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

Abstract

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 (m2,2G26), 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 mutants with reduced 1-methyladenosine (m1A58) specifically target pre-tRNAiMet(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 tRNAiMet(CAU) in both S. pombe and S. cerevisiae. We find that S. pombe trm6Δ mutants lacking m1A58 are temperature sensitive due to decay of tRNAiMet(CAU) by the RTD pathway. Thus, trm6Δ mutants had reduced levels of tRNAiMet(CAU) and not of eight other tested tRNAs, overexpression of tRNAiMet(CAU) restored growth, and spontaneous suppressors that restored tRNAiMet(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 tRNAiMet(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 tRNAiMet(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.Author SummarytRNA modifications are highly conserved, and their lack frequently results in growth defects in the yeast Saccharomyces cerevisiae and neurological disorders in humans. In S. cerevisiae lack of 1-methyladenosine at N58 (m1A58) in the tRNA body is lethal due to 3’-5’ decay of pre-tRNAiMet by the nuclear surveillance pathway. By contrast, lack of any of three other body modifications causes growth defects due to 5’-3’ decay of specific hypomodified tRNAs by the rapid tRNA decay (RTD) pathway. Despite their importance, little is known about either tRNAiMet quality control or tRNA decay pathways in eukaryotes other than S. cerevisiae.Here we show an unexpected role of the RTD pathway in quality control of tRNAiMet lacking m1A58 in the phylogenetically distant yeast species Schizosaccharomyces pombe and S. cerevisiae. We find that S. pombe trm6Δ mutants, lacking m1A58, are temperature sensitive due to decay of tRNAiMet(CAU) primarily by the RTD pathway. Furthermore, re-investigation of S. cerevisiae trm6 mutants revealed a significant role of the RTD pathway, in addition to the nuclear surveillance pathway, in decay of tRNAiMet(CAU). Our results suggest that throughout eukaryotes the RTD pathway has a major role in decay of hypomodified tRNAs and that m1A58 is crucial to tRNAiMet(CAU) biology.