Identification and classification of feline endogenous retroviruses in the cat genome using degenerate PCR and in silico data analysis

Journal of General Virology

Volumn 94, Issue PART7, 2013, Pages 1587-1596

  Song, Ning ^a   Jo, Haiin ^a   Choi, Minkyeung ^a   Kim, Jin Hoi ^a   Seo, Han Geuk ^a   Cha, Se Yeoun ^b   Seo, Kunho ^a   Park, Chankyu ^a  

^a Konkuk University   (South Korea)

^b Chonbuk National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CONTIG; GENOMIC DNA;

ANIMAL EXPERIMENT; ARTICLE; CAT; COMPUTER MODEL; CONTROLLED STUDY; DATA ANALYSIS; FEMALE; GENE LOCATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; RETROVIRUS; SEQUENCE HOMOLOGY; VIRUS CLASSIFICATION; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS MORPHOLOGY; VIRUS REPLICATION;

ANIMALS; CATS; COMPUTER SIMULATION; DNA PRIMERS; ENDOGENOUS RETROVIRUSES; GENE PRODUCTS, POL; GENOME; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

FELIDAE; FELIS CATUS; MURINAE;

EID: 84879157292     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.051862-0     Document Type: Article

References (64)

1. Anai, Y., Ochi, H., Watanabe, S., Nakagawa, S., Kawamura, M., Gojobori, T. & Nishigaki, K. (2012). Infectious endogenous retroviruses in cats and emergence of recombinant viruses. J Virol 86, 8634-8644.
2. Baillie, G. J. & Wilkins, R. J. (2001). Endogenous type D retrovirus in a marsupial, the common brushtail possum (Trichosurus vulpecula). J Virol 75, 2499-2507.
3. Bénit, L., Lallemand, J. B., Casella, J. F., Philippe, H. & Heidmann, T. (1999). ERV-L elements: a family of endogenous retrovirus-like elements active throughout the evolution of mammals. J Virol 73, 3301-3308.
4. Bénit, L., Dessen, P. & Heidmann, T. (2001). Identification, phylogeny, and evolution of retroviral elements based on their envelope genes. J Virol 75, 11709-11719.
5. Beyer, W., Möhring, R., Drescher, B., Nötzel, U. & Rosenthal, S. (1987). Molecular cloning of an endogenous cat retroviral element (ECE 1)-a recombinant between RD-114 and FeLV-related sequences. Brief report. Arch Virol 96, 297-301.
6. Blikstad, V., Benachenhou, F., Sperber, G. O. & Blomberg, J. (2008). Evolution of human endogenous retroviral sequences: a conceptual account. Cell Mol Life Sci 65, 3348-3365.
7. Blomberg, J., Benachenhou, F., Blikstad, V., Sperber, G. & Mayer, J. (2009). Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations. Gene 448, 115-123.
8. Bolisetty, M., Blomberg, J., Benachenhou, F., Sperber, G. & Beemon, K. (2012). Unexpected diversity and expression of avian endogenous retroviruses. mBio 3, e00344-12.
9. Bonner, T. I. & Todaro, G. J. (1979). Carnivores have sequences in their cellular DNA distantly related to the primate endogenous virus, MAC-1. Virology 94, 224-227.
10. Boonyaratanakornkit, J., Chew, A., Ryu, D. D., Greenhalgh, D. G. & Cho, K. (2004). Murine endogenous retroviruses and their transcriptional potentials. Mamm Genome 15, 914-923.
11. Chakrabarti, R., Hofman, F. M., Pandey, R., Mathes, L. E. & Roy- Burman, P. (1994). Recombination between feline exogenous and endogenous retroviral sequences generates tropism for cerebral endothelial cells. Am J Pathol 144, 348-358.
12. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G. & Thompson, J. D. (2003). Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31, 3497-3500.
13. Craven, R. C., Leure-duPree, A. E., Weldon, R. A., Jr & Wills, J. W. (1995). Genetic analysis of the major homology region of the Rous sarcoma virus Gag protein. J Virol 69, 4213-4227.
14. Cui, J. & Holmes, E. C. (2012). Endogenous lentiviruses in the ferret genome. J Virol 86, 3383-3385.
15. Dangel, A. W., Baker, B. J., Mendoza, A. R. & Yu, C. Y. (1995). Complement component C4 gene intron 9 as a phylogenetic marker for primates: long terminal repeats of the endogenous retrovirus ERV-K(C4) are a molecular clock of evolution. Immunogenetics 42, 41-52.
16. Driscoll, C. A., Menotti-Raymond, M., Roca, A. L., Hupe, K., Johnson, W. E., Geffen, E., Harley, E. H., Delibes, M., Pontier, D. & other authors (2007). The Near Eastern origin of cat domestication. Science 317, 519-523.
17. Dunwiddie, C. T., Resnick, R., Boyce-Jacino, M., Alegre, J. N. & Faras, A. J. (1986). Molecular cloning and characterization of gag-, pol-, and env-related gene sequences in the ev- chicken. J Virol 59, 669-675.
