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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  3 methyl-cytidine-32 (m 3 C32), 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 m 3 C32 depends on a single gene,  TRM140 , the m 3 C32 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 m 3 C 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 m 3 C32 on the three tRNAs Ser  that contain anticodon base A36, requires  N   6  -isopentenyl modification of A37 (i 6 A37). This new C32–A37 ACL circuitry indicates that i 6 A37 is a pre- or corequisite for m 3 C32 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.

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