title: Codon usage bias in human cytomegalovirus and its biological implication.
abstract: Human cytomegalovirus (HCMV) infection, a worldwide contagion, causes a serious disorder in infected individuals. Analysis of codon usage can reveal much molecular information about this virus. The effective number of codon (ENC) values, relative synonymous codon usage (RSCU) values, codon adaptation index (CAI), and nucleotide contents was investigated in approximately 160 coding sequences (CDS) among 17 human cytomegalovirus genomes using the software CodonW. Linear regression analysis and logistic regression were performed to explore the preliminary data. The results showed that, overall, HCMV genomes had low codon usage bias (mean ENC=47.619). However, the ENC of individual CDS varied widely and was distributed unevenly between host-related genes and viral-self-function genes (P=0.002, odds ratio (OR)=3.194), as did the GC content (P=0.016, OR=2.178). The ENC values correlated with CAI, GC content, and the nucleotide composing at the 3rd codon position (GC3s) (P<0.001). There was a significant variation in the codon preference that depended on the RSCU data. The predicted ENC curve suggested that mutational pressure, rather than natural selection, was one of the main factors that determined the codon usage bias in HCMV. Among 123 genes with known function, the genes related to viral self-replication and viral-host interaction showed different ENC and CAI values, and GC and GC3s contents. In conclusion, the detailed codon usage bias theoretically revealed information concerning HCMV evolution and could be a valuable additional parameter for HCMV gene function research.
authors.affiliation: Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China.
authors.forename: Changyuan
authors.initials: C
authors.lastname: Hu
authors.affiliation: Department of Rheumatism and Immunology, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China.
authors.forename: Lulu
authors.initials: L
authors.lastname: Ye
authors.affiliation: Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China.
authors.forename: Renpin
authors.initials: R
authors.lastname: Chen
authors.affiliation: Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China.
authors.forename: Lifang
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, Wenzhou Medical University, Ouhai District 325035, Wenzhou City, Zhejiang Province, China. Electronic address: wzxxy@aliyun.com.
authors.forename: Xiangyang
authors.initials: X
authors.lastname: Xue
mesh_terms: D003062:Codon; D003587:Cytomegalovirus / Q000235:genetics*; D005814:Genes, Viral; D016679:Genome, Viral; D054884:Host-Pathogen Interactions / Q000235:genetics; D006801:Humans; D009154:Mutation; D009711:Nucleotides / Q000235:genetics
chemical_list: D003062:Codon; D009711:Nucleotides
keywords: Codon usage bias; Host-relating protein; Human herpesvirus 5