18. Garcia-Etxebarria, K. & Jugo, B. M. (2010). Genome-wide detection and characterization of endogenous retroviruses in Bos taurus. J Virol 84, 10852-10862.
19. Gifford, R. & Tristem, M. (2003). The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26, 291-315.
20. Greenwood, A. D., Englbrecht, C. C. & MacPhee, R. D. (2004). Characterization of an endogenous retrovirus class in elephants and their relatives. BMC Evol Biol 4, 38.
21. Haapala, D. K., Robey, W. G., Oroszlan, S. D. & Tsai, W. P. (1985). Isolation from cats of an endogenous type C virus with a novel envelope glycoprotein. J Virol 53, 827-833.
22. Hall, T. A. (1999). BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
23. Han, G.-Z. & Worobey, M. (2012a). An endogenous foamy virus in the aye-aye (Daubentonia madagascariensis). J Virol 86, 7696-7698.
24. Han, G.-Z. & Worobey, M. (2012b). An endogenous foamy-like viral element in the coelacanth genome. PLoS Pathog 8, e1002790.
25. Han, G.-Z. & Worobey, M. (2012c). Endogenous lentiviral elements in the weasel family (Mustelidae). Mol Biol Evol 29, 2905-2908.
26. Harada, F., Tsukada, N. & Kato, N. (1987). Isolation of three kinds of human endogenous retrovirus-like sequences using tRNAPro as a probe. Nucleic Acids Res 15, 9153-9162.
27. Herniou, E., Martin, J., Miller, K., Cook, J., Wilkinson, M. & Tristem, M. (1998). Retroviral diversity and distribution in vertebrates. J Virol 72, 5955-5966.
28. Hughes, J. F. & Coffin, J. M. (2001). Evidence for genomic rearrangements mediated by human endogenous retroviruses during primate evolution. Nat Genet 29, 487-489.
29. Jo, H., Choi, H., Choi, M. K., Song, N., Kim, J. H., Oh, J. W., Seo, K., Seo, H. G., Chun, T. & other authors (2012). Identification and classification of endogenous retroviruses in the canine genome using degenerative PCR and in-silico data analysis. Virology 422, 195-204.
30. Johnson, W. E. & Coffin, J. M. (1999). Constructing primate phylogenies from ancient retrovirus sequences. Proc Natl Acad Sci U S A 96, 10254-10260.
31. Katzourakis, A., Tristem, M., Pybus, O. G. & Gifford, R. J. (2007). Discovery and analysis of the first endogenous lentivirus. Proc Natl Acad Sci U S A 104, 6261-6265.
32. Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111-120.
33. Klymiuk, N., Müller, M., Brem, G. & Aigner, B. (2002). Characterization of porcine endogenous retrovirus c pro-pol nucleotide sequences. J Virol 76, 11738-11743.
34. Klymiuk, N., Müller, M., Brem, G. & Aigner, B. (2003). Characterization of endogenous retroviruses in sheep. J Virol 77, 11268-11273.
35. Kröger, B. & Horak, I. (1987). Isolation of novel human retrovirusrelated sequences by hybridization to synthetic oligonucleotides complementary to the tRNA(Pro) primer-binding site. J Virol 61, 2071-2075.
36. Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V., Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G. & Sverdlov, E. D. (2000). Differences in HERV-K LTR insertions in orthologous loci of humans and great apes. Gene 247, 265-277.
37. Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., Clamp, M., Chang, J. L., Kulbokas, E. J., III & other authors (2005). Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803-819.
38. Löwer, R., Löwer, J. & Kurth, R. (1996). The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences. Proc Natl Acad Sci U S A 93, 5177-5184.
39. Lueders, K. K. & Kuff, E. L. (1980). Intracisternal A-particle genes: identification in the genome of Mus musculus and comparison of multiple isolates from a mouse gene library. Proc Natl Acad Sci U S A 77, 3571-3575.
40. McAllister, R. M., Nicolson, M., Gardner, M. B., Rongey, R. W., Rasheed, S., Sarma, P. S., Huebner, R. J., Hatanaka, M., Oroszlan, S. & other authors (1972). C-type virus released from cultured human rhabdomyosarcoma cells. Nat New Biol 235, 3-6.
41. McDonald, J. F. (1993). Evolution and consequences of transposable elements. Curr Opin Genet Dev 3, 855-864.
42. Mi, S., Lee, X. H., Li, X. P., Veldman, G. M., Finnerty, H., Racie, L., LaVallie, E., Tang, X. Y., Edouard, P. & other authors (2000). Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 403, 785-789.
