Zhou Tong, Gu Wanjun, Ma Jianmin, Sun Xiao, Lu Zuhong
Key Laboratory of Molecular and Biomolecular Electronics of the Ministry of Education, Southeast University, Nanjing, Jiangsu 210096, China.
Biosystems. 2005 Jul;81(1):77-86. doi: 10.1016/j.biosystems.2005.03.002. Epub 2005 Apr 7.
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.
在本研究中，我们计算了H5N1病毒的密码子使用偏好，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基因组中的密码子使用偏好略显轻微，这主要由密码子第三位的碱基组成决定。通过比较不同病毒的同义密码子使用模式，我们观察到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，并且甲型流感病毒基因中的同义密码子使用在系统发育上是保守的，而非毒株特异性的。不同甲型流感病毒编码的基因中的同义密码子使用是属保守的。组成限制可以解释这些病毒基因之间同义密码子使用的大部分变异，而基因功能在一定程度上也与同义密码子使用相关。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异没有影响。
