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Ribosome collisions trigger subunit splitting in E. coli

ABSTRACT: Ribosome collisions trigger subunit splitting in E. coli

PROVIDER: PRJNA1126309 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29481523.fastq.gz	Fastqsanger.gz
	SRR29481524.fastq.gz	Fastqsanger.gz
	SRR29481525.fastq.gz	Fastqsanger.gz
	SRR29481526.fastq.gz	Fastqsanger.gz
	SRR29481527.fastq.gz	Fastqsanger.gz

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Ribosome collisions trigger subunit splitting in E. coli

Project description:Although many clinically important antibiotics inhibit bacterial ribosomes, the mechanisms by which bacterial cells rescue ribosomes stalled by antibiotics remain poorly understood. Ribosome stalling leads to collisions that recruit ribosome quality control (RQC) factors that recycle the ribosome subunits and target nascent proteins for degradation. Surprisingly, loss of known RQC factors in E. coli does not lead to significant antibiotic sensitivity, even though antibiotics stall ribosomes and induce collisions, suggesting the existence of additional, uncharacterized RQC mechanisms. Here we report a novel mechanism for ribosome quality control (RQC) in bacteria in which the DExH-box ATPase HrpA splits stalled ribosomes into subunits. HrpA selectively acts on collided ribosomes and its activity is dependent on ATP hydrolysis. The cryo-EM structure of HrpA bound to collided ribosomes reveals insight into its selectivity and mechanism: the C-terminal domain of HrpA senses the collision and its helicase domain bind mRNA downstream of the ribosomes, where it likely exerts a pulling force that destabilizes the stalled ribosome. These studies highlight the importance of ribosome splitting as a highly conserved RQC mechanism across all three domains of life and identify an important pathway in proteobacteria that allows proteobacteria to tolerate ribosome-targeting antibiotics.

2024-10-10 | GSE270401 | 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

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

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

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

| PRJNA744552 | ENA

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

Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo

Project description:As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting and folding factors. Here we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone Trigger Factor (TF) reveal that, while TF can interact with many polypeptides, Î²-barrel outer membrane proteins are the most prominent substrates. Loss of TF leads to broad outer membrane defects and premature, cotranslational protein translocation. While in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting ad folding factors. Examination of translation in the Gram-negative bacterium Escherichia coli, as well as an analysis of the interactions between nascent chains and the molecular chaperone Trigger Factor.

2011-12-09 | E-GEOD-33671 | biostudies-arrayexpress

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 5A and Figure 5-source data 1. Files detail: See attached Search Engine file named "Sample info and Maxquant summary"

2020-05-15 | MSV000085424 | 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 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 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

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