Codon usage in nucleopolyhedroviruses
Codon usage in nucleopolyhedroviruses
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DOI：
10.1099/0022-1317-81-9-2313
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发表时间：
2000-09-01
影响因子：
3.8
通讯作者：
Whittome, B
中科院分区：
文献类型：
--
作者：
Levin, DB;Whittome, B
基于杆状病毒多角体蛋白核苷酸和氨基酸序列的系统发育分析揭示了两个主要的核多角体病毒（NPV）分支，分别被命名为类群I和类群II。随后的系统发育分析揭示了三个类群II亚支系，分别为A、B和c。氨基酸频率的变化决定了不同但在结构和功能上保守的基因的不同程度，因此显著影响系统发育关系的分析。因此，考虑氨基酸密码子使用的变化是很重要的。基因组假说认为，在任何给定的基因组中，基因对于同义密码子使用相同的编码模式，并且在系统发育相关的物种中，基因通常显示相同的密码子使用模式。我们对来自6个npv的6个基因的密码子使用情况进行了研究，发现：(1)同一病毒基因组内基因的密码子使用存在显著差异；(2)不同npv编码的同源基因密码子使用存在显著差异；(3) npv基因表达水平与密码子偏倚无相关性；(4) npv基因长度与密码子偏倚无相关性；(5)虽然密码子使用偏好在系统发育密切相关的病毒之间似乎是保守的，但密码子使用模式似乎也是病毒编码基因gc含量的直接功能。
Phylogenetic analyses based on baculovirus polyhedrin nucleotide and amino acid sequences revealed two major nucleopolyhedrovirus (NPV) clades, designated Group I and Group II. Subsequent phylogenetic analyses have revealed three Group II subclades, designated A, B and C. Variations in amino acid frequencies determine the extent of dissimilarity for divergent but structurally and functionally conserved genes and therefore significantly influence the analysis of phylogenetic relationships. Hence, it is important to consider variations in amino acid codon usage. The Genome Hypothesis postulates that genes in any given genome use the same coding pattern with respect to synonymous codons and that genes in phylogenetically related species generally show the same pattern of codon usage. We have examined codon usage in six genes from six NPVs and found that: (1) there is significant variation in codon use by genes within the same virus genome; (2) there is significant variation in the codon usage of homologous genes encoded by different NPVs; (3) there is no correlation between the level of gene expression and codon bias in NPVs; (4) there is no correlation between gene length and codon bias in NPVs; and (5) that while codon use bias appears to be conserved between viruses that are closely related phylogenetically, the patterns of codon usage also appear to be a direct function of the GC-content of the virus-encoded genes.