Analyses of P-like transposable element sequences from the genome of Anopheles gambiae

Insect Molecular Biology

Volumn 13, Issue 1, 2004, Pages 55-63

  Oliveira De Carvalho, M ^a   Silva, J C ^b   Loreto, E L S ^a  

^a FEDERAL UNIVERSITY OF SANTA MARIA   (Brazil)

^b J CRAIG VENTER INSTITUTE   (United States)

Author keywords

'P element'; 'Transposable element'; Repressor; Transposase; Transposon

Indexed keywords

AMINO ACID SEQUENCE; ANIMAL; ANOPHELES; ARTICLE; CLUSTER ANALYSIS; COMPARATIVE STUDY; GENE STRUCTURE; GENETIC DATABASE; GENETICS; MOLECULAR GENETICS; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TRANSPOSON;

AMINO ACID SEQUENCE; ANIMALS; ANOPHELES; CLUSTER ANALYSIS; DATABASES, GENETIC; DNA TRANSPOSABLE ELEMENTS; GENE COMPONENTS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

ANIMALIA; ANOPHELES GAMBIAE; DROSOPHILA MELANOGASTER; DROSOPHILIDAE; HEXAPODA; MELANOGASTER; MUSCA DOMESTICA; TRANSPOSONS;

EID: 1242277814     PISSN: 09621075     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2583.2004.00461.x     Document Type: Article

References (41)

