Escherichia coli
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ABSTRACT:
PROVIDER: PRJNA93017 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The Escherichia coli endoribonucleases RNase E (Rne) and RNase G (Rng) have sequence similarity and broadly similar sequence specificity. Whereas the absence of Rne normally is lethal, we show here that E. coli bacteria that lack the rne gene can be made viable by overexpression of Rng. Rng-complemented cells accumulated precursors of 5S ribosomal RNA (rRNA) and the RNA component of RNase P (i.e. M1 RNA), indicating that normal processing of these Rne-cleaved RNAs was not restored by RNase G; additionally, neither 5S rRNA nor M1 RNA was generated from precursors by RNase G cleavage in vitro. Using DNA microarrays containing 4405 Escherichia coli open reading frames (ORFs), we identified mRNAs whose steady-state level was affected by Rne, Rng or the N-terminal catalytic domain of RNase E. Most transcript species affected by RNase E deficiency were also elevated in an rne deletion mutant complemented by Rng. However, approximately 100 mRNAs that accumulated in Rne-deficient cells were decreased by rng-complemention, thus identifying targets whose processing or degradation may be the basis for RNase E essentiality. Remarkably prominent in this group were mRNAs implicated in energy-generating pathways or in the synthesis or degradation of macromolecules.
2005-07-11 | E-SMDB-1515 | biostudies-arrayexpress
Project description:The Escherichia coli endoribonucleases RNase E (Rne) and RNase G (Rng) have sequence similarity and broadly similar sequence specificity. Whereas the absence of Rne normally is lethal, we show here that E. coli bacteria that lack the rne gene can be made viable by overexpression of Rng. Rng-complemented cells accumulated precursors of 5S ribosomal RNA (rRNA) and the RNA component of RNase P (i.e. M1 RNA), indicating that normal processing of these Rne-cleaved RNAs was not restored by RNase G; additionally, neither 5S rRNA nor M1 RNA was generated from precursors by RNase G cleavage in vitro. Using DNA microarrays containing 4405 Escherichia coli open reading frames (ORFs), we identified mRNAs whose steady-state level was affected by Rne, Rng or the N-terminal catalytic domain of RNase E. Most transcript species affected by RNase E deficiency were also elevated in an rne deletion mutant complemented by Rng. However, approximately 100 mRNAs that accumulated in Rne-deficient cells were decreased by rng-complemention, thus identifying targets whose processing or degradation may be the basis for RNase E essentiality. Remarkably prominent in this group were mRNAs implicated in energy-generating pathways or in the synthesis or degradation of macromolecules. Set of arrays that are part of repeated experiments Keywords: Biological Replicate
2005-08-13 | GSE3123 | GEO
Project description:RNase E is involved in the post-transcriptional gene regulation of a broad spectrom of RNA species involving in different biological processes. Frequently RNase E cooperates with other protein components to form a RNA degradosome to regulate gene expression. Here, we aim to study the impact of RNA degradosome formation on E. coli gene expression by comparing the whole transcriptiome isolate from wildtype Rne strain and Rne C-terminal truncated strain that deleting the RNA degradosome binding domain. We choose to study the bacterial growth conditions in soft-agar culture because it is a condition more silimar to that in the gut of warm-blooded organism compared to merely liquid culture condition.Here we found different groups of transcript that was affected by Rne C-termianl truncation mutant. Altogether, our data give insight into the complex regulation of RNase E/RNA degradosome in transcripts involved in different biological processes of soft-agar growing system.
2025-12-04 | GSE282514 | GEO
Project description:RNase P is an essential enzyme found across all domains of life that is responsible for the 5’-end maturation of precursor tRNA transcripts. Since its discovery in the 1970s, numerous studies have sought to elucidate the mechanisms and biochemistry governing RNase P function. However, much remains unknown about the regulation of RNase P expression, the turnover and degradation of the enzyme, and the mechanisms underlying the phenotypes and complementation of specific RNase P mutations. In Escherichia coli, the temperature-sensitive rnpA49 mutation in the protein subunit of RNase P has arguably been one of the most well-studied and commonly used mutations for examining the enzyme’s activity in vivo. Here we report for the first time naturally-occurring temperature-resistant suppressor mutations of E. coli strains carrying the rnpA49 allele. We find that rnpA49 strains can partially compensate the temperature-sensitive defect via gene amplifications of either RNase P subunit (rnpA49 or rnpB) or by the acquisition of loss-of-function mutations in Lon protease or RNase R. Our results agree with previous plasmid overexpression and gene deletion complementation studies and importantly suggest the involvement of Lon protease in the degradation and/or regulatory pathway(s) of the mutant protein subunit of RNase P. This work offers novel insight into the behavior and complementation of the rnpA49 allele in vivo and provides direction for follow-up studies regarding RNase P regulation and turnover.
