ArticleGenome biology2018
Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 39 citations in OpenAlex.
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- The genomic basis of host and vector specificity in non-pathogenic trypanosomatids.Biology open · 2022Article
- Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals.Journal of molecular evolution · 2022Article
- Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off.Molecular biology and evolution · 2021Article
- Cost-efficiency tradeoff is optimized in various cancer types revealed by genome-wide analysis.Molecular genetics and genomics : MGG · 2021Article
- Compelling Evidence Suggesting the Codon Usage of SARS-CoV-2 Adapts to Human After the Split From RaTG13.Evolutionary bioinformatics online · 2021Article
- Interplay between Position-Dependent Codon Usage Bias and Hydrogen Bonding at the 5' End of ORFeomes.mSystems · 2020Article
- Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation.Frontiers in microbiology · 2020Article
- Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in themSystems · 2019Article
- Evolutionary genomics: the fruits of genomic approaches applied to evolutionary biology.Genome biology · 2019Article
- Selection-driven cost-efficiency optimization of transcripts modulates gene evolutionary rate in bacteria.Genome biology · 2018Article
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2 authors at 1 institution in 1 country.
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Abstract
backgroundMost amino acids are encoded by multiple synonymous codons. However, synonymous codons are not used equally, and this biased codon use varies between different organisms. It has previously been shown that both selection acting to increase codon translational efficiency and selection acting to decrease codon biosynthetic cost contribute to differences in codon bias. However, it is unknown how these two factors interact or how they affect molecular sequence evolution.
resultsThrough analysis of 1320 bacterial genomes, we show that bacterial genes are subject to multi-objective selection-driven optimization of codon use. Here, selection acts to simultaneously decrease transcript biosynthetic cost and increase transcript translational efficiency, with highly expressed genes under the greatest selection. This optimization is not simply a consequence of the more translationally efficient codons being less expensive to synthesize. Instead, we show that transfer RNA gene copy number alters the cost-efficiency trade-off of synonymous codons such that, for many species, selection acting on transcript biosynthetic cost and translational efficiency act in opposition. Finally, we show that genes highly optimized to reduce cost and increase efficiency show reduced rates of synonymous and non-synonymous mutation.
conclusionsThis analysis provides a simple mechanistic explanation for variation in evolutionary rate between genes that depends on selection-driven cost-efficiency optimization of the transcript. These findings reveal how optimization of resource allocation to messenger RNA synthesis is a critical factor that determines both the evolution and composition of genes.
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