Genome Annotation and Comparative Genomics of ORF Virus
Author(s)
A. K. M. Firoj Mahmud1,
K. M. Zillur Rahman2,
Shuvra Kanti Dey2,
Tahsina Islam2,
Ali Azam Talukder2*
Affiliation(s)
1 Molecular Biology Department, Umea University, Umea, Sweden. 2 Deptartment of Microbiology, Jahangirnagar University, Savar, Bangladesh.
1 Molecular Biology Department, Umea University, Umea, Sweden. 2 Deptartment of Microbiology, Jahangirnagar University, Savar, Bangladesh.
ABSTRACT
ORF virus (ORFV), the etiological agent of contagious pustular dermatitis in small ruminants, belongs to members of the genus Parapoxvirus of the Poxviridae. The genome of the ORFV is dsDNA of 139,962 bp which has about 89% coding region, 63% GC content and codes 130 proteins. There are four unique genes within the genome revealed by homology search of them two posses’ strong regulatory region and transmembrane helices. One of the ORF-039 contains signal peptide indicating the possibilities to be secretory protein coding gene. Comparative genomic analysis reveals significant differences in Bovine Papular Stomatitis Virus (BPSV) strain BV-AR02 and ORFV strain OV-SA00, and these may account for differences in host range. Interspecies sequence variability is observed in all functional classes of genes but is the highest in putative virulence/host range genes. Notably, ORFV contains genes which are homologous of Vaccinia virus. Phylogenetic analysis reveals that although divergent, ORFV virus is distinct from other known mammalian cowpox virus. An improved understanding of Parapoxvirus (PPV) biology will permit the engineering of novel vaccine viruses and expression vectors with enhanced efficacy and greater versatility. The novel vaccine will have a significant role in the economy of a country through the control of disease in an economically important and small ruminant caused by ORFV.
ORF virus (ORFV), the etiological agent of contagious pustular dermatitis in small ruminants, belongs to members of the genus Parapoxvirus of the Poxviridae. The genome of the ORFV is dsDNA of 139,962 bp which has about 89% coding region, 63% GC content and codes 130 proteins. There are four unique genes within the genome revealed by homology search of them two posses’ strong regulatory region and transmembrane helices. One of the ORF-039 contains signal peptide indicating the possibilities to be secretory protein coding gene. Comparative genomic analysis reveals significant differences in Bovine Papular Stomatitis Virus (BPSV) strain BV-AR02 and ORFV strain OV-SA00, and these may account for differences in host range. Interspecies sequence variability is observed in all functional classes of genes but is the highest in putative virulence/host range genes. Notably, ORFV contains genes which are homologous of Vaccinia virus. Phylogenetic analysis reveals that although divergent, ORFV virus is distinct from other known mammalian cowpox virus. An improved understanding of Parapoxvirus (PPV) biology will permit the engineering of novel vaccine viruses and expression vectors with enhanced efficacy and greater versatility. The novel vaccine will have a significant role in the economy of a country through the control of disease in an economically important and small ruminant caused by ORFV.
KEYWORDS
ORF Virus, Contagious Pustular Dermatitis, Comparative Genomics, GLIMMER, ACT, Uniue Genes, Novel Vaccine
ORF Virus, Contagious Pustular Dermatitis, Comparative Genomics, GLIMMER, ACT, Uniue Genes, Novel Vaccine
Cite this paper
Mahmud, A. , Rahman, K. , Dey, S. , Islam, T. and Talukder, A. (2014) Genome Annotation and Comparative Genomics of ORF Virus. Advances in Microbiology, 4, 1117-1131. doi: 10.4236/aim.2014.415122.
Mahmud, A. , Rahman, K. , Dey, S. , Islam, T. and Talukder, A. (2014) Genome Annotation and Comparative Genomics of ORF Virus. Advances in Microbiology, 4, 1117-1131. doi: 10.4236/aim.2014.415122.
