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.

The origin of the genetic code: theories and their relationships, a review

“…There are a number of observations and suggestions pointing out that the biosynthetic pathways of amino acids played a fundamental role in structuring the organization of the genetic code table (Nirenberg et al, 1963;Pelc, 1965;Jukes, 1966;Dillon, 1973;Wong, 1975Wong, , 1976Wong, , 1980Wong, , 1981Brack and Orgel, 1975;McClendon, 1986McClendon, , 1987Jurka and Smith, 1987a,b;Wachtershauser, 1988;de Duve, 1991;Miseta, 1989;Taylor and Coates, 1989;Danchin, 1989;Szathmary and Zintzaras, 1992;Morowitz, 1992;Szathmary, 1993;Di Giulio, 1992a,b, 1993, 1994, 1997a-c, 1999, 2000a,b, 2001, 2003Di Giulio and Medugno, 1998, 2000Di Giulio et al, 1994;Edwards, 1996;Chaley et al, 1999;Bermudez et al, 1999;Ardell and Sella, 2002;Zhu et al, 2003;Archetti, 2004;Klipcan and Safro, 2004), thus corroborating the coevolution theory.…”

Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability

“…Along this line, Zhu et al [15] also took into consideration the codon usage of individual species in the code optimization for error minimization and Marquez et al [16] checked whether organisms optimize the genetic code at the same time that the codon usage.…”

Codons Support the Maintenance of Intrinsic DNA Polymer Flexibility over Evolutionary Timescales

“…However, more recently, it has been demonstrated that the genetic code is quite nonrandom with respect to its ability to minimize the effects of single-base substitutions on proteins, especially at the first and third positions of the codon (Freeland and Hurst 1998). Both the source and degree of this nonrandomness are still debated (Zhu et al 2003; Archetti 2004; Stoltzfus and Yampolsky 2007); however, most would agree that this nonrandomness ultimately implies some level of evolutionary constraint evident in both the overall distribution of codon assignments and local choice of codons (i.e., codon bias) within genes and genomes (Hershberg and Petrov 2008). …”