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Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [stabilome]

ABSTRACT: Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [stabilome]

PROVIDER: PRJNA479437 | ENA |

REPOSITORIES: ENA

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Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [stabilome]

Project description:Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives compared to wild type (stabilome) in the stationary phase. The stabilome is an original dynamic transcriptome-based analysis to measure the rates of mRNA degradation at the genome scale. We have combined the analysis of stabilome with the steady state concentrations of mRNAs (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. The stabilome demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. This work allowed the roles of RNase R and PNPase in coordinating E. coli RNA metabolism to be discussed and PNPase to be identified as a central player of the degradation machinery in stationary phase.

2018-12-10 | GSE116576 | GEO

Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [transcriptome]

2018-12-10 | GSE116577 | GEO

Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase

Project description:Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase

| PRJNA479820 | ENA

Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [transcriptome]

Project description:Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase [transcriptome]

| PRJNA479436 | ENA

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.

2019-11-13 | GSE117635 | GEO

Exoribonucleases coordinate degradation and expression of mRNAs in Escherichia coli at the stationary phase

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-12-10 | GSE116652 | GEO

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

2005-12-03 | GSE3729 | GEO

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

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

| PRJNA482775 | ENA

Acinetobacter oleivorans DR1 : WT stationary phase vs. aqsR mutant stationary phase

Project description:Transcriptional profiling of A. oleivorans DR1 cells comparing wild type stationary phase cells with aqsR mutant stationary phase cells.

2013-02-16 | GSE44347 | GEO

The roles of 3’-exoribonucleases and the exosome in trypanosome mRNA degradation

Project description:The roles of 3’-exoribonucleases and the exosome in trypanosome mRNA degradation; 30 min after actinomycin D +sinefungin, RNAi against CAf1, CNOT10, PAN2. These are really old data that hadn't been deposited.The datasets called RNA1, RNA2, RNA3 and RNA4 are almost certainly, from their location in the folder and from new alignment results, from the RRP45 RNAi.

2021-03-11 | E-MTAB-10260 | biostudies-arrayexpress

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