The evolution of Ty1-copia group retrotransposons in eukaryote genomes

Genetica

Volumn 100, Issue 1-3, 1997, Pages 185-195

  Flavell, Andrew J ^a   Pearce, Stephen R ^a,b   Pat Heslop Harrison, J S ^c   Kumar, Amar ^b  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^c JOHN INNES CENTRE   (United Kingdom)

Author keywords

Biodiversity; Copia; Evolution; Genome organization; Retrotransposon; Ty element

Indexed keywords

EMBRYOPHYTA; EUKARYOTA; VERTEBRATA;

EID: 0031451221     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1018385713293     Document Type: Article

References (94)

1. Arkhipova, I.R. & Y.V. Ilyin, 1992. Control of transcription of Drosophila retrotransposons. Bioessays 14: 161-168.
2. Ashburner, M., 1989. Drosophila, A laboratory Handbook. Cold Spring Harbor Press, Cold Spring Harbor, New York.
3. Bennetzen J.L., 1996. The contributions of retroelements to plant genome organisation, function and evolution. Trends Microbiol. 4: 347-353.
4. Bingham, P.M. & Z. Zachar, 1989. Retrotransposons and the FB element from Drosophila melanogaster, pp. 485-502 in Mobile DNA edited by D.E. Berg & M.M. Howe, American Society for Microbiology, Washington USA.
5. Boeke, J.D., D. Eichinger, D. Castrillon & G.R. Fink, 1988. The Saccharomyces cerevisiae genome contains functional and non-functional copies of transposon Ty1. Mol. Cell. Biol. 8: 1432-1442.
6. Boeke, J., 1989. Transposable elements in Saccharomyces cerevisiae, pp. 335-374 in Mobile DNA edited by D.E. Berg & M.M. Howe. American Society for Microbiology, Washington USA.
7. Boeke J.D. & K.B. Chapman, 1991. Retrotransposition mechanisms. Curr. Opin.-Cell. Biol. 3: 502-507.
8. Brandes A., J.S. Heslop-Harrison, A. Kamm, S. Kubis, R.L. Doudrick & T. Schmidt, 1997. Comparative analysis of the chromosomal and genomic organization of the Ty1-copia-like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol. Biol. (in press).
9. Brookfield, J.F.Y., 1995. Transposable elements as selfish DNA, pp. 130-153in 'Mobile Genetic Elements' edited by D.J. Sherratt. Oxford University Press.
10. Brookfield, J.F.Y & R.M. Badge, 1997. Population genetics models of transposable elements. Gentica 100: 281-294.
11. Capy, P., D. Anxolabéhere & T. Langin, 1994. The strange phylogenies of transposable elements: are horizontal transfers the only explanation? Trends Genetics 10: 7-12.
12. Camirand, A. & N. Brisson, 1990. The complete nucleotide sequence of the Tst1 retrotransposon of potato. Nucleic Acids Res. 18: 4929-4935.
13. Carmena, M. & C. Gonzalez, 1995. Transposable elements map in a conserved pattern of distribution extending from beta-heterochromatin to centromeres in Drosophila melanogaster. Chromosoma 103: 676-684.
14. Casacuberta, J.M., S. Vernhettes, C. Audeon & M.-A. Grandbastien, 1997. Quasispecies in retrotransposons: a role for sequence variability in Tnt1 evolution. Genetica 100: 109-117.
15. Cavalier-Smith T., 1985. John Wiley and Sons Ltd. London
16. Charlesworth, B., 1986. Genetic divergence between transposable elements. Genet. Res. Camb. 48: 111-118.
17. Charlesworth, B. & C.H. Langley, 1989. The population genetics of Drosophila transposable elements. Ann. Rev. Genet. 23: 251-287.
18. Charlesworth, Sniegowski & Stephan, 1994. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215-220.
19. Clare, J. & P. Farabaugh, 1985. Nucleotide sequence of a yeast Ty element: evidence for an unusual mechanism of gene expression. Proc. Natl. Acad. Sci. USA 82: 2829-2833.
20. Coffin, J., P.N. Tsichlis, C.S. Barker, S. Voynow & H.L. Robinson, 1980. Variation in avian retrovirus genomes. Ann. N.Y. Acad. Sci. 354: 410-425.
21. Curcio, M.J. & R.H. Morse, 1996. Tying together integration and chromatin. Trends Genetics. 12: 436-438.
22. Daboussi, M.J., 1997. Fungal transposable elements and genome evolution. Genetica 100: 253-260.
23. Daniels, S.B., L.D. Strausbaugh, L. Ehrman & R. Armstrong, 1984. Sequences homologous to P elements occur in Drosophila paulistorum. Proc. Natl. Acad. Sci. USA 81: 6794-6797.
