Phylogenetic and structural studies of a novel equine papillomavirus identified from aural plaques

Veterinary Microbiology

Volumn 162, Issue 1, 2013, Pages 85-93

  Taniwaki, Sueli A ^a   Magro, Angelo J ^a   Gorino, Ana Claudia ^a   Oliveira Filho, José P ^a   Fontes, Marcos R M ^a   Borges, Alexandre S ^a   Araujo, João P ^a  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

Author keywords

Aural plaques; Horses; L1 loops; Papillomavirus; Phylogenetic analysis

Indexed keywords

AMINO ACID; CAPSID PROTEIN; NUCLEOTIDE;

AMINO ACID SEQUENCE; ARTICLE; DNA EXTRACTION; GENE AMPLIFICATION; GENE SEQUENCE; GENOME; HORSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PAPILLOMA VIRUS; PHYLOGENY; POLYMERASE CHAIN REACTION; SKIN; VIRUS MORPHOLOGY;

AMINO ACID SEQUENCE; ANIMALS; BAYES THEOREM; CAPSID PROTEINS; CLUSTER ANALYSIS; DNA PRIMERS; DNA, VIRAL; EAR, EXTERNAL; GENETIC VARIATION; HORSE DISEASES; HORSES; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PAPILLOMAVIRIDAE; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT;

ANIMALIA; EQUIDAE; EQUUS CABALLUS PAPILLOMAVIRUS - 1; MIRIDAE; PAPILLOMAVIRIDAE;

EID: 84872181309     PISSN: 03781135     EISSN: 18732542     Source Type: Journal    
DOI: 10.1016/j.vetmic.2012.08.025     Document Type: Article

References (34)

1. Ashrafi G.H., Piuko K., Burden F., Yuan Z., Gault E.A., Müller M., Trawford A., Reid S.W., Nasir L., Campo M.S. Vaccination of sarcoid-bearing donkeys with chimeric virus-like particles of bovine papillomavirus type 1. J. Gen. Virol. 2008, 89:148-157.
2. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Hermans J. Interaction models for water in relation to protein hydration. Intermolecular Forces 1981, 331-342. D. Reidel Publishing Company, Dordrecht. B. Pullman (Ed.).
3. Berendsen H.J.C., Postma J.P.M., van Gunsteren A., DiNola A., Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81:3684-3690.
4. Bernard H.U., Burk R.D., Chen Z., van Doorslaer K., Hausen H., de Villiers E.M. Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 2010, 401:70-79.
5. Bishop B., Dasgupta J., Klein M., Garcea R.L., Christensen N.D., Zhao R., Chen X.S. Crystal structures of four types of human papillomavirus L1 capsid proteins: understanding the specificity of neutralizing monoclonal antibodies. J. Biol. Chem. 2007, 282:31803-31811.
6. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T., Warren G.L. Crystallography & NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallogr. D: Biol. Crystallogr. 1998, 54:905-921.
7. Chen V.B., Arendall W.B., Headd J.J., Keedy D.A., Immormino R.M., Kapral G.J., Murray L.W., Richardson J.S., Richardson D.C. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D: Biol. Crystallogr. 2010, 66:12-21.
8. Chen X.J., Garcea B., Goldberg I., Casini G., Harrison S.C. Structure of small virus-like particles assembled from the L1 protein of human papillomavirus 16. Mol. Cell. 2000, 5:557-567.
9. Delano W.L. The PyMOL Molecular Graphics System 2002, DeLano Scientific, San Carlos.
10. de Villiers E.M., Fauquet C., Broker T.R., Bernard H.U., zur Hausen H. Classification of papillomaviruses. Virology 2004, 324:17-27.
11. Ghim S.J., Rector A., Delius H., Sundberg J.P., Jenson A.B., Van Ranst M. Equine papillomavirus type 1: complete nucleotide sequence and characterization of recombinant virus-like particles composed of the EcPV-1 L1 major capsid protein. Biochem. Biophys. Res. Commun. 2004, 324:1108-1115.
12. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 1999, 41:95-98.
13. Hess B., Kutzner C., van der Spoel D., Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 2008, 4:435-447.
14. Kainzbauer C., Rushton J., Tober R., Scase T., Nell B., Sykora S., Brandt S. Bovine papillomavirus type 1 and Equus caballus papillomavirus 2 in equine squamous cell carcinoma of the head and neck in a Connemara mare. Equine Vet. J. 2012, 44:112-115.
15. Kidney B.A., Haines D.M., Ellis J.A., Burnham M.L., Teifke J.P., Czerwinski G., Jackson M.L. Evaluation of formalin-fixed paraffin-embedded tissues from vaccine site-associated sarcomas of cats for papillomavirus DNA and antigen. Am. J. Vet. Res. 2001, 62:833-839.
16. Knight C.G., Munday J.S., Peters J., Dunowska M. Equine penile squamous cell carcinomas are associated with the presence of equine papillomavirus type 2 DNA sequences. Vet. Pathol. 2011, 48:1190-1194.
17. Lange C.E., Tobler K., Ackermann M., Favrot C. Identification of two novel equine papillomavirus sequences suggests three genera in one cluster. Vet. Microbiol. 2011, 149:85-90.
18. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
19. Marti-Renom M.A., Stuart A., Fiser A., Sánchez R., Melo F., Sali A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 2000, 29:291-325.
20. Miller M.A., Pfeiffer W., Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments Workshop (GCE) 2010, 1-8.
21. Munday J.S., Kiupel M. Papillomavirus-associated cutaneous neoplasia in mammals. Vet. Pathol. 2010, 47:254-264.
22. Niel C., Diniz-Mendes L., Devalle S. 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. 2005, 86:1343-1347.
23. Oostenbrink C., Soares T.A., van der Vegt N.F.A., van Gunsteren W.F. Validation of the 53A6 GROMOS force field. Eur. Biophys. J. 2005, 34:273-284.
24. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
25. Postey R.C., Appleyard G.D., Kidney B.A. Evaluation of equine papillomas, aural plaques, and sarcoids for the presence of Equine papillomavirus DNA and Papillomavirus antigen. Can. J. Vet. Res. 2007, 71:28-33.
26. Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19:1572-1574.
27. Scase T., Brandt S., Kainzbauer C., Sykora S., Bijmholt S., Hughes K., Sharpe S., Foote A. Equus caballus papillomavirus-2 (EcPV-2): an infectious cause for equine genital cancer?. Equine Vet. J. 2010, 42:738-745.
28. Scott D.W., Miller W.H. Equine Dermatology 2011, Elsevier Saunders, Maryland Heights, pp. 468-516. 2nd ed.
29. Söding J., Biegert A., Lupas A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005, 33:244-248.
30. Sousa N.R., Adorno V.B., Marcondes J.S., Oliveira-Filho J.P., Conceição L.G., Amorim R.L., Borges A.S. Clinical and histopathological characteristics of the aural plaque in Mangalarga and Quarter Horses. Pesq. Vet. Bras. 2008, 28:279-284.
31. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
32. Togawa R.C., Brigido M.M. PHPH: Web based tool for simple electropherogram quality analysis. 1st International Conference on Bioinformatics and Computational Biology 2003, http://asparagin.cenargen.embrapa.br/phph/ribeirao_preto_poster.pdf.
33. Wiederstein M., Sippl M.J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007, 35:407-410.
34. Wolf M., Garcea R.L., Grigorieff N., Harrison S.C. Subunit interactions in bovine papillomavirus. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:6298-6303.