The Characteristics of Context-Dependent Codon Usage Bias for Cleavage Sites in the Polyprotein of Foot and Mouth Disease Virus

摘要

The results of analysis of context-dependent codon bias designed to identify the relationship between codon bias model for the context surrounding the cleavage site and the model for the corresponding cleavage site, applied to genome data form 66 isolates of Foot and Mouth Disease Virus (FMDV) representing all seven serotypes were reported. The cleavage sites in the polyprotein were identified from all parts of the FMDV genome and the similarity of Codon Bias Model for regions flanking the cleavage sites was estimated. Although, the two amino acid residues which was comprised of the cleavage site were not conserved, one residue always tended to be conserved, suggesting that the conserved residue was essential for the cleavage process. In addition, although the similarity of Codon Bias Model for some positions in the most target contexts was ensured, the scale of similarity of Codon Bias Model was larger in the regions flanking the 2A/2B, 2C/3A, 3A/3B, 3B/3C and 3C/3D sites than that of the rest. Furthermore, correlation analysis between the Codon Bias Model for each position in the target context surrounding the cleavage site and that of the corresponding site was performed it was concluded that the significant relationship existed in the VP4/VP2, 2A/2B, 2B/2C and 3A/3B sites, respectively. The interesting phenomena probably suggested that context-dependent codon bias surrounding some cleavage sites was existence in FMDV and the Codon Bias Model for these regions played potential roles in shaping specific characteristics of these corresponding sites at the level of transcription or translation.