Synonymous codon usage is subject to selection in thermophilic bacteria
نویسندگان
چکیده
منابع مشابه
Synonymous codon usage in bacteria.
In most bacteria, synonymous codons are not used with equal frequencies. Different factors have been proposed to contribute to codon usage preference, including translational selection, GC composition, strand-specific mutational bias, amino acid conservation, protein hydropathy, transcriptional selection and even RNA stability. The review discusses these factors and their contribution to bias i...
متن کاملSynonymous codon usage and selection on proteins
Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed `volatility', to estimate selection pressures on protein sequences from their synonymous codon usage (Plotkin and Dushoff 2003, Plotkin et al 2004a). Here we provide a theoretical foundation for this approach. We derive t...
متن کاملSynonymous codon usage in Escherichia coli: selection for translational accuracy.
In many organisms, selection acts on synonymous codons to improve translation. However, the precise basis of this selection remains unclear in the majority of species. Selection could be acting to maximize the speed of elongation, to minimize the costs of proofreading, or to maximize the accuracy of translation. Using several data sets, we find evidence that codon use in Escherichia coli is bia...
متن کاملEstimating selection on synonymous codon usage from noisy experimental data.
A key goal in molecular evolution is to extract mechanistic insights from signatures of selection. A case study is codon usage, where despite many recent advances and hypotheses, two longstanding problems remain: the relative contribution of selection and mutation in determining codon frequencies and the relative contribution of translational speed and accuracy to selection. The relevant target...
متن کاملThe selection-mutation-drift theory of synonymous codon usage.
It is argued that the bias in synonymous codon usage observed in unicellular organisms is due to a balance between the forces of selection and mutation in a finite population, with greater bias in highly expressed genes reflecting stronger selection for efficiency of translation. A population genetic model is developed taking into account population size and selective differences between synony...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2002
ISSN: 1362-4962
DOI: 10.1093/nar/gkf546