1. 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.
2. Andrews, J.D. and Gloor, G.B. (1995) A role for the KP leucine zipper in regulating P element transposition in Drosophila melanogaster. Genetics 141: 587-594.
3. Anxolabéhère, D., Nouaud, D. and Périquet, G. (1985) Séquences homologues a l'élement P chez des espèces de Drosophila du group obscura et Scaptomyza pallida (Drosophilidae). Génét Sél Evol 17: 579-584.
4. Bailey, T. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, vol. 2, pp. 28-36. AAAI Press.
5. Bailey, T. and Gribskov, M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14: 48-54.
6. Bingham, P.M. (1997) Cosuppression comes to the animals. Cell 90: 385-387.
7. Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
8. Clark, J.B., Silva, J.C. and Kidwell, M.G. (2002) Evidence for horizontal transfer of P transposable elements. In Horizontal Gene Transfer (Syvanen, M. and Kado, C.I., eds), pp. 161-171. Academic Press, London.
9. Daniels, S.B., Peterson, K.R., Strausbaugh, L.D., Kidwell, M.G. and Chovnick, An. (1990) Evidence for horizontal transmission of the P transposable element between Drosophila species. Genetics 124: 339-355.
10. Engels, W. (1989) P elements in Drosophila melanogaster. In Mobile DNA (Berg, D.E. and Howe, M.M., eds), pp. 437-484. American Society of Microbiology, Washington, DC.
11. Enright, A.J., Van Dongen, S. and Ouzounis, C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1584.
12. Finnegan, D.J. (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5: 103-107.
13. Hagemann, S. and Pinsker, W. (2001) Drosophila P transposons in the human genome? Mol Biol Evol 18: 1979-1982.
14. Haring, E., Hagemann, S. and Pinsker, W. (2000) Ancient and recent horizontal invasions of drosophilids by P elements. J Mol Evol 51: 577-586.
15. Holt, R.A., Subramanian, G.M., Halpern, A., Sutton, G.G., Charlab, R., Nusskern, D.R., Wincker, P., Clark, A.G., Ribeiro, J.M., Wides, R., Salzberg, S.L., Loftus, B., Yandell, M., Majoros, W.H., Rusch, D.B., Lai, Z., Kraft, C.L., Abril, J.F., Anthouard, V., Arensburger, P., Atkinson, P.W., Baden, H., de Berardinis, V., Baldwin, D., Benes, V., Biedler, J., Blass, C., Bolanos, R., Boscus, D., Barnstead, M., Cai, S., Center, A., Chatuverdi, K., Christophides, G.K., Chrystal, M.A., Clamp, M., Cravchik, A., Curwen, V., Dana, A., Delcher, A., Dew, I., Evans, C.A., Flanigan, M., Grundschober-Freimoser, A., Friedli, L., Gu, Z., Guan, P., Guigo, R., Hillenmeyer, M.E., Hladun, S.L., Hogan, J.R., Hong, Y.S., Hoover, J., Jaillon, O., Ke, Z., Kodira, C., Kokoza, E., Koutsos, A., Letunic, I., Levitsky, A., Liang, Y., Lin, J.J., Lobo, N.F., Lopez, J.R., Malek, J.A., McIntosh, T.C., Meister, S., Miller, J., Mobarry, C., Mongin, E., Murphy, S.D., O'Brochta, D.A., Pfannkoch, C., Qi, R., Regier, M.A., Remington, K., Shao, H., Sharakhova, M.V., Sitter, C.D., Shetty, J., Smith, T.J., Strong, R., Sun, J., Thomasova, D., Ton, L.Q., Topalis, P., Tu, Z., Unger, M.F., Walenz, B., Wang, A., Wang, J., Wang, M., Wang, X., Woodford, K.J., Wortman, J.R., Wu, M., Yao, A., Zdobnov, E.M., Zhang, H., Zhao, Q., Zhao, S., Zhu, S.C., Zhimulev, I., Coluzzi, M., della Torre, A., Roth, C.W., Louis, C., Kalush, F., Mural, R.J., Myers, E.W., Adams, M.D., Smith, H.O., Broder, S., Gardner, M.J., Fraser, C.M., Birney, E., Bork, P., Brey, P.T., Venter, J.C., Weissenbach, J., Kafatos, F.C., Collins, F.H. and Hoffman, S.L. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149.
16. Karplus, K., Barrett, C. and Hughey, R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics 14: 846-856.
17. Klug, A. and Rhodes, D. (1987) Zinc fingers: a novel protein fold for nucleic acid recognition. Cold Spring Harb Symp Quant Biol 52: 473-482.
18. Kolpakov, R., Bana, G. and Kucherov, G. (2003) mreps: Efficient and flexible detection of tandem repeats in DNA. Nucleic Acids Res 31: 3672-3678.
19. Kulp, D., Haussler, D., Reese, M. and Eeckman, F (1996) A generalized hidden Markov model for the recognition of human genes in DNA. In 4th Conference on Intelligent Systems in Molecular Biology, St. Louis USA. AAAI/MIT Press.
20. Kumar, S., Tamura, K., Jakobsen, I.B. and Nei, M. (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245.
21. Lansman, R.A., Stacey, S.N., Grigliatti, T.A., et al. (1985) Sequences Homologous to the P-mobile element of Drosophila melanogaster are widely distributed in the subgenus sophophora. Nature 318(6046): 561-563.
22. Lee, S.H., Clark, J.B. and Kidwell, M.G. (1999) A P element-homologous sequence in the house fly, Musca domestica. Insect Mol Biol 8: 491-500.
23. Loreto, E.L., da Silva, L.B., Zaha, A. and Valente, V.L. (1997-98) Distribution of transposable elements in neotropical species of Drosophila. Genetica 101: 153-165.
24. Loreto, E.L., Valente, V.L., Zaha, A., Silva, J.C. and Kidwell, M.G. (2001) Drosophila mediopunctata P elements: a new example of horizontal transfer. J Hered 92: 375-381.
25. Makalowski, W. (2000) Genomic scrap yard: how genomes utilize all that junk. Gene 259: 61-67.
26. Mul, Y.M. and Rio, D.C. (1997) Reprogramming the purine nucleotide cofactor requirement of Drosophila P element transposase in vivo. EMBO J 16: 4441-4447.
27. Nei, M. and Gojobori, T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.
28. Nekrutenko, A. and Li, W.H. (2001) Transposable elements are found in a large number of human protein-coding genes. Trends Genet 17: 619-621.
29. Ning, Z., Cox, A.J. and Mullikin, J.C. (2001) SSAHA: a fast search method for large DNA databases. Genome Res 11: 1725-1729.
30. O'Hare, K. and Rubin, G.M. (1983) Structures of P transposable elements and their sites of insertion and excision in the Drosophila melanogaster genome. Cell 34: 25-35.
31. Perkins, H.D. and Howells, A.J. (1992) Genomic sequences with homology to the P element of Drosophila melanogaster occur in the blowfly Lucilia cuprina. Proc Natl Acad Sci USA 89: 10753-10757.
32. Rio, D.C., Laski, F.A. and Rubin, G.M. (1986) Identification and immunochemical analysis of biologically active Drosophila P element transposase. Cell 44: 21-32.
33. Robertson, H.M. (1993) The mariner transposable element is widespread in insects. Nature 362: 241-245.
34. Robertson, H.M. and Engels, W.R. (1989) Modified P elements that mimic the P cytotype in Drosophila melanogaster. Genetics 123: 815-824.
35. Rost, B., Fariselli, P. and Casadio, R. (1996) PROFhtm. Prot Sci 7: 1704-1718.
36. Sarkar, A., Sengupta, R., Krzywinski, J., Wang, X., Roth, C. and Collins, F.H. (2003) P elements are found in the genomes of nematoceran insects of the genus Anopheles. Insect Biochem Mol Biol 33: 381-387.
37. Silva, J.C., Shabalina, S.A., Harris, D.G., Spouge, J.L. and Kondrashov, A.S. (2003) Conserved fragments of transposable elements in intergenic regions: evidence for widespread recruitment of MIR- and L2-derived sequences within the mouse and human genomes. Genet Res 82: 1-18.
38. Struhl, K. (1989) Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem Sci 14: 137-140.
39. Thelen, M.P., Venclovas, C. and Fidelis, K. (1999) A sliding clamp model for the Rad1 family of cell cycle checkpoint proteins. Cell 96: 769-770.
40. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (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.
41. Wu, C., Shivakumar, S., Shivakumar, C.V. and Chen, S. (1998) GeneFIND web server for protein family identification and information retrieval. Bioinformatics 14: 223-224.