Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria

Abstract
Article and author information
Metrics

Abstract

Ribosome stalling on mRNAs can decrease protein expression. To decipher ribosome kinetics at stall sites, we induced ribosome stalling at specific codons by starving the bacterium Escherichia coli for the cognate amino acid. We measured protein synthesis rates from a reporter library of over 100 variants that encoded systematic perturbations of translation initiation rate, the number of stall sites, and the distance between stall sites. Our measurements are quantitatively inconsistent with two widely-used kinetic models for stalled ribosomes: ribosome traffic jams that block initiation, and abortive (premature) termination of stalled ribosomes. Rather, our measurements support a model in which collision with a trailing ribosome causes abortive termination of the stalled ribosome. In our computational analysis, ribosome collisions selectively stimulate abortive termination without fine-tuning of kinetic rate parameters at ribosome stall sites. We propose that ribosome collisions serve as a robust timer for translational quality control pathways to recognize stalled ribosomes.

Article and author information

Author details

Michael A Ferrin

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States

Competing interests
The authors declare that no competing interests exist.
Arvind R Subramaniam

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States

For correspondence
rasi@fredhutch.org

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-6145-4303

Funding

National Institute of General Medical Sciences (R35 GM119835,R00 GM107113)

Michael A Ferrin
Arvind R Subramaniam

Fred Hutchinson Cancer Research Center

Michael A Ferrin
Arvind R Subramaniam

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.