The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay

Translation of problematic sequences in mRNAs leads to ribosome collisions that trigger a sequence of quality control events including ribosome rescue, degradation of the stalled nascent polypeptide via the Ribosome-mediated Quality control Complex (RQC), and targeting of the mRNA for decay (No Go Decay or NGD). Previous studies provide strong evidence for the existence of an endonuclease involved in the process of NGD though the identity of the endonuclease and the extent to which it contributes to mRNA decay remain unknown. Using a reverse genetic screen in yeast, we identify Cue2 as the conserved endonuclease that is recruited to stalled ribosomes to promote NGD. Ribosome profiling and biochemistry provide strong evidence that Cue2 cleaves mRNA within the A site of the colliding ribosome. Finally, we show that NGD primarily proceeds via Xrn1-mediated exonucleolytic decay. Cue2-mediated endonucleolytic decay normally constitutes a secondary decay pathway, but becomes a major contributor in cells depleted of factors required for the resolution of stalled ribosome complexes (the RQT factors including Slh1). Together these results provide insights into how multiple decay processes converge to process problematic mRNAs in eukaryotic cells. One Sentence Summary Cue2 is the endonuclease that cleaves mRNA at ribosome stall sites.