Tec3, a new developmentally eliminated DNA element in Euplotes crassus

Eukaryotic Cell

Volumn 2, Issue 1, 2003, Pages 103-114

  Jacobs, Mary Ellen ^a   Sánchez Blanco, Adolfo ^a   Katz, Laura A ^b   Klobutcher, Lawrence A ^a  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

^b SMITH COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALS; BASE SEQUENCE; DNA; DNA NUCLEOTIDYLTRANSFERASES; DNA TRANSPOSABLE ELEMENTS; EUPLOTES; EVOLUTION, MOLECULAR; GENOME; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PHYLOGENY; PROTOZOAN PROTEINS; RECOMBINASES; RECOMBINATION, GENETIC; RIBOSOMAL PROTEINS; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EUPLOTES; MONEUPLOTES CRASSUS; PROTOZOA; TRANSPOSONS;

EID: 0038482194     PISSN: 15359778     EISSN: None     Source Type: Journal    
DOI: 10.1128/EC.2.1.103-114.2003     Document Type: Article

References (53)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Baird, S. E., G. M. Fino, S. L. Tausta, and L. A. Klobutcher. 1989. Micronuclear genome organization in Euplotes crassus: a transposonlike element is removed during macronuclear development. Mol. Cell. Biol. 9:3793-3807.
3. Baird, S. E., and L. A. Klobutcher. 1989. Characterization of chromosome fragmentation in two protozoans and identification of a candidate fragmentation sequence in Euplotes crassus. Genes Dev. 3:585-597.
4. Bernhard, D., A. Stechmann, W. Foissner, D. Ammermann, M. Hehn, and M. Schlegel. 2001. Phylogenetic relationships within the class Spirotrichea (Ciliophora) inferred from small subunit rRNA gene sequences. Mol. Phylogenet. Evol. 21:86-92.
5. Boswell, R. E., L. A. Klobutcher, and D. M. Prescott. 1982. Inverted terminal repeats are added to genes during macronuclear development in Oxytricha nova. Proc. Natl. Acad. Sci. USA 79:3255-3259.
6. Caparon, M. G., and J. R. Scott. 1989. Excision and insertion of the conjugative transposon Tn916 involves a novel recombination mechanism. Cell 59:1027-1034.
7. Doak, T. G., F. P. Doerder, C. L. Jahn, and G. Herrick. 1994. A proposed superfamily of transposase genes: transposon-like elements in ciliated protozoa and a common "D35E"motif. Proc. Natl. Acad. Sci. USA 91:942-946.
8. Doak, T. G., D. J. Witherspoon, C. L. Jahn, and G. Herrick. 2003. Selection on the genes of Euplotes crassus Tec1 and Tec2 transposons: evolutionary appearance of a programmed frameshift in a Tec2 gene encoding a tyrosine family site-specific recombinase. Eukaryot. Cell 2:95-102.
9. Dreyfus, D. H. 1992. Evidence suggesting an evolutionary relationship between transposable elements and the immune system recombination sequences. Mol. Immunol. 29:807-810.
10. Esposito, D., and J. J. Scocca. 1997. The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Nucleic Acids Res. 25:3605-3614.
11. Feinberg, A. P., and B. Vogelstein. 1983. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal. Biochem. 132:6-13.
12. Frels, J. S., and C. L. Jahn. 1995. DNA rearrangements in Euplotes crassus coincide with discrete periods of DNA replication during the polytene chromosome stage of macronuclear development. Mol. Cell. Biol. 15:6488-6495.
13. Frels, J. S., C. M. Tebeau, S. Z. Doktor, and C. L. Jahn. 1996. Differential replication and DNA elimination in the polytene chromosomes of Euplotes crassus. Mol. Biol. Cell 7:755-768.
14. Fugmann, S. D., A. I. Lee, P. E. Shockett, I. J. Villey, and D. G. Schatz. 2000. The RAG proteins and V(D)J recombination: complexes, ends, and transposition. Annu. Rev. Immunol. 18:495-527.
15. Gratias, A., and M. Bétermier. 2001. Developmentally programmed excision of internal DNA sequences in Paramecium aurelia. Biochimie 83:1009-1022.
16. Grindley, N. D. F. 1994. Resolvase-mediated site-specific recombination. Nucleic Acids Mol. Biol. 8:236-267.
17. Higgins, D. G., and P. M. Sharp. 1988. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244.
18. Jacobs, M. E., and L. A. Klobutcher. 1996. The long and the short of developmental DNA deletion in Euplotes crassus. J. Eukaryot. Microbiol. 43:442-452.
19. Jahn, C. L., S. Z. Doktor, J. S. Frels, J. W. Jaraczewski, and M. F. Krikau. 1993. Structures of the Euplotes crassus Tec1 and Tec2 elements: identification of putative transposase coding regions. Gene 133:71-78.
20. Jahn, C. L., M. Erbeznik, J. W. Jaraczewski, M. Melek, and D. E. Shippen. 1994. Sequence of the macronuclear DNA encoding large subunit ribosomal protein 29 (L29) in Euplotes crassus and cycloheximide sensitivity. Gene 151:231-235.
21. Jahn, C. L., and L. W. Klobutcher. 2002. Genome remodeling in ciliated protozoa. Annu. Rev. Microbiol. 56:489-520.
22. Jahn, C. L., M. F. Krikau, and S. Shyman. 1989. Developmentally coordinated en masse excision of a highly repetitive element in E. crassus. Cell 59:1009-1018.
23. Jahn, C. L., L A. Nilles, and M. F. Krikau. 1988. Organization of the Euplotes crassus micronuclear genome. J. Protozool. 35:590-601.
