Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation

  1. Anthony J Veltri
  2. Karole N D'Orazio
  3. Laura N Lessen
  4. Raphael Loll-Krippleber
  5. Grant W Brown
  6. Rachel Green  Is a corresponding author
  1. Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, United States
  2. University of Toronto, Canada

Abstract

Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully-designed reporter mRNAs to perform genetic screens and functional assays in S. cerevisiae. We characterize the roles of Hel2, Syh1, and Smy2 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 and, to a lesser extent its paralog Smy2, act in a distinct pathway from Hel2. This Syh1/Smy2-mediated pathway acts as a redundant, compensatory pathway to elicit NGD when Hel2-dependent NGD is impaired. Importantly, we observe that these NGD factors are not involved in the degradation of mRNAs enriched in non-optimal codons. Further, we establish that a key factor previously implicated in COMD, Not5, contributes modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new insight into the role of Syh1 and Smy2 in NGD and into the ribosomal states that correlate with the activation of distinct pathways targeting mRNAs for degradation in yeast.

Data availability

Ribo-seq data is available in the NCBI Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/) database with the accession GSE189404. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al. 2019) partner repository with the dataset identifier PXD030076. Code to process sequencing data is available at https://github.com/greenlabjhmi/2022_syh1/.

The following data sets were generated

Article and author information

Author details

  1. Anthony J Veltri

    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.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7067-1796
  2. 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
    Karole N D'Orazio, is affiliated with Regeneron Pharmaceuticals.
  3. Laura N Lessen

    Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
    Competing interests
    Laura N Lessen, is affiliated with GlaxoSmithKline.
  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.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9002-5003
  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
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9337-2003

Funding

Canadian Institutes of Health Research (FDN-159913)

  • Grant W Brown

National Institutes of Health (R37GM059425)

  • Rachel Green

National Institutes of Health (5T32GM135131-02)

  • Anthony J Veltri

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

Reviewing Editor

  1. Alan G Hinnebusch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States

Version history

  1. Preprint posted: December 1, 2021 (view preprint)
  2. Received: December 2, 2021
  3. Accepted: July 25, 2022
  4. Accepted Manuscript published: July 27, 2022 (version 1)
  5. Version of Record published: August 4, 2022 (version 2)

Copyright

© 2022, Veltri 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. Anthony J Veltri
  2. Karole N D'Orazio
  3. Laura N Lessen
  4. Raphael Loll-Krippleber
  5. Grant W Brown
  6. Rachel Green
(2022)
Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation
eLife 11:e76038.
https://doi.org/10.7554/eLife.76038

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https://doi.org/10.7554/eLife.76038

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