Bioinformatics study involving characterization of synonymous codon usage bias in the duck enteritis virus glycoprotein D (gD) gene

Asian Journal of Animal and Veterinary Advances

Volumn 9, Issue 4, 2014, Pages 229-242

  Aravind, S ^a   Kamble, N M ^a   Gaikwad, S S ^a   Khulape, S A ^a   Dey, Sohini ^a   Dhama, K ^a   Madhan Mohan, C ^a  

^a INDIAN VETERINARY RESEARCH INSTITUTE   (India)

Author keywords

Bioinformatics; Codon adaptation index; Codon usage bias; Duck enteritis virus; Glycoprotein D (gD); Synonymous codon usage

Indexed keywords

EID: 84899024177     PISSN: 16839919     EISSN: None     Source Type: Journal    
DOI: 10.3923/ajava.2014.229.242     Document Type: Article

References (48)

1. Aragones, L, A. Bosch and R. M. Pinto, 2008. Hepatitis A virus mutant spectra under the selective pressure of monoclonal antibodies: Codon usage constraints limit capsid variability. J. Virol, 82: 1688-1700.
2. Aragones, L, S. Guix, E. Ribes, A. Bosch and R. M. Pinto, 2010. Fine-tuning translation kinetics selection as the driving force of codon usage bias in the hepatitis A virus capsid. PLoS Pathogens, Vol. 6, No. 3. 10.1371/journal.ppat. 1000797
3. Babiuk, L. A, D. H. S. van Drunen Little-Van and S. K. Tikoo, 1996. Immunology of bovine herpesvirus 1 infection. Vet. Microbiol, 53: 31-42.
4. Banerjee, T, S. Basak, S. K. Gupta and T. C. Ghosh, 2004. Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus. J. Biomol. Struct. Dyn, 22: 13-24.
5. Basak, S, T. Banerjee, S. K. Gupta and T. C. Ghosh, 2004. Investigation on the causes of codon and amino acid usages variation between thermophilic Aquifex aeolicus and mesophilic Bacillus subtilis. J. Biomol. Struct. Dyn, 22: 205-214.
6. Bishal, A. K., R. Mukherjee and C. Chakraborty, 2013. Synonymous codon usage pattern analysis of Hepatitis D virus. Virus Res., 173: 350-353.
7. Blake, W. J., M. Kaern, C. R. Cantor and J. J. Collins, 2003. Noise in eukaryotic gene expression. Nature, 422: 633-637.
8. Burgess, E. C., J. Ossa and T. M. Yuill, 1979. Duck plague: A carrier state in waterfowl. Avian Dis., 23: 940-949.
9. Carbone, A., A. Zinovyev and F. Kepes, 2003. Codon adaptation index as a measure of dominating codon bias. Bioinformatics, 19: 2005-2015.
10. Csellner, H., C. Walker, J. E. Wellington, L. E. McLure, D. N. Love and J. M. Whalley, 2000. EHV-1 glycoprotein D (EHV-1 gD) is required for virus entry and cell-cell fusion and an EHV-1 gD deletion mutant induces a protective immune response in mice. Arch. Virol., 145: 2371-2385.
11. Dasika, G. K. and G. J. Letchworth III, 1999. Cellular expression of bovine herpesvirus 1 gD inhibits cell-to-cell spread of two closely related viruses without blocking their primary infection. Virology, 245: 24-36.
12. Fu, M. H., R. Q. Deng, J. W. Wang and X. Z. Wang, 2008. Whole-genome phylogenetic analysis of herpesviruses. Acta Virol., 52: 31-40.
13. Gouy, M. and C. Gautier, 1982. Codon usage in bacteria: Correlation with gene expressivity. Nucl. Acids Res., 10: 7055-7074.
14. Grosjean, H. and W. Fliers, 1982. Preferential codon usage in prokaryotic genes: The optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene, 18: 209-299.
15. Gu, W., T. Zhou, J. Ma, X. Sun and Z. Lu, 2004. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Res., 101: 155-161.
16. 1. Experimental approach to study the role of biased codon usage in gene expression. Mol. Cell Biol., 7: 2914-2924.
17. Ikemura, T., 1985. Codon usage and transfer-RNA content in unicellular and multicellular organisms. Mol. Biol. Evol., 2: 13-34.
18. Jia, R. Y., A. C. Cheng, M. S. Wang, H. Y. Xin and Y. F. Guo et al., 2009. Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus. Virus Genes, 38: 96-103.
19. Jiang, Y., F. Deng, H. L. Wang and Z. H. Hu, 2008. An extensive analysis on the global codon usage pattern of baculoviruses. Arch. Virol., 153: 2273-2282.
20. Karlin, S. and J. Mrazek, 1996. What drives codon choices in human genes? J. Mol. Biol., 262: 459-472.
