Analysis of synonymous codon usage in spike protein gene of infectious bronchitis virus

Canadian Journal of Microbiology

Volumn 61, Issue 12, 2015, Pages 983-989

  Makhija, Aditi ^a   Kumar, Sachin ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY GUWAHATI   (India)

Author keywords

Aliphaticity; Aromaticity; Evolution; IBV; Mutational pressure

Indexed keywords

VIRUS SPIKE PROTEIN; CODON; CORONAVIRUS SPIKE GLYCOPROTEIN;

AVIAN INFECTIOUS BRONCHITIS VIRUS; CODON USAGE; CORRELATION ANALYSIS; DNA BASE COMPOSITION; GENE MUTATION; HYDROPHOBICITY; NATURAL SELECTION; NONHUMAN; NOTE; PRIORITY JOURNAL; VIRUS GENE; ANIMAL; BIOLOGY; CHEMISTRY; CHICKEN; CODON; CORONAVIRUS INFECTION; GENETICS; MUTATION; VIROLOGY;

AVES; AVIAN INFECTIOUS BRONCHITIS VIRUS;

ANIMALS; CHICKENS; CODON; COMPUTATIONAL BIOLOGY; CORONAVIRUS INFECTIONS; INFECTIOUS BRONCHITIS VIRUS; MUTATION; SPIKE GLYCOPROTEIN, CORONAVIRUS;

EID: 84948756955     PISSN: 00084166     EISSN: 14803275     Source Type: Journal    
DOI: 10.1139/cjm-2015-0418     Document Type: Note

References (36)

