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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift
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Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift

机译：通过选择翻译效率，突变偏倚和遗传漂移来解释复杂的密码子使用方式

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摘要

The genetic code is redundant with most amino acids using multiple codons. In many organisms, codon usage is biased toward particular codons. Understanding the adaptive and nonadaptive forces driving the evolution of codon usage bias (CUB) has been an area of intense focus and debate in the fields of molecular and evolutionary biology. However, their relative importance in shaping genomic patterns of CUB remains unsolved. Using a nested model of protein translation and population genetics, we show that observed gene level variation of CUB in Saccharomyces cerevisiae can be explained almost entirely by selection for efficient ribosomal usage, genetic drift, and biased mutation. The correlation between observed codon counts within individual genes and our model predictions is 0.96. Although a variety of factors shape patterns of CUB at the level of individual sites within genes, our results suggest that selection for efficient ribosome usage is a central force in shaping codon usage at the genomic scale. In addition, our model allows direct estimation of codon-specific mutation rates and elongation times and can be readily applied to any organism with high-throughput expression datasets. More generally, we have developed a natural framework for integrating models of molecular processes to population genetics models to quantitatively estimate parameters underlying fundamental biological processes, such a protein translation.
机译：对于大多数使用多个密码子的氨基酸而言，遗传密码是多余的。在许多生物中，密码子使用偏向于特定密码子。在分子和进化生物学领域中，了解驱动密码子使用偏倚（CUB）进化的适应性和非适应性力量一直是人们关注的焦点和争论的领域。但是，它们在塑造CUB基因组模式方面的相对重要性仍未解决。使用蛋白质翻译和群体遗传学的嵌套模型，我们显示观察到的酿酒酵母中CUB的基因水平变异几乎可以完全通过选择有效的核糖体使用，遗传漂移和偏向突变来解释。单个基因中观察到的密码子计数与我们的模型预测之间的相关性是0.96。尽管多种因素会在基因中单个位点的水平上影响CUB的模式，但我们的研究结果表明，有效利用核糖体的选择是在基因组规模上塑造密码子使用的核心力量。此外，我们的模型可以直接估计密码子特异的突变率和延伸时间，并且可以容易地应用于具有高通量表达数据集的任何生物。更一般而言，我们已经开发出了一个自然的框架，可以将分子过程模型与种群遗传学模型集成在一起，以定量估算基本生物学过程（例如蛋白质翻译）的参数。

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  • 作者

    Premal Shah; Michael A. Gilchrist;

  • 作者单位

    Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville TN 37996,National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville TN 37996;

    Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville TN 37996,National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville TN 37996;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    ribosome overhead cost; protein production rate;

    机译：核糖体间接费用;蛋白质产生率;

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