Transposable elements as the key to a 21st century view of evolution

Genetica

Volumn 107, Issue 1-3, 1999, Pages 171-179

  Shapiro, James A ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

Evolutionary feedback; Genome wide transposition; Genomic systems; Natural genetic engineering; Transcriptional regulatory circuits

Indexed keywords

ARTICLE; GENOME; MOLECULAR EVOLUTION; SIGNAL TRANSDUCTION; TRANSPOSON;

DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENOME; SIGNAL TRANSDUCTION;

EID: 0033288598     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1003977827511     Document Type: Article

References (75)

1. Agrawal, A., Q.M. Eastman & D.G. Schatz, 1998. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature, 394: 744-751.
2. Alberts, B., D. Bray, J. Lewis, M. Raff, K. Roberts & J.D. Watson, 1994. Molecular Biology of the Cell, 3rd edn., Garland, New York.
3. Avery, O.T., C.M. MacLeod & M. McCarty, 1944. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a deoxyribonucleic acid fraction isolated from pneumococcus type III. J. Exp. Med. 79: 137-157.
4. Behe, M., 1996. Darwin's Black Box: the biochemical challenge to evolution, Free Press, New York.
5. Berg, D.E. & M.M. Howe, 1989. Mobile DNA. American Society for Microbiology, Washington, D.C.
6. Bestor, T.H., 1999. Sex brings transposons and genomes into conflict. Genetica 107: 289-295.
7. Blackwell, T.K. & F.W. Alt, 1989. Mechanism and developmental program of immunoglobulin gene rearrangement in mammals. Ann. Rev. Genet. 23: 605-636.
8. Bradshaw, V.A. & K. McEntee,1989. DNA damage activates transcription and transposition of yeast Ty retrotransposons. Mol. Gen. Genet. 218: 465-474.
9. Bray, D., 1990. Intracellular signalling as a parallel distributed process. J. Theoret. Biol. 143: 215-231.
10. Bregliano, J.-C. & M.G. Kidwell, 1983. Hybrid dysgenesis determinants, pp. 363-410 in Mobile Genetic Elements, edited by J.A. Shapiro, Academic Press, New York.
11. Britten, R.J., 1997. Mobile elements inserted in the distant past have taken on important functions. Gene 205: 177-182.
12. Britten, R. J. & E.H. Davidson, 1969. Gene regulation for higher cells: a theory, Science 165: 349-357.
13. Britten, R.J. & D.E. Kohne, 1968. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms, Science 161: 529-540.
14. Brosius, J., 1999a. RNAs from all categories generate retrosequences that may be accepted as novel genes or regulatory elements. Gene 238: 115-134.
15. Brosius, J., 1999b. Vertebrate genomes were forged by massive bombardments with retroelements and retrosequences. Genetica 107: 209-238
16. Costa, A.P.P., K.C. Scortecci, R.Y. Hashimoto, P.G. Araujo, M.-A. Grandbastien & M.-A. Van Sluys, 1999. Retrolycl-1, a member of the Tnt1 retrotransposon super-family in the Lycopersicon peruvianum genome. Genetica 107: 65-72.
17. Echols, H., 1986. Multiple DNA-protein interactions governing high-precision DNA transactions. Science 233: 1050-1056.
18. Engels, W.R., 1989. P elements in Drosophila melanogaster, pp. 437-484 in Mobile DNA, edited by D.E. Berg, and M.M. Howe, American Society for Microbiology, Washington, D.C.
19. Errede, B., T.S. Cardillo, G. Wever & F. Sherman, 1981. ROAM mutations causing increased expression of yeast genes: Their activation by signals directed toward conjugation functions and their formation by insertions of Ty1 repetitive elements. Cold Spr. Harb. Symp. Quant. Biol. 45: 593-607.
20. Fauvarque, M.O. & J.M. Dura, 1993. Polyhomeotic regulatory sequences induce developmental regulator-dependent variegation and targeted P-element insertions in Drosophila. Genes Dev. 7: 1508-1520.
21. Felsenfeld, G., J. Boyes, J. Chung, D. Clark & V. Studitsky, 1996. Chromatin structure and gene expression. Proc. Natl. Acad. Sci. USA 93: 9384-9388.
