Characterization of Codon Usage Bias in UL13 Gene of the Duck Plague Virus

Abstract:

A comprehensive analysis of codon usage bias of DPV UL13 gene (GenBank Accession No. EU195098) was performed to provide a basis for understanding the relevant mechanism for its biased usage of synonymous codons and for selecting suitable expression systems to improve the expression of UL13 genes. Our study showed that codon usage bias of DPV UL13 gene strongly prefered to the synonymous with A and T at the third codon position. And ENC value and GC3s contents of the codon usage bias of UL13 gene in DPV were significantly different compared with those in other 21 reference herpesviruses. The phylogentic analysis about the putative protein of DPV UL13 and the 21 reference herpesviruses revealed that DPV was evolutionarily closer to the AnHV-1. In addition, the codon usage bias of DPV UL13 gene was compared with those of E. coli, yeast and human. There are 23 codons showing distinct usage differences between DPV and E. coli, 12 codons between DPV and yeast, 21 codons between DPV and human. Therefore, the yeast expression system is more appropriate for heterologous expression of the DPV UL13 gene.

• Periodical: Advanced Materials Research (Volumes 393-395)
• Pages: 641-650
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.393-395.641
• Online since: November 2011
• Authors: Xi Xia Hu, An Chun Cheng, Ming Shu Wang
• Keywords: Codon Usage Bias, Duck Plague Virus, UL13 Gene

References

[1] T.S. Sandhu and S.A. Metwally in: Duck Virus Enteritis (Duck Plague). Saif YM(ed) Diseases of Poultry, 11th ed, Wiley-Blackwell, American, 2003, pp.355-363.

[2] L. Duret: Evolution of synonymous codon usage in metazoans. Curr Opin Genet . Vol. 12(2002), pp.640-649.

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

[3] P.M. Sharp, M. Averof, A.T. Lloyd et al.: DNA sequence evolution: the sounds of silence. Philos Trans: Biol Sci. Vol. 349(1995), pp.241-247.

[4] R.Y. Jia, A.C. Cheng, M.S. Wang et al.: Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus. Virus Genes. Vol. 38(2009), pp.96-103.

DOI: 10.1007/s11262-008-0295-0

[5] F. Wright: The effective number of codons' used in a gene. Gene. Vol. 87(1990), pp.23-29.

DOI: 10.1016/0378-1119(90)90491-9

[6] J. Zhang, M. Wang, W.Q. Liu et al.: Analysis of codon usage and nucleotide composition bias in polioviruses. Virology Journal. Vol. 8(2011), p.146.

[7] H. Lu, W.M. Zhao, Y. Zheng et al.: Analysis of synonymous codon usage bias in Chlamydia. Acta Biochim Biophys Sin. Oxford University Press, Oxford, Vol. 37(2005), pp.1-10.

[8] X.H. Xia: An improved implementation of codon adaptation index. Evolutionary Bioinformatics. Vol. 3(2007), pp.53-58.

[9] S.L. Fennoy, and J. Bailey-Serres: Synonymous codon usage in Zea mays L. Nuclear genes is varied by levels of C and G-ending codons. Nucleic Acids Research. Vol. 21(1993), pp.5294-5300.

DOI: 10.1093/nar/21.23.5294

[10] P. Jiang, X. Sun, Z. Lu et al.: Genomics. Vol. 34(2007), pp.275-284.

[11] N. Sueoka, and Y. Kawanishi: DNA G+C content of the third codon position and codon usage biases of human genes. Gene. Elsevier Ltd, Oxford, Vol. 261(2000), pp.53-62.

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

[12] X.F. Wan, D. Xu, A. Kleinhofs et al.: Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evolutionary Biology. BioMed Central Ltd., England and Wales, Vol. 4(2004), p.19.

[13] A. Eyre-Walker: Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?. Molecular Biology and Evolution. Oxford University Press, New York, Vol. 13(1996), pp.864-872.

DOI: 10.1093/oxfordjournals.molbev.a025646

[14] S. Noguchi and Y. Satow: Purification of human β2-adrenergic receptor expressed in methylotrophic yeast Pichia pastoris. Journal of Biochemistry. Oxford University Press, New York, Vol. 140(2006), pp.799-804.

