Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing

Abstract
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Abstract

Shine-Dalgarno (SD) motifs are thought to play an important role in translational initiation in bacteria. Paradoxically, ribosome profiling studies in E. coli show no correlation between the strength of an mRNA's SD motif and how efficiently it is translated. Performing profiling on ribosomes with altered anti-Shine-Dalgarno sequences, we reveal a genome-wide correlation between SD strength and ribosome occupancy that was previously masked by other contributing factors. Using the antibiotic retapamulin to trap initiation complexes at start codons, we find that the mutant ribosomes select start sites correctly, arguing that start sites are hard-wired for initiation through the action of other mRNA features. We show that A-rich sequences upstream of start codons promote initiation. Taken together, our genome-wide study reveals that SD motifs are not necessary for ribosomes to determine where initiation occurs, though they do affect how efficiently initiation occurs.

Data availability

Sequencing data have been deposited in the GEO under accession code GSE135906.

The following data sets were generated

(2019) Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing
NCBI Gene Expression Omnibus, GSE135906.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135906

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

Japan Society for the Promotion of Science

Kazuki Saito

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.