An extraordinary retrotransposon family encoding dual endonucleases

Genome Research

Volumn 15, Issue 8, 2005, Pages 1106-1117

  Kojima, Kenji K ^a   Fujiwara, Haruhiko ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE PROTEINASE; DNA (APURINIC OR APYRIMIDINIC SITE) LYASE; ENDONUCLEASE; RIBONUCLEASE H; RNA DIRECTED DNA POLYMERASE;

ARTICLE; CHLAMYDOMONAS REINHARDTII; GENOME; MONOPHYLY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RETROPOSON;

AMINO ACID SEQUENCE; ANIMALS; CATALYTIC DOMAIN; CHLAMYDOMONAS REINHARDTII; CONSERVED SEQUENCE; CYSTEINE ENDOPEPTIDASES; ENDONUCLEASES; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; RETROELEMENTS; RIBONUCLEASE H, CALF THYMUS; RNA SPLICING; RNA, ANTISENSE;

CHLAMYDOMONAS REINHARDTII;

EID: 23744469909     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3271405     Document Type: Article

References (38)

1. Albrecht, M., Hoffmann, D., Evert, B.O., Schmitt, I., Wullner, U., and Lengauer, T. 2003. Structural modeling of ataxin-3 reveals distant homology to adaptins. Proteins 50: 355-370.
2. 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.
3. Anantharaman, V. and Aravind, L. 2003. Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes. Genome Biol. 4: R11.
4. Anzai, T., Takahashi, H., and Fujiwara, H. 2001. Sequence-specific recognition and cleavage of telomeric repeat (TTAGG)n by endonuclease of non-long terminal repeat retrotransposon TRAS1. Mol. Cell. Biol. 21: 100-108.
5. Arabidopsis Genome Initiative 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
6. Arkhipova, I. and Meselson, M. 2000. Transposable elements in sexual and ancient asexual taxa. Proc. Natl. Acad. Sci. 97: 14473-14477.
7. Bouneau, L., Fischer, C., Ozouf-Costaz, C., Froschauer, A., Jaillon, O., Coutanceau, J.P., Korting, C., Weissenbach, J., Bernot, A., and Volff, J.N. 2003. An active non-LTR retrotransposon with tandem structure in the compact genome of the pufferfish Tetraodon nigroviridis. Genome Res. 13: 1686-1695.
8. Burke, W.D., Malik, H.S., Rich, S.M., and Eickbush, T.H. 2002. Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia. Mol. Biol. Evol. 19: 619-630.
9. Burnett, B., Li, F., and Pittman, R.N. 2003. The polyglutamine neurodegenerative protein ataxin-3 binds polyubiquitylated proteins and has ubiquitin protease activity. Hum. Mol. Genet. 12: 3195-3205.
10. Cost, G.J., Feng, Q., Jacquier, A., and Boeke, J.D. 2002. Human L1 element target-primed reverse transcription in vitro. EMBO J. 21: 5899-5910.
11. Douady, C.J., Delsuc, F., Boucher, Y., Doolittle, W.F., and Douzery, E.J. 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20: 248-254.
12. Eickbush, T.H. and Malik, H.S. 2002. Origins and evolution of retrotransposons. In Mobile DNA II (eds. N.L. Craig et al.), pp. 1111-1144. American Society of Microbiology Press, Washington, DC.
13. Feng, Q., Moran, J.V., Kazazian Jr., H.H., and Boeke, J.D. 1996. Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition. Cell 87: 905-916.
14. Guarné, A., Tormo, J., Kirchweger, R., Pfistermueller, D., Fita, I., and Skern, T. 1998. Structure of the foot-and-mouth disease virus leader protease: A papain-like fold adapted for self-processing and eIF4G recognition. EMBO J. 17: 7469-7479.
15. Kojima, K.K. and Fujiwara, H. 2003. Evolution of target specificity in R1 clade non-LTR retrotransposons. Mol. Biol. Evol. 20: 351-361.
