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MRNA Decay in E. Coli Degradosome Mutants and their Parental Strains

ABSTRACT: mRNA decay in E. Coli degradosome mutants and their parental strains following transcriptional arrest with rifampicin. 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. An RNA stablity experiment design type examines stability and/or decay of RNA transcripts. Keywords: RNA_stability_design

ORGANISM(S): Escherichia coli

PROVIDER: GSE3978 | GEO | 2006/01/06

SECONDARY ACCESSION(S): PRJNA104883

REPOSITORIES: GEO

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mRNA Decay in E. Coli Degradosome Mutants and their Parental Strains

Project description:mRNA decay in E. Coli degradosome mutants and their parental strains following transcriptional arrest with rifampicin. 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. An RNA stablity experiment design type examines stability and/or decay of RNA transcripts. User Defined

2006-01-05 | E-GEOD-3978 | biostudies-arrayexpress

Global analysis of Escherichia coli RNA degradosome function

Project description:This SuperSeries is composed of the following subset Series: GSE3977: Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains GSE3978: mRNA Decay in E. Coli Degradosome Mutants and their Parental Strains 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 Refer to individual Series

2006-03-07 | E-GEOD-4394 | biostudies-arrayexpress

Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains

Project description:Comparative transcript abundance in E. Coli degradosome mutants and their parental strains. 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. A genetic modification design type is where an organism(s) has had genetic material removed, rearranged, mutagenized or added, such as knock out. Computed

2006-01-05 | E-GEOD-3977 | biostudies-arrayexpress

Global analysis of Escherichia coli RNA degradosome function

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

Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains

2006-01-06 | GSE3977 | GEO

Small RNA interactome revealed through crosslinking of the degradosome

Project description:UV-crosslining of protein-RNA complexes was employed to capture sRNA-mRNA interactions occuring on the RNA degradosome protein, RNase E, in enterohaemorhaggic E. coli. Abstract from associated mansucript: In many organisms small regulatory RNAs (sRNA) play important roles in the regulation of gene expression by base-pairing to specific target mRNAs. In enterohaemorrhagic E. coli (EHEC), sRNAs are encoded by both the “core” genome and in numerous horizontally acquired pathogenicity islands. To identify functionally important sRNA-target RNA interactions we applied crosslinking and sequencing of hybrids (CLASH) to the core degradosome component RNase E in EHEC. RNase E was shown to bind to many classes of RNA, confirming the wide distribution of degradosome targets. These included several hundred sRNA-mRNA duplexes, and the distribution of non-templated oligo(A) tails indicated that the sRNA target RNase E-mediated cleavage at these interaction sites. Functional repression of target mRNAs was confirmed for the core sRNA RyhB, and the pathogenicity-associated sRNA Esr41. In the case of Esr41, three confirmed target mRNAs participate in iron accumulation and the ∆esr41 strain showed increased growth under conditions of iron limitation. We conclude that CLASH can be used to identify functional targets for bacterial sRNAs.

2017-02-14 | GSE77463 | GEO

RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli

Project description:Abstract: Ribonuclease E (RNase E) has a key role in mRNA degradation and the processing of catalytic and structural RNAs in E. coli. We report the discovery of an evolutionarily conserved 17.4 kDa protein, here named RraA (regulator of ribonuclease activity A) that binds to RNase E and inhibits RNase E endonucleolytic cleavages without altering cleavage site specificity or interacting detectably with substrate RNAs. Overexpression of RraA circumvents the effects of an autoregulatory mechanism that normally maintains the RNase E cellular level within a narrow range, resulting in the genome-wide accumulation of RNase E-targeted transcripts. While not required for RraA action, the C-terminal RNase E region that serves as a scaffold for formation of a multiprotein degradosome complex modulates the inhibition of RNase E catalytic activity by RraA. Our results reveal a possible mechanism for the dynamic regulation of RNA decay and processing by inhibitory RNase binding proteins. This SuperSeries is composed of the SubSeries listed below.