21. Karlin, S., B. E. Blaisdell and G. A. Schachtel, 1990. Contrasts in codon usage of latent versus productive genes of Epstein-Barr virus: Data and hypotheses. J. Virol., 64: 4264-4273.
22. Lesnik, T., J. Solomovici, A. Deana, R. Ehrlich and C. Reiss, 2000. Ribosome traffic in E. coli and regulation of gene expression. J. Theor. Biol., 202: 175-185.
23. Lu, H., W. M. Zhao, Y. Zheng, H. Wang, M. Qi and X. P. Yu, 2005. Analysis of synonymous codon usage bias in Chlamydia. Acta Biochim. Biophys. Sin., 371: 1-10.
24. Matis, J. and M. Kudelova, 2001. Early shutoff of host protein synthesis in cells infected with herpes simplex viruses. Acta Virol., 45: 269-277.
25. McGeoch, D. J., A. Dolan and A. C. Ralph, 2000. Toward a comprehensive phylogeny for mammalian and avian herpesviruses. J. Virol., 74: 10401-10406.
26. Novembre, J. A, 2002. Accounting for background nucleotide composition when measuring codon usage bias. Mol. Biol. Evol, 19: 1390-1394.
27. Roizman, B. and P. E. Pellet, 2001. The Family Herpesviridae: A Brief Introduction. In: Fields Virology, Knipe, D. M, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman and S. E. Strauss (Eds.). 4th Edn, Lippincott Williams and Wilkins, Philadelphia, USA, pp: 2381-2397.
28. Romero, H, A. Zavala, H. Musto and G. Bernardi, 2003. The influence of translational selection on codon usage in fishes from the family Cyprinidae. Gene, 317: 141-147.
29. Shackelton, L. A, C. R. Parrish and E. C. Holmes, 2006. Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J. Mol. Evol, 62: 551-563.
30. Sharp, P. M. and W. H. Li, 1986. Codon usage in regulatory genes in Escherichia coli does not reflect selection for rare codons. Nucleic Acids Res, 14: 7737-7749.
31. Sharp, P. M., T. M. F. Tuohy and K. R. Mosurski, 1986. Codon usage in yeast cluster-analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res, 14: 5125-5143.
32. Shawky, S. A. and K. Schat, 2002. Latency sites and reactivation of duck enteritis virus. Avian Dis, 46: 308-313.
33. Shawky, S. A. and T. S. Sandhu, 1997. Inactivated vaccine for protection against duck virus enteritis. Avian Dis, 41: 461-468.
34. Shawky, S. A, T. Sandhu and H. L. Shivaprasad, 2000. Pathogenicity of a low virulence duck virus enteritis isolate with immunosuppressive ability. Avian. Dis, 44: 590-599.
35. Smiley, R. J, 2004. Herpes simplex virus virion host shutoff protein: Immune evasion mediated by a viral RNase? J. Virol, 78: 1063-1068.
36. Spear, P. G. and R. Longnecker, 2003. Herpesvirus entry: An update. J. Virol, 77: 10179-10185.
37. Spear, P. G, 1993. Entry of alphaherpesviruses into cells. Semin. Virol, 4: 167-180.
38. Strand, S. S, T. K. Vanheyningen and D. A. Leib, 2004. The virion host shutoff protein of herpes simplex virus type 1 has RNA degradation activity in primary neurons. J. Virol, 78: 8400-8403.
39. Sueoka, N, 1988. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci, 85: 2653-2657.
40. + monocytes. J. Immunol, 174: 2273-2279.
41. Tsai, C. T, C. H. Lin and C. Y. Chang, 2007. Analysis of codon usage bias and base compositional constraints in iridovirus genomes. Virus Res, 126: 196-206.
42. Wan, X. F, D. Xu, A. Kleinhofs and J. Zhou, 2004. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol. Biol, Vol. 4. 10.1186/1471-2148-4-19
43. Whitley, R. J, 1996. Herpesviruses. In: Baron's Medical Microbiology, Baron, S. (Ed.). 4th Edn, University of Texas. Galveston, USA.
44. Wong, E. H, D. K. Smith, R. Rabadan, M. Peiris amd L. L. Poon, 2010. Codon usage bias and the evolution of influenza A viruses. Codon usage biases of influenza virus. BMC Evol. Biol, Vol: 10. 10.1186/1471-2148-10-253
45. Wright, F, 1990. The effective number of codons used in a gene. Gene, 87: 23-29.
46. Wu, Y, A. Cheng, M. Wang, Q. Yang and D. Zhu et al., 2012. Complete genomic sequence of Chinese virulent duck enteritis virus. J. Virol, 86: 5965-5965.
47. Xia, X. H, 2007. An improved implementation of codon adaptation index. Evol. Bioinform, 3: 53-58.
48. Zhao, L, A. Cheng, M. Wang, G. Yuan and M. Cai, 2008. Characterization of codon usage bias in the dUTPase gene of duck enteritis virus. Progr. Nat. Sci, 18: 1069-1076.