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Acetylation regulates the oligomerization state and activity of RNase J, the major ribonuclease of Helicobacter pylori

ABSTRACT: In Helicobacter pylori, the major actor in post-transcriptional regulation is an RNA degradosome assembly composed of the essential ribonuclease RNase J and the DEAD-box RNA helicase RhpA. Here, we describe the oligomeric state and post-translational modifications of this protein complex. Our crystal structure of RNase J at 2.75 Å resolution reveals a homotetrameric quaternary state, and solution studies show that purified RNase J forms monomers and dimers, that RhpA is a monomer, and that the two proteins interact to form a stable complex with a 1:1 stoichiometry. Using mass spectrometry, we observed that RNase J is acetylated on multiple residues, one of which, K649, is important for RNase J oligomerization. Mutations targeting this residue and others affect the dimerization and in vitro activity of RNase J, suggesting that the dimer is the active form. In H. pylori, we observed that several of the identified acetylated residues impact on cell morphology, suggesting their importance for RNase J cellular function. Using H. pylori mutants, we found that several pathways contribute to RNase J acetylation. We propose acetylation as a regulatory level controlling RNase J properties and as a consequence the activity of the H. pylori RNA degradosome.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Helicobacter Pylori B8

SUBMITTER: Thibaut Douché

LAB HEAD: Hilde De Reuse

PROVIDER: PXD027670 | Pride | 2023-12-12

REPOSITORIES: Pride

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RNase R is associated in a functional complex with the RhpA DEAD-box RNA helicase in Helicobacter pylori

Project description:Ribonucleases (RNases) are central actors in post-transcriptional regulation, a major level of regulation of gene expression in all cells. This control plays an important role in the bacterial pathogen Helicobacter pylori, although only the function of RNase J was characterized so far. Here, we studied the RNase R enzyme from H. pylori, a 3’-5’ exoribonuclease whose ortholog in Escherichia coli was reported to display, in addition, helicase activity and to be able to hydrolyze RNA substrates with double stranded structures. We observed that HpRNase R protein does not carry the domains responsible for helicase activity in E. coli and accordingly that the purified protein is unable to degrade in vitro RNA molecules with secondary structures. The RNase R helicase domain loss is widespread among the Campylobacterota and occurred gradually during their evolution. Furthermore, an in vivo interaction between HpRNase R and RhpA, the sole DEAD-box RNA helicase of H. pylori, was discovered. Phylogenomics suggests that this interaction might occur in other bacteria of the phylum Campylobacterota. Purified RhpA facilitates the degradation of double stranded RNA substrates by HpRNase R, showing that this complex is functional. HpRNase R has a minor role of in 5S rRNA maturation and, as shown by RNA-Seq, few targets in H. pylori all of them being included in the RhpA regulon. In conclusion, we describe a new type of RNase R that lacks some of the features that were considered as hallmarks of RNase R proteins, but that has co-opted another RNA helicase, which we hypothesize helps it accomplish some of its functions in vivo.

2021-06-19 | E-MTAB-10045 | biostudies-arrayexpress

The acetylated lysine residues of RNase II (TPA&control)

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Salt regulated gene expression in Helicobacter pylori

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2010-06-25 | E-GEOD-7183 | biostudies-arrayexpress

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2016-07-27 | PXD003285 | Pride

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. Keywords: RNA_stability_design

2006-01-06 | GSE3978 | GEO

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

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

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

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