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

ABSTRACT: 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.

ORGANISM(S): Escherichia coli K-12 Escherichia coli BL21(DE3)

PROVIDER: GSE100022 | GEO | 2019/06/01

REPOSITORIES: GEO

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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

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2006-03-08 | GSE4394 | GEO

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

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2006-01-06 | GSE3978 | GEO

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

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

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

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

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

2006-01-06 | GSE3977 | GEO

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2019-04-01 | PXD012662 | Pride

Small RNA interactome revealed through crosslinking of the degradosome

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2017-02-14 | GSE77463 | GEO

Attachment of the RNA degradosome to the inner cytoplasmic membrane of Escherichia coli prevents wasteful degradation of rRNA intermediates in ribosome assembly.

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2023-01-16 | PXD038317 | Pride

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