22. Finnegan, D.J., 1989. Eukaryotic transposable elements and genome evolution. Trends Genet. 5: 103-107.
23. Foster P.L., 1993. Adaptive mutation: the uses of adversity. Ann. Rev. Microbiol. 47: 467-504.
24. Foster, P.L. & W.A. Rosche, 1999. Increased episomal replication accounts for the high rate of adaptive mutation in recD mutants of Escherichia coli. Genetics 152: 15-30.
25. Galitski, T. & J.R. Roth, 1995. Evidence that F plasmid transfer replication underlies apparent adaptive mutation. Science 268: 421-423.
26. Gerhart, J. & M. Kirschner, 1997. Cells, Embryos & Evolution: toward a cellular and developmental understanding of phenotypic variation and evolutionary adaptability. Blackwell Science, Malden, Mass.
27. Green, M.M., 1988. Mobile DNA elements and spontaneous gene mutation, In Eukaryotic Transposable Elements as Mutagenic Agents, Banbury Report 30: 41-50.
28. Hall, B.G., 1999. Transposable elements as activators of cryptic genes in E. coli. Genetica 107: 181-187.
29. Hama C, Z. Ali & T.B. Kornberg, 1990. Region-specific recombination and expression are directed by portions of the Drosophila engrailed promoter. Genes Dev. 4: 1079-1093.
30. Hiom, K., M. Melek & M. Gellert, 1998. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94: 463-470.
31. Jacob, F. & J. Monod, 1961. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3: 318-356.
32. Kassis, J.A., E. Noll, E.P. Vansickle, W.F. Odenwald & N. Perrimon, 1992. Altering the insertional specificity of a Drosophila transposable element. Proc. Natl. Acad. Sci. USA 89: 1919-1923.
33. Kenter, A. & R. Wuerffel, 1999. Immunoglobulin switch recombination may occur by a DNA end-joining mechanism. Annal. N.Y. Acad. Sci. 870: 206-217.
34. Kidwell, M.G. & M.B. Evgen'ev, 1999. How valuable are model organisms for transposable element studies? Genetica 107: 103-111.
35. Kinsey P.T. & S.B. Sandmeyer, 1995. Ty3 transposes in mating populations of yeast: a novel transposition assay for Ty3. Genetics 139: 81-94.
36. Kirchner, J., C.M. Connolly & S.B. Sandmeyer, 1995. Requirement of RNA polymerase III transcription factors for in vitro position-specific integration of a retrovirus like element. Science 267: 1488-1491.
37. Lamrani, S., C. Ranquet, M.-J. Gama, H. Nakai, J.A. Shapiro, A. Toussaint & G. Maenhaut-Michel, 1999. Starvation-induced Mucts62-mediated Coding Sequence Fusion: Roles for ClpXP, Lon, RpoS and Crp. Molec. Microbiol. 32, 327-343.
38. Lerat, E., F. Brunet, C. Bazin & P. Capy, 1999. Is the evolution of transposable elements modular? Genetica 107: 15-25.
39. Lewis, S.M., 1999. Evolution of immunoglobulin and T-cell receptor gene assembly. Annal. N.Y. Acad. Sci. 870: 58-67.
40. MacNab, R., 1992. Genetics and biogenesis of bacterial flagella. Annu. Rev. Genet. 26: 131-158.
41. Maenhaut-Michel, G. & J. A. Shapiro, 1994. The roles of starvation and selective substrates in the emergence of araB-lacZ fusion clones. EMBO J. 13: 5229-5239.
42. Maenhaut-Michel, G., C.E. Blake, D.R.F. Leach & J.A. Shapiro, 1997. Different structures of selected and unselected araB-lacZ fusions. Molec. Micro. 23: 1133-1146.
43. Matzke, M.A., M.F. Mette, W. Aufsatz, J. Jakowitsch & A.J.M. Matzke, 1999. Host defenses to parasitic sequences and the evolution of epigenetic control mechanisms. Genetica 107: 271-287.
44. Mazel, D, B. Dychinco, V.A. Webb & J. Davies, 1998. A distinctive class of integron in the Vibrio cholerae genome. Science 280: 605-608.
45. McClintock, B., 1950. The origin and behavior of mutable loci in maize. Proc. Natl. Acad. Sci. USA 36: 344-355.
46. McClintock, B., 1951. Chromosome organization and genie expression. Cold Spr. Harb. Symp. Quant. Biol. 16: 13-47.
