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RNase G complementation of rne null mutation identifies functional interrelationships with RNase E

ABSTRACT: 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

ORGANISM(S): Escherichia coli

PROVIDER: GSE3123 | GEO | 2005/08/13

SECONDARY ACCESSION(S): PRJNA93017

REPOSITORIES: GEO

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RNase G complementation of rne null mutation identifies functional interrelationships with RNase E

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

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Project description:Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the post-transcriptional regulation of gene expression. A key endoribonuclease in many bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria such as E. coli have evolved a tightly functioning feedback regulation of RNase E, which is mediated in cis by the rne 5′-untranslated region (5′UTR); however, the mechanisms involved in the control of RNase E in other bacteria have largely remained unknown. Cyanobacteria rely on solar light as energy source for their photosynthetic lifestyle, despite the inherent ultraviolet (UV) irradiation. Here, we revealed the global gene expression response in the cyanobacterium Synechocystis sp. PCC 6803 after exposure to UV light and discovered a unique response of RNase E: a rapidly increasing enzymatic activity although stability of the protein was lowered . In parallel, we observed a substantial stabilization of the full-length mRNA specifically after UV-C treatment, while the 5′UTR accumulated under all conditions. Mapping of RNA 3′ends and in vitro cleavage assays revealed that RNase E cleaves within a stretch of six consecutive uridine residues within the rne 5′UTR, indicating the autoregulation of RNase E via its own 5′UTR. These observations imply that RNase E in cyanobacteria evolved as a substantial contributor in re-shaping the transcriptome during the UV stress response, that its required activity level is maintained despite enhanced turnover of the protein, and that the underlying mechanism involves a feedback mechanism acting on a uridine-rich element within the rne 5′UTR.

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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.

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