Woo Patrick C Y, Wong Beatrice H L, Huang Yi, Lau Susanna K P, Yuen Kwok-Yung
State Key Laboratory of Emerging Infectious Diseases, Hong Kong; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong; Department of Microbiology, The University of Hong Kong, Hong Kong.
Virology. 2007 Dec 20;369(2):431-42. doi: 10.1016/j.virol.2007.08.010. Epub 2007 Sep 19.
Using the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G+C content in CoV-HKU1 warrants further studies.
利用19种冠状病毒基因组的完整序列，我们分析了冠状病毒基因组中的密码子使用偏好、二核苷酸相对丰度和胞嘧啶脱氨作用。在包含CpG的八个密码子中，有六个被显著抑制。使用NNC或NNU作为密码子的六种氨基酸的平均NNU/NNC比率为3.262，提示胞嘧啶脱氨。在16种二核苷酸中，CpG被抑制得最为显著（平均相对丰度0.509）。未观察到CpG丰度与平均NNU/NNC比率之间存在相关性。在这19种冠状病毒中，HKU1冠状病毒表现出最极端的密码子使用偏好，其NNU/NNC比率极高，达8.835。胞嘧啶脱氨以及免疫系统对CpG抑制克隆的选择是塑造冠状病毒基因组密码子使用偏好的两个主要独立生化和生物学选择力量。HKU1冠状病毒中极端密码子使用偏好、胞嘧啶脱氨和G+C含量的潜在机制有待进一步研究。
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