Codon Usage Influences Fitness Through RNA Toxicity

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2018 Aug 8

PMID 30082392

Citations 41

Authors

Pragya Mittal

James Brindle

Julie Stephen

Joshua B Plotkin

Grzegorz Kudla

Affiliations

Soon will be listed here.

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 , and used quantitative growth and viability assays to estimate bacterial fitness. Unexpectedly, we found many synonymous variants whose expression was toxic to 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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References

Goodman D, Church G, Kosuri S . Causes and effects of N-terminal codon bias in bacterial genes. Science. 2013; 342(6157):475-9. DOI: 10.1126/science.1241934. View

Raghavan R, Kelkar Y, Ochman H . A selective force favoring increased G+C content in bacterial genes. Proc Natl Acad Sci U S A. 2012; 109(36):14504-7. PMC: 3437849. DOI: 10.1073/pnas.1205683109. View

Miroux B, Walker J . Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J Mol Biol. 1996; 260(3):289-98. DOI: 10.1006/jmbi.1996.0399. View

Plotkin J, Kudla G . Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet. 2010; 12(1):32-42. PMC: 3074964. DOI: 10.1038/nrg2899. View

Schlegel S, Genevaux P, Gier J . De-convoluting the Genetic Adaptations of E. coli C41(DE3) in Real Time Reveals How Alleviating Protein Production Stress Improves Yields. Cell Rep. 2015; 10(10):1758-1766. DOI: 10.1016/j.celrep.2015.02.029. View

Brandis G, Hughes D . The Selective Advantage of Synonymous Codon Usage Bias in Salmonella. PLoS Genet. 2016; 12(3):e1005926. PMC: 4786093. DOI: 10.1371/journal.pgen.1005926. View

Akashi H . Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics. 1994; 136(3):927-35. PMC: 1205897. DOI: 10.1093/genetics/136.3.927. View

Drummond D, Wilke C . Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell. 2008; 134(2):341-52. PMC: 2696314. DOI: 10.1016/j.cell.2008.05.042. View

Gu W, Zhou T, Wilke C . A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol. 2010; 6(2):e1000664. PMC: 2816680. DOI: 10.1371/journal.pcbi.1000664. View

10.

Kwon S, Kim S, Lee D, Kim J . Comparative genomics and experimental evolution of Escherichia coli BL21(DE3) strains reveal the landscape of toxicity escape from membrane protein overproduction. Sci Rep. 2015; 5:16076. PMC: 4632034. DOI: 10.1038/srep16076. View

11.

Kudla G, Murray A, Tollervey D, Plotkin J . Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009; 324(5924):255-8. PMC: 3902468. DOI: 10.1126/science.1170160. View

12.

Knoppel A, Nasvall J, Andersson D . Compensating the Fitness Costs of Synonymous Mutations. Mol Biol Evol. 2016; 33(6):1461-77. PMC: 4868123. DOI: 10.1093/molbev/msw028. View

13.

Neme R, Amador C, Yildirim B, McConnell E, Tautz D . Random sequences are an abundant source of bioactive RNAs or peptides. Nat Ecol Evol. 2017; 1(6):0217. PMC: 5447804. DOI: 10.1038/s41559-017-0127. View

14.

Kelsic E, Chung H, Cohen N, Park J, Wang H, Kishony R . RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq. Cell Syst. 2016; 3(6):563-571.e6. PMC: 5234859. DOI: 10.1016/j.cels.2016.11.004. View

15.

Sorensen M, Kurland C, Pedersen S . Codon usage determines translation rate in Escherichia coli. J Mol Biol. 1989; 207(2):365-77. DOI: 10.1016/0022-2836(89)90260-x. View

16.

Boel G, Letso R, Neely H, Price W, Wong K, Su M . Codon influence on protein expression in E. coli correlates with mRNA levels. Nature. 2016; 529(7586):358-363. PMC: 5054687. DOI: 10.1038/nature16509. View

17.

Agashe D, Sane M, Phalnikar K, Diwan G, Habibullah A, Martinez-Gomez N . Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium. Mol Biol Evol. 2016; 33(6):1542-53. PMC: 4868122. DOI: 10.1093/molbev/msw035. View

18.

Frumkin I, Schirman D, Rotman A, Li F, Zahavi L, Mordret E . Gene Architectures that Minimize Cost of Gene Expression. Mol Cell. 2016; 65(1):142-153. PMC: 5506554. DOI: 10.1016/j.molcel.2016.11.007. View

19.

Stemmer W . DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci U S A. 1994; 91(22):10747-51. PMC: 45099. DOI: 10.1073/pnas.91.22.10747. View

20.

Salis H, Mirsky E, Voigt C . Automated design of synthetic ribosome binding sites to control protein expression. Nat Biotechnol. 2009; 27(10):946-50. PMC: 2782888. DOI: 10.1038/nbt.1568. View