1. Abro, S.H., Renstrom, L.H., Ullman, K., Isaksson, M., Zohari, S., Jansson, D.S., et al. 2012. Emergence of novel strains of avian infectious bronchitis virus in Sweden. Vet. Microbiol. 155(2–4): 237–246. doi:10.1016/j.vetmic.2011.09.022. PMID:22005179.
2. Babbitt, G.A., Alawad, M.A., Schulze, K.V., and Hudson, A.O. 2014. Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid. Nucleic Acids Res. 42(17): 10915–10926. doi:10.1093/nar/gku811. PMID:25200075.
3. Boursnell, M.E., Brown, T.D., Foulds, I.J., Green, P.F., Tomley, F.M., and Binns, M.M. 1987. Completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus. J. Gen. Virol. 68(1): 57–77. doi:10.1099/0022-1317-68-1-57. PMID:3027249.
4. Butt, A.M., Nasrullah, I., and Tong, Y. 2014. Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. PLoS One, 9(3): e90905. doi:10.1371/journal.pone.0090905. PMID:24595095.
5. Casais, R., Dove, B., Cavanagh, D., and Britton, P. 2003. Recombinant avian infectious bronchitis virus expressing a heterologous spike gene demonstrates that the spike protein is a determinant of cell tropism. J. Virol. 77(16): 9084–9089. doi: 10.1128/JVI.77.16.9084-9089.2003. PMID:12885925.
6. Cavanagh, D. 2007. Coronavirus avian infectious bronchitis virus. Vet. Res. 38(2): 281–297. doi:10.1051/vetres:2006055. PMID:17296157.
7. Deka, H., and Chakraborty, S. 2014. compositional constraint is the key force in shaping codon usage bias in hemagglutinin gene in H1N1 subtype of influenza A Virus. Int. J. Genomics, 2014: 349139. doi:10.1155/2014/349139. PMID:25140301.
8. Ding, Y.Z., You, Y.N., Sun, D.J., Chen, H.T., Wang, Y.L., Chang, H.Y., et al. 2014. The effects of the context-dependent codon usage bias on the structure of the nsp1alpha of porcine reproductive and respiratory syndrome virus. Biomed. Res. Int. 2014: 765320. doi:10.1155/2014/765320. PMID:25162025.
9. Epstein, R.J., Lin, K., and Tan, T.W. 2000. A functional significance for codon third bases. Gene, 245(2): 291–298. doi:10.1016/S0378-1119(00)00042-1. PMID:10717480.
10. Ermolaeva, M.D. 2001. Synonymous codon usage in bacteria. Curr. Issues Mol. Biol. 3(4): 91–97. PMID:11719972.
11. Grantham, R., Gautier, C., and Gouy, M. 1980. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 8(9): 1893–1912. doi:10.1093/nar/8.9.1893. PMID:6159596.
12. Greenacre, M.J. 1984. Theory and applications of correspondence analysis. Academic Press, London, UK.
13. Gu, W., Zhou, T., Ma, J., Sun, X., and Lu, Z. 2004. The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens. Biosystems, 73(2): 89–97. doi: 10.1016/j.biosystems.2003.10.001. PMID:15013221.
14. Hu, C., Chen, J., Ye, L., Chen, R., Zhang, L., and Xue, X. 2014. Codon usage bias in human cytomegalovirus and its biological implication. Gene, 545(1): 5–14. doi:10.1016/j.gene.2014.05.018. PMID:24814188.
15. Ikai, A. 1980. Thermostability and aliphatic index of globular proteins. J. Biochem. 88(6): 1895–1898. PMID:7462208.
16. Jackwood, M.W. 2012. Review of infectious bronchitis virus around the world. Avian Dis.56(4):634–641. doi:10.1637/10227-043012-Review.1. PMID:23397833.
17. Jenkins, G.M., and Holmes, E.C. 2003. The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res. 92(1): 1–7. doi:10.1016/S0168-1702(02)00309-X. PMID:12606071.
18. Kant, A., Koch, G., van Roozelaar, D.J., Kusters, J.G., Poelwijk, F.A., and van der Zeijst, B.A. 1992. Location of antigenic sites defined by neutralizing monoclonal antibodies on the S1 avian infectious bronchitis virus glycopolypeptide. J. Gen. Virol. 73(3): 591–596. doi:10.1099/0022-1317-73-3-591. PMID:1372036.
19. Kober, K.M., and Pogson, G.H. 2013. Genome-wide patterns of codon bias are shaped by natural selection in the purple sea urchin, Strongylocentrotus purpuratus. G3 (Bethesda), 3(7): 1069–1083. doi:10.1534/g3.113.005769. PMID:23637123.
20. Kumar, C.S., and Kumar, S. 2014. Species based synonymous codon usage in fusion protein gene of Newcastle disease virus. PLoS One, 9(12): e114754. doi:10.1371/journal.pone.0114754. PMID:25479071.
21. Kumar, C.S., Hazarika, N.M., and Kumar, S. 2015. Analysis of synonymous codon usage in the VP2 protein gene of infectious bursal disease virus. Arch. Virol. 160(9): 2359–2366. doi: 10.1007/s00705-015-2505-0. PMID:26123923.
22. Kyte, J., and Doolittle, R.F. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157(1): 105–132. doi:10.1016/0022-2836(82)90515-0. PMID:7108955.
23. Li, W.H. 1997. Molecular evolution. 2nd ed. Sinauer Associates, Sunderland, Mass., USA.
24. Li, Y., Wang, C., Cheng, X., Wu, T., and Zhang, C. 2011. Synonymous codon usage of the VP2 gene of a very virulent infectious bursal disease virus isolate serial passaged in chicken embryos. Biosystems, 104(1): 42–47. doi:10.1016/j.biosystems.2010.12.009. PMID:21216278.
25. Lobry, J.R., and Gautier, C. 1994. Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res. 22(15): 3174–3180. doi:10.1093/nar/22.15.3174. PMID: 8065933.
26. Lynn, D.J., Singer, G.A., and Hickey, D.A. 2002. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res. 30(19): 4272–4277. doi:10.1093/nar/gkf546. PMID:12364606.
27. Martin, E.A., Brash, M.L., Hoyland, S.K., Coventry, J.M., Sandrock, C., Guerin, M.T., and Ojkic, D. 2014. Genotyping of infectious bronchitis viruses identified in Canada between 2000 and 2013. Avian Pathol. 43(3): 264–268. doi:10.1080/03079457.2014.916395. PMID:24754612.
28. Paul, S., Bag, S.K., Das, S., Harvill, E.T., and Dutta, C. 2008. Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes. Genome Biol. 9(4): R70. doi:10.1186/gb-2008-9-4-r70. PMID: 18397532.
29. Rimondi, A., Craig, M.I., Vagnozzi, A., Konig, G., Delamer, M., and Pereda, A. 2009. Molecular characterization of avian infectious bronchitis virus strains from outbreaks in Argentina (2001–2008). Avian Pathol. 38(2): 149–153. doi:10.1080/03079450902737821. PMID:19322714.
30. Sharp, P.M., and Li, W.H. 1986. Codon usage in regulatory genes in Escherichia coli does not reflect selection for ‘rare’ codons. Nucleic Acids Res. 14(19): 7737–7749. doi:10.1093/nar/14.19.7737. PMID:3534792.
31. Sharp, P.M., and Lloyd, A.T. 1993. Codon usage. In An atlas of Drosophila genes. Edited by G. Maroni. Oxford University Press, New York, USA. pp. 378–397.
32. Sun, L., Zhang, G.H., Jiang, J.W., Fu, J.D., Ren, T., Cao, W.S., et al. 2007. A Massachusetts prototype like coronavirus isolated from wild peafowls is pathogenic to chickens. Virus Res. 130(1–2): 121–128. doi:10.1016/j.virusres.2007.06.003. PMID: 17629993.
33. Tao, P., Dai, L., Luo, M., Tang, F., Tien, P., and Pan, Z. 2009. Analysis of synonymous codon usage in classical swine fever virus. Virus Genes, 38(1): 104–112. doi:10.1007/s11262-008-0296-z. PMID:18958611.
34. Wang, M., Liu, Y.S., Zhou, J.H., Chen, H.T., Ma, L.N., Ding, Y.Z., et al. 2011. Analysis of codon usage in Newcastle disease virus. Virus Genes, 42(2): 245–253. doi:10.1007/s11262-011-0574-z. PMID:21249440.
35. Wright, F. 1990. The‘effective number of codons’ used in a gene. Gene, 87(1): 23–29. doi:10.1016/0378-1119(90)90491-9. PMID: 2110097.
36. Zhong, J., Li, Y., Zhao, S., Liu, S., and Zhang, Z. 2007. Mutation pressure shapes codon usage in the GC-rich genome of footand- mouth disease virus. Virus Genes, 35(3): 767–776. doi:10.1007/s11262-007-0159-z. PMID:17768673.