2006-03-08 | GSE4383 | GEO

A natively unstructured RNA/protein-recognition core in the E. coli RNA degradosome facilitates riboregulation

Project description:The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. The core of the assembly is provided by the endoribonuclease RNase E, one of the largest E. coli proteins. The C-terminal half of RNase E is predicted to be predominantly unstructured and is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane. We demonstrate that a subassembly of the degradosome - comprising a 248-residue segment of the C-terminal part of RNase E, the DEAD-box helicase RhlB, and the glycolytic enzyme enolase - serves as a flexible recognition centre that can co-recruit small regulatory RNA (sRNA) molecules and the RNA chaperone Hfq into an effector complex. The association of enolase with the degradosome impacts on carbon utilisation pathways under changing metabolic conditions, most likely by facilitating recruitment and the activity of sRNAs. Our results support a model in which the degradosome captures substrates and regulatory RNAs through the recognition core, facilitates pairing to cognate transcripts, and presents the target to the ribonuclease active sites of the greater assembly for cooperative degradation or processing.

2019-06-01 | GSE100022 | GEO

RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli

Project description:This SuperSeries is composed of the following subset Series: GSE3869: Effects of rraA deletion on transcription GSE3870: Effects of rraA overexpression on transcription Abstract: Ribonuclease E (RNase E) has a key role in mRNA degradation and the processing of catalytic and structural RNAs in E. coli. We report the discovery of an evolutionarily conserved 17.4 kDa protein, here named RraA (regulator of ribonuclease activity A) that binds to RNase E and inhibits RNase E endonucleolytic cleavages without altering cleavage site specificity or interacting detectably with substrate RNAs. Overexpression of RraA circumvents the effects of an autoregulatory mechanism that normally maintains the RNase E cellular level within a narrow range, resulting in the genome-wide accumulation of RNase E-targeted transcripts. While not required for RraA action, the C-terminal RNase E region that serves as a scaffold for formation of a multiprotein degradosome complex modulates the inhibition of RNase E catalytic activity by RraA. Our results reveal a possible mechanism for the dynamic regulation of RNA decay and processing by inhibitory RNase binding proteins. Refer to individual Series

2006-03-07 | E-GEOD-4383 | biostudies-arrayexpress

Analysis of mRNA decay intermediates in Bacillus subtilis 3' exoribonuclease and RNA helicase mutant strains

Project description:The Bacillus subtilis genome encodes four 3’ exoribonucleases: polynucleotide phosphorylase (PNPase), RNase R, RNase PH, and YhaM. Previous work showed that PNPase, encoded by the pnpA gene, is the major 3’ exonuclease involved in mRNA turnover; in a pnpA deletion strain, numerous mRNA decay intermediates accumulate. Whether B. subtilis mRNA decay occurs in the context of a degradosome complex is controversial. In this study, global mapping of mRNA decay intermediate 3’ ends within coding sequences was performed in strains that were either deleted for, or had an inactivating point mutation in, the pnpA gene. The pattern of 3’ end accumulation in these strains was highly similar, suggesting that mRNA decay was not occurring in the context of a degradosome, whose structure would be affected by the absence of PNPase. A comparison with mapped 3’ ends in a strain lacking CshA, the major RNA helicase, indicated that different mRNAs may require both PNPase and CshA for efficient decay. RNA-seq analysis of strains lacking RNase R suggested that this enzyme did not play a major role in mRNA turnover in the wild-type strain. Strains were constructed that contained only one of the four known 3’ exoribonucleases. When RNase R was the only 3’ exonuclease present, it was able to degrade a model mRNA efficiently, showing processive decay even through a strong stem-loop structure that inhibits PNPase processivity. Strains containing only RNase PH or only YhaM were also insensitive to this RNA secondary structure, suggesting the existence of another, as-yet unidentified, 3’ exoribonuclease.

2022-01-03 | GSE192670 | GEO

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