Characterization of Synonymous Codon Usage Bias in the Riemerella Anatipestifer OmpA/MotB Gene

Abstract:

The analysis on codon usage bias of OmpA/MotB gene of Riemerella anatipestifer (RA) may provide a basis for understanding the evolution and pathogenesis of RA and for selecting appropriate host expression systems to improve the expression of target genes in vivo and in vitro. In our study, a comparative analysis of the codon usage bias in the newly discovered RA OmpA/MotB gene and the OmpA/MotB gene of 20 reference flavobacteriaceae was performed. The results of the codon adaptation indes (CAI), effective number of codon (ENC), and GC3s values indicated that synonymous codon usage bias in the OmpA/MotB gene of flavobacteriaceae. The results showed that codon usage bias in the RA OmpA/MotB gene was strong bias towards the synonymous codons with A and T at the third codon position. A high level of diversity in codon usage bias existed, and the effective number of codons used in a gene plot revealed that the G+C compositional constraint is the main factor that determines the codon usage bias in OmpA/MotB gene of flavobacteriaceae. Comparison of the codon usage in the OmpA/MotB gene of different organisms revealed that there were 31 codons showing distinct codon usage differences between the RA and E. coli, 41 between the RA and humans, but 29 between the RA and yeast. Therefore the yeast expression system may be more suitable for the expression of RA OmpA/MotB gene. These results may improve our understanding of the evolution, pathogenesis and functional studies of RA, as well as contribute significantly to the area of flavobacteriaceae research.

• Periodical: Advanced Materials Research (Volumes 641-642)
• Pages: 684-692
• DOI: https://doi.org/10.4028/www.scientific.net/AMR.641-642.684
• Online since: January 2013
• Authors: Pan Xu, An Chun Cheng, Ming Shu Wang, De Kang Zhu, Xiao Jia Wang
• Keywords: Codon Usage Bias, Flavobacteriaceae, OmpA/MotB Gene, RA

References

[1] T. Ikemur: Mol Biol Vol. 146 (1981), pp.1-21.

[2] F.F. Liang: Animal Husbandry and Feed Science Vol. 31 (2010), pp.118-119.

[3] R.J. Grocock and P. M. Sharp: International Journal for Parasitology, Elsevier Science, Amsterdam Vol. 4 (2001), pp.402-412.

[4] M. Oresic, D. Shalloway: Mol Biol Vol. 281 (1998), pp.31-48.

[5] S. Das, S. Paul, C. Dutta: Virus Res Vol. 117 (2006), pp.227-236.

[6] W. Gu, T. Zhou, J. Ma, X. Sun, Z. Lu: Biosystems Vol. 73 (2004), pp.89-97.

[7] S.K. Gupta, S. Majumdar, T.K. Bhattacharya, T.C. Ghosh: Biochem Biophys Res Commun Vol. 269 (2000), pp.692-696.

[8] P. Mukhopadhyay, S. Basak and T.C. Ghosh: Biosci Vol. 32 (2007), pp.947-963.

[9] H. Romero, A. Zavala, H. Musto: Gene Vol. 242 (2000), pp.307-311.

[10] J.O. McInerney: Natl. Proc, Sci. Acad Vol. 95 (1998), pp.10689-10703.

[11] R. Grantham, C. Gautier, M. Gouy, M. Jacobzone and R. Mercier: Nucleic Acids Res Vol. 9 (1981), pp.43-74.

[12] T. Ikemura: Mol Biol Evol Vol. 2 (1985), pp.13-34.

[13] P.M. Sharp, E. Cowe: Yeast Vol. 7 (1991), pp.657-678.

[14] T.C. Ghosh, SK. Gupta, S. Majumdar: Int J Parasitol Vol. 30 (2000), pp.715-722.

[15] D.B. Levin, B. Whittome: Gen Virol Vol. 81 (2000), pp.2313-2325.

[16] G.M. Jenkins, M. Pagel, E.A. Gould, P.M. deA. Zanotto and E.C. Holmes: Mol Evol Vol. 52 (2001), pp.383-390.

