Molecular phylogeny of leader proteinase gene of type A of Foot-and-mouth disease virus from India

Archives of Virology

Volumn 149, Issue 3, 2004, Pages 523-536

  Tosh, C ^a   Mittal, M ^a   Sanyal, A ^a   Hemadri, D ^a   Bandyopadhyay, S K ^a  

^a Indian Veterinary Research Institute Campus   (India)

Author keywords

[No Author keywords available]

Indexed keywords

LEADER PROTEINASE, FOOT AND MOUTH DISEASE VIRUS; LEADER PROTEINASE, FOOT-AND-MOUTH DISEASE VIRUS; PROTEINASE;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BUFFALO; CATTLE; CATTLE DISEASE; CELL LINE; CHEMISTRY; DNA SEQUENCE; FOOT AND MOUTH DISEASE; FOOT AND MOUTH DISEASE VIRUS; GENETIC SELECTION; GENETICS; HAMSTER; INDIA; MOLECULAR GENETICS; PHYLOGENY; STATISTICAL MODEL; VIROLOGY;

AMINO ACID SEQUENCE; ANIMALS; BUFFALOES; CATTLE; CATTLE DISEASES; CELL LINE; CRICETINAE; ENDOPEPTIDASES; FOOT-AND-MOUTH DISEASE; FOOT-AND-MOUTH DISEASE VIRUS; INDIA; LIKELIHOOD FUNCTIONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA;

ANIMALIA; BOS TAURUS; BUBALUS; CRICETINAE; FOOT-AND-MOUTH DISEASE VIRUS; PROKARYOTA;

EID: 1542350824     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-003-0224-4     Document Type: Article

References (50)

