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.

Reviewing Editor

  1. Nahum Sonenberg, McGill University, Canada

Version history

  1. Received: June 7, 2019
  2. Accepted: June 19, 2019
  3. Accepted Manuscript published: June 20, 2019 (version 1)
  4. Version of Record published: June 28, 2019 (version 2)

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.

Metrics

  • 7,989
    views
  • 1,263
    downloads
  • 138
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  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

Further reading

    1. Genetics and Genomics
    2. Neuroscience
    Yifei Weng, Shiyi Zhou ... Coleen T Murphy
    Research Article

    Cognitive decline is a significant health concern in our aging society. Here, we used the model organism C. elegans to investigate the impact of the IIS/FOXO pathway on age-related cognitive decline. The daf-2 Insulin/IGF-1 receptor mutant exhibits a significant extension of learning and memory span with age compared to wild-type worms, an effect that is dependent on the DAF-16 transcription factor. To identify possible mechanisms by which aging daf-2 mutants maintain learning and memory with age while wild-type worms lose neuronal function, we carried out neuron-specific transcriptomic analysis in aged animals. We observed downregulation of neuronal genes and upregulation of transcriptional regulation genes in aging wild-type neurons. By contrast, IIS/FOXO pathway mutants exhibit distinct neuronal transcriptomic alterations in response to cognitive aging, including upregulation of stress response genes and downregulation of specific insulin signaling genes. We tested the roles of significantly transcriptionally-changed genes in regulating cognitive functions, identifying novel regulators of learning and memory. In addition to other mechanistic insights, a comparison of the aged vs young daf-2 neuronal transcriptome revealed that a new set of potentially neuroprotective genes is upregulated; instead of simply mimicking a young state, daf-2 may enhance neuronal resilience to accumulation of harm and take a more active approach to combat aging. These findings suggest a potential mechanism for regulating cognitive function with age and offer insights into novel therapeutic targets for age-related cognitive decline.

    1. Genetics and Genomics
    Samuel Pattillo Smith, Gregory Darnell ... Lorin Crawford
    Research Article

    LD score regression (LDSC) is a method to estimate narrow-sense heritability from genome-wide association study (GWAS) summary statistics alone, making it a fast and popular approach. In this work, we present interaction-LD score (i-LDSC) regression: an extension of the original LDSC framework that accounts for interactions between genetic variants. By studying a wide range of generative models in simulations, and by re-analyzing 25 well-studied quantitative phenotypes from 349,468 individuals in the UK Biobank and up to 159,095 individuals in BioBank Japan, we show that the inclusion of a cis-interaction score (i.e. interactions between a focal variant and proximal variants) recovers genetic variance that is not captured by LDSC. For each of the 25 traits analyzed in the UK Biobank and BioBank Japan, i-LDSC detects additional variation contributed by genetic interactions. The i-LDSC software and its application to these biobanks represent a step towards resolving further genetic contributions of sources of non-additive genetic effects to complex trait variation.