16. _. 2004. Cross-genome screening of novel sequence-specific non-LTR retrotransposons: Various multicopy RNA genes and microsatellites are selected as targets. Mol. Biol. Evol. 21: 207-217.
17. Li, S.J. and Hochstrasser, M. 1999. A new protease required for cell-cycle progression in yeast. Nature 398: 246-251.
18. Malik, H.S. and Eickbush, T.H. 2000. NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans. Genetics 154: 193-203.
19. _. Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res. 11: 1187-1197.
20. Malik, H.S., Burke, W.D., and Eickbush, T.H. 1999. The age and evolution of non-LTR retrotransposable elements. Mol. Biol. Evol. 16: 793-805.
21. Malik, H.S., Henikoff, S., and Eickbush, T.H. 2000. Poised for contagion: Evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res. 10: 1307-1318.
22. Mandal, P.K., Bagchi, A., Bhattacharya, A., and Bhattacharya, S. 2004. An Entamoeba histolytica LINE/SINE pair inserts at common target sites cleaved by the restriction enzyme-like LINE-encoded endonuclease. Eukaryot. Cell 3: 170-179.
23. Marchler-Bauer, A., Anderson, J.B., DeWeese-Scott, C., Fedorova, N.D., Geer, L.Y., He, S. Hurwitz, D.I., Jackson, J.D., Jacobs, A.R., Lanczycki, C.J., et al. 2003. CDD: A curated Entrez database of conserved domain alignments. Nucleic Acids Res. 31: 383-387.
24. Morrish, T.A., Gilbert, N., Myers, J.S., Vincent, B.J., Stamato, T.D., Taccioli, G.E., Batzer, M.A., and Moran, J.V. 2002. DNA repair mediated by endonuclease-independent LINE-1 retrotransposition. Nat. Genet. 31: 159-165.
25. Ronquist, F. and Huelsenbeck, J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
26. Scheel, H., Tomiuk, S., and Hofmann, K. 2003. Elucidation of ataxin-3 and ataxin-7 function by integrative bioinformatics. Hum. Mol. Genet. 12: 2845-2852.
27. Sewell, E. and Kinsey, J.A. 1996. Tad, a Neurospora LINE-like retrotransposon exhibits a complex pattern of transcription. Mol. Gen. Genet. 252: 137-145.
28. Symer, D.E., Connelly, C., Szak, S.T., Caputo, E.M., Cost, G.J., Parmigiani, G., and Boeke, J.D. 2002. Human L1 retrotransposition is associated with genetic instability in vivo. Cell 110: 327-338.
29. Takahashi, H. and Fujiwara, H. 2002. Transplantation of target site specificity by swapping the endonuclease domains of two LINEs. EMBO J. 21: 408-417.
30. 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.
31. Waugh, D.S. and Sauer, R.T. 1993. Single amino acid substitutions uncouple the DNA binding and strand scission activities of Fok I endonuclease. Proc. Natl. Acad. Sci. 90: 9596-9600.
32. Weichenrieder, O., Repanas, K., and Perrakis, A. 2004. Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon. Structure 12: 975-986.
33. Yamamoto, Y., Fujimoto, Y., Arai, R., Fujie, M., Usami, S., and Yamada, T. 2003. Retrotransposon-mediated restoration of Chlorella telomeres: Accumulation of Zepp retrotransposons at termini of newly formed minichromosomes. Nucleic Acids Res. 31: 4646-4653.
34. Yang, J., Malik, H.S., and Eickbush, T.H. 1999. Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements. Proc. Natl. Acad. Sci. 96: 7847-7852.
35. http://www.ncbi.nlm.nih.gov/BLAST; The BLAST server at the National Center for Biotechnology Information.
36. http://aluminum.jgi-psf.org/prod/bin/runBlast.pl?db=chlre1; Chlamydomonas reinhardtii BLAST server at the US Department of Energy Joint Genome Institute.
37. http://www.jgi.doe.gov/; the US Department of Energy Joint Genome Institute.
38. http://www.biol.s.u-tokyo.ac.jp/users/animal/kojima/sequence.html; authors' Web site.