Initiator tRNA lacking 1-methyladenosine is targeted by the rapid tRNA decay pathway in evolutionarily distant yeast species

All tRNAs have numerous modifications, lack of which often results in growth defects in the budding yeast Saccharomyces cerevisiae and neurological or other disorders in humans. In S. cerevisiae, lack of tRNA body modifications can lead to impaired tRNA stability and decay of a subset of the hypomodified tRNAs. Mutants lacking 7-methylguanosine at G₄₆ (m⁷G₄₆), N₂,N₂-dimethylguanosine (m^2,2G₂₆), or 4-acetylcytidine (ac⁴C₁₂), in combination with other body modification mutants, target certain mature hypomodified tRNAs to the rapid tRNA decay (RTD) pathway, catalyzed by 5’-3’ exonucleases Xrn1 and Rat1, and regulated by Met22. The RTD pathway is conserved in the phylogenetically distant fission yeast Schizosaccharomyces pombe for mutants lacking m⁷G₄₆. In contrast, S. cerevisiae trm6/gcd10 mutants with reduced 1-methyladenosine (m¹A₅₈) specifically target pre-tRNA_i^Met(CAU) to the nuclear surveillance pathway for 3’-5’ exonucleolytic decay by the TRAMP complex and nuclear exosome. We show here that the RTD pathway has an unexpected major role in the biology of m¹A₅₈ and tRNA_i^Met(CAU) in both S. pombe and S. cerevisiae. We find that S. pombe trm6Δ mutants lacking m¹A₅₈ are temperature sensitive due to decay of tRNA_i^Met(CAU) by the RTD pathway. Thus, trm6Δ mutants had reduced levels of tRNA_i^Met(CAU) and not of eight other tested tRNAs, overexpression of tRNA_i^Met(CAU) restored growth, and spontaneous suppressors that restored tRNA_i^Met(CAU) levels had mutations in dhp1/RAT1 or tol1/MET22. In addition, deletion of cid14/TRF4 in the nuclear surveillance pathway did not restore growth. Furthermore, re-examination of S. cerevisiae trm6 mutants revealed a major role of the RTD pathway in maintaining tRNA_i^Met(CAU) levels, in addition to the known role of the nuclear surveillance pathway. These findings provide evidence for the importance of m¹A₅₈ in the biology of tRNA_i^Met(CAU) throughout eukaryotes, and fuel speculation that the RTD pathway has a major role in quality control of body modification mutants throughout fungi and other eukaryotes.