Molecules and Cells

Korean Society for Molecular and Cellular Biology (한국분자세포생물학회)
권호 표지

Characterization of the Bovine Endogenous Retrovirus β3 Genome

  • Xiao, Rui (Laboratory of Mammalian Genomics, Department of Animal Biotechnology, Konkuk University) ;
  • Kim, Juhyun (Laboratory of Mammalian Genomics, Department of Animal Biotechnology, Konkuk University) ;
  • Choi, Hojun (Laboratory of Mammalian Genomics, Department of Animal Biotechnology, Konkuk University) ;
  • Park, Kwangha (Laboratory of Mammalian Genomics, Department of Animal Biotechnology, Konkuk University) ;
  • Lee, Hoontaek (Laboratory of Mammalian Genomics, Department of Animal Biotechnology, Konkuk University) ;
  • Park, Chankyu (Laboratory of Mammalian Genomics, Department of Animal Biotechnology, Konkuk University)
  • Received : 2007.05.30
  • Accepted : 2007.07.31
  • Published : 2008.02.29
⟨ Previous Next ⟩

Abstract

We recently used degenerate PCR and locus-specific PCR methods to identify the endogenous retroviruses (ERV) in the bovine genome. Using the ovine ERV classification system, the bovine ERVs (BERVs) could be classified into four families. Here, we searched the most recently released bovine genome database with the partial nucleotide sequence of the pro/pol region of the BERV ${\beta}3$ family. This allowed us to obtain and analyze the complete genome of BERV ${\beta}3$. The BERV ${\beta}3$ genome is 7666 nucleotides long and has the typical retroviral organization, namely, 5'-long terminal repeat (LTR)-gag-pro-pol-env-LTR-3'. The deduced open reading frames for gag, pro, pol and env of BERV ${\beta}3$ en- code 507, 271, 879 and 603 amino acids, respectively. BERV ${\beta}3$ showed little amino acid similarity to other betaretroviruses. Phylogenetic analysis showed that it clusters with HERV-K. This is the first report describing the genetic structure and sequence of an entire BERV.