[17] G.M. Jenkins, E.C. Holmes: Virus Res Vol. 92 (2003), pp.1-7.

[18] N. Sueoka, Y. Kawanishi: Gene, Elsevier Ltd, Oxford Vol. 261 (2000), pp.53-62.

[19] X.F. Wan, D. Xu, A. Kleinhofs and J.Z. Zhou: BMC Evolutionary Biology, BioMed Central Ltd., England and Wales Vol. 4 (2004), p.19.

[20] Bains W: Mol Biol Vol. 197 (1987), pp.379-388.

[21] S. Basak, T. Banerjee, S.K. Gupta, T.C. Ghosh: Biomol Struct Dyn Vol. 22 (2004), pp.205-214.

[22] D.J. Lynn, G.A.C. Singer, D.A. Hickey: Nucleic Acids Res Vol. 30 (2002), pp.4272-4277.

[23] M. Gouy, C. Gautier: Nucleic Acids Res Vol. 10 (1982), pp.7055-7074.

[24] P.M. Sharp, T.M. Tuohy and K.R. Mosurski: Nucleic Acids Res, Oxford University Press, Oxford Vol. 14 (1986), pp.5125-5143.

[25] A. Hoekema, R.A. Kastelein, M. Vasser and H.A. de Boer: Mol Cell Biol Vol. 7 (1987), pp.2914-2924.

[26] P.M. Sharp, W.H. Li: Mol Biol Evol Vol. 4 (1987), pp.222-230.

[27] S. Karlin, I. Ladunga and B.E. Blaisdell: Proc Natl Acad Sci. USA Vol. 91 (1994), pp.12837-12841.

DOI: 10.1073/pnas.91.26.12837

[28] S.D. Hooper, O.G. Berg: Nucleic Acids Res, Oxford University Press, Oxford Vol. 28 (2000), pp.3517-3523.

[29] P. Segers, W. Mannheim, M. Vancanneyt, K. De Brandt, K.H. Hinz, K. Kersters and P. Vandamme: Int. J. Syst. Bacteriol Vol. 43 (1993), pp.768-776.

[30] A. C. cheng, M. S. wang, X. Y. chen, D. K. zhu, C. huang, F. liu, Y. zhou, Y. F. guo, Z. Y. liu, and P. F. Fang: Chinese Journal of Veterinary Science Vol. 23 (2003), pp.320-232.

[31] X. J. Wang, D. K. Zhu, M.S. Wang, A.C. Cheng, R.Y. Jia, Y. Zhou, Z.L. Chen, Q.H. Luo, F. Liu, Y. Wang, X.Y. Chen: Journal of Bacteriology Vol. 194 (2012), pp.3270-3271.

DOI: 10.1128/jb.00366-12

[32] J.A. Novembre: Mol Biol Evol Vol. 19 (2002), pp.1390-1394.

[33] F. Wright: Gene Vol. 87 (1990), pp.23-29.

[34] H. Lu, W.M. Zhao, Y. Zheng , H, Wang, M. Qi and X.P. Yu: Acta Biochim Biophys Sin, Shanghai Vol. 37 (2005), pp.1-10.

[35] S. Karlin, I. Ladunga, B.E. Blaisdell: ProcNatl Acad Sci. USA Vol. 91 (1994), pp.12837-12841.

DOI: 10.1073/pnas.91.26.12837

[36] J.R. Lobry, C. Gautier: Nucleic Acids Res Vol. 22 (1994), pp.3174-3180.

[37] P. M. Sharp, W. H. Li: Nucleic. Acids. Res, Oxford University Press, Oxford Vol. 15 (1987), pp.1281-1295.

[38] W. Gu, T. Zhou, J. Ma, X. Sun and Z. Lu: Res Vol. 101 (2004), p.155–161.

[39] Q. Liu, S. Dou, J. Zhijuan and Q. Xue: BioSystems, Elsevier Science, Amsterdam Vol. 80(2005), pp.123-131.