Different modification pathways for m(1)A58 incorporation in yeast elongator and initiator tRNAs

As essential components of the protein synthesis machinery, tRNAs undergo a tightly controlled biogenesis process, which include the incorporation of numerous posttranscriptional modifications. Defects in these tRNA maturation steps may lead to the degradation of hypomodified tRNAs by the rapid tRNA decay (RTD) and nuclear surveillance pathways. We previously identified m(1)A58 as a late modification introduced after modifications Ψ55 and T54 in yeast elongator tRNA(Phe). However, previous reports suggested that m(1)A58 is introduced early during the tRNA modification process, in particular on primary transcripts of initiator tRNA(i)(Met), which prevents its degradation by RNA decay pathways. Here, aiming to reconcile this apparent inconsistency on the temporality of m(1)A58 incorporation, we examined its introduction into yeast elongator and initiator tRNAs. We used specifically modified tRNAs to report on the molecular aspects controlling the Ψ55 → T54 → m(1)A58 modification circuit in elongator tRNAs. We also show that m(1)A58 is efficiently introduced on unmodified tRNA(i)(Met), and does not depend on prior modifications. Finally, we show that m(1)A58 has major effects on the structural properties of initiator tRNA(i)(Met), so that the tRNA elbow structure is only properly assembled when this modification is present. This observation provides a structural explanation for the degradation of hypomodified tRNA(i)(Met) lacking m(1)A58 by the nuclear surveillance and RTD pathways.