Characteristics of Nucleotide and Codon Usage Bias of 2A Sequence of Foot and Mouth Disease Virus

The cleavage at 2A/2B junction of Foot and Mouth Disease Virus (FMDV) is mediated by the 2A sequence. Here researchers calculate some data of the 2A sequence including the nucleotide usage bias (R-value), the Authentic Codon Bias (ACB value) and accumulation of Codon Bias (CUB2A value) to estimate potential effects of nucleotide and codon bias on the auto-cleavage of this junction. Researchers find that a high nucleotide usage bias exists in the 2A sequence (R-value = 0.856±0.113), ten positions 3, 5, 8, 9, 11, 14-18 show a stable codon usage tendency in the 2A sequence across all serotype while the accumulation of Codon Bias (CUB2A = 0.293±0.043) is low. It is interesting that an obvious downward trend of accumulation of codon bias in C-termini is present in the 2A sequence. These phenomena suggest that the nucleotide and codon usage models play potential roles in impairing the formation of the peptide bond linking the 2A/2B junction during co-translation by affecting conformation changes of A and P sites in the ribosome.