Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons

Journal of Virology

Volumn 73, Issue 6, 1999, Pages 5186-5190

  Malik, Harmit S ^a   Eickbush, Thomas H ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE;

ARTICLE; LONG TERMINAL REPEAT; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; RETROPOSON; RETROVIRUS; VERTEBRATE; VIRUS GENOME;

EID: 0033057257     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/jvi.73.6.5186-5190.1999     Document Type: Article

References (31)

1. Aasland, R., and A. F. Stewart. 1995. The chromo shadow domain, a second chromo domain in heterochromatin-binding protein 1, HP1. Nucleic Acids Res. 23:3168-3173.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Ball, L. J., N. V. Murzina, R. W. Broadhurst, A. R. Raine, S. J. Archer, F. J. Stott, A. G. Murzin, P. B. Singh, P. J. Domaille, and E. D. Laue. 1997. Structure of the chromatin binding (chromo) domain from mouse modifier protein 1. EMBO J. 16:2473-2481.
4. Bushman, F. 1995. Targeting retroviral integration. Science 267:1443-1444.
5. Chalker, D. L., and S. B. Sandmeyer. 1992. Ty3 integrates within the region of RNA polymerase III transcription initiation. Genes Dev. 6:117-128.
6. Craigie, R. 1992. Hotspots and warm spots: integration specificity of retroelements. Trends Genet. 8:187-190.
7. Dej, K. J., T. Gerasimova, V. G. Corces, and J. D. Boeke. 1998. A hotspot for the Drosophila Gypsy retroelement in the ovo locus. Nucleic Acids Res. 26:4019-4025.
8. Dildine, S. L., J. Respess, D. Jolly, and S. B. Sandmeyer. 1998. A chimeric Ty3/Moloney murine leukemia virus integrase protein is active in vivo. J. Virol. 72:4297-4307.
9. Doolittle, W. F., and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284:601-603.
10. EMBL Database Website. Modified 16 March 1999. [Online.] http://www.e-bi.ac.uk. [30 March 1999, last date accessed.]
11. Engelman, A., A. B. Hickman, and R. Craigie. 1994. The core and carboxyl-terminal domains of the integrase protein of human immunodeficiency virus type 1 each contribute to nonspecific DNA binding. J. Virol. 68:5911-5917.
12. Gai, X., and D. F. Voytas. 1998. A single amino acid change in the yeast Ty5 abolishes targeting to silent chromatin. Mol. Cell 1:1051-1055.
13. Khan, E., J. P. Mack, R. A. Katz, J. Kulkosky, and A. M. Skalka. 1991. Retroviral integrase domains: DNA binding and the recognition of LTR sequences. Nucleic Acids Res. 19:851-850.
14. Kinsey, P. T., and S. B. Sandmeyer. 1995. Ty3 transposes in mating populations of yeast: a novel transposition assay for Ty3. Genetics 139:81-94.
15. Kirchner, J., C. M. Connolly, and S. B. Sandmeyer. 1995. Requirement of RNA polymerase III transcription factors for in vitro position-specific integration of a retroviruslike element. Science 267:1488-1491.
16. Koonin, E. V., S. Zhou, and J. C. Lucchesi. 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.
17. Labrador, M., and A. Fontdevila. 1994. High transposition rates of Osvaldo, a new Drosophila buzzatii retrotransposon. Mol. Gen. Genet. 245:661-674.
18. Messmer, S., A. Franke, and R. Paro. 1992. Analysis of the functional role of the Polycomb chromo domain in Drosophila melanogaster. Genes Dev. 6:1241-1254.
19. Nymark-McMahon, M. H., and S. B. Sandmeyer. 1999. Mutations in non-conserved domains of Ty3 integrase affect multiple stages of the Ty3 life cycle. J. Virol. 73:453-465.
20. Orgel, L. E., and F. H. Crick. 1980. Selfish DNA: the ultimate parasite. Nature 284:604-607.
21. Paro, R., and D. S. Hogness. 1991. The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila. Proc. Natl. Acad. Sci. USA 88:263-267.
22. Platero, J. S., T. Hartnett, and J. C. Eissenberg. 1995. Functional analysis of the chromo domain of HP1. EMBO J. 14:3977-3986.
23. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
24. Shub, D. A., H. Goodrich-Blair, and S. R. Eddy. 1994. Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem. Sci. 19:402-404.
25. Song, S. U., T. Gerasimova, M. Kurkulos, J. D. Boeke, and V. G. Corces. 1994. An env-like protein encoded by a Drosophila retroelement: evidence that Gypsy is an infectious retrovirus. Genes Dev. 8:2046-2057.
26. Springer, M. S., and R. J. Britten. 1993. Phylogenetic relationships of reverse transcriptase and RNase H sequences and aspects of genome structure in the Gypsy group of retrotransposons. Mol. Biol. Evol. 10:1370-1379.
27. Steele, S. J. S., and H. L. Levin. 1998. A map of interactions between the proteins of a retrotransposon. J. Virol. 72:9318-9322.
28. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
29. Wright, D. A., and D. F. Voytas. 1998. Potential retroviruses in plants. Tat1 is related to a group of Arabidopsis thaliana Ty3/Gypsy retrotransposons that encode envelope-like proteins. Genetics 149:703-715.
30. Xiong, Y., and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9:3353-3362.
31. Yang, J., H. S. Malik, and T. H. Eickbush. The endonucleases encoded by site-specific non-LTR retrotransposons are related to restriction enzymes. Submitted for publication.