Evolving specificity of tRNA 3-methyl-cytidine-32 (m3C32) modification: a subset of tRNAsSer 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 tRNAsSer and tRNAsThr. In contrast to that reported for Saccharomyces cerevisiae in which all m3C32 depends on a single gene, TRM140, the m3C32 of tRNAsSer and tRNAsThr 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 tRNAsArg and C47:3 in the variable arm of tRNAsSer. More significantly, by examining S. pombe mutants deficient for other modifications, we found that m3C32 on the three tRNAsSer 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.