Identification and Sequence Analysis of the Duck Plague Virus UL46 Gene

Abstract

The DPV UL46 gene( GenBank accession No. EU195108) isolated by our laboratory was amplified by PCR and cloned into pMD18-T vector. The recombinant plasmid pMD18-T-UL46 was identified by PCR, restriction enzymes (BamHⅠ+XhoⅠ), sequencing and nucleic acid dot-hybridization. Then the gene was analyzed by bioinformatics tools. The results showed that a 2220bp complete open reading frame of 739 amino acids with Mr 81.8 kDa and PI 9.00 was discovered and it shared low homology with 24 strains other herpesvirus UL46 gene. The phylogenetic tree of the amino acids sequences indicated that the DPV should be placed into a single cluster within the subfamily Alphaherpesvirinae. The DPV UL46 had 10 transcription promo-ter sequences and a functional domains between 17-470aa. Codon bias analysis showed that the UL46 gene was biased in some codons, especially those codons encoding amino acids Trp, Met, His, Lys and Glu. The 35 epitopes covered the whole polypeptide chains of VP11/12, where hydrophilicity regions took the most parts. It had better hydrophilicity, flexible regions and higher antigen indexs. The DPV UL46 gene was predicted to be situated outside of membrane, locating throughout the cytoplasm with concentrations in the perinuclear region. It had 72 phospho-rylation sites and 2 N-Glycosylation potential sites but signal peptide. The protein had many flexible regions, α-helices and β-strands, but only a few of random coils. The tertiary structure had not been gained by the way of homology modelling of molecular confirmation. These results provided elementary data to research the biological function of this gene.