EDF1 coordinates cellular responses to ribosome collisions
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, United States
- Harvard Medical School, United States
- Ludwig Maximilian University of Munich, Germany
- University of California, San Diego, United States
- Gene Center, Ludwig-Maximilians-Universität München, Germany
Abstract
Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation.
Data availability
Raw mass spectrometry data associated with the following Figures have been deposited in MassIVE repository: Source data for all proteomics-based plots are provided in Source data tables.Figure 1, Figure 1-figure supplement 1: https://doi.org/doi:10.25345/C5T70C(Username: MSV000085423_reviewer | Password: a)Figure 2, Figure 2-figure supplement 1: https://doi.org/doi:10.25345/C5B71D(Username: MSV000085419_reviewer | Password: a)Figure 2-figure supplement 2A: https://doi.org/doi:10.25345/C5Z11X(Username: MSV000085422_reviewer | Password: a)Figure 2H, Figure 2-figure supplement 2F: https://doi.org/doi:10.25345/C5JQ47(Username: MSV000085425_reviewer | Password: a)Figure 5A: https://doi.org/doi:10.25345/C5PH7J(Username: MSV000085424_reviewer | Password: a)Figure 5B, Figure 5-figure supplement 1B-1C: https://doi.org/doi:10.25345/C52Q58(Username: MSV000085421_reviewer | Password: a)Figure 6B-6C, Figure 6-figure supplement 1: https://doi.org/doi:10.25345/C56H6T(Username: MSV000085420_reviewer | Password: a)Raw sequencing data were deposited in the GEO database under the accession number GSE149565. Secure token for reviewers: uzajoeeultgrpsr.The cryo-EM structures reported here have been deposited in the Protein Data Bank under the accession codes 6ZVH (EDF1•ribosome) and 6ZVI (Mbf1•ribosome), and in the Electron Microscopy Data Bank under the accession codes EMD-11456 (EDF1•ribosome) and EMD-11457 (Mbf1•ribosome).
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EDF1 coordinates cellular responses to ribosome collisions, related to Figure 5B, Figure 5-figure supplement 1B-1CMassIVE, MSV000085421_reviewer | Password: a).
Article and author information
Author details
Elayanambi Sundaramoorthy
Danielle M Garshott
Funding
Howard Hughes Medical Institute
- Rachel Green
Deutsche Forschungsgemeinschaft (GRK 1721)
- Roland Beckmann
Deutsche Forschungsgemeinschaft (QBM (Quantitative Biosciences Munich) Graduate School Fellowships)
- Katharina Best
Deutsche Forschungsgemeinschaft (QBM (Quantitative Biosciences Munich) Graduate School Fellowships)
- Timo Denk
National Institute of General Medical Sciences (R37GM059425)
- Rachel Green
National Institute of Neurological Disorders and Stroke (R37NS083524)
- Wade Harper
National Institute on Aging (AG011085)
- Wade Harper
National Institute of General Medical Sciences (DP2GM119132)
- Eric J Bennett
National Institute of General Medical Sciences (5K99GM135450-02)
- Boris Zinshteyn
Jane Coffin Childs Memorial Fund for Medical Research
- Niladri K Sinha
National Institute of General Medical Sciences (T32GM007240)
- Danielle M Garshott
National Science Foundation (DGE-1650112)
- Danielle M Garshott
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Nahum Sonenberg, McGill University, Canada
Version history
- Received: May 12, 2020
- Accepted: August 2, 2020
- Accepted Manuscript published: August 3, 2020 (version 1)
- Version of Record published: September 11, 2020 (version 2)
Copyright
© 2020, Sinha 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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EDF1 coordinates cellular responses to ribosome collisions
eLife 9:e58828.
https://doi.org/10.7554/eLife.58828
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