Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA248095 | ENA |
REPOSITORIES: ENA
Similar Datasets
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Project description:We measured the mRNA abundance in E.coli using RNAseq to calculate mRNA lifetimes. The data is used in support of a larger paper on the proteome and transcriptome of E.coli.
2010-07-30 | GSE21341 | GEO
Project description:DNA damage induces the mutations that drive bacterial adaption, evolution, and antibiotic escape. Both mutagenic and non-mutagenic DNA damage repair is coordinated by the SOS response, but despite extensive work, the functions of some SOS-induced genes remain obscure. Here, we clarify the function of Escherichia coli SbmC (GyrI). Despite its proposed function as a gyrase inhibitor, cells either lacking or overexpressing SbmC instead exhibit phenotypes consistent with a role in limiting DNA damage and cellular variation. Importantly, SbmC levels inversely correlate with E. coli mutation rate. Excess SbmC limits mutation whereas loss of SbmC increases mutation, possibly because ∆sbmC cells variably induce the SOS response, including mutagenic DNA Pol V. We additionally show that SbmC is dispensable for survival in the presence of double-strand break inducing drugs but is required to limit their mutational effects. Finally, evolutionary analysis indicates that bacterial SbmC homologs maintain their small molecule-binding domain but not the gyrase interacting residues identified in E. coli. Together, our findings suggest that SbmC-like proteins may bind to a yet-unknown cofactor to limit DNA damage and organismal evolution.
2026-03-11 | GSE324174 | GEO
Project description:We measured the mRNA abundance in E.coli using RNAseq to calculate mRNA lifetimes. The data is used in support of a larger paper on the proteome and transcriptome of E.coli. Comparison of mRNA abundance over time, after the addition of transcription inhibitor, rifampicin. Center: Harvard University
2010-07-30 | E-GEOD-21341 | biostudies-arrayexpress
Project description:Abstract: RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes This SuperSeries is composed of the SubSeries listed below.
2006-03-08 | GSE4394 | GEO
Project description:Mutation accumulation evolution experiment
| PRJNA295762 | ENA
Project description:Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains
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