References
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http://dx.doi.org/10.1371/journal.pone.0066958 [12] Kumar, N., Wadhwa, A., Chaubey, K.K., Singh, S.V., Gupta, S., Sharma, S., et al. (2014) Isolation and Phylogenetic Analysis of an Orf Virus from Sheep in Makhdoom, India. Virus Genes, 48, 312-319.
http://dx.doi.org/10.1007/s11262-013-1025-9 [13] Robinson, A.J. and Lyttle, D.J. (1992) Parapoxviruses. Their Biology and Potential as Recombinant Vaccines. Recombinant Poxviruses, 28, 285-327. [14] Lyttle, D.J., Fraser, K.M., Fleming, S.B., Mercer, A.A. and Robinson, A.J. (1994) Homologs of Vascular Endothelial Growth Factor Are Encoded by the Poxvirus Orf Virus. Journal of Virology, 68, 84-92. [15] Savory, L.J., Stacker, S.A., Fleming, S.B., Niven, B.E and Mercer, A.A. (2000) Viral Vascular Endothelial Growth Factor Plays a Critical Role in Orf Virus Infection. Journal of Virology, 74, 699-706.
http://dx.doi.org/10.1128/JVI.74.22.10699-10706.2000 [16] Fleming, S.B., McCaughan, C.A., Andrews, A.E., Nash, A.D. and Mercer, A.A. (1997) A Homolog of Interleukin-10 Is Encoded by the Poxvirus Orf Virus. Journal of Virology, 71, 4857-4861. [17] McInnes, C.J., Wood, A.R. and Mercer, A.A. (1998) Orf Virus Encodes a Homolog of the Vaccinia Virus Interferon- Resistance Gene E3L. Virus Genes, 17, 107-115.
http://dx.doi.org/10.1023/A:1026431704679 [18] Delhon, G., Tulman, E.R., Afonso, C.L., Lu, Z., de la Concha-Bermejillo, A., Lehmkuhl, H.D., et al. (2004) Genomes of the Parapoxviruses Orf Virus and Bovine Papular Stomatitis Virus. Journal of Virology, 78, 168-177.http://dx.doi.org/10.1128/JVI.78.1.168-177.2004 [19] Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A. and Barrell, B. (2000) Artemis, Sequence Visualization and Annotation. Bioinformatics, 16, 944-945.
http://dx.doi.org/10.1093/bioinformatics/16.10.944 [20] DeGrado, W.F., Gratkowski, H. and Lear, J.D. (2003) How Do Helix-Helix Interactions Help Determine the Folds of Membrane Proteins? Perspectives from the Study of Homo-Oligomeric Helical Bundles. Protein Science, 12, 647-665. http://dx.doi.org/10.1110/ps.0236503 [21] Delcher, A.L., Harmon, D., Kasif, S., White, O. and Salzberg, S.L. (1998) Improved Microbial Gene Identification with GLIMMER. Nucleic Acids Research, 27, 36-41. [22] Durbin, R., Eddy, S.R., Krogh, A. and Mitchison, G.J. (1998) Biological Sequence Analysis, Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge. [23] Gershenzon, N.I. and Ioshikhes, I.P. (2006) Synergy of Human Pol II Core Promoter Elements Revealed by Statistical Sequence Analysis. Bioinformatics, 21, 295-300. [24] Fatemi, M., Pao, M.M., Jeong, S., Gal-Yam, E.N., Egger, G., Weisenberger, D.J. and Jones, P.A. (2005) Footprinting of Mammalian Promoters, Use of a CpG DNA Methyltransferase Revealing Nucleosome Positions at a Single Molecule Level. Nucleic Acids Research, 33, 176-188.
http://dx.doi.org/10.1093/nar/gni180 [25] Guigó, R., Knudsen, S., Drake, N. and Smith, T. (1992) Prediction of Gene Structure. Journal of Molecular Biology, 226, 141-157. http://dx.doi.org/10.1016/0022-2836(92)90130-C [26] Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B.C. and Herrmann, R. (1996) Complete Sequence Analysis of the Genome of the Bacterium Mycoplasma Pneumoniae. Nucleic Acids Research, 24, 4420-4449.http://dx.doi.org/10.1093/nar/24.22.4420 [27] Nakai, K., Kanehisa, M. and Doolittle, R.F. (1991) Signal Peptide and Cytokine Receptor, Function and Regulation. Proteins Structure Function Genetics, 11, 95-110.
http://dx.doi.org/10.1002/prot.340110203 [28] Zhang, K., Liu, Y., Kong, H., Shang, Y. and Liu, X. (2014) Comparison and Phylogenetic Analysis Based on the B2L Gene of Orf Virus from Goats and Sheep in China during 2009-2011. Archives of Virology, 159, 1475-1479.http://dx.doi.org/10.1007/s00705-013-1946-6 [29] Amann, R., Rohde, J., Wulle, U., Conlee, D., Raue, R., Martinon, O. and Rziha, H.J. (2013) A New Rabies Vaccine Based on a Recombinant ORF Virus (Parapoxvirus) Expressing the Rabies Virus Glycoprotein. Journal of Virology, 87, 1618-1630. http://dx.doi.org/10.1128/JVI.02470-12 [30] Zhao, K., He, W., Gao, W., Lu, H.J., Han, T., Li, J., et al. (2011) Orf Virus DNA Vaccines Expressing ORFV 011 and ORFV 059 Chimeric Protein Enhances Immunogenicity. Journal of Virology, 8, 562.
