Analysis of Synonymous Codon Usage in the newly identified DPV UL43 Gene

Abstract

In this paper, we analyzed the UL43 gene of duck plague virus (DPV) of codon usage bias. The results may provide a basis for understanding the evolution and pathogenesis of DPV and for selecting appropriate host expression systems to improve the expression of target gene in vitro. In this study, the synonymous codon usage bias of UL43 gene in the 24 herpesviruses have been analyzed and the results showed obvious differences by the Codon Adaptation Index (CAI), effective number of codons (ENC) and the value of G + C content at the 3rd codon position (GC3s). In addition, the results revealed that the synonymous codons with A and T at the third codon positon have widely usage in the codon of UL43 gene of DPV. G + C compositional constraint is the main factor that determines the codon usage bias in UL43 gene. The phylogenetic analysis suggested that DPV was evolutionarily closer to fowl herpesviruses which further clustered into Alphaherpesvirinae. Furthermore the ORF of UL43 gene has sequential rare codons. There were 25 codons showing distinct usage differences between DPV with Escherichia coli, 24 codons showing distinct usage differences between DPV with yeast, and 32 between DPV and H. sapiens. Therefore the yeast and E. coli expression system may be suitable for the expression of DPV UL43 gene if some codons could be optimized.