Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine

• Published in: Nature communications 2022-10, Vol.13 (1), p.5994-15, Article 5994
• Main Authors: Kimura, Satoshi, Srisuknimit, Veerasak, McCarty, Kacie L., Dedon, Peter C., Kranzusch, Philip J., Waldor, Matthew K.
• Format: Article
• Language: English
• Subjects: 38/88; 631/337/1645/1944; 631/45/173; 631/45/500; 82/58; 82/80; Anticodon; Availability; Catalysis; Conversion; Cytidine - metabolism; Cytidine deaminase; Cytidine Deaminase - genetics; Domains; Editing; Enzymes; Gene expression; Humanities and Social Sciences; Iron; multidisciplinary; Nutrient availability; Post-transcription; Pseudouridine - metabolism; Pseudouridylation; Ribonucleic acid; RNA; RNA editing; RNA, Transfer - metabolism; Science; Science (multidisciplinary); Substrates; Transfer RNA; tRNA; tRNA Ala
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-33714-x

Post-transcriptional RNA editing modulates gene expression in a condition-dependent fashion. We recently discovered C-to-Ψ editing in Vibrio cholerae tRNA. Here, we characterize the biogenesis, regulation, and functions of this previously undescribed RNA editing process. We show that an enzyme, TrcP, mediates the editing of C-to-U followed by the conversion of U to Ψ, consecutively. AlphaFold-2 predicts that TrcP consists of two globular domains (cytidine deaminase and pseudouridylase) and a long helical domain. The latter domain tethers tRNA substrates during both the C-to-U editing and pseudouridylation, likely enabling a substrate channeling mechanism for efficient catalysis all the way to the terminal product. C-to-Ψ editing both requires and suppresses other modifications, creating an interdependent network of modifications in the tRNA anticodon loop that facilitates coupling of tRNA modification states to iron availability. Our findings provide mechanistic insights into an RNA editing process that likely promotes environmental adaptation. C-to-Ψ conversion is a previously uncharacterized form of base editing. Here, the authors describe how the TrcP enzyme catalyzes this process in a stepwise fashion and how this editing process is controlled by a network of modifications and nutrient availability to optimize translation efficiency.