Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
Viruses. 2013 Jan 15;5(1):162-81. doi: 10.3390/v5010162.
Viral codon usage bias may be the product of a number of synergistic or antagonistic factors, including genomic nucleotide composition, translational selection, genomic architecture, and mutational or repair biases. Most studies of viral codon bias evaluate only the relative importance of genomic base composition and translational selection, ignoring other possible factors. We analyzed the codon preferences of ssRNA (luteoviruses and potyviruses) and ssDNA (geminiviruses) plant viruses that infect translationally distinct monocot and dicot hosts. We found that neither genomic base composition nor translational selection satisfactorily explains their codon usage biases. Furthermore, we observed a strong relationship between the codon preferences of viruses in the same family or genus, regardless of host or genomic nucleotide content. Our results suggest that analyzing codon bias as either due to base composition or translational selection is a false dichotomy that obscures the role of other factors. Constraints such as genomic architecture and secondary structure can and do influence codon usage in plant viruses, and likely in viruses of other hosts.
病毒密码子使用偏好可能是多种协同或拮抗因素的产物，包括基因组核苷酸组成、翻译选择、基因组结构以及突变或修复偏向。大多数病毒密码子偏向性的研究仅评估基因组碱基组成和翻译选择的相对重要性，而忽略了其他可能的因素。我们分析了感染翻译上不同的单子叶和双子叶宿主的 ssRNA（线病毒和马铃薯 Y 病毒）和 ssDNA（双生病毒）植物病毒的密码子偏好性。我们发现，基因组碱基组成和翻译选择都不能很好地解释它们的密码子使用偏好。此外，我们观察到同一科或属的病毒之间的密码子偏好性之间存在很强的关系，而与宿主或基因组核苷酸含量无关。我们的结果表明，将密码子偏向性归因于碱基组成或翻译选择是一种错误的二分法，掩盖了其他因素的作用。诸如基因组结构和二级结构等限制因素可以并且确实会影响植物病毒中的密码子使用，并且可能会影响其他宿主的病毒。
