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

Abstract
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Abstract

Translation of problematic sequences in mRNAs leads to ribosome collisions that trigger a series 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. We demonstrate that NGD primarily proceeds via Xrn1-mediated exonucleolytic decay and Cue2-mediated endonucleolytic decay normally constitutes a secondary decay pathway. Finally, we show that the Cue2-dependent pathway becomes a major contributor to NGD 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.

Data availability

Sequencing data have been deposited in NCBI Gene Expression Omnibus under accession code GSE129128.

The following data sets were generated

(2019) Cue2 and Slh1 define parallel pathways to rescue stalled ribosomes
NCBI Gene Expression Omnibus, GSE129128.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129128

Article and author information

Author details

Karole N D'Orazio

Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States

Competing interests
No competing interests declared.
Colin Chih-Chien Wu

Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States

Competing interests
No competing interests declared.
Niladri K Sinha

Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States

Competing interests
No competing interests declared.
Raphael Loll-Krippleber

Department of Biochemistry, University of Toronto, Toronto, Canada

Competing interests
No competing interests declared.
Grant W Brown

Department of Biochemistry, University of Toronto, Toronto, Canada

Competing interests
No competing interests declared.
Rachel Green

Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States

For correspondence
ragreen@jhmi.edu

Competing interests
Rachel Green, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0001-9337-2003

Funding

National Institutes of Health (R37GM059425)

Rachel Green

National Institutes of Health (5T32GM007445-39)

Rachel Green

Canadian Institutes of Health Research (FDN-159913)

Grant W Brown

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.