The Effects of the Context-Dependent Codon Usage Bias on the Structure of the nsp1αof Porcine Reproductive and Respiratory Syndrome Virus

The information about the crystal structure of porcine reproductive and respiratory syndrome virus (PRRSV) leader protease nsp1 α 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 nsp1 α 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 nsp1 α , 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 nsp1 α was found, and the phenomenon of CDCB exists in the specific folding units of the nsp1 α . These findings provide an insight into the roles of the synonymous codon usage and CDCB in the formation of PRRSV nsp1 α structure.