ArticleGenome biology2014
Inferring gene function from evolutionary change in signatures of translation efficiency.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
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- Comparative Analysis of Genomic and Transcriptome Sequences Reveals Divergent Patterns of Codon Bias in Wheat and Its Ancestor Species.Frontiers in genetics · 2021Article
- Protein structure, amino acid composition and sequence determine proteome vulnerability to oxidation-induced damage.The EMBO journal · 2020Article
- Short- and Long-Term Transcriptomic Responses of Escherichia coli to Biocides: a Systems Analysis.Applied and environmental microbiology · 2020Article
- Genes and Proteomes Associated With Increased Mutation Frequency and Multidrug Resistance of Naturally Occurring Mismatch Repair-DeficientFrontiers in microbiology · 2020Article
- Variation and selection on codon usage bias across an entire subphylum.PLoS genetics · 2019Article
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- The evolutionary signal in metagenome phyletic profiles predicts many gene functions.Microbiome · 2018Article
- Diversity of Translation Initiation Mechanisms across Bacterial Species Is Driven by Environmental Conditions and Growth Demands.Molecular biology and evolution · 2018Article
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- Overlap of Promoter Recognition Specificity of Stress Response Sigma Factors SigD and SigH inFrontiers in microbiology · 2018Article
- Codon-Resolution Analysis Reveals a Direct and Context-Dependent Impact of Individual Synonymous Mutations on mRNA Level.Molecular biology and evolution · 2017Article
- Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe genetic code is redundant, meaning that most amino acids can be encoded by more than one codon. Highly expressed genes tend to use optimal codons to increase the accuracy and speed of translation. Thus, codon usage biases provide a signature of the relative expression levels of genes, which can, uniquely, be quantified across the domains of life.
resultsHere we describe a general statistical framework to exploit this phenomenon and to systematically associate genes with environments and phenotypic traits through changes in codon adaptation. By inferring evolutionary signatures of translation efficiency in 911 bacterial and archaeal genomes while controlling for confounding effects of phylogeny and inter-correlated phenotypes, we linked 187 gene families to 24 diverse phenotypic traits. A series of experiments in Escherichia coli revealed that 13 of 15, 19 of 23, and 3 of 6 gene families with changes in codon adaptation in aerotolerant, thermophilic, or halophilic microbes. Respectively, confer specific resistance to, respectively, hydrogen peroxide, heat, and high salinity. Further, we demonstrate experimentally that changes in codon optimality alone are sufficient to enhance stress resistance. Finally, we present evidence that multiple genes with altered codon optimality in aerobes confer oxidative stress resistance by controlling the levels of iron and NAD(P)H.
conclusionsTaken together, these results provide experimental evidence for a widespread connection between changes in translation efficiency and phenotypic adaptation. As the number of sequenced genomes increases, this novel genomic context method for linking genes to phenotypes based on sequence alone will become increasingly useful.
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