Synonymous codon usage in TTSuV2: Analysis and comparison with TTSuV1

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Zhang, Zhicheng ^a   Dai, Wei ^b   Dai, Dingzhen ^a  

^a JINLING INSTITUTE OF TECHNOLOGY   (China)

^b ANHUI AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLUSTER ANALYSIS; CODON USAGE; CONTROLLED STUDY; DNA BASE COMPOSITION; GEOGRAPHIC DISTRIBUTION; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; SYNONYMOUS CODON USAGE; TORQUE TENO SUS VIRUS 1; TORQUE TENO SUS VIRUS 2; TORQUE TENO VIRUS; VIRUS GENOME; VIRUS RECOMBINATION;

BASE COMPOSITION; CODON; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, VIRAL; GENOTYPE; OPEN READING FRAMES; PHYLOGENY; RECOMBINATION, GENETIC; TORQUE TENO VIRUS;

EID: 84896734157     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0081469     Document Type: Article

References (50)

1. Gupta SK, Bhattacharyya TK, Ghosh TC (2004) Synonymous codon usage in Lactococcus lactis: mutational bias versus translational selection. J Biomol Struct Dyn 21: 527-536. doi: 10.1080/07391102.2004.10506946. PubMed: 14692797.
2. Lloyd AT, Sharp PM (1992) Evolution of codon usage patterns: the extent and nature of divergence between Candida albicans and Saccharomyces cerevisiae. Nucleic Acids Res 20: 5289-5295. doi: 10.1093/nar/20.20.5289. PubMed: 1437548.
3. Chen R, Holmes EC (2006) Avian influenza virus exhibits rapid evolutionary dynamics. Mol Biol Evol 23: 2336-2341. doi:10.1093/molbev/msl102. PubMed: 16945980. (Pubitemid 44737127)
4. Zhong J, Li Y, Zhao S, Liu S, Zhang Z (2007) Mutation pressure shapes codon usage in the GC-Rich genome of foot-and-mouth disease virus. Virus Genes 35: 767-776. doi:10.1007/s11262-007-0159-z. PubMed: 17768673. (Pubitemid 350012787)
5. Sau K, Sau S, Mandal SC, Ghosh TC (2005) Factors influencing the synonymous codon and amino acid usage bias in AT-rich Pseudomonas aeruginosa phage PhiKZ. Acta Biochim Biophys Sin (Shanghai) 37: 625-633. doi:10.1111/j.1745-7270.2005.00089.x. PubMed: 16143818. (Pubitemid 43002368)
6. Sharp PM, Li WH (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res 14: 7737-7749. doi:10.1093/nar/14.19.7737. PubMed: 3534792.
7. Shackelton LA, Parrish CR, Holmes EC (2006) Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol 62: 551-563. doi:10.1007/s00239-005-0221-1. PubMed: 16557338. (Pubitemid 43965543)
8. Naya H, Romero H, Carels N, Zavala A, Musto H (2001) Translational selection shapes codon usage in the GC-rich genome of Chlamydomonas reinhardtii. FEBS Lett 501: 127-130. doi:10.1016/S0014-5793(01)02644-8. PubMed: 11470270.
9. Chiapello H, Lisacek F, Caboche M, Henaut A (1998) Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene 209: GC1-GC38 (Pubitemid 28149640)
10. Ma ES, Chow EY, Chan AY, Chu CM, Lin SY et al. (2002) Low affinity and unstable hemoglobin variant caused by AAC - ATC (Asn - Ile) mutation at codon 108 of the beta-globin gene. Haematologica 87: 553-554. PubMed: 12010673. (Pubitemid 34533285)
11. McInerney JO (1998) Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci U S A 95: 10698-10703. doi:10.1073/pnas.95.18.10698. PubMed: 9724767.
12. Chiusano ML, Alvarez-Valin F, Di Giulio M, D'Onofrio G, Ammirato G et al. (2000) Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code. Gene 261: 63-69. (Pubitemid 32103524)
13. Gupta SK, Majumdar S, Bhattacharya TK, Ghosh TC (2000) Studies on the relationships between the synonymous codon usage and protein secondary structural units. Biochem Biophys Res Commun 269: 692-696. doi:10.1006/bbrc. 2000.2351. PubMed: 10720478. (Pubitemid 30440363)
14. Levin DB, Whittome B (2000) Codon usage in nucleopolyhedroviruses. J Gen Virol 81: 2313-2325. PubMed: 10950991.
15. Mushahwar IK, Erker JC, Muerhoff AS, Leary TP, Simons JN et al. (1999) Molecular and biophysical characterization of TT virus: evidence for a new virus family infecting humans. Proc Natl Acad Sci U S A 96: 3177-3182. doi:10.1073/pnas.96.6.3177. PubMed: 10077657. (Pubitemid 29148864)
