RNase J depletion leads to massive changes in mRNA abundance in<i>Helicobacter pylori</i>

Redko, Yulia; Galtier, Eloïse; Arnion, Hélène; Darfeuille, Fabien; Sismeiro, Odile; Coppée, Jean‐Yves; Médigue, Claudine; Weiman, Marion; Cruveiller, Stéphane; Reuse, Hilde De

doi:10.1080/15476286.2015.1132141

Cited by 24 publications

(33 citation statements)

References 43 publications

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“…Finally, it must be remembered that aRNase J is the homolog of bacterial RNase J (bRNase J) which was shown to be critical in mRNA decay and rRNA maturation pathways and to be part of a degradosome-like complex (29,62,63). bRNase J which can carry 5'-3' exo-and endo-RNase activities was shown to associate with proteins identified as, among others, helicase-like proteins and a polynucleotide phosphorylase (PNPase).…”

Section: Discussionmentioning

confidence: 99%

RNA processing machineries in Archaea: the 5’-3’ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’ exoribonucleolytic RNA exosome machinery

Phung

Etienne

Batista

et al. 2019

Preprint

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A network of RNA helicases, endoribonucleases, and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focused on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5'-3' exoribonuclease of the β-CASP family conserved in Euryarchaea, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, and that this occurs in the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses demonstrated that aRNase J interplay with ASH-Ski2 and the Csl4 cap exosome subunit. These in vitro data are strengthened by our phylogenomic studies showing a taxonomic co-distribution of aRNase J and ASH-Ski2 among the archaeal phylogeny. Finally, our T. barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome or polysomes that is stressed in absence of ASH-Ski2. While aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest, for the first time, a fundamental role of β-CASP RNase/helicase complex in archaeal RNA metabolism. Finally, our results position aRNase J at the junction of RNA surveillance and translation processes, thus opening new perspectives and evolutionary scenario on RNA processing players in Archaea.

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Section: Discussionmentioning

confidence: 99%

RNA processing machineries in Archaea: the 5’-3’ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’ exoribonucleolytic RNA exosome machinery

Phung

Etienne

Batista

et al. 2019

Preprint

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“…Like E. coli, it is a proteobacterium, and it therefore contains an ortholog of EcRppH. However, as an epsilonproteobacterium, other aspects of RNA turnover in H. pylori more closely resemble B. subtilis, as it lacks RNase E and instead is thought to utilize two other ribonucleases, RNase J and the endonuclease RNase Y, to degrade RNA (5,8,9). As a result, it is likely that the monophosphorylated decay intermediates generated by HpRppH are degraded exonucleolytically by RNase J, probably with help from RhpA, a DEXD-box RNA helicase with which RNase J forms a complex in H. pylori (8).…”

Section: Journal Of Biological Chemistry 1943mentioning

confidence: 99%

“…As a result, it is likely that the monophosphorylated decay intermediates generated by HpRppH are degraded exonucleolytically by RNase J, probably with help from RhpA, a DEXD-box RNA helicase with which RNase J forms a complex in H. pylori (8). Indeed, Ͼ80% of the likely and possible RppH targets that were previously examined for RNase J sensitivity (5,8,9) appear to be degraded by an RNase J-dependent mechanism (supplemental Tables S2 and S3). RNase J is also capable of functioning as an endonuclease (8), but this activity is not dependent on the 5Ј-phosphorylation state of RNA (11) and therefore is unlikely to contribute significantly to the degradation of transcripts productively targeted by RppH.…”

Section: Journal Of Biological Chemistry 1943mentioning

confidence: 99%

Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets

Bischler

Hsieh

Resch

et al. 2017

Journal of Biological Chemistry

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Edited by Patrick SungRNA degradation is crucial for regulating gene expression in all organisms. Like the decapping of eukaryotic mRNAs, the conversion of the 5-terminal triphosphate of bacterial transcripts to a monophosphate can trigger RNA decay by exposing the transcript to attack by 5-monophosphate-dependent ribonucleases. In both biological realms, this deprotection step is catalyzed by members of the Nudix hydrolase family. The genome of the gastric pathogen Helicobacter pylori, a Gramnegative epsilonproteobacterium, encodes two proteins resembling Nudix enzymes. Here we present evidence that one of them, HP1228 (renamed HpRppH), is an RNA pyrophosphohydrolase that triggers RNA degradation in H. pylori, whereas the other, HP0507, lacks such activity. In vitro, HpRppH converts RNA 5-triphosphates and diphosphates to monophosphates. It requires at least two unpaired nucleotides at the 5 end of its substrates and prefers three or more but has only modest sequence preferences. The influence of HpRppH on RNA degradation in vivo was examined by using RNA-seq to search the H. pylori transcriptome for RNAs whose 5-phosphorylation state and cellular concentration are governed by this enzyme. Analysis of cDNA libraries specific for transcripts bearing a 5-triphosphate and/or monophosphate revealed at least 63 potential HpRppH targets. These included mRNAs and sRNAs, several of which were validated individually by half-life measurements and quantification of their 5-terminal phosphorylation state in wild-type and mutant cells. These findings demonstrate an important role for RppH in post-transcriptional gene regulation in pathogenic Epsilonproteobacteria and suggest a possible basis for the phenotypes of H. pylori mutants lacking this enzyme.

