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

Abstract

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. ...

A peptide of a type I toxin−antitoxin system induces Helicobacter pylori morphological transformation from spiral shape to coccoids

“…Fractionation and Immunoblotting. H. pylori fractionation was performed as in Tejada-Arranz et al (57). H. pylori strains were grown in the absence or presence of 1 mM IPTG.…”

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

“…pylori to obtain crystals were unsuccessful. As we previously reported (Tejada-Arranz et al, 2020b), the N-terminal part of RNase J (first 120 amino acids) that is specific of the Helicobacter species is predicted to be an intrinsically disordered region (IDR). After truncating this region, well diffracting crystals were obtained from this RNase J form comprising residues 137-691 (from H. pylori strain 26695, uniprot P56185).…”

“…RhpA is the sole DEAD-box RNA helicase encoded by the H. pylori genome and is essential for colonization in the mouse infection model (El Mortaji et al, 2018). Furthermore, we recently demonstrated that, in H. pylori , the RNA degradosome is compartmentalized into clusters at the inner membrane whose formation is regulated and likely represents a major level of control of its activity (Tejada-Arranz et al, 2020b).…”

“…B. subtilis and S. aureus encode two paralogues of RNase J, called J1 and J2 while H. pylori, Streptomyces pyogenes and D. radiodurans possess only one gene for this protein. Compared to the RNase J proteins of these three organisms, the H. pylori enzyme possesses a unique N-terminal extension of 132 residues that is predicted to be predominantly disordered (Redko et al, 2013; Tejada-Arranz et al, 2020b). In B. subtilis , while both RNase J paralogues have equivalent endoribonuclease activities, RNase J2 seems to lack the 5’-3’ exoribonuclease activity that predominates in RNase J1 (Mathy et al, 2010).…”