures

Project description:Background: As carbon sources are exhausted, Saccharomyces cerevisiae cells exhibit reduced metabolic activity and cultures enter stationary phase. We asked whether cells in stationary-phase cultures respond to additional stress at the level of transcript abundance. Results: Microarrays were used to quantify changes in transcript abundance in cells from stationary-phase cultures. In response to oxidative stress, more than 800 mRNAs increased within 1 minute. A significant number of these mRNAs encode proteins involved in stress responses. We tested whether mRNA increases were due to new transcription, rapid poly-adenylation of message (which would not be detected by microarrays), or potential release of mature mRNA sequestered in the cell but insoluble during RNA isolation. Examination of the response to oxidative stress in an RNA polymerase II mutant, rpb1-1 suggested new transcription was not required. Quantitative RT-PCR analysis of a subset of these transcripts further suggested that essentially all isolated transcripts were polyadenylated. In contrast, over 1000 transcripts increased after protease treatment of cell-free lysates from stationary-phase but not exponentially growing cultures. We also determined that oxidative stress and temperature upshift led to the release of different transcripts, suggesting that mRNA release is stress specific. Conclusions: A large number of mRNAs are sequestered in a protease-labile, rapidly releasable form in cells in stationary-phase cultures but not exponentially growing cultures. The differences between mRNAs released by protease treatment and those observed with oxidative stress and temperature upshift, suggest different stresses cause the release of different transcripts. We hypothesize that P-bodies are involved in this sequestration. Keywords: stress response

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