The Gypsy Database (GyDB) of mobile genetic elements

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Lloréns, Carlos ^a,b   Futami, R ^a   Bezemer, D ^c   Moya, A ^b,d  

^a Biotech Vana   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c STICHTING HIV MONITORING   (Netherlands)

^d CIBER EPIDEMIOLOGÍA Y SALUD PÚBLICA CIBERESP   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

GAG PROTEIN; POL PROTEIN; RNA DIRECTED DNA POLYMERASE;

ARTICLE; DATA BASE; EUKARYOTE; GENUS; GYPSY DATABASE; INTERNET; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; MONOPHYLY; NOMENCLATURE; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; RETROPOSON; RETROVIRUS; VERTEBRATE; VIRUS CLASSIFICATION;

DATABASES, GENETIC; GENES, VIRAL; INTERNET; PHYLOGENY; RETROELEMENTS; RETROVIRIDAE; RETROVIRIDAE PROTEINS; SEQUENCE ALIGNMENT; TERMINAL REPEAT SEQUENCES; USER-COMPUTER INTERFACE;

EUKARYOTA; RETROVIRIDAE; VERTEBRATA;

EID: 38549109509     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm697     Document Type: Article

References (64)

1. McClintock, B. (1948) Mutable loci in maize. Carnegie Inst. Wash. Year book, 47, 155-169.
2. Kazazian, H.H. Jr (2004) Mobile elements: Drivers of genome evolution. Science, 303, 1626-1632.
3. Temin, H.M. (1989) Reverse transcriptases. Retrons in bacteria. Nature, 339, 254-255.
4. Craig, N.L., Craigie, R., Gellert, M. and Lambowitz, A.M. (2002) Mobile DNA II. ASM Press, Washington, DC.
5. Mizuuchi, K. (1992) Transpositional recombination: Mechanistic insights from studies of mu and other elements. Annu. Rev. Biochem., 61 1011-1051.
6. Wessler, S.R., Bureau, T.E. and White, S.E. (1995) LTR-retrotransposons and MITEs: Important players in the evolution of plant genomes. Curr. Opin. Genet. Dev., 5, 814-821.
7. Bureau, T.E., Ronald, P.C. and Wessler, S.R. (1996) A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc. Natl Acad. Sci. USA, 93 8524-8529.
8. Lynch, M. and Conery, J.S. (2003) The origins of genome complexity. Science, 302, 1401-1404.
9. Poiesz, B.J., Ruscetti, F.W., Gazdar, A.F., Bunn, P.A., Minna, J.D. and Gallo, R.C. (1980) Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma. Proc. Natl Acad. Sci. USA, 77, 7415-7419.
10. Yoshida, M., Miyoshi, I. and Hinuma, Y. (1982) Isolation and characterization of retrovirus from cell lines of human adult T-cell leukemia and its implication in the disease. Proc. Natl Acad. Sci. USA, 79, 2031-2035.
11. Barre-Sinoussi, F., Chermann, J.C, Rey, F., Nugeyre, M.T., Chamaret, S., Gruest, J., Dauguet, C., xler-Blin, C., Vezinet-Brun, F. et al. (1983) Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science, 220 868-871.
12. Gallo, R.C., Salahuddin, S.Z., Popovic, M., Shearer, G.M., Kaplan, M., Haynes, B.F., Palker, T.J., Redfield, R., Oleske, J. et al. (1984) Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS. Science, 224, 500-503.
13. Levy, J.A. and Shimabukuro, J. (1985) Recovery of AIDS-associated retroviruses from patients with AIDS or AIDS-related conditions and from clinically healthy individuals. J. Infect. Dis., 152, 734-738.
14. Edwards, C.M., Edwards, S.J., Bhumbra, R.P. and Chowdhury, T.A. (2003) Severe refractory hypercalcaemia in HTLV-1 infection. J. R. Soc. Med. 96, 126-127.
15. UNAIDS. (2007) 06 Annual Report. Making the Money Work. UNAIDS, WHO, Geneva.
16. Saigo, K., Kugimiya, W., Matsuo, Y., Inouye, S., Yoshioka, K. and Yuki, S. (1984) Identification of the coding sequence for a reverse transcriptase-like enzyme in a transposable genetic element in Drosophila melanogaster. Nature, 312, 659-661.
17. Mount, S.M. and Rubin, G.M. (1985) Complete nucleotide sequence of the Drosophila transposable element copia: Homology between copia and retroviral proteins. Mol. Cell. Biol., 5, 1630-1638.