24. Jaraczewski, J. W., J. S. Frels, and C. L. Jahn. 1994. Developmentally regulated, low abundance Tec element transcripts in Euplotes crassus - implications for DNA elimination and transposition. Nucleic Acids Res. 22:4535-4542.
25. Jaraczewski, J. W., and C. L. Jahn. 1993. Elimination of Tec elements involves a novel excision process. Genes Dev. 7:95-105.
26. Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
27. Kishino, H., and M. Hasegawa. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J. Mol. Evol. 29:170-179.
28. Klobutcher, L. A., S. E. Gygax, J. D. Podoloff, J. R. Vermeesch, C. M. Price, C. M. Tebeau, and C. L. Jahn. 1998. Conserved DNA sequences adjacent to chromosome fragmentation and telomere addition sites in Euplotes crassus. Nucleic Acids Res. 26:4230-4240.
29. Klobutcher, L. A., and G. Herrick. 1995. Consensus inverted terminal repeat sequence of Paramecium IESs: resemblance to termini of Tc1-related and Euplotes Tec transposons. Nucleic Acids Res. 23:2006-2013.
30. Klobutcher, L. A., and G. Herrick. 1997. Developmental genome reorganization in ciliated protozoa: the transposon link. Prog. Nucleic Acid Res. Mol. Biol. 56:1-62.
31. Klobutcher, L. A., and D. M. Prescott. 1986. The special case of the hypotrichs, p. 111-154. In J. G. Gall (ed.), The molecular biology of ciliated protozoa. Academic Press, Inc., New York, N.Y.
32. Klobutcher, L. A., M. T. Swanton, P. Donini, and D. M. Prescott. 1981. All gene-sized DNA molecules in four species of hypotrichs have the same terminal sequence and an unusual 3′ terminus. Proc. Natl. Acad. Sci. USA 78:3015-3019.
33. Klobutcher, L. A., L. R. Turner, and J. LaPlante. 1993. Circular forms of developmentally excised DNA in Euplotes crassus have a heteroduplex junction. Genes Dev. 7:84-94.
34. Knecht, K., and L. A. Klobutcher. 1995. Telomeric repeat sequences are not associated with Tec1 elements in Euplotes crassus. Eur. J. Protistol. 31:201-207.
35. Krikau, M. F., and C. L. Jahn. 1991. Tec2, a second transposon-like element demonstrating developmentally programmed excision in Euplotes crassus. Mol. Cell. Biol. 11:4751-4759.
36. Ling, Z., S. Ghosh, M. E. Jacobs, and L. A. Klobutcher. 1997. Conjugation-specific genes in the ciliate Euplotes crassus: gene expression from the old macronucleus. J. Eukaryot. Microbiol. 44:1-11.
37. Mahillon, J., and D. Lereclus. 1988. Structural and functional analysis of Tn4430: identification of an integrase-like protein involved in the co-integrate-resolution process. EMBO J. 7:1515-1526.
38. Meyer, E., and O. Garnier. 2002. Non-Mendelian inheritance and homology-dependent effects in ciliates. Adv. Genet. 46:305-337.
39. Nunes-Düby, S. E., H. J. Kwon, R. S. Tirumalai, T. Ellenberger, and A. Landy. 1998. Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res. 26:391-406.
40. Prescott, D. M. 1994. The DNA of ciliated protozoa. Microbiol. Rev. 58:233-267.
41. Quan, L., and M. Wilkinson. 1991. DNA fragment purification from LMP agarose. BioTechniques 10:737-738.
42. Roth, M., M. Lin, and D. M. Prescott. 1985. Large scale synchronous mating and the study of macronuclear development in Euplotes crassus. J. Cell Biol. 101:79-84.
43. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
44. Smith, R. F., B. A. Wiese, M. K. Wojzynski, D. B. Davison, and K. C. Worley. 1996. BCM Search Launcher - an integrated interface to molecular biology data base search and analysis services available on the World Wide Web. Genome Res. 6:454-462.
45. Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
46. Tamura, K., and M. Nei. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526.
47. Tausta, S. L., and L. A. Klobutcher. 1989. Detection of circular forms of eliminated DNA during macronuclear development in E. crassus. Cell 59:1019-1026.
48. Tausta, S. L., and L. A. Klobutcher. 1990. Internal eliminated sequences are removed prior to chromosome fragmentation during development in Euplotes crassus. Nucleic Acids Res. 18:845-853.
49. Tausta, S. L., L. R. Turner, L. K. Bucldey, and L. A. Klobutcher. 1991. High fidelity developmental excision of Tec1 transposons and internal eliminated sequences in Euplotes crassus. Nucleic Acids Res. 19:3229-3236.
50. Taylor, K., and G. Churchward. 1997. Specific DNA cleavage mediated by the integrase of conjugative transposon Tn916. J. Bacteriol. 179:1117-1125.
51. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
52. Vermeesch, J. R., and C. M. Price. 1994. Telomeric DNA sequence and structure following de novo telomere synthesis in Euplotes crassus. Mol. Cell. Biol. 14:554-566.
53. Yao, M.-C., S. Duharcourt, and D. L. Chalker. 2002. Genome-wide rearrangements of DNA in ciliates, p. 730-758. In N. L. Craig, R. Craigie, M. Gellert, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.