24. Devereux, J., P. Haeberli & O. Smithies, 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12: 387-395.
25. Doolittle, R.F. D.F. Feng, M.S. Johnson & M.A. McClure, 1989. Origins and evolutionary relationships of retroviruses. Quarterly Rev. Biol. 64: 1-29.
26. Doolittle, R.F., D.F. Feng, M.A. McClure & M.S. Johnson, 1990. Retrovirus phylogeny and evolution. Curr. Top. Microbiol. Immunol. 157: 1-18.
27. Emori, Y., T. Shiba, S. Kanaya, S. Inouye, S. Yuki & K. Saigo, 1985. Determination of the nucleotide sequences of copia and copia-related RNA in Drosophila VLP. Nature 315: 773-776.
28. Finnegan, D.J., 1989. Eukaryotic transposable elements and genome evolution. Trends Genet. 5: 103-107.
29. Flavell, A.J., R. Levis, M.A. Simon & G.M. Rubin, 1981. The 5′ termini of RNAs encoded by the transposable element copia. Nucleic Acids Res. 9: 6279-6291.
30. Flavell, A.J., D.B. Smith & A. Kumar, 1992. Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol. Gen. Genet. 231: 233-242.
31. Flavell, A.J. & D.B. Smith, 1992. A Ty1-copia groupretrotransposon sequence in a vertebrate. Mol. Gen. Genet. 233: 322-326.
32. Flavell, A.J., E. Dunbar, R. Anderson, S.R. Pearce, R. Hartley & A. Kumar, 1992. Ty1-copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res. 20: 3639-3644.
33. Flavell, A.J., 1992. Ty1-copia group retrotransposons and the evolution of retroelements in the eukaryotes. Genetica 86: 203-214.
34. Flavell, A.J., S.R. Pearce & A. Kumar, 1994. Plant transposable elements and the genome. Current Opinion in Genet. 4: 838-844.
35. Flavell, A.J., V. Jackson, M.P. Iqbal, I. Riach & S. Waddell, 1995. Ty1-copia group retrotransposon sequences in amphibia and reptilia. Mol. Gen. Genet. 246: 65-71.
36. Fourcade-Peronnet, F., L. D'Auriol, J. Becker, F. Galibert & M. Best-Belpomme, 1988. Primary structure and functional organization of Drosophila 1731 retrotransposon. Nucleic Acids Res. 11: 6113-25.
37. Gerasimova, T.I., L.J. Mizrokhiand, G.P. Georgiev, 1984. Transposition bursts in genetically unstable Drosophila melanogaster. Nature 309: 714-716.
38. Gojobori, T. & S. Yokohama, 1985. Rates of evolution of the retroviral oncogene of Moloney murine sarcome virus and of its cellular homologues. Proc. Natl. Acad. Sci. USA 82: 4198-4201.
39. Grandbastien, M-A., A. Spielman & M. Caboche, 1989. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature 337: 376-380.
40. Grandbastien, M-A., 1992. Retroelements in higher plants. Trends in Genetics 8: 103-108.
41. Grandbastien, M-A., H. Lucas, J.-B. Morel, C. Mhiri, S. Vernhettes & J.M. Casacuberta, 1997. The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses. Genetica 100: 241-252.
42. Harada, K., K. Yukohiro & T. Mukai, 1990. Transposition rates of movable genetic elements in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 87: 3248-3252.
43. Heidmann, O. & T. Heidmann, 1991. Retrotransposition of a mouse IAP sequence tagged with an indicator gene. Cell 64: 159-170.
44. Heslop-Harrison J.S.(R), A. Brandes, S. Taketa, T. Schmidt, A.V. Vershinin, E.G. Alkhimova, A. Kamm, R.L. Doudrick, T. Schwarzacher, A. Katsiotis, S. Kubis, A. Kumar, S.R. Pearce, A.J. Flavell & G.E. Harrison, 1997. The chromosomal distributions of Ty1-copia group retrotransponsable elements in higher plants and their implications for genome evolution. Genetica 100: 197-204.
45. Hirochika, H. & R. Hirochika, 1993. Ty1-copia group retrotransposons as ubiquitous components of plant genomes. Jpn. J. Genet. 68: 35-46.
46. Hirochika H., H. Otsuki, M. Yoshikawa, Y. Otsuki, K. Sugimoto & S. Takeda, 1996, Autonomous transposition of the tobacco retrotransposon Tto1 in rice. Plant Cell. 8: 725-734.
47. Hutchison, C.A., S.C. Hardies, D.D. Loeb, W.R. Shehee & M.R. Edgell, 1989. LINEs and related retroposons: long interspersed repeat sequence in the eucaryotic genome, pp. 593-617 in Mobile DNA, edited by D.E. Berg and M.M. Howe. American Society for Microbiology, Washington USA.
