Patterns and influencing factor of synonymous codon usage in porcine circovirus

Virology Journal

Volumn 9, Issue , 2012, Pages

  Liu, Xin Sheng ^a   Zhang, Yong Guang ^a   Fang, Yu Zhen ^a   Wang, Yong Lu ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; OLIGONUCLEOTIDE;

AROMA; AROMATICITY; ARTICLE; CALCULATION; CIRCOVIRUS; CODON USAGE; CONTROLLED STUDY; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHICAL VARIATION (SPECIES); HYDROPHOBICITY; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; VIRUS GENOME; ANIMAL; CODON; DNA BASE COMPOSITION; GENETICS; HOST PATHOGEN INTERACTION;

PORCINE CIRCOVIRUS; SUIDAE;

ANIMALS; BASE COMPOSITION; CIRCOVIRUS; CODON; EVOLUTION, MOLECULAR; GENOME, VIRAL; HOST-PATHOGEN INTERACTIONS;

EID: 84862824670     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-9-68     Document Type: Article

References (42)

1. Tissue-specific differences in human transfer RNA expression. Dittmar KA, Goodenbour JM, Pan J, PLoS Genet 2006 2 2107 2115 (Pubitemid 46045190)
2. Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae. Lloyd AT, Sharp PM, Nucleic Acids Res 1992 20 5289 5295 10.1093/nar/20.20.5289 1437548
3. The relationship between synonymous codon usage and protein structure. Xie T, Ding D, Tao X, Dafu D, FEBS Lett 1998 434 93 96 10.1016/S0014-5793(98) 00955-7 9738458 (Pubitemid 28404669)
4. Codon usage and gene function are related in sequences of Arabidopsisthaliana. Chiapello H, Lisacek F, Caboche M, Gene 1998 209 1-2 C1 GC38 10.1016/S0378-1119(97)00671-9 9583944 (Pubitemid 28149640)
5. Codon usage bias amongst plant viruses. Adams MJ, Antoniw JF, Arch Virol 2003 149 1 113 135 10.1007/s00705-003-0186-6 14689279 (Pubitemid 38162103)
6. Heterogeneity in codon usages of sobemovirus genes. Zhou H, Wang H, Huang LF, Arch Virol 2005 150 8 1591 1605 10.1007/s00705-005-0510-4 15834656 (Pubitemid 41187181)
7. Codon usage in nucleopolyhedroviruses. Levin DB, Whittome B, J Gen Virol 2000 81 2313 2325 10950991
8. Gene expressivity is the main factor in dictating the codon usage variation among the genes in Pseudomonas aeruginosa. Gupta SK, Ghosh TC, Gene 2001 273 1 63 70 10.1016/S0378-1119(01)00576-5 11483361 (Pubitemid 32718727)
9. The base composition of the genes is correlated with the secondary structures of the encoded Proteins. D'Onofrio G, Ghosh TC, Bernardi G, Gene 2002 300 1 179 187 10.1016/S0378-1119(02)01045-4 12468099 (Pubitemid 35441173)
10. The relationship between synonymous codon usage and Protein structure in Escherichia coli and Homo sapiens. Gu W, Zhou T, Ma J, Sun X, Lu Z, Biosystems 2004 73 2 89 97 10.1016/j.biosystems.2003.10.001 15013221 (Pubitemid 38175406)
11. Analysis of codon usage in bovine viral diarrhea virus. Wang Meng, Zhang Jie, Zhou Jian-hua, Chen Hao-tai, Ma Li-na, Ding Yao-zhong, Liu Wen-qian, Liu Yong-sheng, Arch Virol 2010 156 1 153 160 21069395
12. Compositional pressure and translational selection determine codon usage in the extremely GC poor unicellular eukaryote Entamoeba histolytica. Romero H, Zavala A, Musto H, Gene 2000 242 1-2 307 311 10.1016/S0378-1119(99)00491-6 10721724 (Pubitemid 30064516)
13. Correlation between codon usage and thermostability. Van der Linden MG, de Farias ST, Extremophiles 2006 10 5 479 481 10.1007/s00792-006-0533-0 16830074 (Pubitemid 44564011)
14. Mapping and characterization of the origin of DNA replication of porcine circovirus. Mankertz A, Persson F, Mankertz J, Blaess G, Buhk HJ, J Virol 1997 71 3 2562 2566 9032401 (Pubitemid 27078647)
15. ORF3 of porcine circovirus 2 enhances the in vitro and in vivo spread of the of the virus. Karuppannan AK, Kwang J, Virology 2011 410 248 256 10.1016/j.virol.2010.11.009 21144544
16. The ORF3 protein of porcine circovirus type 2 is involved in viral pathogenesis in vivo. Liu J, Chen I, Du Q, Virol 2006 80 10 5065 5073 10.1128/JVI.80.10.5065-5073.2006
17. Nucleotide sequence of porcine circovirus associated with postweaning multisystemic wasting syndrome in pigs. Andre L, Hamel, Lihua L, Lin, Gopi PS, Nayar, J Virol 1998 72 5262 5267 9573301 (Pubitemid 28215711)
18. Characterization of novel circovirus DNAs associated with wasting syndromes in pigs. Meehan BM, McNeilly F, Todd D, Kennedy S, Jewhurst VA, Ellis JA, Hassard LE, Clark EG, Haines DM, Allan GM, J Gen Virol 1998 79 2171 2179 9747726 (Pubitemid 28423412)
19. Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. Zhou T, Wanjun Gu, Ma J, Sun X, Zuhong Lu, Biosystems 2005 81 77 86 10.1016/j.biosystems.2005.03.002 15917130 (Pubitemid 40726202)
20. Second codon positions of genes and the secondary structures of proteins.Relationships and implications for the origin of the genetic code. Chiusano Maria Luisa, Alvarez-Valin Fernando, Giulio Massimo Di, D'Onofrio Giuseppe, Ammirato Gaetano, Colonna Giovanni, Bernardi Giorgio, Gene 2000 261 63 69 10.1016/S0378-1119(00)00521-7 11164038 (Pubitemid 32103524)
21. Codon usage in yeast:cluster analysis clearly differentiates highly and lowly expressed genes. Sharp PM, Tuohy TM, Mosurski KR, Nucleic Acids Res 1986 14 5125 5143 10.1093/nar/14.13.5125 3526280
22. Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Gu WJ, Zhou T, Ma JM, Sun X, Lu ZH, Virus Res 2004 101 2 155 161 10.1016/j.virusres.2004.01.006 15041183 (Pubitemid 38369316)
23. Compare the differences of synonymous codon usage between the two species within cardiovirus. Liu Wen-qian, Zhang Jie, Zhang Yi-qiang, Zhou Jian-hua, Chen Hao-tai, Ma Li-na, Ding Yao-zhong, Liu Yongsheng, Virol J 2011 8 325 10.1186/1743-422X-8-325 21708006
24. Evolution of base composition and codon usage bias in the genus Flavivirus. Gareth M, Jenkins, Pagel Mark, Ernest A, Gould, Zanotto DeA, Paolo M, Edward C, Holmes, J Mol Evol 2001 52 383 390 11343134 (Pubitemid 32372397)
25. The strength of translational selection for codon usage varies in the three replicons of Sinorhizobium meliloti. Peixoto L, Zavala A, Romero H, Musto H, Gene 2003 320 27 109 116 14597394 (Pubitemid 37352760)
26. The influence of translational selection on codon usage in fishes from the family cyprinidae. Romero H, Zavala A, Musto H, Bernardi G, Gene 2003 317 1-2 141 147 14604802 (Pubitemid 37356928)
27. Studies on the relationships between the synonymous codon usage and protein secondary structural units. Gupta SK, Majumdar S, Bhattacharya TK, Ghosh TC, Biochem Biophys Res Commun 2000 269 692 696 10.1006/bbrc.2000.2351 10720478 (Pubitemid 30440363)
28. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. James O, McInerney, PNAS 1998 95 18 10698 10703 10.1073/pnas.95.18.10698 9724767 (Pubitemid 28413131)
29. Codon usage and secondary strueture of mRNA. Zama M, Nucleic Acids Symp Ser 1990 22 93 94 2101925
30. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Stoletzki N, Eyre-Walker A, Mol Biol Evol 2007 24 2 374 381 17101719 (Pubitemid 46204370)
31. Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. Rocha PC, Eduardo, Genome Res 2004 14 11 2279 2281 10.1101/gr.2896904 15479947 (Pubitemid 39517335)
32. Synonymous codon usage is subject to selection in thermophilic bacteria. Lynn DJ, GAC, Nucleic Acids Res 2002 30 19 4272 4277 10.1093/nar/gkf546 12364606 (Pubitemid 35189536)
33. Codon usage bias in herpesvirus. Minghui Fu, Arch Virol 2010 155 391 396 10.1007/s00705-010-0597-0 20107845
34. Analysis of codon usage bias and base compositional constraints in iridovirus genomes. Tsai C-T, Lin C-H, Chang C-Y, Virus Res 2007 126 196 206 10.1016/j.virusres.2007.03.001 17434639 (Pubitemid 46726713)
35. Characterization of Synonymous Codon Usage Bias in the Duck Plague Virus UL35 Gene. Cai M-S, An-Chun Cheng, Wang M-S, Li-Chan Zhao, Intervirology 2009 52 266 278 10.1159/000231992 19672100
36. Analysis of synonymous codon usage in the UL24 gene of duck enteritis virus. Jia R, Cheng A, Wang M, Virus Genes 2009 38 96 103 10.1007/s11262-008- 0295-0 18958612
37. The effective number of codons used in a gene. Wright F, Gene 1990 87 23 29 10.1016/0378-1119(90)90491-9 2110097 (Pubitemid 20139850)
38. Analysis of synonymous codon usage in classical swine fever virus. Tao P, Dai L, Luo M, Tien Fangqiang Tang Po, Pan Z, Virus Genes 2009 38 104 112 10.1007/s11262-008-0296-z 18958611
39. Analysis of synonymous codon usage in 11 Human Bocavirus isolates. Hao S, Zhang Q, Liu X, Wang X, Zhang H, Wu Y, Jiang F, Biosystems 2008 92 207 214 10.1016/j.biosystems.2008.01.006 18378386
40. Factors influencing synonymous codon and amino acid usage biases in Mimivirus. Sau K, Gupta SK, Sau S, Mandal SC, Ghosh TC, Biosystems 2006 85 107 113 10.1016/j.biosystems.2005.12.004 16442213 (Pubitemid 44040957)
41. Ewens WJ, Grant GR, Statistical Methods in Bioinformatics New York: Springer 2001
42. Mutation rates among RNA viruses. Drake JW, Holland JJ, Proc Natl Acad Sci USA 1999 96 13910 13913 10.1073/pnas.96.24.13910 10570172