The effects of the context-dependent codon usage bias on the structure of the nsp1 α of porcine reproductive and respiratory syndrome virus

Yao Zhong Ding, Ya Nan You, Dong Jie Sun, Hao Tai Chen, Yong Lu Wang, Hui Yun Chang, Li Pan, Yu Zhen Fang, Zhong Wang Zhang, Peng Zhou, Jian Liang Lv, Xin Sheng Liu, Jun Jun Shao, Fu Rong Zhao, Tong Lin, Laszlo Stipkovits, Zygmunt Pejsak, Yong Guang Zhang, Jie Zhang

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4 Citations (Scopus)

Abstract

The information about the crystal structure of porcine reproductive and respiratory syndrome virus (PRRSV) leader protease nsp1α is available to analyze the roles of tRNA abundance of pigs and codon usage of the nsp1 α gene in the formation of this protease. The effects of tRNA abundance of the pigs and the synonymous codon usage and the context-dependent codon bias (CDCB) of the nsp1 α on shaping the specific folding units (α-helix, β-strand, and the coil) in the nsp1α were analyzed based on the structural information about this protease from protein data bank (PDB: 3IFU) and the nsp1 α of the 191 PRRSV strains. By mapping the overall tRNA abundance along the nsp1 α, we found that there is no link between the fluctuation of the overall tRNA abundance and the specific folding units in the nsp1α, and the low translation speed of ribosome caused by the tRNA abundance exists in the nsp1 α. The strong correlation between some synonymous codon usage and the specific folding units in the nsp1α was found, and the phenomenon of CDCB exists in the specific folding units of the nsp1α. These findings provide an insight into the roles of the synonymous codon usage and CDCB in the formation of PRRSV nsp1α structure.

Original languageEnglish
Article number765320
JournalBioMed research international
Volume2014
DOIs
Publication statusPublished - 2014

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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    Ding, Y. Z., You, Y. N., Sun, D. J., Chen, H. T., Wang, Y. L., Chang, H. Y., Pan, L., Fang, Y. Z., Zhang, Z. W., Zhou, P., Lv, J. L., Liu, X. S., Shao, J. J., Zhao, F. R., Lin, T., Stipkovits, L., Pejsak, Z., Zhang, Y. G., & Zhang, J. (2014). The effects of the context-dependent codon usage bias on the structure of the nsp1 α of porcine reproductive and respiratory syndrome virus. BioMed research international, 2014, [765320]. https://doi.org/10.1155/2014/765320