48. Kim, A., E.S. Belyaeva & M.M. Aslanian, 1990. Autonomous transposition of gypsy mobile elements and genetic instability in Drosophila melanogaster. Mol. Gen. Genet. 224: 303-308.
49. Kim, A, C. Terzian, P. Santamaria, A. Pélisson, N. Prudhomme & A. Bucheton, 1994. Retroviruses in invertebrates: The gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 91: 1285-1289.
50. Konieczny, A., D.F. Voytas, M.P. Cummings & F.M. Ausubel, 1991. A superfamily of Arabidopsis thaliana retrotransposons. Genetics 127: 801-809.
51. Kuff, E.L. & K.K. Leuders, 1988. The intracisternal A particle gene family: structural and functional aspects. Adv. Cancer Res. 51: 183-276.
52. Kumar, A., 1996. The adventures of the Ty1-copia group of retrotransposons in plants. Trends Genet. 12: 41-43.
53. Kumar A., S.R. Pearce, K. McLean, G. Harrison, J.S.(P) HeslopHarrison, R. Waugh & A.J. Flavell, 1997. The Ty1-copia group of retrotransposons in plants: genomic organisation, evolution, and use as molecular markers. Genetica 100: 205-217.
54. Kupiec, M. & T.D. Petes, 1988. Meiotic recombination between repeated transposable elements in Saccharomyces cerevisiae. Mol. Cell. Biol. 8: 2942-2954.
55. Langley, C.H., E. Montgomery, R. Hudson, N. Kaplan & B. Charlesworth, 1988. On the role of unequal exchange in the containment of transposable element copy number. Genet. Res. Camb. 52: 223-235.
56. Li, W-H. & D. Graur, 1991. 'Fundamentals of Molecular Evolution', pp. 67-98. Sinauer Associates, Sunderland, MA, USA.
57. Lindauer, A, D. Fraser, M. Bruderlein & R. Schmitt, 1993. Reverse transcriptase families and a copia-like retrotransposon, Osser, in the green alga Volvox carteri. FEES Lett. 319: 261-6.
58. Meyer zu Altenschildesche, G., H. Heller, P. Wilgenbus, S. Tjia & W. Doerfler, 1996. Chromosoma 104: 341-344.
59. Minton S.A. & M.G. Minton, 1969. Venomous reptiles, pp. 8-19. Charles Scribner's Sons, New York.
60. Mizrokhi L.J. & A.M. Mazo, 1990. Evidence for horizontal transmission of the mobile elementjockey between distant Drosophila species. Proc. Natl. Acad. Sci. USA 87: 9216-9220.
61. Montchamp-Moreau, C., S. Jaques, M. Lehmann & D. Anxolabere, 1993. Distribution and conservation of sequences homologous to the 1731 retrotransposon in Drosophila. Mol. Biol. Evol. 10: 791-803.
62. Mount, S.M. & G.M. Rubin, 1985. Complete nucleotide sequence of the Drosophila transposable element copia: Homology between copia and retroviral proteins. Mol. Cell. Biol. 5: 1630-1638.
63. Nuzhdin, S.S. & T.F.C. Mackay, 1994. Direct determination of retrotransposon transposition rates in Drosophila melanogaster. Genet. Res. Camb. 63: 139-144.
64. Pasyukova, E.G. & S.V. Nuzhdin, 1993. Doc and copia instability in an isogenic Drosophila melanogaster stock. Mol. Gen. Genet. 240: 302-305.
65. Pearce, S.R., G. Harrison, D. Li, J.S. Heslop-Harrison, A. Kumar & A.J.Flavell, 1996a. The Ty1-copia group retrotransposons in Vicia species: copy number, sequence heterogeneity and chromosomal localisation. Mol. Gen. Genet. 250: 305-315.
66. Pearce S.R., G. Harrison, A.J. Flavell, J.S. Heslop-Harrison, I. Schubert & A. Kumar, 1996b. The Ty1-copia group retrotransposons of Allium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin. Chromosome Res. 4: 357-364.
67. Pearce, S.R., G. Harrison, J.S. Heslop-Harrison, A.J. Flavell & A. Kumar, 1997. Characterization and genomic organization of Ty1-copia group retrotransposons in rye (Secale cereale). Genome (In press).
68. Pélissier, T., S. Tutois, J-M. Deragon & G. Picard, 1995. Athila, a new retroelement from Arabidopsis thaliana. Plant Mol. Biol. 29: 441-452.
69. Pélissier, T., S. Tutois, S. Tourmente, J-M. Deragon & G. Picard, 1996. DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences. Genetica 97: 141-151
70. Pimpinelli, S., M. Berloco, L. Fanti, P. Dimitri, S. Bonaccorsi, E. Marchetti, R. Caizzi, C. Caggese & M. Gatti, 1995. Transposable elements are stable structural components of Drosophila melanogaster heterochromatin. Proc. Natl. Acad. Sci. USA 92: 3804-8.