2024-05-15 | PXD047498 | Pride
Project description:The Escherichia coli endoribonucleases RNase E (Rne) and RNase G (Rng) have sequence similarity and broadly similar sequence specificity. Whereas the absence of Rne normally is lethal, we show here that E. coli bacteria that lack the rne gene can be made viable by overexpression of Rng. Rng-complemented cells accumulated precursors of 5S ribosomal RNA (rRNA) and the RNA component of RNase P (i.e. M1 RNA), indicating that normal processing of these Rne-cleaved RNAs was not restored by RNase G; additionally, neither 5S rRNA nor M1 RNA was generated from precursors by RNase G cleavage in vitro. Using DNA microarrays containing 4405 Escherichia coli open reading frames (ORFs), we identified mRNAs whose steady-state level was affected by Rne, Rng or the N-terminal catalytic domain of RNase E. Most transcript species affected by RNase E deficiency were also elevated in an rne deletion mutant complemented by Rng. However, approximately 100 mRNAs that accumulated in Rne-deficient cells were decreased by rng-complemention, thus identifying targets whose processing or degradation may be the basis for RNase E essentiality. Remarkably prominent in this group were mRNAs implicated in energy-generating pathways or in the synthesis or degradation of macromolecules. Set of arrays that are part of repeated experiments Biological Replicate
2005-08-13 | E-GEOD-3123 | biostudies-arrayexpress
Project description:We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of different strains of the cyanobacterium Synechocystis sp. PCC6803. Comparison encompassed wild-type Synechocystis (WT), a strain overexpressing RNase E and RNase HII (rne(WT)) and a strain overexpressing 5’-sensing-deficient RNase E and RNase HII (rne(5p)). Analysis of changing 5'-monophosphorylated ends revealed 5’ sensing depedent processing sites on a transcriptome-wide level.
2023-01-20 | GSE184824 | GEO
Project description:We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of a thermo-sensitive and a wild-typic RNase E mutant strain of the cyanobacterium Synechocystis sp. PCC6803 (rne(Ts) and rne(WT)) before and after a heat shock. Analysis of changing 5'-monophosphorylated ends revealed RNase E depedent processing sites on a transcriptome-wide level.
2021-07-30 | GSE180316 | GEO
Project description:Localization of RNase E to the inner membrane in Escherichia coli is well documented, but the functional consequences of this localization are largely unknown. Here we characterize the rne∆MTS strain, which expresses cytoplasmic RNase E (cRNase E). CsrB and CsrC regulatory RNAs are stabilized in the rne∆MTS strain resulting in leaky glycogen expression. There is a small but significant global slowdown in mRNA degradation with no bias considering function or localization of encoded proteins. RNase E is a stable protein, but cRNase E is unstable with a half-life equal to the doubling time of exponentially growing cells. cRNase E instability is compensated by increased synthesis. Co-purification experiments show that cRNase E associates with RhlB, enolase and PNPase to form a cytoplasmic RNA degradosome. Measurements in multiple turnover assays show that there is no difference in Km or kcat between cRNase E and RNase E. In contrast to the global slowdown of mRNA degradation, the inactivation of a ribosome-free lacZ transcript is faster in the rne∆MTS strain. We discuss how the association of RNase E with the inner cytoplasmic membrane is important for carbon storage regulation, degradation of polyribosomal mRNA, protection of ribosome-free transcripts from inactivation and stability of RNase E.
2019-11-25 | GSE118058 | GEO
Project description:The ribonucleases (RNases) E and J are essential in Escherichia coli and Bacillus subtilis, respectively. Sinorhizobium meliloti contains both, the rne gene encoding RNase E and the rnj gene encoding RNase J. The transcriptomes of the S. meliloti Rm2011 wild type, and rne and rnj mutants were compared.
2017-01-21 | E-MTAB-5435 | biostudies-arrayexpress
Project description:Fitness and functional landscapes of the E. coli RNase III gene rnc
| PRJNA887445 | ENA