Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses
Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses
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DOI：
10.1016/j.biosystems.2005.03.002
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发表时间：
2005-07-01
期刊：
影响因子：
1.6
通讯作者：
Lu, ZH
中科院分区：
文献类型：
--
作者：
Zhou, T;Gu, WJ;Lu, ZH
在这项研究中，我们计算了H5N1病毒的密码子使用偏差，并对H5N1病毒、其他五种进化相关的甲型流感病毒和一种乙型流感病毒的同义密码子使用模式进行了比较分析。H5N1基因组的密码子使用偏向性稍弱，这主要是由第三个密码子位置的碱基组成决定的。通过比较不同病毒的同义密码子使用模式，我们发现H5N1病毒的密码子使用模式与其他甲型流感病毒相似，但与乙型流感病毒不同；甲型流感病毒基因的同义密码子使用在系统发育上是保守的，但不是株特异性的。在不同甲型流感病毒编码的基因中使用同义密码子是属保守的。这些病毒基因中同义密码子使用的变异大部分可以用组成约束来解释，而基因功能也与同义密码子使用在一定程度上相关。然而，翻译选择和基因长度对这些病毒基因中同义密码子使用的变化没有影响。2005爱思唯尔爱尔兰有限公司版权所有。
In this study, we calculated the codon usage bias in H5N1 virus and performed a comparative analysis of synonymous codon usage patterns in H5N1 virus, five other evolutionary related influenza A viruses and a influenza B virus. Codon usage bias in H5N1 genome is a little slight, which is mainly determined by the base compositions on the third codon position. By comparing synonymous codon usage patterns in different viruses, we observed that the codon usage pattern of H5N1 virus is similar with other influenza A viruses, but not influenza B virus, and the synonymous codon usage in influenza A virus genes is phylogenetically conservative, but not strain-specific. Synonymous codon usage in genes encoded by different influenza A viruses is genus conservative. Compositional constraints could explain most of the variation of synonymous codon usage among these virus genes, while gene function is also correlated to synonymous codon usages to a certain extent. However, translational selection and gene length have no effect on the variations of synonymous codon usage in these virus genes. (c) 2005 Elsevier Ireland Ltd. All rights reserved.