Codon usage influences fitness through RNA toxicity

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 quant...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 115; no. 34; pp. 8639 - 8644
Main Authors Mittal, Pragya, Brindle, James, Stephen, Julie, Plotkin, Joshua B., Kudla, Grzegorz
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 21.08.2018
Subjects
Analgesics
Angiotensin
Angiotensin II
Biological Sciences
Biology
Cellular structure
Codon - genetics
Codon - metabolism
Escherichia coli - genetics
Escherichia coli - metabolism
Fitness
Ganglia
Gene expression
Genes
Hypersensitivity
Immune system
Inflammation
Macrophages
Mutation
Neuralgia
Pain
Pain perception
Peripheral neuropathy
Proteins
Ribonucleic acid
RNA
RNA, Bacterial - genetics
RNA, Bacterial - metabolism
Sensory neurons
Structural damage
Toxicity
Transplantation
synthetic biology
experimental evolution
RNA
codon usage
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Summary: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.
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Author contributions: P.M. and G.K. designed research; P.M., J.B., J.S., and G.K. performed research; P.M., J.B.P., and G.K. analyzed data; and P.M. and G.K. wrote the paper.
Edited by Gisela Storz, National Institute of Child Health and Human Development, Bethesda, MD, and approved July 18, 2018 (received for review June 13, 2018)
ISSN:0027-8424
1091-6490
1091-6490
DOI:10.1073/pnas.1810022115