47. McClintock, B., 1953. Induction of instability at selected loci in maize. Genetics 38: 579-599.
48. McClintock, B., 1956a. Intranuclear systems controlling gene action and mutation. Brookhaven Symp. Biol. 8: 58-74.
49. McClintock, B., 1956b. Controlling elements and the gene. Cold Spr. Harb. Symp. Quant. Biol. 21: 197-216.
50. McClintock, B., 1965. The control of gene action in maize. Brookhaven Symp. Biol. 18: 162-184.
51. McClintock, B., 1978. Mechanisms that rapidly reorganize the genome. Stadler Genetics Symp. 10: 25-48.
52. McClintock, B., 1984. Significance of responses of the genome to challenge. Science 226: 792-801.
53. Monod, J. & F. Jacob, 1961. Teleonomic mechanisms in cellular metabolism, growth and differentiation. Cold Spr. Harb. Symp. Quant. Biol. 26: 389-401.
54. Moran, J.V., 1999. Human L1 retrotransposition: insights and peculiarities learned from a cultured cell retrotransposition assay. Genetica 107: 39-51.
55. Pardue, M.-L. & P.G. DeBaryshe, 1999. Drosophila telomeres: two transposable elements with important roles in chromosomes. Genetica 107: 189-196.
56. Peters, J.E. & S.A. Benson. 1995. Redundant transfer of F' plasmids occurs between Escherichia coli cells during nonlethal selection. J. Bacteriol. 177: 847-850.
57. Radicella, J.P., P.U. Park & M.S. Fox, 1995. Adaptive mutation in Escherichia coli: A role for conjugation. Science 268: 418-420.
58. Recchia, G.D. & R. Hall, 1995. Gene cassettes: a new class of mobile element. Microbiology 141: 3015-3027.
59. Reznikoff, W.S., 1992. The lactose operon-controlling elements: a complex paradigm. Mol. Microbiol. 6: 2419-2422.
60. Roy, A.M., M.L. Carroll, D.H. Kass, S.V. Nguyen, A.-H. Salem, M.A. Batzer & P.L. Deininger, 1999. Recently integrated human Alu repeats: finding needles in the haystack. Genetica 107: 149-161.
61. Saier, M.H., Jr., T.M. Ramseier & J. Reizer, 1996. Regulation of carbon utilization, pp. 1325-1343 in Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn., edited by P.C. Neidhardt et al., ASM Press, Washington, B.C.
62. Shapiro, J.A. 1982, Changes in gene order and gene expression. Natl. Cancer Inst. Monograph 60: 87-110.
63. Shapiro, J.A., 1983. Mobile Genetic Elements, Academic Press, New York.
64. Shapiro, J.A., 1984. Observations on the formation of clones containing araB-lacZ cistron fusions. Molec. Gen. Genet. 194: 79-90.
65. Shapiro, J.A., 1992. Natural genetic engineering in evolution. Genetica 86: 99-111.
66. Shapiro, J.A., 1995, Adaptive mutation: Who's really in the garden? Science 268: 373-374.
67. Shapiro, J.A., 1997. Genome organization, natural genetic engineering and adaptive mutation. Trends Genet. 13: 98-104.
68. Shapiro, J.A., 1999a. Natural genetic engineering, adaptive mutation and bacterial evolution, pp. 259-275, in Microbial Ecology and Infectious Disease, edited by E. Rosenberg, ASM Press, Washington.
69. Shapiro, J.A., 1999b. Genome system architecture and natural genetic engineering in evolution. Annal. N.Y. Acad. Sci. 870: 23-35.
70. Shapiro, J.A. & D. Leach, 1990. Action of a transposable element in coding sequence fusions. Genetics 126: 293-299.
71. Taillebourg, E. & J.M. Dura, 1999. A novel mechanism for P element homing in Drosophila. Proc. Natl. Acad. Sci. USA 96: 6856-6861.
72. Voytas, D.F. & J.D. Boeke, 1993. Yeast retrotransposons and tRNAs. Trends Genet. 9: 421-427.
73. Watson, J.D. & F.H.C. Crick, A structure for deoxyribose nucleic acids. Nature 171: 737-738.
74. Yuh, C.H., H. Bolouri & E.H. Davidson, 1998. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 279: 1896-1902
75. Zou, S., N. KE, J.M. Kim & D.F. Voytas, 1996. The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes Dev. 10: 634-645.