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.
Sequencing data have been deposited in the GEO under accession code GSE135906.
Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairingNCBI Gene Expression Omnibus, GSE135906.
- Allen R Buskirk
- Rachel Green
- Kazuki Saito
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Joseph T Wade, Wadsworth Center, New York State Department of Health, United States
© 2020, Saito et al.
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