71. Price, H.J., 1988. Nuclear DNA content variation within angiosperm species. Evol. Trends. Plants 2: 53-60.
72. Rothnie, H.M., K.J. McCurrach, L.A. Glover & N. Hardman, 1991. Retrotransposon-like nature of Tp1 elements: imlications for the organization of highly repetitive, hypermethylated DNA in the genome of Physarum polycephalum. Nucleic Acids Res. 19: 279-286.
73. Russell, F.E., 1980. Snake Venom Phylogeny, Published by Lippincott. pp. 25-27.
74. SanMiguel, P., A. Tikhonov, Y-K. Jin, N. Motchoulskaia, D. Zakharov, A. Melake-Berhan, P.S. Springer, K.J. Edwards, M. Lee, Z. Avramova & J.L. Bennetzen, 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274: 765-768.
75. Shih, A., R. Misra & M.G. Rush, 1989. Detection of multiple novel reverse transcriptase coding sequences in human nucleic acids: Relation to primate retroviruses. J. Virol. 63: 64-75.
76. Smit, A.F.A., 1993. Identification of a new, abundantsuperfamily of mammalian LTR-transposons. Nucleic Acids Res. 21: 1863-1872
77. Springer, M.S. & 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.
78. Steinhauer, D.A. & J.J. Holland, 1986. Direct method for quantitation of extreme polymerase error frequencies at selected single base sites in viral RNA. J. Virol. 57: 219-228.
79. Strobel, E., P. Dunsmuir, G.M. Rubin, 1979. Polymorphisms in the chromosomal locations of elements of the 412, copia and 297 dispersed repeated gene families in Drosophila melanogaster. Cell 17: 429-439.
80. Suoniemi, A., A. Narvanto & A.M. Schulman, 1996. The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Mol. Biol. 31: 295-306.
81. Suoniemi, A., D. Schmidt & A.H. Schulman, 1997. Bare-1 insertion site preferences and evolutionary conservation of RNA and cDNA processing sites. Genetica 100: 219-230.
82. Tchurikov, N.A., Y.V. Ilyin, E.V. Ananiev & G.P. Georgiev, 1978. The properties of gene Dm225, a representative of dispersed repetitive genes in Drosophila melanogaster. Nucleic Acids Res. 5: 2169-2187.
83. Tchurikov, N.A., Y.V. Ilyin, K.G. Skryabin, E.V. Ananiev, A.A. Bayev, A.S. Krayev, E.S. Zelentsova, V.V. Kulguskin, N.V. Lyubomirskaya & G.P. Georgiev, 1980. General properties of mobile dispersed genetic elements in Drosophila melanogaster. Cold Spring Harbor Symp. Quant. Biol. 43: 655-665.
84. Todaro, G.J., 1975. Evolution and modes of transmission of RNA tumor viruses. Am. J. Pathol. 81: 590-605.
85. Tristem, M., P. Kabat, E. Herniou, A. Karpas & F. Hill, 1995. Easel, A gypsy LTR retrotransposon in the Salmonidae. Mol. Gen. Genet. 249: 229-236.
86. Varmus, H.E. & P. Brown, 1989. Retroviruses, pp. 53-108 in Mobile DNA, edited by D.E. Berg and M.M. Howe. American Society for Microbiology, Washington USA.
87. Voytas, D.F., M.P. Cummings, A. Konieczny, F.M. Ausubel & S.R. Rodermel, 1992. copia-like retrotransposons are ubiquitous among plants Proc. Natl. Acad. Sci. (USA) 89: 7124-7128.
88. Voytas, D.F., 1996. Retroelements in genome organisation. Science 274: 737-738.
89. Warmington, J.R., R.B. Waring, C.S. Newlon, K.J. Indge & S.G. Oliver, 1985. Nucleotide sequence characterization of Ty1-17, a class II transposon from yeast. Nucleic Acids Res. 13: 6679-6693.
90. Wessler, S.R., T.E. Bureau & S.E. White, 1996. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Current Opinion Genet. Development. 5: 814-821.
91. Wichman, H.A., C.T. Payne, T.W. Reeder, 1985. Mys, a family of mammalian transposable elements isolated by phylogenetic screening. Nature 317: 77-81.
92. Xiong, Y. & T.H. Eickbush, 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9: 3353-3362.
93. Zou S., D.A. Wright & D.E. Voytas, 1995. The Saccharomyces Ty5 retrotransposon family is associated with origins of DNA replication at the telomeres and the silent mating locus HMR. Proc Natl. Acad. Sci. USA 92: 920-924.
94. Zou, S., N. Ke & 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.