18. Clare, J. and Farabaugh, P. (1985) Nucleotide sequence of a yeast Ty element: Evidence for an unusual mechanism of gene expression. Proc. Natl. Acad. Sci. USA, 82, 2829-2833.
19. Eiekbush, T.H. (1994) Origin and evolutionary relationships of LTR retroelements. In Morse, S.S. (ed), The Evolutionary Biology of Viruses. Raven, New York, pp. 121-157.
20. Kim, A., Terzian, C., Santamaria, P., Pelisson, A., Purd'homme, N. and Bucheton, A. (1994) Retroviruses in invertebrates: The gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc. Natl Acad. Sci. USA, 91, 1285-1289.
21. Song, S.U., Gerasimova, T., Kurkulos, M., Boeke, J.D. and Corces, V.G. (1994) An env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus. Genes Dev., 8 2046-2057.
22. Pantazidis, A., Labrador, M. and Fontdevila, A. (1999) The retrotransposon Osvaldo from Drosophila buzzatii displays all structural features of a functional retrovirus. Mol. Biol. Evol., 16, 909-921.
23. Bowen, N.J. and McDonald, J.F. (1999) Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res., 9, 924-935.
24. Wright, D.A. and Voytas, D.F. (2002) Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res., 12, 122-131.
25. Volff, J.N., Lehrach, H., Reinhardt, R. and Chourrout, D. (2004) Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica. Mol. Biol. Evol., 21, 2022-2033.
26. Wright, D.A. and Voytas, D.F. (1998) Potential retroviruses in planta: Tat1 is related to a group of Arabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins. Genetics, 149, 703-715.
27. Coffin, J.M., Huges, S.H. and Varmus, H.E. (1997) Retroviruses. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
28. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. and Higgins, D.G. (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
29. Eickbush, T.H. and Malik, H.S. (2002) Origin and evolution of retrotransposons. In Craig, N.L., Craigie, R., Gellert, M. and Lambowitz, A.M. (eds), Mobile DNA II. ASM Press, Washington, DC, pp. 1111-1144.
30. Pearl, L. and Blundell, T. (1984) The active site of aspartic proteinases. FEBS Lett., 174, 96-101.
31. Malik, H.S. and Eickbush, T.H. (1999) Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J. Virol., 73, 5186-5190.
32. Xiong, Y. and Eickbush, T.H. (1990) Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J, 9, 3353-3362.
33. Marin, I. and Llorens, C. (2000) Ty3/Gypsy retrotransposons: Description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. Mol. Biol. Evol., 17, 1040-1049.
34. Gorinsek, b., Gubensek, F. and Kordis, D. (2004) Evolutionary genomics of chromoviruses in eukaryotes. Mol. Biol. Evol., 21, 781-798.
35. Bae, Y.A., Moon, S.Y., Kong, Y, Cho, S.Y. and Rhyu, M.G. (2001) CsRn1, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons. Mol. Biol. Evol., 18, 1474-1483.
36. Boeke, J.D., Eickbush, T.H., Sandmeyer, S. and Voytas, D.F. (1999) Metaviridae. In Murphy, F.A. (ed), Virus Taxonomy. ICTV VIIth report. Springer-Verlag, New York.
37. Hull, R. (1999) Classification of reverse transcribing elements: A discussion document. Arch. Virol., 144, 209-214.
38. Pringle, C.R. (1999) Virus taxonomy, the universal system of virus taxonomy, updated to include the new proposals ratified by the International Committee on Taxonomy of Viruses during 1998. Arch. Virol., 144, 421-429.
39. Britten, R.J. (1995) Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans. Proc. Natl Acad. Sci. USA, 92, 599-601.
