1. Chromosomes and Gene Expression
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Ribosome recycling is not critical for translational coupling in E. coli

  1. Kazuki Saito
  2. Rachel Green
  3. Allen R Buskirk  Is a corresponding author
  1. Johns Hopkins University School of Medicine, United States
  2. Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, United States
Research Article
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Cite this article as: eLife 2020;9:e59974 doi: 10.7554/eLife.59974

Abstract

We used ribosome profiling to characterize the biological role of ribosome recycling factor (RRF) in E. coli. As expected, RRF depletion leads to enrichment of post-termination 70S complexes in 3'-UTRs. We also observe that elongating ribosomes are unable to complete translation because they are blocked by non-recycled ribosomes at stop codons. Previous studies have suggested a role for recycling in translational coupling within operons; if a ribosome remains bound to an mRNA after termination, it may re-initiate downstream. We found, however, that RRF depletion did not significantly affect coupling efficiency in reporter assays or in ribosome density genome-wide. These findings argue that re-initiation is not a major mechanism of translational coupling in E. coli. Finally, RRF depletion has dramatic effects on the activity of ribosome rescue factors tmRNA and ArfA. Our results provide a global view of the effects of the loss of ribosome recycling on protein synthesis in E. coli.

Data availability

Sequencing data have been deposited in GEO under accession codes GSE151688.

The following data sets were generated

Article and author information

Author details

  1. Kazuki Saito

    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
    Competing interests
    No competing interests declared.
  2. Rachel Green

    Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
    Competing interests
    Rachel Green, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9337-2003
  3. Allen R Buskirk

    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States
    For correspondence
    buskirk@jhmi.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2720-6896

Funding

National Institute of General Medical Sciences (GM110113)

  • Allen R Buskirk

Howard Hughes Medical Institute

  • Rachel Green

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Joseph T Wade, Wadsworth Center, New York State Department of Health, United States

Publication history

  1. Received: June 13, 2020
  2. Accepted: September 22, 2020
  3. Accepted Manuscript published: September 23, 2020 (version 1)
  4. Version of Record published: October 6, 2020 (version 2)

Copyright

© 2020, Saito 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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