Evolving specificity of tRNA 3-methyl-cytidine-32 (m³C32) modification: a subset of tRNAs^Ser requires N⁶-isopentenylation of A37

Abstract

Post-transcriptional modifications of anticodon loop (ACL) nucleotides impact tRNA structure, affinity for the ribosome, and decoding activity, and these activities can be fine-tuned by interactions between nucleobases on either side of the anticodon. A recently discovered ACL modification circuit involving positions 32, 34, and 37 is disrupted by a human disease-associated mutation to the gene encoding a tRNA modification enzyme. We used tRNA-HydroSeq (-HySeq) to examine ³methyl-cytidine-32 (m³C32), which is found in yeast only in the ACLs of tRNAs^Ser and tRNAs^Thr. In contrast to that reported for Saccharomyces cerevisiae in which all m³C32 depends on a single gene, TRM140, the m³C32 of tRNAs^Ser and tRNAs^Thr of the fission yeast S. pombe, are each dependent on one of two related genes, trm140⁺ and trm141⁺, homologs of which are found in higher eukaryotes. Interestingly, mammals and other vertebrates contain a third homolog and also contain m³C at new sites, positions 32 on tRNAs^Arg and C47:3 in the variable arm of tRNAs^Ser. More significantly, by examining S. pombe mutants deficient for other modifications, we found that m³C32 on the three tRNAs^Ser that contain anticodon base A36, requires N⁶-isopentenyl modification of A37 (i⁶A37). This new C32–A37 ACL circuitry indicates that i⁶A37 is a pre- or corequisite for m³C32 on these tRNAs. Examination of the tRNA database suggests that such circuitry may be more expansive than observed here. The results emphasize two contemporary themes, that tRNA modifications are interconnected, and that some specific modifications on tRNAs of the same anticodon identity are species-specific.