synonymous codon usage in hepatitis B virus and the effects of host

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原帖由yangcao 发表于 2011-12-20 11:08 、

这是关于HBV的一篇密码子分析的文章：The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern
出自：Virology Journal 2011, 8:544 doi:10.1186/1743-422X-8-544
Abstract
Background: Hepatitis B virus (HBV) infection is one of the main human health problem and causes a large-scale of patients chronic infection worldwide.. As the replication of HBV depends on its host cell system, codon usage pattern for the viral gene might be susceptible to two main selections, namely mutation pressure and translation selection. In this case, a deeper investigation between HBV evolution and host adaptive response might assist control this disease.
Result: Relative synonymous codon usage (RSCU) values for the whole HBV coding sequence were studied by Principal component analysis (PCA). The characteristics of the synonymous codon usage patterns, nucleotide contents and the comparison between ENC values of the whole HBV coding sequence indicated that the interaction between virus mutation pressure and host
translation selection exists in the processes of HBV evolution. The synonymous codon usage pattern of HBV is a mixture of coincidence and antagonism to that of host cell. But the difference of genetic characteristic of HBV failed to be observed to its different epidemic areas or subtypes, suggesting that geographic factor is limited to influence the evolution of this virus, while genetic characteristic based on HBV genotypes could be divided into three groups, namely (i) genotyps A
and E, (ii) genotype B, (iii) genotypes C, D and G.
Conclusion: Codon usage patterns from PCA for identification of evolutionary trends in HBV provide an alternative approach to understand the evolution of HBV. Further more, a combined selection of mutation pressure with translation selection on codon usage might shed a light on understanding the evolutionary trends of HBV genotypes.
Keywords: Hepatitis B virus, codon usage pattern, evolution, mutation pressure, translation selection

背景:乙型肝炎病毒(HBV)感染是一种主要的人类健康问题并造成世界范围内大规模的慢性感染. HBV的复制依赖其宿主细胞体系,病毒基因的密码子使用模式主要有两个,即突变压力和翻译的选择。在这种情况下,对乙肝病毒进化和宿主适应性反应能力的研究可能会帮助控制这种疾病。
结果:相对同义密码子使用频率(RSCU值)对整个HBV编码序列进行主成分分析(PCA)。对乙肝病毒整个编码序列同义密码子使用模式、核苷酸组成和ENC值的分析较表明,病毒突变压力和宿主翻译选择存在于乙肝病毒进化过程。他们同义密码子使用模式是宿主细胞巧合和对立的产物。但在不同的流行地区或亚型间对HBV病毒的基因特征的差异未被发现,表明地理因素对病毒演化的影响是有限的,而基于HBV基因型可将其遗传特征分为三组,分别为(1)genotyps A和E,(2)基因型B,(3)基因型C、D和G。
结论:研究HBV的主码使用模式的鉴定其进化趋势对研究HBV的进化提供一个可选的方法。突变压力与翻译的选择共同作用于密码子使用模式也会更进一步了解HBV基因型的进化趋势。
关键词:乙型肝炎病毒、密码子使用模式、进化、突变压力、翻译选择


  在现代化进程中，人们生活多姿多样，疾病也越来越多越来越复杂，病原处于不断进化的过程中，乙肝病毒是危害国民健康的一大杀手，对病毒密码子使用模式的研究可以更深入的了解病毒特征，为病毒的培养，基因的表达及研发抗病毒药物都是很有帮助的。

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