1. Beck E, Forss S, Strebel K, Cattaneo R, Feil G (1983) Structure of the FMDV translation initiation site and of the structural proteins. Nucleic Acids Res 11: 7873-7885
2. Brown CC, Piccone ME, Mason PW, McKenna TSC, Grubman MJ (1996) Pathogenesis of wild-type and leaderless foot-and-mouth disease virus in bovines. J Virol 70: 5638-5641
3. Cao X, Bergmann I, Fullkrug R, Beck E (1995) Functional analysis of the two alternate translation initiation sites of foot-and-mouth disease virus. J Virol 69: 560-563
4. Chinsangaram J, Koster M, Grubman MJ (2001) Inhibition of L-deleted foot-and-mouth disease virus replication by alpha/beta interferon involves double-stranded RNA-dependent protein kinase. J Virol 75: 5498-5503
5. Chinsangaram J, Piccone ME, Grubman MJ (1999) Ability of foot-and-mouth disease virus to form plaques in cell culture is associated with suppression of alpha/beta interferon. J Virol 73: 9891-9898
6. Clarke BE, Sangar DV, Burroughs JN, Newton SE, Carroll AR, Rowlands DJ (1985) Two initiation sites for foot-and-mouth disease virus polyprotein in vivo. J Gen Virol 66: 2615-2626
7. Devaney MA, Vakharia VN, Lloyd RE, Ehrenfeld E, Grubman MJ (1988) Leader protein of foot-and-mouth disease virus is required for cleavage of the p220 component of the cap-binding complex. J Virol 62: 4407-4409
8. Domingo E, Escarmis C, Martinez MA, Martinez-Salas E, Mateu MG (1992) Foot-and-mouth disease virus populations are quasispecies. Curr Top Microbiol Immunol 176: 33-47
9. Fares ML, Moya A, Cristina E, Baranowski E, Domingo E, Barrio E (2001) Evidence of positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens. Mol Biol Evol 18: 10-21
10. Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22: 521-565
11. Foeger N, Glaser W, Skern T (2002) Recognition of eukaryotic initiation factor 4G isoforms by Picornaviral proteinases. J Biol Chem 277: 44300-44309
12. George M, Venkataramanan R, Gurumurthy CB, Hemadri D (2001) The non-structural leader protein gene of foot-and-mouth disease virus is highly variable between serotypes. Virus Genes 22: 271-278
13. Glaser W, Cencic R, Skern T (2001) Foot-and-mouth disease leader proteinase. J Biol Chem 276: 35473-35481
14. Guarne A, Hampoelz B, Glaser W, Carpena X, Tormo J, Fita I, Skern T (2000) Structural and Biochemical features distinguishing the foot-and-mouth disease virus leader proteinase from other papain-like enzymes. J Mol Biol 302: 1227-1240
15. Guarne A, Tormo J, Kirchweger R, Pfistermueller D, Fita I, Skern T (1998) Structure of the foot-and-mouth disease virus leader protease: a papain-like fold adapted for self-processing and eIF4G recognition. EMBO J 17: 7469-7479
16. Gurumurthy CB, Sanyal A, Venkataramanan R, Tosh C, George M, Hemadri D (2002) Genetic diversity in the VP1 gene of foot-and-mouth disease virus serotype Asia 1. Arch Virol 147: 85-102
17. Hemadri D, Tosh C, Sanyal A, Venkataramanana R (2002) Emergences of a new strain of type O foot-and-mouth disease virus: its phylogenetic and evolutionary relationship with PanAsia pandemic strain. Virus Genes 25: 23-34
18. Hemadri D, Tosh C, Venkataramanan R, Sanyal A, Samuel AR, Knowles NJ, Kitching RP (2000) Genetic analysis of foot-and-mouth disease virus type O isolates responsible for field outbreaks in India between 1993 and 1999. Epidemiol Infect 125: 729-736
19. Huelsenbeck JP, Crandall KA (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Syst 28: 437-466
20. King AMQ (1988) Recombination in positive strand RNA viruses. In: Domingo E, Holland JJ, Ahlquist P (eds) RNA Genetics, vol. 2. CRC, Boca Raton, pp 149-165
21. Kitching RP (1999) Foot-and-mouth disease: Current world situation. Vaccine 26: 1772-1774
22. Knowles NJ, Samuel AR (1995) Polymerase chain reaction amplification and cycle sequencing of the ID (VP1) gene of foot-and-mouth disease viruses. Rpt Sess Res Gp Stand Tech Comm Eur Comm Control of FMD (FAO), Vienna, Austria, pp 45-53
23. Kosakovsky SL, Muse SV (2000) HY-PHY: hypothesis testing using phylogenies. Version 0.95b. Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh
24. Krebs O, Marquardt O (1993) Identification and characterization of foot-and-mouth disease virus O1 Burgwedel/1987 as an intertypic recombinant. J Gen Virol 73: 613-619
25. Medina M, Domingo E, Brangwyn K, Belsham GJ (1993) The two species of the foot-and-mouth disease virus leader protein, expressed individually, exhibit the same activities. Virology 194: 355-359
26. Mohapatra JK, Sanyal A, Hemadri D, Tosh C, Venkataramanan R (2002) Sequence and phylogenetic analysis of the L and VP1 genes of foot-and-mouth disease virus serotype Asia 1. Virus Res 87: 107-118
27. Page RDM (1996) TREEVIEW: An application to display phylogenetic trees on personal computers. Comput Appl Biosci 12: 357-358
28. Pattnaik B, Venkataramanan R, Tosh C, Sanyal A, Hemadri D, Samuel AR, Knowles NJ, Kitching RP (1998) Genetic heterogeneity of Indian field isolates of foot-and-mouth disease virus serotype O as revealed by partial sequencing of 1D gene. Virus Res 55: 115-127
29. Pereira HG (1977) Subtyping of foot-and-mouth disease virus. Dev Biol Stand 35: 167-174
30. Piccone M, Zellner M, Kumosinski TF, Mason P, Grubman MJ (1995) Identification of the active-site residues of the L proteinase of foot-and-mouth disease virus. J Virol 69: 4950-4956
31. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818
32. th edn, vol 1. Lippincott Williams and Wilkins, Philadelphia, pp 685-722
33. Roberts PJ, Belsham GJ (1995) Identification of critical amino acids within the foot-and-mouth disease virus leader protein, a cysteine protease. Virology 213: 140-146
34. Sabarinath GP (2001) Comparison of nucleotide sequence of structural protein encoding (P1) region of foot-and-mouth disease virus serotype O isolates. M.V.Sc. Thesis. Deemed University, IVRI-Izatanagar, Uttar Pradesh, India
35. Sangar DV, Newton SE, Rowlands DJ, Clarke BE (1987) All foot-and-mouth disease virus serotypes initiate protein synthesis at two separate AUGs. Nucleic Acids Res 15: 3305-3315
36. Schlick P, Kronovetr J, Hampoelz B, Skern T (2002) Modulation of the electrostatic charge at the active site of foot-and-mouth virus leader proteinase, an unusual papain-like enzyme. Biochem J 363: 493-501
37. Seipelt J, Guarne A, Bergmann E, James M, Sommergruber W, Fita I, Skern T (1999) The structure of Picornaviral proteinases. Virus Res 62: 159-168
38. Strebel K, Beck E (1986) A second protease of foot-and-mouth disease virus. J Virol 58: 893-899
39. Strimmer K, von Haeseler A (1996) Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13: 964-969
40. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitution in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526
41. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680
42. Tosh C, Hemadri D, Sanyal A (2002b) Evidence of recombination in the capsid-coding region of type A foot-and-mouth disease virus. J Gen Virol 83: 2455-2460
43. Tosh C, Hemadri D, Sanyal A, Bandyopadhyay SK (2003) Genetic and antigenic analysis of two recently circulating genotypes of type A foot-and-mouth disease virus in India: evidence for positive selection in the capsid-encoding genes. Arch Virol 148: 853-869
44. Tosh C, Sanyal A, Hemadri D (2002c) Genetic and antigenic analysis of a recombinant foot-and-mouth disease virus. Curr Sci 83: 1016-1019
45. Tosh C, Sanyal A, Hemadri D, Venkataramanan R (2002a) Phylogenetic analysis of serotype A foot-and-mouth disease virus isolated in India between 1977 and 2000. Arch Virol 147: 493-513
46. van Rensburg H, Haydon D, Joubert F, Bastos A, Heath L, Nel L (2002) Genetic heterogeneity in the foot-and-mouth disease virus Leader and 3C proteinases. Gene 289: 19-29
47. Yang Z (1997) Phylogenetic analysis by maximum likelihood (PAML) http:// abacus.gene.ucl.ac.uk/software/paml.html. University College London, London
48. Yang Z, Goldman N, Friday A (1994) Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol Biol Evol 11: 316-324
49. Yang Z, Nielsen R, Goldman N, Pedersen AMK (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155: 431-449
50. Zhang J (1999) Performance of likelihood ratio test of evolutionary hypotheses under inadequate substitution models. Mol Biol Evol 16: 868-875