http://dx.doi.org/10.1186/1743-422X-8-562 [31] Ogata1, H. and Claverie, J.M. (2007) Unique Genes in Giant Viruses: Regular Substitution Pattern and Anomalously Short Size. Genome Research, 17, 1353-1361. http://dx.doi.org/10.1101/gr.6358607 [32] Renesto, P., Abergel, C., Decloquement, P., Moinier, D., Azza, S., Ogata, H., Fourque, P., Gorvel, J.P. and Claverie, J.M. (2006) Mimivirus Giant Particles Incorporate a Large Fraction of Anonymous and Unique Gene Products. Journal of Virology, 80, 11678-11685. http://dx.doi.org/10.1128/JVI.00940-06 [33] Dung, N.T., Chi, D.H., Thao, L.T., Dung, T.K., Nhi, N.B. and Chi, P.V. (2013) Identification and Characterization of Membrane Proteins from Mouse Brain Tissue. Journal of Proteomics Bioinformatics, 6, 142-147. [34] Chakraborty, S. (2014) In Silico Analysis Identifies Genes Common between Five Primarygastrointestinal Cancer Sites with Potential Clinical Applications. Annals of Gastroenterology, 27, 231-236. [35] Dutta, A., Singh, S.K., Ghosh, P., Mukherjee, R., Mitter, S. and Bandyopadhyay, D. (2006) In Silico Identification of Potential Therapeutic Targets in the Human Pathogen. In Silico Biology, 6, 43-47. [36] Wang, T.T., Mendoza, L.T., Laperriere, D., Libby, E., MacLeod, N.B., Nagai, Y., Bourdeau, V., Konstorum, A., Lallemant, B., Zhang, R., et al. (2005) Large-Scale in Silico and Microarray-Based Identification of Direct 1,25-Dihydroxyvitamin D3 Target Genes. Molecular Endocrinology, 19, 2685-2695. http://dx.doi.org/10.1210/me.2005-0106 [37] Das, S. and Chaudhuri, K. (2003) Identification of a Unique IAHP (IcmF Associated Homologous Proteins) Cluster in Vibrio Cholerae and Other Proteobacteria through in Silico Analysis. In Silico Biology, 3, 287-300.
[1] Delcher, A.L., Harmon, D., Kasif, S., White, O. and Salzberg, S.L. (1999) Improved Microbial Gene Identification with GLIMMER. Nucleic Acids Research, 27, 4636-4641.
http://dx.doi.org/10.1093/nar/27.23.4636 [2] Besemer, J., Lomsadze, A. and Borodovsky, M. (2001) GeneMarkS: A Self-Training Method for Prediction of Gene Starts in Microbial Genomes. Implications for Finding Sequence Motifs in Regulatory Regions. Nucleic Acids Research, 29, 2607-2618.
http://dx.doi.org/10.1093/nar/29.12.2607 [3] Stothard, P. (2000) The Sequence Manipulation Suite: JavaScript Programs for Analyzing and Formatting Protein and DNA Sequences. Biotechniques, 28, 1102-1104. [4] Schiex, T., Gouzy, J., Moisan, A. and Oliveira, Y. (2003) Frame D: A Flexible Program for Quality Check and Gene Prediction in Prokaryotic Genomes and Noisy Matured Eukaryotic Sequences. Nucleic Acids Research, 31, 3738-3741.http://dx.doi.org/10.1093/nar/gkg610 [5] Neumann, R.S., Kumar, S. and Tabrizi, K.S. (2014) BLAST Output Visualization in the New Sequencing Era. Brief Bioinformatics, 15, 484-503. http://dx.doi.org/10.1093/bib/bbt009 [6] Yandell, M. and Ence, D. (2012) A Beginner’s Guide to Eukaryotic Genome Annotation. Nature Reviews Genetics, 13, 329-342. http://dx.doi.org/10.1038/nrg3174 [7] Robinson, A.J. and Balassu, T.C. (1981) Contagious Pustular Dermatitis (Orf). Veterinary Bulletin, 51, 771-782. [8] Haig, D.M. and Mercer, A.A. (1998) Ovine Diseases. Orf. Veterinary Research, 29, 311-326. [9] Fleming, S.B., Blok, J., Fraser, K.M., Mercer, A.A. and Robinson, A.J. (1993) Conservation of Gene Structure and Arrangement between Vaccinia Virus and Orf Virus. Virology, 195, 175-184.