Keywords

Acknowledgement

Supported by : Rural Development Administration

References

  1. Andrake, M.D. and Skalka, A.M. (1996). Retroviral integrase, putting the pieces together. J. Biol. Chem. 271, 19633-19636 https://doi.org/10.1074/jbc.271.33.19633
  2. Baillie, G.J. and Wilkins, R.J. (2001). Endogenous type D retrovirus in a marsupial, the common brushtail possum (Trichosurus vulpecula). J. Virol. 75, 2499-2507 https://doi.org/10.1128/JVI.75.5.2499-2507.2001
  3. Baillie, G.J., van de Lagemaat, L.N., Baust, C., and Mager, D.L. (2004). Multiple groups of endogenous beta retroviruses in mice, rats, and other mammals. J. Virol. 78, 5784-5798 https://doi.org/10.1128/JVI.78.11.5784-5798.2004
  4. Chen, R. (1982). Complete amino acid sequence and glycosylation sites of glycoprotein gp71A of Friend murine leukemia virus. Proc. Natl. Acad. Sci. USA 79, 5788-5792
  5. Choi, Y., Kappler, J.W., and Marrack, P. (1991). A superantigen encoded in the open reading frame of the 3′ long terminal repeat of mouse mammary tumour virus. Nature 350, 203-207 https://doi.org/10.1038/350203a0
  6. Coffin, J.M. (1990). Retroviridae and their replication. In Virology, Fields, B.N., Knipe, D.M. et al., eds. (New York, USA: Raven Press), pp. 1437-1500
  7. Coffin, J.M., Hughes, S.H., and Varmus, H.E. (1997). Retroviruses (New York, Cold Spring Harbor Laboratory Press)
  8. Cousens, C., Minguijon, E., Dalziel, R.G., Ortin, A., Garcia, M., Park, J., Gonzalez, L., Sharp, J.M., and de las Heras, M. (1999). Complete sequence of enzootic nasal tumor virus, a retrovirus associated with transmissible intranasal tumors of sheep. J. Virol. 73, 3986-3993
  9. Craven, R.C., Leure-duPree, A.E., Weldon, R.A. Jr., and Wills, J.W. (1995). Genetic analysis of the major homology region of the Rous sarcoma virus Gag protein. J. Virol. 69, 4213-4227
  10. Elder, J.H., Lerner, D. L., Hasselkus-Light, C. S., Fontenot, D. J., Hunter, E., Luciw, P.A., Montelaro, R.C., and Phillips, T.R. (1992). Distinct subsets of retroviruses encode dUTPase. J. Virol. 66, 1791-1794
  11. Herniou, E., Martin, J., Miller, K., Cook, J., Wilkinson, M., and Tristem, M. (1998). Retroviral diversity and distribution in vertebrates. J. Virol. 72, 5955-5966
  12. Huh, J.W., Kim, D.S., Ha, H.S., Kim, T.H., Kim, W., and Kim, H.S. (2006). Formation of a new solo-LTR of the human endogenous retrovirus H family in human chromosome 21. Mol. Cells 22, 360-363
  13. Kang, S.M., Zhang, Z., and Morrow, C.D. (1999). Identification of a human immunodeficiency virus type 1 that stably uses tRNALys1,2 rather than tRNALys,3 for initiation of reverse transcription. Virology 257, 95-105 https://doi.org/10.1006/viro.1999.9615
  14. Klymiuk, N., Müller, M., Brem, G., and Aigner, B. (2003). Characterization of endogenous retroviruses in sheep. J. Virol. 77, 11268-11273 https://doi.org/10.1128/JVI.77.20.11268-11273.2003
  15. Kumar, S., Tamura, K., and Nei, M. (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5, 150-163 https://doi.org/10.1093/bib/5.2.150
  16. Mager, D.L. and Freeman, J.D. (2000). Novel mouse type D endogenous proviruses and ETn elements share long terminal repeat and internal sequences. J. Virol. 74, 7221-7229 https://doi.org/10.1128/JVI.74.16.7221-7229.2000
  17. McGeoch, D.J. (1990). Protein sequence comparisons show that the 'pseudoproteases'encoded by poxviruses and certain retroviruses belong to the deoxyuridine triphosphatase family. Nucleic Acids Res. 18, 4105-4110 https://doi.org/10.1093/nar/18.14.4105
  18. Ono, M., Yasunaga, T., Miyata, T., and Ushikubo, H. (1986). Nucleotide sequence of human endogenous retrovirus genome related to the mouse mammary tumor virus genome. J. Virol. 60, 589-598
  19. Palmarini, M., Hallwirth, C., York, D., Murgia, C., de Oliveira, T., Spencer, T., and Fan, H. (2000). Molecular cloning and functional analysis of three type D endogenous retroviruses of sheep reveal a different cell tropism from that of the highly related exogenous jaagsiekte sheep retrovirus. J. Virol. 74, 8065-8076 https://doi.org/10.1128/JVI.74.17.8065-8076.2000
  20. Patience, C., Wilkinson, D.A., and Weiss, R.A. (1997). Our retroviral heritage. Trends Genet. 13, 116-120 https://doi.org/10.1016/S0168-9525(97)01057-3
  21. Power, M.D., Marx, P.A., Bryant, M.L., Gardner, M.B., Barr, P.J., and Luciw, P.A. (1986). Nucleotide sequence of SRV-1, a type D simian acquired immune deficiency syndrome virus. Science 231, 1567-1572 https://doi.org/10.1126/science.3006247
  22. Reus, K., Mayer, J., Sauter, M., Scherer, D., Muller-Lantzsch, N., and Meese, E. (2001). Genomic organization of the human endogenous retrovirus HERV-K (HML-2.HOM) (ERVK6) on chromosome 7. Genomics 72, 314-320 https://doi.org/10.1006/geno.2000.6488
  23. Robert, G. and Michael, T. (2003). The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26, 291-315 https://doi.org/10.1023/A:1024455415443
  24. Seiki, M., Hattori, S., Hirayama, Y., and Yoshida, M. (1983). Human adult T-cell leukemia virus: complete nucleotide sequence of the provirus genome integrated in leukemia cell DNA. Proc. Natl. Acad. Sci. USA 80, 3618-3622
  25. Temin, H.M. (1981). Structure, variation and synthesis of retrovirus long terminal repeat. Cell 27, 1-3 https://doi.org/10.1016/0092-8674(81)90353-6
  26. van der Kuyl, A.C., Mang, R., Dekker, J.T., and Goudsmit, J. (1997). Complete nucleotide sequence of simian endogenous type D retrovirus with intact genome organization: evidence for ancestry to simian retrovirus and baboon endogenous virus. J. Virol. 71, 3666-3676
  27. Van Regenmortel, M.H., Fauquet, C.M., Bishop, D.H.L., Carsten, E.B., and Estes, M.K. (2000). Virus Taxonomy: The Classification and Nomenclature of Viruses (California; Academic Press)
  28. Xiao, R., Park, K., Lee, H., Kim, J., and Park, C. (2008). Identification and classification of endogenous retroviruses in cattle. J. Virol. 82, 582-587 https://doi.org/10.1128/JVI.01451-07
  29. York, D.F., Vigne, R., Verwoerd, D.W., and Querat, G. (1992). Nucleotide sequence of the Jaagsiekte retrovirus, an exogenous and endogenous type D and B retrovirus of sheep and goats. J. Virol. 66, 4930-4939