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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.

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