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

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