Dual pathways of tRNA hydroxylation ensure efficient translation by expanding decoding capability

• Published in: Nature communications 2019-06, Vol.10 (1), p.2858-16, Article 2858
• Main Authors: Sakai, Yusuke, Kimura, Satoshi, Suzuki, Tsutomu
• Format: Article
• Language: English
• Subjects: 101/58; 38/90; 45/41; 631/326/41/2482; 631/326/41/2530; 631/337/1645/2570; 631/337/574/1793; 82/80; Aerobic conditions; Biosynthesis; Codons; Decoding; E coli; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Evolution, Molecular; Gene Deletion; Gene Expression Regulation, Bacterial - physiology; Genetics; Genomics; Guanosine; Humanities and Social Sciences; Hydroxylation; multidisciplinary; Peptidase; Phenotypes; Phylogeny; Protein biosynthesis; Protein Biosynthesis - physiology; Protein synthesis; Proteins; Pyrimidines; Rhodanese; RNA, Bacterial; RNA, Transfer - metabolism; Science; Science (multidisciplinary); tRNA
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-10750-8

In bacterial tRNAs, 5-carboxymethoxyuridine (cmo 5 U) and its derivatives at the first position of the anticodon facilitate non-Watson–Crick base pairing with guanosine and pyrimidines at the third positions of codons, thereby expanding decoding capabilities. However, their biogenesis and physiological roles remained to be investigated. Using reverse genetics and comparative genomics, we identify two factors responsible for 5-hydroxyuridine (ho 5 U) formation, which is the first step of the cmo 5 U synthesis: TrhP (formerly known as YegQ), a peptidase U32 family protein, is involved in prephenate-dependent ho 5 U formation; and TrhO (formerly known as YceA), a rhodanese family protein, catalyzes oxygen-dependent ho 5 U formation and bypasses cmo 5 U biogenesis in a subset of tRNAs under aerobic conditions. E. coli strains lacking both trhP and trhO exhibit a temperature-sensitive phenotype, and decode codons ending in G (GCG and UCG) less efficiently than the wild-type strain. These findings confirm that tRNA hydroxylation ensures efficient decoding during protein synthesis. 5-carboxymethoxyuridine (cmo5U) is one of the RNA modifications found in bacterial tRNA anticodons. Here the authors show that the first step of cmo5U biosynthesis from uridine is mediated by either one of two parallel factors, TrhP or TrhO, and that cmo5U modification is required for efficient translation.