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“…In the Gram-negative pathogen Helicobacter pylori , we recently demonstrated the existence of a minimal RNA degradosome composed of two partners ( 11 – 13 ). H. pylori is a spiral-shaped bacterium that persistently colonizes the stomach of more than half of the human population worldwide ( 14 ) and causes chronic gastritis, peptic ulcers, mucosa-associated lymphoid tissue (MALT) lymphoma, and gastric carcinoma, which is responsible for 800,000 deaths per year in the world ( 15 , 16 ).…”

Section: Introductionmentioning

confidence: 99%

“…The RNA degradosome of H. pylori is composed of the essential RNase J protein and of RhpA, its sole DEAD box RNA helicase ( 11 – 13 ). In vitro , each protein of this complex stimulates the activity of the other, demonstrating that they form a functional RNA degradosome ( 11 ).…”

Section: Introductionmentioning

confidence: 99%

The RNase J-Based RNA Degradosome Is Compartmentalized in the Gastric Pathogen Helicobacter pylori

Tejada-Arranz

Galtier

Mortaji

et al. 2020

mBio

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Posttranscriptional regulation is a major level of gene expression control in any cell. In bacteria, multiprotein machines called RNA degradosomes are central for RNA processing and degradation, and some were reported to be compartmentalized inside these organelleless cells. The minimal RNA degradosome of the important gastric pathogen Helicobacter pylori is composed of the essential ribonuclease RNase J and RhpA, its sole DEAD box RNA helicase, and plays a major role in the regulation of mRNA decay and adaptation to gastric colonization. Here, the subcellular localization of the H. pylori RNA degradosome was investigated using cellular fractionation and both confocal and superresolution microscopy. We established that RNase J and RhpA are peripheral inner membrane proteins and that this association was mediated neither by ribosomes nor by RNA nor by the RNase Y membrane protein. In live H. pylori cells, we observed that fluorescent RNase J and RhpA protein fusions assemble into nonpolar foci. We identified factors that regulate the formation of these foci without affecting the degradosome membrane association. Flotillin, a bacterial membrane scaffolding protein, and free RNA promote focus formation in H. pylori. Finally, RNase J-GFP (RNase J-green fluorescent protein) molecules and foci in cells were quantified by three-dimensional (3D) single-molecule fluorescence localization microscopy. The number and size of the RNase J foci were found to be scaled with growth phase and cell volume as previously reported for eukaryotic ribonucleoprotein granules. In conclusion, we propose that membrane compartmentalization and the regulated clustering of RNase J-based degradosome hubs represent important levels of control of their activity and specificity. IMPORTANCE Helicobacter pylori is a bacterial pathogen that chronically colonizes the stomach of half of the human population worldwide. Infection by H. pylori can lead to the development of gastric pathologies such as ulcers and adenocarcinoma, which causes up to 800,000 deaths in the world each year. Persistent colonization by H. pylori relies on regulation of the expression of adaptation-related genes. One major level of such control is posttranscriptional regulation, which, in H. pylori, largely relies on a multiprotein molecular machine, an RNA degradosome, that we previously discovered. In this study, we established that the two protein partners of this machine are associated with the membrane of H. pylori. Using cutting-edge microscopy, we showed that these complexes assemble into hubs whose formation is regulated by free RNA and scaled with bacterial size and growth phase. Organelleless cellular compartmentalization of molecular machines into hubs emerges as an important regulatory level in bacteria.

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RNase J depletion leads to massive changes in mRNA abundance inHelicobacter pylori

Cited by 24 publications

References 43 publications

RNA processing machineries in Archaea: the 5’-3’ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’ exoribonucleolytic RNA exosome machinery

RNA processing machineries in Archaea: the 5’-3’ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’ exoribonucleolytic RNA exosome machinery

Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets

The RNase J-Based RNA Degradosome Is Compartmentalized in the Gastric Pathogen Helicobacter pylori

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