http://dx.doi.org/10.1006/viro.1993.1358 [10] Rziha, H.J., Henkel, M., Cottone, R., Meyer, M., Dehio, C. and Büttner, M. (1999) Parapoxviruses, Potential Alternative Vectors for Directing the Immune Response in Permissive and Non-Permissive Hosts. Journal of Biotechnology, 73, 235-242. http://dx.doi.org/10.1016/S0168-1656(99)00141-8 [11] Chi, X., Zeng, X., Hao, W., Li, M., Li, W., Huang, X.H., et al. (2013) Heterogeneity among Orf Virus Isolates from Goats in Fujian Province, Southern China. PLoS ONE, 8, 1-12.
http://dx.doi.org/10.1371/journal.pone.0066958 [12] Kumar, N., Wadhwa, A., Chaubey, K.K., Singh, S.V., Gupta, S., Sharma, S., et al. (2014) Isolation and Phylogenetic Analysis of an Orf Virus from Sheep in Makhdoom, India. Virus Genes, 48, 312-319.
http://dx.doi.org/10.1007/s11262-013-1025-9 [13] Robinson, A.J. and Lyttle, D.J. (1992) Parapoxviruses. Their Biology and Potential as Recombinant Vaccines. Recombinant Poxviruses, 28, 285-327. [14] Lyttle, D.J., Fraser, K.M., Fleming, S.B., Mercer, A.A. and Robinson, A.J. (1994) Homologs of Vascular Endothelial Growth Factor Are Encoded by the Poxvirus Orf Virus. Journal of Virology, 68, 84-92. [15] Savory, L.J., Stacker, S.A., Fleming, S.B., Niven, B.E and Mercer, A.A. (2000) Viral Vascular Endothelial Growth Factor Plays a Critical Role in Orf Virus Infection. Journal of Virology, 74, 699-706.
http://dx.doi.org/10.1128/JVI.74.22.10699-10706.2000 [16] Fleming, S.B., McCaughan, C.A., Andrews, A.E., Nash, A.D. and Mercer, A.A. (1997) A Homolog of Interleukin-10 Is Encoded by the Poxvirus Orf Virus. Journal of Virology, 71, 4857-4861. [17] McInnes, C.J., Wood, A.R. and Mercer, A.A. (1998) Orf Virus Encodes a Homolog of the Vaccinia Virus Interferon- Resistance Gene E3L. Virus Genes, 17, 107-115.
http://dx.doi.org/10.1023/A:1026431704679 [18] Delhon, G., Tulman, E.R., Afonso, C.L., Lu, Z., de la Concha-Bermejillo, A., Lehmkuhl, H.D., et al. (2004) Genomes of the Parapoxviruses Orf Virus and Bovine Papular Stomatitis Virus. Journal of Virology, 78, 168-177.http://dx.doi.org/10.1128/JVI.78.1.168-177.2004 [19] Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A. and Barrell, B. (2000) Artemis, Sequence Visualization and Annotation. Bioinformatics, 16, 944-945.
http://dx.doi.org/10.1093/bioinformatics/16.10.944 [20] DeGrado, W.F., Gratkowski, H. and Lear, J.D. (2003) How Do Helix-Helix Interactions Help Determine the Folds of Membrane Proteins? Perspectives from the Study of Homo-Oligomeric Helical Bundles. Protein Science, 12, 647-665. http://dx.doi.org/10.1110/ps.0236503 [21] Delcher, A.L., Harmon, D., Kasif, S., White, O. and Salzberg, S.L. (1998) Improved Microbial Gene Identification with GLIMMER. Nucleic Acids Research, 27, 36-41. [22] Durbin, R., Eddy, S.R., Krogh, A. and Mitchison, G.J. (1998) Biological Sequence Analysis, Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge. [23] Gershenzon, N.I. and Ioshikhes, I.P. (2006) Synergy of Human Pol II Core Promoter Elements Revealed by Statistical Sequence Analysis. Bioinformatics, 21, 295-300. [24] Fatemi, M., Pao, M.M., Jeong, S., Gal-Yam, E.N., Egger, G., Weisenberger, D.J. and Jones, P.A. (2005) Footprinting of Mammalian Promoters, Use of a CpG DNA Methyltransferase Revealing Nucleosome Positions at a Single Molecule Level. Nucleic Acids Research, 33, 176-188.
