Clustering of low usage codons in the translation initiation region of hepatitis C virus

Jian hua Zhou, Jun hong Su, Hao tai Chen, Jie Zhang, Li na Ma, Yao zhong Ding, L. Stipkovits, Susan Szathmary, Zygmunt Pejsak, Yong sheng Liu

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)8-12
Number of pages5
JournalInfection, Genetics and Evolution
Volume18
DOIs
Publication statusPublished - Aug 2013

Fingerprint

hepatitis
Hepatitis C virus
codons
Codon
Hepacivirus
translation (genetics)
Cluster Analysis
virus
Viruses
viruses
secondary structure

Keywords

  • Hepatitis C virus
  • Overall codon usage pattern
  • Synonymous codon usage value
  • Translation initiation region

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Molecular Biology
  • Microbiology
  • Infectious Diseases
  • Microbiology (medical)

Cite this

Clustering of low usage codons in the translation initiation region of hepatitis C virus. / Zhou, Jian hua; Su, Jun hong; Chen, Hao tai; Zhang, Jie; Ma, Li na; Ding, Yao zhong; Stipkovits, L.; Szathmary, Susan; Pejsak, Zygmunt; Liu, Yong sheng.

In: Infection, Genetics and Evolution, Vol. 18, 08.2013, p. 8-12.

Research output: Contribution to journalArticle

Zhou, JH, Su, JH, Chen, HT, Zhang, J, Ma, LN, Ding, YZ, Stipkovits, L, Szathmary, S, Pejsak, Z & Liu, YS 2013, 'Clustering of low usage codons in the translation initiation region of hepatitis C virus', Infection, Genetics and Evolution, vol. 18, pp. 8-12. https://doi.org/10.1016/j.meegid.2013.03.043
Zhou, Jian hua ; Su, Jun hong ; Chen, Hao tai ; Zhang, Jie ; Ma, Li na ; Ding, Yao zhong ; Stipkovits, L. ; Szathmary, Susan ; Pejsak, Zygmunt ; Liu, Yong sheng. / Clustering of low usage codons in the translation initiation region of hepatitis C virus. In: Infection, Genetics and Evolution. 2013 ; Vol. 18. pp. 8-12.
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