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EDF1 coordinates cellular responses to ribosome collisions

ABSTRACT: Raw mass spectrometry data associated with the following paper: EDF1 coordinates cellular responses to ribosome collisions. Related to Figure 5A and Figure 5-source data 1. Files detail: See attached Search Engine file named "Sample info and Maxquant summary"

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: J. Wade Harper Rachel Green Eric J. Bennett

PROVIDER: MSV000085424 | MassIVE | Fri May 15 19:44:00 BST 2020

SECONDARY ACCESSION(S): PXD019229

REPOSITORIES: MassIVE

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EDF1 coordinates cellular responses to ribosome collisions.

Sinha Niladri K NK Ordureau Alban A Best Katharina K Saba James A JA Zinshteyn Boris B Sundaramoorthy Elayanambi E Fulzele Amit A Garshott Danielle M DM Denk Timo T Thoms Matthias M Paulo Joao A JA Harper J Wade JW Bennett Eric J EJ Beckmann Roland R Green Rachel R

eLife 20200803

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 ...[more]

PMID: 32744497

Similar Datasets

EDF1 coordinates cellular responses to ribosome collisions

Project description:Raw mass spectrometry data associated with the following paper: EDF1 coordinates cellular responses to ribosome collisions. Related to Figure 5B, Figure 5-figure supplement 1B-1C and Figure 5-source data 2. Files detail: See attached Search Engine file named "Sample info and Maxquant summary"

2020-05-15 | MSV000085421 | MassIVE

EDF1 coordinates cellular responses to ribosome collisions

Project description:Raw mass spectrometry data associated with the following paper: EDF1 coordinates cellular responses to ribosome collisions. Related to Figure 2-figure supplement 2A and Figure 2-source data 2. Files detail: See attached Search Engine File named "Sample info and Maxquant summary"

2020-05-15 | MSV000085422 | MassIVE

EDF1 coordinates cellular responses to ribosome collisions

Project description:Raw mass spectrometry data associated with the following paper: EDF1 coordinates cellular responses to ribosome collisions. Related to Figure 2H and Figure 2-figure supplement 2F.

2020-05-15 | MSV000085425 | MassIVE

EDF1 coordinates cellular responses to ribosome collisions

Project description:Raw mass spectrometry data associated with the following paper: EDF1 coordinates cellular responses to ribosome collisions. Related to Figure 1, Figure 1-figure supplement 1 and Figure 1-source data 1. Files detail: 11 sucrose gradient fractions (Fr1-11 respectively labeled AO3038-3048)

2020-05-15 | MSV000085423 | MassIVE

EDF1 coordinates cellular responses to ribosome collisions

Project description:Raw mass spectrometry data associated with the following paper: EDF1 coordinates cellular responses to ribosome collisions. Related to Figure 2, Figure 2-figure supplement 1 and Figure 2-source data 1. Files detail: Monosome (6 BPRP fractions - labeled AO3104-3109); Polysome (6 BPRP fractions - labeled AO3098-3103)

2020-05-15 | MSV000085419 | MassIVE

EDF1 coordinates cellular responses to ribosome collisions

Project description:Raw mass spectrometry data associated with the following paper: EDF1 coordinates cellular responses to ribosome collisions. Related to Figure 6B-6C, Figure 6-figure supplement 1 and Figure 6-source data 1. Files detail: Light-Polysome (12 BPRP fractions - labeled AO3310-3321); Heavy-Polysome (12 BPRP fractions - labeled AO3322-3333)

2020-05-15 | MSV000085420 | MassIVE

EDF1 coordinates cellular responses to ribosome collisions.

Project description: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.

| S-EPMC7486125 | biostudies-literature

Ribosome collisions trigger cis-acting feedback inhibition of translation initiation

Project description:Translation of aberrant mRNAs can cause ribosomes to stall, leading to collisions with trailing ribosomes. Collided ribosomes are specifically recognized by ZNF598 to initiate protein and mRNA quality control pathways. Here we found using quantitative proteomics of collided ribosomes that EDF1 is a ZNF598-independent sensor of ribosome collisions. EDF1 recruits and stabilizes GIGYF2 at collisions to inhibit translation initiation in cis via 4EHP. The GIGYF2 axis acts independently of the ZNF598 axis, but each pathway’s output is more pronounced without the other. We propose that the widely conserved and highly abundant EDF1 monitors the transcriptome for excessive ribosome density, then triggers a GIGYF2-mediated response to locally and temporarily reduce ribosome loading. Only when collisions persist is translation abandoned to initiate ZNF598-dependent quality control. This tiered response to ribosome collisions would allow cells to dynamically tune translation rates while ensuring fidelity of the resulting protein products.

2020-07-14 | PXD020239 | Pride

EDF1 binds collided ribosomes and facilitates recruitment of translational repressors GIGYF2/EIF4E2 and initiates JUN-mediated transcriptional response

Project description:RNA-seq analyses of wild-type and DEDF1 cell lines show that the immediate-early JUN-dependent transcriptional response to collisions is dependent on EDF1.

2020-08-02 | GSE149565 | GEO

Ribosome collisions in bacteria promote ribosome rescue by triggering mRNA cleavage by SmrB

Project description:Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes. In a genetic screen in E. coli, we discovered a novel rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNA) to rescue upstream ribosomes. SmrB is recruited by ribosome collisions. Cryo-EM structures of collided disomes from E. coli and B. subtilis reveal interactions between the 30S subunits and a possible SmrB binding site. These findings show that ribosome collisions trigger ribosome rescue in bacteria and reveal the mechanism by which this occurs.

2022-08-01 | GSE179691 | GEO

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