ArticleJournal of molecular evolution2004
Selection on codon usage for error minimization at the protein level.
Article in Journal of molecular evolution, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 54 citations in OpenAlex.
- A comprehensive analysis of translational misdecoding pattern and its implication on genetic code evolution.Nucleic acids research · 2023Article
- Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes.Nature communications · 2022Article
- Large-scale in silico mutagenesis experiments reveal optimization of genetic code and codon usage for protein mutational robustness.BMC biology · 2020Article
- Experimental solutions to problems defining the origin of codon-directed protein synthesis.Bio Systems · 2019Review
- Thawing out frozen metabolic accidents.BMC biology · 2019Review
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- Decoding mechanisms by which silent codon changes influence protein biogenesis and function.The international journal of biochemistry & cell biology · 2015Review
- Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint.Life (Basel, Switzerland) · 2015Article
- Selection shapes the robustness of ligand-binding amino acids.Journal of molecular evolution · 2013Article
- High-density transcriptional initiation signals underline genomic islands in bacteria.PloS one · 2012Article
- Specialization versus adaptation: two strategies employed by cyanophages to enhance their translation efficiencies.Nucleic acids research · 2011Article
- Modeling compositional dynamics based on GC and purine contents of protein-coding sequences.Biology direct · 2010Article
- Codon usage is associated with the evolutionary age of genes in metazoan genomes.BMC evolutionary biology · 2009Article
- Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage.Nucleic acids research · 2009Article
- The evolutionary consequences of erroneous protein synthesis.Nature reviews. Genetics · 2009Review
- Differential selective constraints shaping codon usage pattern of housekeeping and tissue-specific homologous genes of rice and arabidopsis.DNA research : an international journal for rapid publication of reports on genes and genomes · 2008Article
- The tri-frame model.Journal of theoretical biology · 2008Article
- OPTIMIZER: a web server for optimizing the codon usage of DNA sequences.Nucleic acids research · 2007Article
- Identification of conflicting selective effects on highly expressed genes.Evolutionary bioinformatics online · 2007Article
- Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation.Genome biology · 2007Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Given the structure of the genetic code, synonymous codons differ in their capacity to minimize the effects of errors due to mutation or mistranslation. I suggest that this may lead, in protein-coding genes, to a preference for codons that minimize the impact of errors at the protein level. I develop a theoretical measure of error minimization for each codon, based on amino acid similarity. This measure is used to calculate the degree of error minimization for 82 genes of Drosophila melanogaster and 432 rodent genes and to study its relationship with CG content, the degree of codon usage bias, and the rate of nucleotide substitution. I show that (i) Drosophila and rodent genes tend to prefer codons that minimize errors; (ii) this cannot be merely the effect of mutation bias; (iii) the degree of error minimization is correlated with the degree of codon usage bias; (iv) the amino acids that contribute more to codon usage bias are the ones for which synonymous codons differ more in the capacity to minimize errors; and (v) the degree of error minimization is correlated with the rate of nonsynonymous substitution. These results suggest that natural selection for error minimization at the protein level plays a role in the evolution of coding sequences in Drosophila and rodents.
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