The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNA

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 116; no. 4; pp. 1394 - 1403
• Main Authors: Kimura, Satoshi, Waldor, Matthew K.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 22.01.2019
• Series: PNAS Plus
• Subjects: Abundance; Archaea - genetics; Bacteria; Bacteria - genetics; Biodegradation; Biological Sciences; Decay; Degradation; Elongation; Elongation factor EF-Tu; Endoribonucleases - genetics; Genetic analysis; Insertion; Kinetics; Modifications; Multienzyme Complexes - genetics; Mutants; Peptide Elongation Factor Tu - genetics; PNAS Plus; Polyribonucleotide Nucleotidyltransferase - genetics; Post-transcription; Quality Control; Ribonucleic acid; RNA; RNA Helicases - genetics; RNA Processing, Post-Transcriptional - genetics; RNA, Transfer - genetics; Stability analysis; Stationary phase; Thiouridine - metabolism; tRNA; tRNA Ala; Viability; Vibrio cholerae - genetics; Waterborne diseases; thiI; stationary phase; tRNA modification; Vibrio cholerae; RNA degradosome
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1814130116

The factors and mechanisms that govern tRNA stability in bacteria are not well understood. Here, we investigated the influence of posttranscriptional modification of bacterial tRNAs (tRNA modification) on tRNA stability. We focused on Thil-generated 4-thiouridine (s⁴U), a modification found in bacterial and archaeal tRNAs. Comprehensive quantification of Vibrio cholerae tRNAs revealed that the abundance of some tRNAs is decreased in a Δthil strain in a stationary phase-specific manner. Multiple mechanisms, including rapid degradation of a subset of hypomodified tRNAs, account for the reduced abundance of tRNAs in the absence of thil. Through transposon insertion sequencing, we identified additional tRNA modifications that promote tRNA stability and bacterial viability. Genetic analysis of suppressor mutants as well as biochemical analyses revealed that rapid degradation of hypomodified tRNA is mediated by the RNA degradosome. Elongation factor Tu seems to compete with the RNA degradosome, protecting aminoacyl tRNAs from decay. Together, our observations describe a previously unrecognized bacterial tRNA quality control system in which hypomodification sensitizes tRNAs to decay mediated by the RNA degradosome.