Analysis of Synonymous Codon Usage in the US2 Gene of Duck Plague Virus

Abstract:

The codon usage bias of DPV-CHv US2 gene (GenBank Accession No. EU195086) will be analysed in this study, and a comparative analysis of DPV-CHv US2 gene and those of other 15 alphaherpesvirus US2 genes was performed. We also analysed the RSCU, ENC, GC3s value of those US2 genes in herpesvirus, some data were analysed specifically in the article. Consequently, we found that the eukaryotic expression system——the yeast is more suitable for the expression of DPV US2 gene.

• Periodical: Advanced Materials Research (Volume 647)
• Pages: 220-226
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.647.220
• Online since: January 2013
• Authors: Jie Gao, An Chun Cheng, Ming Shu Wang
• Keywords: Codon Usage Bias, Duck Plague Virus, US2 Gene

References

[1] E. R Campagnolo., M Banerjee., B Panigrahy., R. L Jones. An outbreak of duck viral enteritis (duck plague) in domestic Muscovy ducks(Cairina moschata domesticus) in Illinois. Avian Dis. Vol. 2(2001), pp.522-528.

DOI: 10.2307/1592999

[2] S Davison., K. A Converse., A. N Hamir., R. J Eckroade. Duck viral enteritis in domestic muscovy ducks in Pennsylvania. Avian Dis. Vol. 4(1993), pp.1142-1146.

DOI: 10.2307/1591927

[3] TS Sandhu, SA Metwally. Duck Virus Enteritis (Duck Plague). 12 ed. (Singapore: Blackwell 2008).

[4] M S Paul., A Michalis, L Andrew T., M Giorgio, P John F. DNA Sequence Evolution: The Sounds of Silence. Philosophical Transactions of the Royal Society of London Series B: Biological Sciences. Vol. 1329(1995), pp.241-247.

DOI: 10.1098/rstb.1995.0108

[5] D Laurent. Evolution of synonymous codon usage in metazoans. Current Opinion in Genetics & Development. Vol. 6(2002), pp.640-649.

DOI: 10.1016/s0959-437x(02)00353-2

[6] W Frank. The effective number of codons, used in a gene. Gene. Vol. 1(1990), pp.23-29.

[7] A Carbone., A Zinovyev., F Képès. Codon adaptation index as a measure of dominating codon bias. Bioinformatics. Vol. 16(2003), p.2005-(2015).

DOI: 10.1093/bioinformatics/btg272

[8] S Noboru, K Yuichi. DNA G+C content of the third codon position and codon usage biases of human genes. Gene. Vol. 1(2000), pp.53-62.

DOI: 10.1016/s0378-1119(00)00480-7

[9] K Naeem, B Rachel, Taylor Graham S., Cobbold Mark, Jones Thomas R., Rickinson Alan B., et al. Identification of Cytomegalovirus-Specific Cytotoxic T Lymphocytes In Vitro Is Greatly Enhanced by the Use of Recombinant Virus Lacking the US2 to US11 Region or Modified Vaccinia Virus Ankara Expressing Individual Viral Genes. J Virol. Vol. 5(2005).

DOI: 10.1128/jvi.79.5.2869-2879.2005

[10] G Wanjun, Z Tong, M Jianmin, S Xiao, L Zuhong. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Research. Vol. 2(2004), pp.155-161.

DOI: 10.1016/j.virusres.2004.01.006

[11] J Peng, S Xiao, L Zuhong. Analysis of Synonymous Codon Usage in Aeropyrum pernix K1 and Other Crenarchaeota Microorganisms. Journal of Genetics and Genomics. Vol. 3(2007), pp.275-284.

DOI: 10.1016/s1673-8527(07)60029-0

[12] K Robin, F Stephen, L Laura. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biology. Vol. 4(2001), pp.011-013.

[13] M S Paul., L Wen-Hsiung. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research. Vol. 3(1987), pp.1281-1295.

DOI: 10.1093/nar/15.3.1281

[14] G Andreas, H Karsten, S Maurice, Münch Richard, Nörtemann Bernd, Hempel Dietmar C., et al. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Research. Vol. 33(2005) 38. p. W526-W531.

DOI: 10.1093/nar/gki376

[15] J Renyong, C Anchun, WMingshu, X Hongyi, G Yufei, Z Dekang, et al. Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus. Virus Genes. Vol. 1(2009), pp.96-103.

DOI: 10.1007/s11262-008-0295-0

[16] M. S Cai., A. C Cheng., M. S. Wang, L. C. Zhao, D. K. Zhu, Q. H. Luo, et al. Characterization of Synonymous Codon Usage Bias in the Duck Plague Virus UL35 Gene. Intervirology. Vol. 5(2009), pp.266-278.

DOI: 10.1159/000231992

[17] M S Paul., B Elizabeth, G Russell J., P John F., S R. Elizabeth. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Research. Vol. 4(2005), pp.1141-1153.

DOI: 10.1093/nar/gki242

[18] Y Hsiao , L Chorng-Horng, L Jong-Kang, W Tit-Yee and J Kuo. Analysis of codon usage patterns in toxic dinoflagellate alexandrium tamarense through expressed sequence tag data. Comparative and Functional Genomics. Vol. (2010), pp.138538-138546.

DOI: 10.1155/2010/138538

[19] Z Jie, W Meng, L Wen-qian, Z Jian-hua, C Hao-tai, M Li-na, et al. Analysis of codon usage and nucleotide composition bias in polioviruses. Virology Journal. Vol. 1(2011), p.146.

[20] F.X. Shen A.C. Cheng, M.S. Wang et al.:. Factors affecting synonymous codon usage bias in the gC gene of DPV CHv strain. African Journal of Microbiology Research. Vol. (2010), pp.343-353.

[21] H. Chang A.C. Cheng, M.S. Wang et al. Characterization of codon usage bias in the newly identified DPV gE gene. IEEE the 2nd International Conference on BioMedical Engineering and Informatics (2009), IEEE in Press.

DOI: 10.1109/bmei.2009.5305045