The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1α of Porcine Reproductive and Respiratory Syndrome Virus

• Main Authors: 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
• Format: Article
• Language: English
• Published: Hindawi Limited 2014-01-01
• Series: BioMed Research International
• Online Access: http://dx.doi.org/10.1155/2014/765320
• ISSN: 2314-6133; 2314-6141

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 nsp1α 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 nsp1α 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 nsp1α of the 191 PRRSV strains. By mapping the overall tRNA abundance along the nsp1α, 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 nsp1α. 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.