Characterization of codon usage bias in the dUTPase gene of duck enteritis virus

The analysis on codon usage bias of UL17 gene of duck enteritis virus (DEV) may provide a basis for understanding the relevant mechanism for its biased usage of synonymous codons and for selecting appropriate host expression systems to improve the expression of DEV UL17 gene. In this study the results indicate that codon usage bias of DEV UL17 gene strongly preferred to the synonymous with A and T at third codon position. The ENC values and GC3S contents of the codon usage bias of UL17 genes in DEV and the 20 reference herpesviruses were obviously different. In addition, we compared the codon usage bias of DEV UL17 gene with E.coli, yeast and human. There are 25 codons showing distinct usage differences between DEV and E. coli, 17 codons between DEV and yeast, 23 codons between DEV and human. Therefore, the yeast expression system is more suitable for heterologous expression of the DEV UL17 gene.

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Characterization of Codon Usage Bias in the UL55 Gene of Duck Enteritis Virus

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.204-210.649 ◽

2011 ◽

Vol 204-210 ◽

pp. 649-662 ◽

Cited By ~ 1

Author(s):

Ying Wu ◽

An Chun Cheng ◽

Ming Shu Wang ◽

De Kang Zhu ◽

Xiao Yue Chen

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Duck Enteritis Virus ◽

Codon Usage Pattern ◽

Usage Pattern ◽

E Coli ◽

Usage Patterns ◽

Enteritis Virus

The analysis of codon usage may improve our understanding of the evolution and pathogenesis of DEV（Duck enteritis virus） and allow reengineering of target gene to improve their expression for gene therapy.In this study,we calculated the codon usage bias in DEV UL55 gene and performed a comparative analysis of synonymous codon usage patterns in other 26 related viruses by EMBOSS CUSP program and Codon W on line.Moreover,statistical methods were used to investigate the correlations of these related parameters. By comparing synonymous codon usage patterns in different viruses,we observed that synonymous codon usage pattern in these virus is virus speciﬁc and phylogenetically conserved, with a strong bias towards the codons with A and T at the third codon position. Phylogenetic analysis based on codon usage pattern suggested that DEV UL55 gene was clustered with the avian Alphaherpesvirus but diverged to form a single branch. The Neutrality-plot suggested GC12 and GC3s adopt the same mutation pattern,meanwhile,the ENC-plot revealed that the genetic heterogeneity in UL55 genes is constrained by the G+C content, while translational selection and gene length have no or micro effect on the variations of synonymous codon usage in these virus genes.Furthermore, we compared the codon preferences of DEV with those of E. coli, yeast and Homo sapiens.Data suggested the eukaryotes system such as human system may be more suitable for the expression of DEV UL55 gene in vitro. If the yeast and E. coli expression system are wanted for the expression of DEV UL55 gene ,codon optimization of the DEV UL55 gene may be required.

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Synonymous Codon Usage Bias in the UL47 Gene of Duck Enteritis Virus

2010 4th International Conference on Bioinformatics and Biomedical Engineering ◽

10.1109/icbbe.2010.5515888 ◽

2010 ◽

Author(s):

Dandan Luo ◽

Anchun Cheng ◽

Mingshu Wang ◽

Aimei Shen ◽

Chang Hua ◽

...

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Duck Enteritis Virus ◽

Enteritis Virus ◽

Synonymous Codon Usage Bias

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Characterization of Synonymous Codon Usage in the R1 Gene of Duck Enteritis Virus

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.641-642.701 ◽

2013 ◽

Vol 641-642 ◽

pp. 701-711

Author(s):

Guo Fu Lu ◽

An Chun Cheng ◽

Ming Shu Wang

Keyword(s):

Codon Usage ◽

Codon Usage Bias ◽

Synonymous Codon ◽

Large Subunit ◽

Expression System ◽

Evolutionary Relationship ◽

Duck Enteritis Virus ◽

Yeast Expression System ◽

R1 Gene ◽

Enteritis Virus

In this paper, a corresponding analysis of the codon usage bias in the large subunit of ribonucleotide reductase (R1), encoded by UL39 gene from duck enteritis virus (DEV) CHv strain (Assigned Accession No.: EU071042) and 33 other reference herpesviruses was performed by using CAI, CHIPS and CUSP program of EMBOSS, aims to provide a basis for understanding the evolution and pathogenesis of DEV and for selecting appropriate host expression systems. The results showed that codon usage bias of DEV R1 gene strongly preferred to the synonymous with A and T at the third codon position; the phylogentic analysis revealed that DEV had a close evolutionary relationship with the avian Alphaherpesvirinae. In addition, the codon usage bias of DEV R1 gene was compared with those of E.coli, yeast and human. There are 17 codons showing distinct usage differences between DEV and E.coli, 13 codons between DEV and yeast, 20 codons between DEV and human. Therefore, the yeast expression system is more suitable for the target gene’s expression. The extent of codon usage bias in the DEV R1 gene was highly correlated with the gene expression level, therefore the results may provide useful information for the study of classification and function of the target gene.

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