40. Van Regenmortel, M.H.V., Fauquet, C.M., Bishop, D.H.L., Carstens, E.B., Estes, M.K., Lemon, S.M., Maniloff, J., Mayo, M.A., McGeoch, D.J. et al. (2000) Virus taxonomy: The classification and nomenclature of viruses. Seventh Report of the International Committee on Taxonomy of Viruses. Academia Press, San Diego, California.
41. Wilkinson, D.A., Mager, D.L. and Leong, J.A. (1994) Endogenous human retroviruses. In Levy, J.A. (ed), The Retroviridae. Plenum Press, New York, pp. 465-535.
42. International Human Genome Consortium. (2002) Initial sequencing and analysis of the human genome. Nature, 420, 520-562.
43. International Human Genome Consortium. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
44. Gifford, R., Kabat, P., Martin, J., Lynch, C. and Tristem, M. (2005) Evolution and distribution of class II-related endogenous retroviruses. J. Virol., 79, 6478-6486.
45. Gifford, R. and Tristem, M. (2003) The evolution, distribution and diversity of endogenous retroviruses. Virus Genes, 26, 291-315.
46. Saitou, N. and Nei, M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
47. Eck, R.V. and Dayhoff, M.O. (1966) Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Silver Spring, Maryland.
48. Kluge, A.G. and Farris, J.S. (1969) Quantitative phyletics and the evolution of anurans. System Zool, 18, 1-32.
49. Margus, T. and McMorris, F.R. (1981) Consensus n-trees. Bull. Math. Biol., 43, 239-244.
50. Koonin, E.V., Zhou, S. and Lucchesi, J.C. (1995) The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. Nucleic Acids Res. 23, 4229-4233.
51. Llorens, C. and Marin, I. (2001) A mammalian gene evolved from the integrase domain of an LTR retrotransposon. Mol. Biol. Evol., 18, 1597-1600.
52. Rawlings, N.D. and Barrett, A.J. (1995) Families of aspartic peptidases, and those of unknown catalytic mechanism. Methods Enzymol., 248 105-120.
53. Altschul, S.F, Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res, 25, 3389-3402.
54. Eddy, S.P. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
55. Huder, J.B., Boni, J., Hatt, J.M., Soldati, G., Lutz, H. and Schupbach, J. (2002) Identification and characterization of two closely related unclassifiable endogenous retroviruses in pythons (Python molurus and Python curtus). J. Virol., 76, 7607-7615.
56. Chatterjee, S. and Hunter, E. (1980) Fusion of normal primate cells: A common biological property of the D-type retroviruses. Virology, 107, 100-108.
57. Sommerfelt, M.A. and Weiss, R.A. (1990) Receptor interference groups of 20 retroviruses plating on human cells. Virology, 176, 58-69.
58. Sonigo, P., Barker, C., Hunter, E. and Wain-Hobson, S. (1986) Nucleotide sequence of Mason-Pfizer monkey virus: An immunosuppressive D-type retrovirus. Cell, 45, 375-385.
59. 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.
60. Bai, J., Bishop, J.V., Carlson, J.O. and DeMartini, J.C. (1999) Sequence comparison of JSRV with endogenous proviruses: Envelope genotypes and a novel ORF with similarity to a G-protein-coupled receptor. Virology 258, 333-343.
61. Rosafi, S., Pittau, M., Alberti, A., Pozzi, S., York, D.F., Sharp, J.M. and Palmarini, M. (2000) An accessory open reading frame (orf-x) of jaagsiekte sheep retrovirus is conserved between different virus isolates. Virus Res., 66, 109-116.
62. Quesneville, H., Bergman, C.M., Andrieu, O., Autard, D., Nouaud, D., Ashburner, M. and Anxolabehere, D. (2005) Combined evidence annotation of transposable elements in genome sequences. PLoS. Comput. Biol., 1, 166-175.
63. Goodwin, T.J. and Poulter, R.T. (2002) A group of deuterostome Ty3/ gypsy-like retrotransposons with Ty1/copia-like pol-domain orders. Mol. Genet. Genomics, 267, 481-491.
64. Gladyshev, E.A., Meselson, M. and Arkhipova, I.R. (2007) A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers. Gene, 390, 136-145.