http://dx.doi.org/10.1093/nar/gni180 [25] Guigó, R., Knudsen, S., Drake, N. and Smith, T. (1992) Prediction of Gene Structure. Journal of Molecular Biology, 226, 141-157. http://dx.doi.org/10.1016/0022-2836(92)90130-C [26] Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B.C. and Herrmann, R. (1996) Complete Sequence Analysis of the Genome of the Bacterium Mycoplasma Pneumoniae. Nucleic Acids Research, 24, 4420-4449.http://dx.doi.org/10.1093/nar/24.22.4420 [27] Nakai, K., Kanehisa, M. and Doolittle, R.F. (1991) Signal Peptide and Cytokine Receptor, Function and Regulation. Proteins Structure Function Genetics, 11, 95-110.
http://dx.doi.org/10.1002/prot.340110203 [28] Zhang, K., Liu, Y., Kong, H., Shang, Y. and Liu, X. (2014) Comparison and Phylogenetic Analysis Based on the B2L Gene of Orf Virus from Goats and Sheep in China during 2009-2011. Archives of Virology, 159, 1475-1479.http://dx.doi.org/10.1007/s00705-013-1946-6 [29] Amann, R., Rohde, J., Wulle, U., Conlee, D., Raue, R., Martinon, O. and Rziha, H.J. (2013) A New Rabies Vaccine Based on a Recombinant ORF Virus (Parapoxvirus) Expressing the Rabies Virus Glycoprotein. Journal of Virology, 87, 1618-1630. http://dx.doi.org/10.1128/JVI.02470-12 [30] Zhao, K., He, W., Gao, W., Lu, H.J., Han, T., Li, J., et al. (2011) Orf Virus DNA Vaccines Expressing ORFV 011 and ORFV 059 Chimeric Protein Enhances Immunogenicity. Journal of Virology, 8, 562.
http://dx.doi.org/10.1186/1743-422X-8-562 [31] Ogata1, H. and Claverie, J.M. (2007) Unique Genes in Giant Viruses: Regular Substitution Pattern and Anomalously Short Size. Genome Research, 17, 1353-1361. http://dx.doi.org/10.1101/gr.6358607 [32] Renesto, P., Abergel, C., Decloquement, P., Moinier, D., Azza, S., Ogata, H., Fourque, P., Gorvel, J.P. and Claverie, J.M. (2006) Mimivirus Giant Particles Incorporate a Large Fraction of Anonymous and Unique Gene Products. Journal of Virology, 80, 11678-11685. http://dx.doi.org/10.1128/JVI.00940-06 [33] Dung, N.T., Chi, D.H., Thao, L.T., Dung, T.K., Nhi, N.B. and Chi, P.V. (2013) Identification and Characterization of Membrane Proteins from Mouse Brain Tissue. Journal of Proteomics Bioinformatics, 6, 142-147. [34] Chakraborty, S. (2014) In Silico Analysis Identifies Genes Common between Five Primarygastrointestinal Cancer Sites with Potential Clinical Applications. Annals of Gastroenterology, 27, 231-236. [35] Dutta, A., Singh, S.K., Ghosh, P., Mukherjee, R., Mitter, S. and Bandyopadhyay, D. (2006) In Silico Identification of Potential Therapeutic Targets in the Human Pathogen. In Silico Biology, 6, 43-47. [36] Wang, T.T., Mendoza, L.T., Laperriere, D., Libby, E., MacLeod, N.B., Nagai, Y., Bourdeau, V., Konstorum, A., Lallemant, B., Zhang, R., et al. (2005) Large-Scale in Silico and Microarray-Based Identification of Direct 1,25-Dihydroxyvitamin D3 Target Genes. Molecular Endocrinology, 19, 2685-2695. http://dx.doi.org/10.1210/me.2005-0106 [37] Das, S. and Chaudhuri, K. (2003) Identification of a Unique IAHP (IcmF Associated Homologous Proteins) Cluster in Vibrio Cholerae and Other Proteobacteria through in Silico Analysis. In Silico Biology, 3, 287-300.