16. Biagini P (2009) Classification of TTV and related viruses (anelloviruses). Curr Top Microbiol Immunol 331: 21-33. doi: 10.1007/978-3-540-70972-5-2. PubMed: 19230555.
17. Nishizawa T, Okamoto H, Konishi K, Yoshizawa H, Miyakawa Y et al. (1997) A novel DNA virus (TTV) associated with elevated transaminase levels in posttransfusion hepatitis of unknown etiology. Biochem Biophys Res Commun 241: 92-97. doi:10.1006/bbrc.1997.7765. PubMed: 9405239. (Pubitemid 28033544)
18. Okamoto H, Nishizawa T, Takahashi M, Tawara A, Peng Y et al. (2001) Genomic and evolutionary characterization of TT virus (TTV) in tupaias and comparison with species-specific TTVs in humans and non-human primates. J Gen Virol 82: 2041-2050. PubMed: 11514713. (Pubitemid 32827584)
19. Okamoto H, Takahashi M, Nishizawa T, Tawara A, Fukai K et al. (2002) Genomic characterization of TT viruses (TTVs) in pigs, cats and dogs and their relatedness with species-specific TTVs in primates and tupaias. J Gen Virol 83: 1291-1297. PubMed: 12029143. (Pubitemid 34591322)
20. Niel C, Diniz-Mendes L, Devalle S (2005) Rolling-circle amplification of Torque teno virus (TTV) complete genomes from human and swine sera and identification of a novel swine TTV genogroup. J Gen Virol 86: 1343-1347. doi:10.1099/vir.0.80794-0. PubMed: 15831945. (Pubitemid 40613251)
21. McKeown NE, Fenaux M, Halbur PG, Meng XJ (2004) Molecular characterization of porcine TT virus, an orphan virus, in pigs from six different countries. Vet Microbiol 104: 113-117. doi:10.1016/j.vetmic.2004.08. 013. PubMed: 15530745. (Pubitemid 39458184)
22. Jelcic I, Hotz-Wagenblatt A, Hunziker A, Zur Hausen H, de Villiers EM (2004) Isolation of multiple TT virus genotypes from spleen biopsy tissue from a Hodgkin's disease patient: genome reorganization and diversity in the hypervariable region. J Virol 78: 7498-7507. doi: 10.1128/JVI.78.14.7498-7507. 2004. PubMed: 15220423. (Pubitemid 38915895)
23. Kakkola L, Bondén H, Hedman L, Kivi N, Moisala S et al. (2008) Expression of all six human Torque teno virus (TTV) proteins in bacteria and in insect cells, and analysis of their IgG responses. Virology 382: 182-189. doi:10.1016/j.virol.2008.09.012. PubMed: 18947848.
24. Ellis JA, Allan G, Krakowka S (2008) Effect of coinfection with genogroup 1 porcine torque teno virus on porcine circovirus type 2-associated postweaning multisystemic wasting syndrome in gnotobiotic pigs. Am J Vet Res 69: 1608-1614. doi:10.2460/ajvr.69.12.1608. PubMed: 19046008.
25. Kekarainen T, Sibila M, Segalés J (2006) Prevalence of swine Torque teno virus in post-weaning multisystemic wasting syndrome (PMWS)-affected and non-PMWS-affected pigs in Spain. J Gen Virol 87: 833-837. doi:10.1099/vir.0.81586-0. PubMed: 16528032.
26. Aramouni M, Segalés J, Sibila M, Martin-Valls GE, Nieto D et al. (2011) Torque teno sus virus 1 and 2 viral loads in postweaning multisystemic wasting syndrome (PMWS) and porcine dermatitis and nephropathy syndrome (PDNS) affected pigs. Vet Microbiol 153: 377-381. doi: 10.1016/j.vetmic.2011.05.046. PubMed: 21719215.
27. Nieto D, Aramouni M, Grau-Roma L, Segalés J, Kekarainen T (2011) Dynamics of Torque teno sus virus 1 (TTSuV1) and 2 (TTSuV2) DNA loads in serum of healthy and postweaning multisystemic wasting syndrome (PMWS) affected pigs. Vet Microbiol 152: 284-290. doi: 10.1016/j.vetmic.2011.05.020. PubMed: 21680113.
28. Taira O, Ogawa H, Nagao A, Tuchiya K, Nunoya T et al. (2009) Prevalence of swine Torque teno virus genogroups 1 and 2 in Japanese swine with suspected post-weaning multisystemic wasting syndrome and porcine respiratory disease complex. Vet Microbiol 139: 347-350. doi:10.1016/j.vetmic.2009.06.010. PubMed: 19570625.
29. Zhang Z, Dai W, Wang Y, Lu C, Fan H (2013) Analysis of synonymous codon usage patterns in torque teno sus virus 1 (TTSuV1). Arch Virol, 158: 145-54. PubMed: 23011310.
30. Marais G, Mouchiroud D, Duret L (2001) Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc Natl Acad Sci U S A 98: 5688-5692. doi:10.1073/pnas.091427698. PubMed: 11320215. (Pubitemid 32435703)
