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

  1. Karole N D'Orazio
  2. Colin Chih-Chien Wu
  3. Niladri K Sinha
  4. Raphael Loll-Krippleber
  5. Grant W Brown
  6. Rachel Green  Is a corresponding author
  1. Johns Hopkins University School of Medicine, United States
  2. University of Toronto, Canada

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

Article and author information

Author details

  1. 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.
  2. 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.
  3. 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.
  4. Raphael Loll-Krippleber

    Department of Biochemistry, University of Toronto, Toronto, Canada
    Competing interests
    No competing interests declared.
  5. Grant W Brown

    Department of Biochemistry, University of Toronto, Toronto, Canada
    Competing interests
    No competing interests declared.
  6. 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.
    ORCID icon "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

© 2019, D'Orazio et al.

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.

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  1. Karole N D'Orazio
  2. Colin Chih-Chien Wu
  3. Niladri K Sinha
  4. Raphael Loll-Krippleber
  5. Grant W Brown
  6. Rachel Green
(2019)
The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay
eLife 8:e49117.
https://doi.org/10.7554/eLife.49117

Share this article

https://doi.org/10.7554/eLife.49117

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