title: Clustering of low usage codons in the translation initiation region of hepatitis C virus.
abstract: The adaptation of the overall codon usage pattern of hepatitis C virus (HCV) to that of human is estimated by the synonymous codon usage value (RSCU). The synonymous codon usage biases for the translation initiation region (TIR) of this virus are also analyzed by calculation of usage fluctuation of each synonymous codon along the TIR (the first 30 codon sites of the whole coding sequence of HCV). As for the overall codon usage pattern of HCV, this virus has a significant tendency to delete the codons with CpG or TpA dinucleotides. Turning to the adaptation of the overall codon usage of HCV to that of human, over half part of codons has a similar usage pattern between this virus and human, suggesting that the host cellular environment of the overall codon usage pattern influences the formation of codon usage for HCV. In addition, there is no obvious phenomenon that the codons with relatively low energy tend to be highly selected in the TIR of HCV, suggesting that the synonymous codon usage patterns for the TIR of HCV might be not affected by the secondary structure of nucleotide sequence, however, the formation of synonymous codons usage in the TIR of HCV is influenced by the overall codon usage patterns of human to some degree.
authors.affiliation: State Key Laboratory of Veterinary Etiological Biology, National Foot-and-Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China.
authors.forename: Jian-hua
authors.initials: JH
authors.lastname: Zhou
authors.forename: Jun-hong
authors.initials: JH
authors.lastname: Su
authors.forename: Hao-tai
authors.initials: HT
authors.lastname: Chen
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.forename: Li-na
authors.initials: LN
authors.lastname: Ma
authors.forename: Yao-zhong
authors.initials: YZ
authors.lastname: Ding
authors.forename: Laszlo
authors.initials: L
authors.lastname: Stipkovits
authors.forename: Susan
authors.initials: S
authors.lastname: Szathmary
authors.forename: Zygmunt
authors.initials: Z
authors.lastname: Pejsak
authors.forename: Yong-sheng
authors.initials: YS
authors.lastname: Liu
mesh_terms: D016000:Cluster Analysis; D003062:Codon; D016174:Hepacivirus / Q000235:genetics* / Q000502:physiology; D006526:Hepatitis C / Q000821:virology*; D054884:Host-Pathogen Interactions / Q000235:genetics; D006801:Humans; D016366:Open Reading Frames; D010442:Peptide Chain Initiation, Translational / Q000235:genetics* / Q000502:physiology
chemical_list: D003062:Codon
keywords: Hepatitis C virus; Overall codon usage pattern; Synonymous codon usage value; Translation initiation region