Ribosome recycling is not critical for translational coupling in E. coli

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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

1. Buskirk
2. AR
(2020) RRF plays critical roles in ribosome homeostasis in E. coli but has little effect on translational coupling
NCBI Gene Expression Omnibus, GSE151688.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE151688

Article and author information

Author details

Kazuki Saito

Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, United States

Competing interests
No competing interests declared.
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.

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

"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.

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.