tRNA ligase structure reveals kinetic competition between non-conventional mRNA splicing and mRNA decay.

Abstract

Yeast tRNA ligase (Trl1) is an essential trifunctional enzyme that catalyzes exon-exon ligation during tRNA biogenesis and the non-conventional splicing of <i>HAC1</i> mRNA during the unfolded protein response (UPR). The UPR regulates the protein folding capacity of the endoplasmic reticulum (ER). ER stress activates Ire1, an ER-resident kinase/RNase, which excises an intron from <i>HAC1</i> mRNA followed by exon-exon ligation by Trl1. The spliced product encodes for a potent transcription factor that drives the UPR. Here we report the crystal structure of Trl1 RNA ligase domain from <i>Chaetomium thermophilum</i> at 1.9 Å resolution. Structure-based mutational analyses uncovered kinetic competition between RNA ligation and degradation during <i>HAC1</i> mRNA splicing. Incompletely processed <i>HAC1</i> mRNA is degraded by Xrn1 and the Ski/exosome complex. We establish cleaved <i>HAC1</i> mRNA as endogenous substrate for ribosome-associated quality control. We conclude that mRNA decay and surveillance mechanisms collaborate in achieving fidelity of non-conventional mRNA splicing during the UPR.