DOI: 10.1093/jb/mvj211

[15] J. Ma, A. Campbell and S. Karlin: Correlations between shine-dalgarno sequences and gene features such as predicted expression levels and operon structures. Journal of Bacteriology, American Society for Microbiology, U.S. A, Vol. 184(2002).

DOI: 10.1128/jb.184.20.5733-5745.2002

[16] M. Nakamura and M. Sugiura: Translation efficiencies of synonymous codons are not always correlated with codon usage in tobacco chloroplasts. The Plant Journal. Blackwell Publishing Ltd., England and Wales, Vol. 49(2007), pp.128-134.

DOI: 10.1111/j.1365-313x.2006.02945.x

[17] S. Kanaya, Y. Yamada, Y. Kudo et al.: Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and speciesspecific diversity of codon usage based on multivariate analysis. Gene. Elsevier Ltd, Oxford, Vol. 238(1999).

DOI: 10.1016/s0378-1119(99)00225-5

[18] J.B. Plotkin, J. Dushoff, M.M. Desai et al.: Codon usage and selection on proteins. Jouranl of Molecular Evolution. Spinger, New York, Vol. 63(2006), pp.635-653.

DOI: 10.1007/s00239-005-0233-x

[19] S. Noboru: Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of A = T and G = C. Journal of Molecular Evolution. Spinger, New York, Vol. 49(1999), pp.49-62.

DOI: 10.1007/pl00006534

[20] M.S. Cai, A.C. Cheng, M.S. Wang et al.: Characterization of synonymous codon usage bias in the duck plague virus UL35 gene. Intervirology. Vol. 52(2009), pp.266-278.

DOI: 10.1159/000231992

[21] Z.H. Yang and R. Nielsen: Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Molecular Biology and Evolution. Vol. 2005(2007), pp.568-579.

DOI: 10.1093/molbev/msm284

[22] N. Rodrigue, H. Philippe and N. Lartillot: Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles. PNAS. Vol. 107(2010), pp.4629-4634.

DOI: 10.1073/pnas.0910915107

[23] K. Sau, S.K. Gupta, S. Sau et al.: Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy. Virus Research. Elsevier Ltd, Oxford, Vol. 113(2005), pp.123-131.

DOI: 10.1016/j.virusres.2005.05.001

[24] Y.S. Liu, J.H. Zhou, H.T. Chen et al.: Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus. Infection. Genetics and Evolution, Vol. 10(2010), pp.797-803.

DOI: 10.1016/j.meegid.2010.04.010

[25] A. Carbone, A. Zinovyev and F. Kepes: Codon adaptation index as a measure of dominating codon bias. Bioinformatics. Vol. 19(2003), p.2005-(2015).

DOI: 10.1093/bioinformatics/btg272

[26] Y.Y. Hsiao, C.H. Lin, J.K. Liu et al.: Analysis of codon usage patterns in toxic dinoflagellate alexandrium tamarense through expressed sequence tag data. Comparative andFunctionalGenomics. Vol. 2010(2010), pp.138538-138546.

DOI: 10.1155/2010/138538

[27] H. Suzuki, R. Saito and M. Tomita: Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria. EURASIP Journal on Bioinform and Systems Biology. Vol. 9(2007).

DOI: 10.1155/2007/61374

[28] S.W. Liu, S.H. Chen, H.X. Li et al.: Molecular characterization of the herpes simplex virus 1 (HSV-1) homologues, UL25 to UL30, in duck enteritis virus (DEV). Gene. Vol. 401(2007), pp.88-96.

DOI: 10.1016/j.gene.2007.06.022

[29] L.C. Zhao, A.C. Cheng, M.S. Wang et al.: Characterization of codon usage bias in the dUTPase gene of duck enteritis virus. Prog Nat Sci. Vol. 18(2008), pp.1069-1076.

DOI: 10.1016/j.pnsc.2008.03.009

[30] 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. 4(2010), pp.343-353.

[31] 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, IEEE Press, Vol. 4(2009), pp.1836-1841.

DOI: 10.1109/bmei.2009.5305045