Cardinale Daniel J, Duffy Siobain
Department of Ecology, Evolution and Natural Resources; School of Environmental and Biological Sciences; Rutgers; The State University of New Jersey; New Brunswick, NJ USA.
Bacteriophage. 2011 Jul;1(4):219-224. doi: 10.4161/bact.1.4.18496. Epub 2011 Jul 1.
Viral codon usage is shaped by the conflicting forces of mutational pressure and selection to match host patterns for optimal expression. We examined whether genomic architecture (single- or double-stranded DNA) influences the degree to which bacteriophage codon usage differ from their primary bacterial hosts and each other. While both correlated equally with their hosts' genomic nucleotide content, the coat genes of ssDNA phages were less well adapted than those of dsDNA phages to their hosts' codon usage profiles due to their preference for codons ending in thymine. No specific biases were detected in dsDNA phage genomes. In all nine of ten cases of codon redundancy in which a specific codon was overrepresented, ssDNA phages favored the NNT codon. A cytosine to thymine biased mutational pressure working in conjunction with strong selection against non-synonymous mutations appears be shaping codon usage bias in ssDNA viral genomes.
病毒密码子使用情况受到突变压力和选择这两种相互冲突的力量的影响，以匹配宿主模式从而实现最佳表达。我们研究了基因组结构（单链或双链DNA）是否会影响噬菌体密码子使用情况与其主要细菌宿主以及彼此之间的差异程度。虽然两者与宿主的基因组核苷酸含量的相关性相同，但由于单链DNA噬菌体对以胸腺嘧啶结尾的密码子的偏好，其外壳基因比双链DNA噬菌体的外壳基因对宿主密码子使用谱的适应性更差。在双链DNA噬菌体基因组中未检测到特定偏差。在十种密码子冗余的情况中有九种，即特定密码子出现频率过高的情况，单链DNA噬菌体偏好NNT密码子。胞嘧啶到胸腺嘧啶的偏向性突变压力与针对非同义突变的强烈选择共同作用，似乎正在塑造单链DNA病毒基因组中的密码子使用偏差。
