Synonymous Codon Usage Bias of E 2 Genes of Classical Swine Fever Virus
Synonymous Codon Usage Bias of E 2 Genes of Classical Swine Fever Virus
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发表时间：
2012
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通讯作者：
Cao
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作者：
Cao
253 Synonymous Codon Usage of Classical Swine Fever Virus INTRODUCTION Synonymous codons are not used randomly as has been previously shown in many prokaryotes and some lower eukaryotes (1, 2, 3). Studies of the synonymous codon usage can reveal information about the molecular evolution of individual genes and provide data to prepare genome-specific gene recognition algorithms (4), which detect protein coding regions in uncharacterized genomic DNA (5). In addition to mutational pressure, translational selection is also influenced by non-random codon usage (6). To date, codon usage bias and nucleotide composition has been studied in great detail for many organisms such as bacteria (7), yeast (8), Drosophila (9, 10), and mammals (1). However, there are only a few reports on factors determining synonymous codon usage bias and nucleotide composition in viruses, especially in animal viruses. Classical swine fever virus (CSFV) an enveloped positive-stranded RNA virus belongs to the Pestivirus genus of the Flaviviridae family. The genome contains a large open reading frame (ORF) which encodes for a unique polyprotein of about 3898 amino acids that give rise to 12 final cleavage proteins (11). Envelope protein E2 is the major envelope glycoprotein exposed on the outer surface of the virion and represents an important target for induction of the immune response during infection (12). Furthermore, the E2 gene is extensively used for evolutionary analysis (13, 14). Phylogenetic analysis indicates CSFV could be classified into 3 groups (Group 1, 2 and 3) and 10 subgroups (15). Recently, Tao et al. have analyzed the positive selection pressure acting on the CSFV envelope protein genes, and identified several specific codons subject to diversifying positive selection (16, 17). In order to better understand the characteristics of the Synonymous Codon Usage Bias of E2 Genes of Classical Swine Fever Virus
