title: Codon usage decreases the error minimization within the genetic code.
abstract: The genetic code is not random but instead is organized in such a way that single nucleotide substitutions are more likely to result in changes between similar amino acids. This fidelity, or error minimization, has been proposed to be an adaptation within the genetic code. Many models have been proposed to measure this adaptation within the genetic code. However, we find that none of these consider codon usage differences between species. Furthermore, use of different indices of amino acid physicochemical characteristics leads to different estimations of this adaptation within the code. In this study, we try to establish a more accurate model to address this problem. In our model, a weighting scheme is established for mistranslation biases of the three different codon positions, transition/transversion biases, and codon usage. Different indices of amino acids' physicochemical characteristics are also considered. In contrast to pervious work, our results show that the natural genetic code is not fully optimized for error minimization. The genetic code, therefore, is not the most optimized one for error minimization, but one that balances between flexibility and fidelity for different species.
authors.affiliation: Department of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY 11794-5245, USA.
authors.forename: Chen-Tseh
authors.initials: CT
authors.lastname: Zhu
authors.forename: Xiao-Bin
authors.initials: XB
authors.lastname: Zeng
authors.forename: Wei-Da
authors.initials: WD
authors.lastname: Huang
mesh_terms: D019943:Amino Acid Substitution; D003062:Codon / Q000235:genetics*; D005815:Genetic Code; D017354:Point Mutation; D014176:Protein Biosynthesis / Q000502:physiology*
chemical_list: D003062:Codon