43. Miller, S. A., Dykes, D. D. & Polesky, H. F. (1988). A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16, 1215.
44. Mullikin, J. C., Hansen, N. F., Shen, L., Ebling, H., Donahue, W. F., Tao, W., Saranga, D. J., Brand, A., Rubenfield, M. J. & other authors (2010). Light whole genome sequence for SNP discovery across domestic cat breeds. BMC Genomics 11, 406.
45. O'Brien, S. J., Johnson, W., Driscoll, C., Pontius, J., Pecon-Slattery, J. & Menotti-Raymond, M. (2008). State of cat genomics. Trends Genet 24, 268-279.
46. Ono, M., Toh, H., Miyata, T. & Awaya, T. (1985). Nucleotide sequence of the Syrian hamster intracisternal A-particle gene: close evolutionary relationship of type A particle gene to types B and D oncovirus genes. J Virol 55, 387-394.
47. Patience, C., Switzer, W. M., Takeuchi, Y., Griffiths, D. J., Goward, M. E., Heneine, W., Stoye, J. P. & Weiss, R. A. (2001). Multiple groups of novel retroviral genomes in pigs and related species. J Virol 75, 2771-2775.
48. Pontius, J. U., Mullikin, J. C., Smith, D. R., Lindblad-Toh, K., Gnerre, S., Clamp, M., Chang, J., Stephens, R., Neelam, B. & other authors (2007). Initial sequence and comparative analysis of the cat genome. Genome Res 17, 1675-1689.
49. Ruebner, M., Langbein, M., Strissel, P. L., Henke, C., Schmidt, D., Goecke, T. W., Faschingbauer, F., Schild, R. L., Beckmann, M. W. & Strick, R. (2012). Regulation of the human endogenous retroviral Syncytin-1 and cell-cell fusion by the nuclear hormone receptors PPARc/RXRa in placentogenesis. J Cell Biochem 113, 2383-2396.
50. Sheets, R. L., Pandey, R., Jen, W. C. & Roy-Burman, P. (1993). Recombinant feline leukemia virus genes detected in naturally occurring feline lymphosarcomas. J Virol 67, 3118-3125.
51. Soe, L. H., Devi, B. G., Mullins, J. I. & Roy-Burman, P. (1983). Molecular cloning and characterization of endogenous feline leukemia virus sequences from a cat genomic library. J Virol 46, 829-840.
52. Stewart, M. A., Warnock, M., Wheeler, A., Wilkie, N., Mullins, J. I., Onions, D. E. & Neil, J. C. (1986). Nucleotide sequences of a feline leukemia virus subgroup A envelope gene and long terminal repeat and evidence for the recombinational origin of subgroup B viruses. J Virol 58, 825-834.
53. Stewart, H., Jarrett, O., Hosie, M. J. & Willett, B. J. (2011). Are endogenous feline leukemia viruses really endogenous? Vet Immunol Immunopathol 143, 325-331.
54. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24, 1596-1599.
55. Tönjes, R. R. & Niebert, M. (2003). Relative age of proviral porcine endogenous retrovirus sequences in Sus scrofa based on the molecular clock hypothesis. J Virol 77, 12363-12368.
56. Tristem, M., Kabat, P., Lieberman, L., Linde, S., Karpas, A. & Hill, F. (1996). Characterization of a novel murine leukemia virus-related subgroup within mammals. J Virol 70, 8241-8246.
57. van der Kuyl, A. C., Dekker, J. T. & Goudsmit, J. (1999). Discovery of a new endogenous type C retrovirus (FcEV) in cats: evidence for RD- 114 being an FcEV(Gag-Pol)/baboon endogenous virus BaEV(Env) recombinant. J Virol 73, 7994-8002.
58. Weiss, R. A. (2006). The discovery of endogenous retroviruses. Retrovirology 3, 67.
59. Weiss, R. A., Friis, R. R., Katz, E. & Vogt, P. K. (1971). Induction of avian tumor viruses in normal cells by physical and chemical carcinogens. Virology 46, 920-938.
60. Xiao, R., Park, K., Oh, Y., Kim, J.-H. & Park, C. (2008a). Structural characterization of the genome of BERV c4, the most abundant endogenous retrovirus family in cattle. Mol Cells 26, 404-408.
61. Xiao, R., Park, K., Lee, H., Kim, J. & Park, C. (2008b). Identification and classification of endogenous retroviruses in cattle. J Virol 82, 582-587.
62. Xiong, Y. & Eickbush, T. H. (1990). Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9, 3353-3362.
63. Yi, J.-M., Kim, T.-H., Huh, J.-W., Park, K. S., Jang, S. B., Kim, H.-M. & Kim, H.-S. (2004). Human endogenous retroviral elements belonging to the HERV-S family from human tissues, cancer cells, and primates: expression, structure, phylogeny and evolution. Gene 342, 283-292.
64. Yuhki, N., Mullikin, J. C., Beck, T., Stephens, R. & O'Brien, S. J. (2008). Sequences, annotation and single nucleotide polymorphism of the major histocompatibility complex in the domestic cat. PLoS ONE 3, e2674.