Mutations in the anticodon stem of tRNA cause accumulation and Met22-dependent decay of pre-tRNA in yeast

During tRNA maturation in yeast, aberrant pre-tRNAs are targeted for 3′–5′ degradation by the nuclear surveillance pathway, and aberrant mature tRNAs are targeted for 5′–3′ degradation by the rapid tRNA decay (RTD) pathway. RTD is catalyzed by the 5′–3′ exonucleases Xrn1 and Rat1, which act on tRNAs with an exposed 5′ end due to the lack of certain body modifications or the presence of destabilizing mutations in the acceptor stem, T-stem, or tRNA fold. RTD is inhibited by mutation of MET22, likely due to accumulation of the Met22 substrate adenosine 3′,5′ bis-phosphate, which inhibits 5′-3′ exonucleases. Here we provide evidence for a new tRNA quality control pathway in which intron-containing pre-tRNAs with destabilizing mutations in the anticodon stem are targeted for Met22-dependent pre-tRNA decay (MPD). Multiple SUP4(οc) anticodon stem variants that are subject to MPD each perturb the bulge-helix-bulge structure formed by the anticodon stem–loop and intron, which is important for splicing, resulting in substantial accumulation of end-matured unspliced pre-tRNA as well as pre-tRNA decay. Mutations that restore exon–intron structure commensurately reduce pre-tRNA accumulation and MPD. The MPD pathway can contribute substantially to decay of anticodon stem variants, since pre-tRNA decay is largely suppressed by removal of the intron or by restoration of exon–intron structure, each also resulting in increased tRNA levels. The MPD pathway is general as it extends to variants of tRNA(Tyr(GUA)) and tRNA(Ser(CGA)). These results demonstrate that the integrity of the anticodon stem–loop and the efficiency of tRNA splicing are monitored by a quality control pathway.