Synonymous codon usage is subject to selection in thermophilic bacteria
Synonymous codon usage is subject to selection in thermophilic bacteria
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DOI：
10.1093/nar/gkf546
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发表时间：
2002-10-01
影响因子：
14.9
通讯作者：
Hickey, DA
中科院分区：
文献类型：
--
作者：
Lynn, DJ;Singer, GAC;Hickey, DA
在过去的二十年中，基因组内部和基因组之间的同义密码子使用模式已被广泛研究。尽管越来越多的证据表明自然选择可以影响密码子的使用，但仍不可能将特定的密码子使用模式与特定的外部选择力联系起来。在这里，我们分析了 40 个完整测序的原核生物基因组中同义密码子的使用模式。通过将多个基因组的基因（总共超过 80,000 个基因）合并到一个数据集中进行分析，我们能够研究基因组内部和基因组之间密码子使用的变化。结果表明，同义密码子的使用受到两个主要因素的影响：（i）基因组的总体G+C含量和（ii）高温下的生长。这项研究的重点是同义密码子使用与高温生长能力之间的关系。我们已经能够消除系统发育历史和横向基因转移作为嗜热菌密码子使用特征模式的可能解释。因此，这些结果证明密码子使用的特定模式与外部选择力之间存在明显的联系。
The patterns of synonymous codon usage, both within and among genomes, have been extensively studied over the past two decades. Despite the accumulating evidence that natural selection can shape codon usage, it has not been possible to link a particular pattern of codon usage to a specific external selective force. Here, we have analyzed the patterns of synonymous codon usage in 40 completely sequenced prokaryotic genomes. By combining the genes from several genomes (more than 80 000 genes in all) into a single dataset for this analysis, we were able to investigate variations in codon usage, both within and between genomes. The results show that synonymous codon usage is affected by two major factors: (i) the overall G+C content of the genome and (ii) growth at high temperature. This study focused on the relationship between synonymous codon usage and the ability to grow at high temperature. We have been able to eliminate both phylogenetic history and lateral gene transfer as possible explanations for the characteristic pattern of codon usage among the thermophiles. Thus, these results demonstrate a clear link between a particular pattern of codon usage and an external selective force.