Identification of a novel tRNA wobble uridine modifying activity in the biosynthesis of 5-methoxyuridine

Derivatives of 5-hydroxyuridine (ho(5)U), such as 5-methoxyuridine (mo(5)U) and 5-oxyacetyluridine (cmo(5)U), are ubiquitous modifications of the wobble position of bacterial tRNA that are believed to enhance translational fidelity by the ribosome. In gram-negative bacteria, the last step in the biosynthesis of cmo(5)U from ho(5)U involves the unique metabolite carboxy S-adenosylmethionine (Cx-SAM) and the carboxymethyl transferase CmoB. However, the equivalent position in the tRNA of Gram-positive bacteria is instead mo(5)U, where the methyl group is derived from SAM and installed by an unknown methyltransferase. By utilizing a cmoB-deficient strain of Escherichia coli as a host and assaying for the formation of mo(5)U in total RNA isolates with methyltransferases of unknown function from Bacillus subtilis, we found that this modification is installed by the enzyme TrmR (formerly known as YrrM). Furthermore, X-ray crystal structures of TrmR with and without the anticodon stemloop of tRNA(Ala) have been determined, which provide insight into both sequence and structure specificity in the interactions of TrmR with tRNA.