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Proc Natl Acad Sci U S A. 2018 Aug 21;115(34):8639-8644. doi: 10.1073/pnas.1810022115. Epub 2018 Aug 6.

Codon usage influences fitness through RNA toxicity.

Author information

1
Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, United Kingdom.
2
Department of Biology, University of Pennsylvania, Philadelphia, PA 19104.
3
Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, United Kingdom; gkudla@gmail.com.

Abstract

Many organisms are subject to selective pressure that gives rise to unequal usage of synonymous codons, known as codon bias. To experimentally dissect the mechanisms of selection on synonymous sites, we expressed several hundred synonymous variants of the GFP gene in Escherichia coli, and used quantitative growth and viability assays to estimate bacterial fitness. Unexpectedly, we found many synonymous variants whose expression was toxic to E. coli Unlike previously studied effects of synonymous mutations, the effect that we discovered is independent of translation, but it depends on the production of toxic mRNA molecules. We identified RNA sequence determinants of toxicity and evolved suppressor strains that can tolerate the expression of toxic GFP variants. Genome sequencing of these suppressor strains revealed a cluster of promoter mutations that prevented toxicity by reducing mRNA levels. We conclude that translation-independent RNA toxicity is a previously unrecognized obstacle in bacterial gene expression.

KEYWORDS:

RNA; codon usage; experimental evolution; synthetic biology

PMID:
30082392
PMCID:
PMC6112741
DOI:
10.1073/pnas.1810022115
[Indexed for MEDLINE]
Free PMC Article

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