31. Etherington GJ, Dicks J, Roberts IN (2005) Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination. Bioinformatics 21: 278-281. doi:10.1093/bioinformatics/ bth500. PubMed: 15333462.
32. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739. doi:10.1093/molbev/msr121. PubMed: 21546353.
33. Sharp PM, Li WH (1986) An evolutionary perspective on synonymous codon usage in unicellular organisms. J Mol Evol 24: 28-38. doi: 10.1007/BF02099948. PubMed: 3104616.
34. Comeron JM, Aguadé M (1998) An evaluation of measures of synonymous codon usage bias. J Mol Evol 47: 268-274. doi:10.1007/PL00006384. PubMed: 9732453. (Pubitemid 28455143)
35. Zhou JH, Zhang J, Chen HT, Ma LN, Liu YS (2010) Analysis of synonymous codon usage in foot-and-mouth disease virus. Vet Res Commun 34: 393-404. doi:10.1007/s11259-010-9359-4. PubMed: 20425142.
36. Posada D, Crandall KA (2002) The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol 54: 396-402. PubMed: 11847565. (Pubitemid 34165424)
37. Krakowka JE, MacIntosh K, Ringler SS, Rings DM,Hartunian C, Zhang Yan, Allan G (2008) Porcine genogroup 1 Torque Teno Virus (G1-TTV) Potentiates PCV2 & PRRSV infections in gnotobiotic swine. Proceedings of the International Pig Veterinary Society (Durban) 1: 99.
38. Krakowka S, Ellis JA (2008) Evaluation of the effects of porcine genogroup 1 torque teno virus in gnotobiotic swine. Am J Vet Res 69: 1623-1629. doi:10.2460/ajvr.69.12.1623. PubMed: 19046010.
39. Zhao S, Zhang Q, Liu X, Wang X, Zhang H et al. (2008) Analysis of synonymous codon usage in 11 human bocavirus isolates. Biosystems 92: 207-214. doi:10.1016/j.biosystems.2008.01.006. PubMed: 18378386.
40. Wang M, Zhang J, Zhou JH, Chen HT, Ma LN et al. (2011) Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus. Biosystems 106: 45-50. doi:10.1016/j.biosystems.2011.06.005. PubMed: 21708221.
41. Wong EH, Smith DK, Rabadan R, Peiris M, Poon LL (2010) Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus. BMC Evol Biol 10: 253. doi: 10.1186/1471-2148-10-253. PubMed: 20723216.
42. Posada D, Crandall KA, Holmes EC (2002) Recombination in evolutionary genomics. Annu Rev Genet 36: 75-97. doi:10.1146/annurev.genet.36.040202.111115. PubMed: 12429687. (Pubitemid 36109184)
43. Shi M, Holmes EC, Brar MS, Leung FC (2013) Recombination is Associated with an Outbreak of Novel Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Viruses in China. J Virol, 87: 10904-7. PubMed: 23885071.
44. Ramos N, Mirazo S, Castro G, Arbiza J (2013) Molecular analysis of Porcine Circovirus Type 2 strains from Uruguay: Evidence for natural occurring recombination. Infect Genet Evol 19C: 23-31. PubMed: 23806516.
45. Li J, Huo X, Dai Y, Yang Z, Lei Y et al. (2012) Evidences for intertypic and intratypic recombinant events in EV71 of hand, foot and mouth disease during an epidemic in Hubei Province, China, 2011. Virus Res 169: 195-202. doi:10.1016/j.virusres.2012.07.028. PubMed: 22922556.
46. Abrantes J, Esteves PJ, van der Loo W (2008) Evidence for recombination in the major capsid gene VP60 of the rabbit haemorrhagic disease virus (RHDV). Arch Virol 153: 329-335. doi: 10.1007/s00705-007-1084-0. PubMed: 18193156.
47. Zhou T, Gu W, Ma J, Sun X, Lu Z (2005) Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. Biosystems 81: 77-86. doi:10.1016/j.biosystems.2005.03.002. PubMed: 15917130. (Pubitemid 40726202)
48. Gu W, Zhou T, Ma J, Sun X, Lu Z (2004) Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Res 101: 155-161. doi:10.1016/j.virusres.2004.01.006. PubMed: 15041183. (Pubitemid 38369316)
49. Zhang Z, Wang Y, Fan H, Lu C (2012) Natural infection with torque teno sus virus 1 (TTSuV1) suppresses the immune response to porcine reproductive and respiratory syndrome virus (PRRSV) vaccination. Arch Virol 157: 927-933. doi:10.1007/s00705-012-1249-3. PubMed: 22327391.
50. Namouchi A, Didelot X, Schöck U, Gicquel B, Rocha EP (2012) After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res 22: 721-734. doi:10.1101/gr.129544.111. PubMed: 22377718.