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    Solving the riddle of codon usage preferences: a test for translational selection

    dos Reis, M. and Savva, Renos and Wernisch, Lorenz (2004) Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Research 32 (17), pp. 5036-5044. ISSN 0305-1048.


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    Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model.


    Item Type: Article
    Additional Information: This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Nucleic Acids Research following peer review. The definitive publisher-authenticated version, v.32 (17), Pp. 5036-5044 is available online at
    School: Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences
    Research Centres and Institutes: Innovation Management Research, Birkbeck Centre for, Structural Molecular Biology, Institute of (ISMB)
    Depositing User: Administrator
    Date Deposited: 20 Jul 2010 11:05
    Last Modified: 02 Aug 2023 16:48


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