EDF1 coordinates cellular responses to ribosome collisions

Abstract
Data availability
Article and author information
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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).

The following data sets were generated

1. Sinha NK
2. Ordureau A
3. Harper JW
4. Bennett EJ
5. Green R.
(2020) EDF1 coordinates cellular responses to ribosome collisions, related to Figure 1, Figure 1-figure supplement 1
MassIVE, MSV000085423.

https://doi.org/doi:10.25345/C5T70C
1. Sinha NK
2. Ordureau A
3. Harper JW
4. Bennett EJ
5. Green R.
(2020) EDF1 coordinates cellular responses to ribosome collisions, related to Figure 2, Figure 2-figure supplement 1
MassIVE, MSV000085419.

https://doi.org/doi:10.25345/C5B71D
1. Sinha NK
2. Ordureau A
3. Harper JW
4. Bennett EJ
5. Green R.
(2020) EDF1 coordinates cellular responses to ribosome collisions, Figure 2-figure supplement 2A
MassIVE, MSV000085422.

https://doi.org/doi:10.25345/C5Z11X
1. Sinha NK
2. Ordureau A
3. Harper JW
4. Bennett EJ
5. Green R.
(2020) EDF1 coordinates cellular responses to ribosome collisions, related to Figure 2H, Figure 2-figure supplement 2F
MassIVE, MSV000085425.

https://doi.org/doi:10.25345/C5JQ47
1. Sinha NK
2. Ordureau A
3. Harper JW
4. Bennett EJ
5. Green R.
(2020) EDF1 coordinates cellular responses to ribosome collisions, related to Figure 5A
MassIVE, MSV000085424.

https://doi.org/doi:10.25345/C5PH7J
1. Sinha NK
2. Ordureau A
3. Harper JW
4. Bennett EJ
5. Green R.
(2020) EDF1 coordinates cellular responses to ribosome collisions, related to Figure 5B, Figure 5-figure supplement 1B-1C
MassIVE, MSV000085421_reviewer | Password: a).

https://doi.org/doi:10.25345/C52Q58
1. Sinha NK
2. Ordureau A
3. Harper JW
4. Bennett EJ
5. Green R.
(2020) EDF1 coordinates cellular responses to ribosome collisions, related to Figure 6B-6C, Figure 6-figure supplement 1
MassIVE, MSV000085420.

https://doi.org/doi:10.25345/C56H6T
(2020) EDF1 binds collided ribosomes and facilitates recruitment of translational repressors GIGYF2/EIF4E2 and initiates JUN-mediated transcriptional response
NCBI Gene Expression Omnibus, GSE149565.

https://www.ncbi.nlm.nih.gov/geo/
1. Best
2. K.M.
3. Denk
4. T.
5. Cheng
6. J.
7. Thoms
8. M.
9. Berninghausen
10. O.
11. Beckmann
12. R.
(2020) EDF1-ribosome complex
PDB, 6ZVH.

https://rcsb.org
1. Best
2. K.M.
3. Denk
4. T.
5. Cheng
6. J.
7. Thoms
8. M.
9. Berninghausen
10. O.
11. Beckmann
12. R.
(2020) Mbf1-ribosome complex
PDB, 6ZVI.

https://rcsb.org
1. Best
2. K.M.
3. Denk
4. T.
5. Cheng
6. J.
7. Thoms
8. M.
9. Berninghausen
10. O.
11. Beckmann
12. R.
(2020) EDF1-ribosome complex
EMDB, EMD-11456.

https://ebi.ac.uk/pdbe/emdb
1. Best
2. K.M.
3. Denk
4. T.
5. Cheng
6. J.
7. Thoms
8. M.
9. Berninghausen
10. O.
11. Beckmann
12. R.
(2020) Mbf1-ribosome complex
EMDB, EMD-11457.

https://ebi.ac.uk/pdbe/emdb

Article and author information

Author details

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.

"This ORCID iD identifies the author of this article:" 0000-0002-9143-495X
Alban Ordureau

Department of Cell Biology, Harvard Medical School, Boston, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-4924-8520
Katharina Best

Gene Center, Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany

Competing interests
No competing interests declared.
James A Saba

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

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-3453-8151
Boris Zinshteyn

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.

"This ORCID iD identifies the author of this article:" 0000-0003-0103-3501
Elayanambi Sundaramoorthy

Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-1256-9758
Amit Fulzele

Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States

Competing interests
No competing interests declared.
Danielle M Garshott

Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-4357-1781
Timo Denk

Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany

Competing interests
No competing interests declared.
Matthias Thoms

Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany

Competing interests
No competing interests declared.
Joao A Paulo

Department of Cell Biology, Harvard Medical School, Boston, United States

Competing interests
No competing interests declared.
Wade Harper

Cell Biology, Harvard Medical School, Boston, United States

Competing interests
Wade Harper, J.W.H. is a reviewing editor, eLife, a founder and advisory board member for Caraway Therapeutics, Inc, and an advisor for X-Chem Inc..

"This ORCID iD identifies the author of this article:" 0000-0002-6944-7236
Eric J Bennett

Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, United States

Competing interests
Eric J Bennett, E.J.B is an advisor and scientific advisory board member for Plexium.

"This ORCID iD identifies the author of this article:" 0000-0002-1201-3314
Roland Beckmann

Gene Center, Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany

For correspondence
beckmann@genzentrum.lmu.de

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-4291-3898
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, eLife, reviewing editor; advisory board member for Moderna, Inc., FL63, and the Cystic Fibrosis Foundation.

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

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.

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.