A minimal bacterial RNase J-based degradosome is associated with translating ribosomes

Abstract

Protein complexes directing messenger RNA (mRNA) degradation are present in all kingdoms of life. In Escherichia coli, mRNA degradation is performed by an RNA degradosome organized by the major ribonuclease RNase E. In bacteria lacking RNase E, the existence of a functional RNA degradosome is still an open question. Here, we report that in the bacterial pathogen Helicobacter pylori, RNA degradation is directed by a minimal RNA degradosome consisting of Hp-RNase J and the only DExD-box RNA helicase of H. pylori, RhpA. We show that the protein complex promotes faster degradation of double-stranded RNA in vitro in comparison with Hp-RNase J alone. The ATPase activity of RhpA is stimulated in the presence of Hp-RNase J, demonstrating that the catalytic capacity of both partners is enhanced upon interaction. Remarkably, both proteins are associated with translating ribosomes and not with individual 30S and 50S subunits. Moreover, Hp-RNase J is not recruited to ribosomes to perform rRNA maturation. Together, our findings imply that in H. pylori, the mRNA-degrading machinery is associated with the translation apparatus, a situation till now thought to be restricted to eukaryotes and archaea.

Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane Region and Cosediments with Degradosome and Polysome Complexes in Synechocystis sp. Strain PCC 6803

“…This association is known to occur in archaea and eukarya (50)(51)(52)(53), and polysome fractionation on sucrose gradients has recently provided evidence for polysome-RNA degradosome association in E. coli (54) and Helicobacter pylori (55). Indeed, other than the results from photosynthesis-associated peptides, our proteomic data set closely resembles that obtained in the E. coli (54) and H. pylori (55) studies. Similarly to the results presented here, the respective RNA helicase peptides were associated with the identified polysome-RNA degradosome complexes (54,55).…”

“…Indeed, other than the results from photosynthesis-associated peptides, our proteomic data set closely resembles that obtained in the E. coli (54) and H. pylori (55) studies. Similarly to the results presented here, the respective RNA helicase peptides were associated with the identified polysome-RNA degradosome complexes (54,55). In E. coli, the degradosome-associated RNA helicase RhlB contributes to ribosome binding and thus to formation of the polysome-RNA degradosome complex (54).…”

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

“…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).…”

“…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). 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).…”

“…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.…”