Examining the Protein Interactome and Subcellular Localization of RNase J2 Complexes in Streptococcus mutans

Mu, Rong; Shinde, Pushkar; Zou, Zhengzhong; Kreth, Jens; Merritt, Justin

doi:10.3389/fmicb.2019.02150

Cited by 10 publications

(18 citation statements)

References 48 publications

(97 reference statements)

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“…Zhang & Hong, 2009), Hfq (Y. Zhang & Hong, 2009) Arabidopsis thaliana (chloroplast) RHON 1 (Stoppel et al, 2012) T A B L E 3 CshA (major) (Mu et al, 2019) Ldh (major) (Mu et al, 2019), Enolase (Mu et al, 2019) FtsZ (Mu et al, 2019), DnaK (Mu et al, 2019), DnaJ (Mu et al, 2019) Streptococcus pyogenes…”

Section: Compositional Variation Of the Rna Degradosomementioning

confidence: 99%

Phase‐separated bacterial ribonucleoprotein bodies organize mRNA decay

et al. 2020

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In bacteria, mRNA decay is controlled by megadalton scale macromolecular assemblies called, "RNA degradosomes," composed of nucleases and other RNA decay associated proteins. Recent advances in bacterial cell biology have shown that RNA degradosomes can assemble into phase-separated structures, termed bacterial ribonucleoprotein bodies (BR-bodies), with many analogous properties to eukaryotic processing bodies and stress granules. This review will highlight the functional role that BR-bodies play in the mRNA decay process through its organization into a membraneless organelle in the bacterial cytoplasm. This review will also highlight the phylogenetic distribution of BRbodies across bacterial species, which suggests that these phase-separated structures are broadly distributed across bacteria, and in evolutionarily related mitochondria and chloroplasts.

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Section: Compositional Variation Of the Rna Degradosomementioning

confidence: 99%

Phase‐separated bacterial ribonucleoprotein bodies organize mRNA decay

et al. 2020

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“…RNase Y is, as expected, membrane associated, but RNase J1, which is one of its proposed interacting partners, does not follow the same distribution, being cytoplasmic ( 25 , 33 ). In contrast, in a recent work, a fraction of RNase J2 of Streptococcus mutans was found to localize at the membrane ( 34 ). In B. subtilis , RNase Y was recently found to assemble at the membrane into dynamic short-lived foci that increased in number and size upon rifampicin treatment or deletion of the Y-complex, a protein complex that modulates RNase Y activity ( 27 ).…”

Section: Discussionmentioning

confidence: 71%

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 Y is, as expected, membrane associated, but RNase J1, which is one of its proposed interacting partners, does not follow the same distribution, being cytoplasmic (26,32). In contrast, in a recent work a fraction of RNase J2 of Streptococcus mutans was found to localize at the membrane (33). In B. subtilis, The RNase J-GFP fusion was further used to identify factors that modify its cellular distribution.…”

Section: Discussionmentioning

confidence: 78%

The RNase J-based RNA degradosome is compartmentalized in the gastric pathogenHelicobacter pylori

Tejada-Arranz

Galtier

Mortaji³

et al. 2020

Preprint

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Importance 46Helicobacter pylori is a bacterial pathogen that chronically colonizes the stomach of 47 half of the human population worldwide. Infection by H. pylori can lead to the 48 development of gastric pathologies such as ulcers and adenocarcinoma, that causes 49 up to 800.000 deaths in the world each year. Persistent colonization by H. pylori relies 50 on regulation of the expression of adaptation-related genes. One major level of such 51 control is post-transcriptional regulation that, in H. pylori, largely relies on a multi-52 protein molecular machine, an RNA-degradosome, that we previously discovered. In 53 this study, we established that the two protein partners of this machine are associated 54 to the membrane of H. pylori. Using cutting-edge microscopy, we showed that these 55 complexes assemble into hubs whose formation is regulated by free RNA and scaled 56 with bacterial size and growth phase. Cellular compartmentalization of molecular 57 machines into hubs emerges as an important regulatory level in the organelle-less 58 bacteria. 59 61Post-transcriptional regulation is one of the most important levels of control of gene 62 expression in every kingdom of life. Ribonucleases (RNases) are key enzymes in post-63 transcriptional regulation, involved in RNA maturation and degradation. RNases often 64 act in multi-protein complexes that are designated exosomes in Eukarya and Archaea 65 and RNA degradosomes in bacteria and chloroplasts [for a review, see (1)]. RNA-66 degradosomes were established in several bacterial species and are defined by two 67 core components, an RNase and an RNA helicase (2). These RNA helicases belong 68 to the DEAD-box family and act by unwinding RNA, thereby allowing access of the 69 ribonucleases to some of their target sites on RNAs. RNA degradosomes are 70 widespread and vary in composition, although only few have been described in detail 71(1). Most RNA degradosomes reported so far are assembled on the essential 72 endoribonuclease RNase E, like in Escherichia coli, Caulobacter crescentus or 73 Mycobacterium tuberculosis (3-5). In the E. coli degradosome, RNase E serves as a 74 scaffold for the binding of the DEAD-box RNA helicase RhlB, the metabolic enzyme 75 enolase and the 3'-5' exoribonuclease PNPase (2, 6). Nevertheless, our recent 76 analysis on a representative set of 1,535 bacterial genomes revealed that RNase E is 77 absent from about half of the bacterial species (1). Most of the remaining bacteria 78 (47%), that lack RNase E, have either RNase Y or RNase J enzymes or both. RNase 79 J and RNase Y, first identified in Bacillus subtilis, both display endoribonucleolytic 80 activities but RNase J acts in addition as a 5'-3' exoribonuclease (7, 8). Although being 81 unrelated proteins, these enzymes constitute functional homologues of RNase E. In 82 the Gram-positive bacteria Staphylococcus aureus and B. subtilis, RNA 83 degradosomes comprising RNase Y and RNase J have been proposed, but to date 84 20). Interestingly, similarly to the situation in H. pylori, the E. ...

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Examining the Protein Interactome and Subcellular Localization of RNase J2 Complexes in Streptococcus mutans

Cited by 10 publications

References 48 publications

Phase‐separated bacterial ribonucleoprotein bodies organize mRNA decay

Phase‐separated bacterial ribonucleoprotein bodies organize mRNA decay

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

The RNase J-based RNA degradosome is compartmentalized in the gastric pathogenHelicobacter pylori

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