Comparison of translation loads for standard and alternative genetic codes

BMC Evolutionary Biology

Research Article

Ugo Bastolla¹  Markus Porto²  Stefanie Gabriele Sammet³ 

[1] Centro de Biología Molecular 'Severo Ochoa', (CSIC-UAM), Cantoblanco, 28049, Madrid, Spain;Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 8, 64289, Darmstadt, Germany;Institut für Theoretische Physik, Universität zu Köln, Zülpicher Str. 77, 50937, Köln, Germany;Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstr. 8, 64289, Darmstadt, Germany;Karlstr. 23, 64283, Darmstadt, Germany;

关键词: Genetic Code;    Fitness Landscape;    Mutation Load;    Mutation Bias;    Standard Genetic Code;   

DOI  :  10.1186/1471-2148-10-178

 received in 2009-08-07, accepted in 2010-06-14,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundThe (almost) universality of the genetic code is one of the most intriguing properties of cellular life. Nevertheless, several variants of the standard genetic code have been observed, which differ in one or several of 64 codon assignments and occur mainly in mitochondrial genomes and in nuclear genomes of some bacterial and eukaryotic parasites. These variants are usually considered to be the result of non-adaptive evolution. It has been shown that the standard genetic code is preferential to randomly assembled codes for its ability to reduce the effects of errors in protein translation.ResultsUsing a genotype-to-phenotype mapping based on a quantitative model of protein folding, we compare the standard genetic code to seven of its naturally occurring variants with respect to the fitness loss associated to mistranslation and mutation. These fitness losses are computed through computer simulations of protein evolution with mutations that are either neutral or lethal, and different mutation biases, which influence the balance between unfolding and misfolding stability. We show that the alternative codes may produce significantly different mutation and translation loads, particularly for genomes evolving with a rather large mutation bias. Most of the alternative genetic codes are found to be disadvantageous to the standard code, in agreement with the view that the change of genetic code is a mutationally driven event. Nevertheless, one of the studied alternative genetic codes is predicted to be preferable to the standard code for a broad range of mutation biases.ConclusionsOur results show that, with one exception, the standard genetic code is generally better able to reduce the translation load than the naturally occurring variants studied here. Besides this exception, some of the other alternative genetic codes are predicted to be better adapted for extreme mutation biases. Hence, the fixation of alternative genetic codes might be a neutral or nearly-neutral event in the majority of the cases, but adaptation cannot be excluded for some of the studied cases.

【 授权许可】

Unknown   
© Sammet et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.