1887

Chapter 28 : Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap28-1.gif /docserver/preview/fulltext/10.1128/9781555817954/9781555812096_Chap28-2.gif

Abstract:

Long terminal repeat (LTR)-containing retrotransposons (LTR-retrotransposons) are a large class of interspersed repeats that multiply by a process that includes reverse transcription. The sequence similarities of LTR-retroelements have allowed several laboratories to characterize the phylogenetic relationships. The most significant regions of homology are seven motifs in reverse transcriptase (RT). Extensive analysis of the sequences among LTR-elements revealed two principal classes of LTR-retrotransposons that are named for their founding members discovered in yeast and drosophila, Ty3/gypsy and Ty1/copia. The phylogenetic analyses also suggest that the Ty3/gypsy class of retrotransposons is more closely related to the retrovirus family than is the Ty1/copia group. The study of transposons in complex hosts such as plants reveals qualitative differences in the population of elements compared with those in single-cell organisms. The vertebrate transposons are a sister clade to several groups of Ty3/gypsy elements from fungal and plant hosts. This relationship may be due to a horizontal transmission event between either fungi or plants and an early species of vertebrate. An alternative model for the evolution of env genes in retroviruses, errantiviruses, and members of the copia and BEL families is that the third open reading frame (ORF) originated independently in each of these classes. It may be that much of the success of LTR-retroelements is that, early in their evolution, they developed a replication pathway and a structure that readily adapts to the introduction of env-like genes.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28

Key Concept Ranking

Rous sarcoma virus
0.47120485
0.47120485
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1
Figure 1

The pathway of LTR-retrotransposition. The LTRs of retroelements are symbolized by triangles, and the unique sequences are represented by a rectangle. The process of transposition is initiated by integrated copies of the element. Fulllength transcripts of the transposon are translated and the protein is processed by PR into Gag, PR, RT, and IN. These proteins and copies of the mRNA assemble into VLPs. The RT reverse transcribes the mRNA into double-stranded cDNA that associates with IN in the preintegration complex. After transport into the nucleus, IN inserts the cDNA into a new position in the genome. The designations provirus and virus refer to analogous intermediates in the propagation of retroviruses.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

The general structure of elements in the Ty1/copia and Ty3/gypsy families. All three categories of elements contain PBS and polypurine tracts (PPT). The ORFs encoding Gag are generally separated from the sequences of Pol by a frameshift. The elements in the Ty1/copia class encode IN upstream of RT. This order is reversed in the Ty3/gypsy family. In some cases, Ty3/gypsy elements possess a third ORF that encodes an env-like protein. This ORF is encoded in a spliced mRNA that lacks the sequences of Pol.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

A genetic assay for Tf1 transposition activity. Transposition of Tf1 is induced from a plasmid that contains the URA3 gene and the nmt promoter fused to Tf1. Transposition is induced by activating the transcription of the element. The neo gene included in Tf1 causes cells to become resistant to G418. Once transposition is complete, cells are grown on medium containing 5-FOA to select for loss of the assay plasmid. Cells that receive transposed copies of Tf1-neo are detected on medium containing G418. A wild-type copy of Tf1 generates confluent growth on plates with G418 while mutations that block the expression of IN (IN fs) or RT and IN (PR fs) cause many fewer cells to become G418R.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

The self-priming mechanism of reverse transcription is required for Tf1 transposition. The first 11 nucleotides of the Tf1 mRNA anneal to the PBS and a nucleolytic cleavage between nucleotides 11 and 12 generates the primer (top). Single nucleotide substitutions in the PBS (5th base PBS, 7th base PBS) and in the first 11 nucleotides (5th base 5′end, 7th base 5′end) cause significant reductions in transposition (bottom). The combination of two of these mutations reestablishes complementarity and results in the rescue of the transposition defect.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

The conservation of priming structures. (Tf1) A large segment of the Tf1 mRNA near the 5′ end folds into an RNA structure that is required for the self-priming of reverse transcription. Single nucleotide substitutions in any of the four duplexes results in reduced cleavage of the mRNA. The arrow indicates the position of the nucleolytic cleavage. (RSV) The 5′ end of retrovirus mRNA folds into structures called the U5-IR and U5-leader stems. This structure is surprisingly similar to the selfpriming structure of Tf1. Mutations in the U5-IRand U5-leader stems cause significant defects in the initiation of reverse transcription.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

A phylogenetic tree of the Ty3/gypsy group of LTR-retrotransposons. Bootstrap values are derived from 100 replicate trees generated by neighbor-joining analysis of an alignment of amino acids that was produced by Clustal X. The sequences used were based on the seven domains of RT (70). This tree was rooted to four elements of the Ty1/copia family.

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817954.chap28
1. Ananiev, E. V.,, R. L. Phillips,, and H. W. Rines. 1998. Complex structure of knob DNA on maize chromosome 9: retrotransposon invasion into heterochromatin. Genetics 149:20252037.
2. Anaya, N.,, and M. I. G. Roncero. 1995. Skippy, a retrotransposon from the fungal plant pathogen Fusarium oxysporum. Mol. Gen. Genet. 249:637647.
3. Atwood, A.,, J. Choi,, and H. L. Levin. 1998. The application of a homologous recombination assay revealed amino acid residues in an LTR-retrotransposon that were critical for integration. J. Virol. 72:13241333.
4. Atwood, A.,, J. Lin,, and H. Levin. 1996. The retrotransposon Tf1 assembles virus-like particles with excess Gag relative to integrase because of a regulated degradation process. Mol. Cell. Biol. 16:338346.
5. Avedisov, S. N.,, V. A. Cherkasova,, and Y. V. Ilyin. 1991. Characteristics of structural organization of Drosophila mdg1 retrotransposon detected during its sequencing. Sov. Genet. (Engl. Transl. Genetika) 26:12231242.
6. Balasundaram, D.,, M. J. Benedik,, M. Morphew,, V. D. Dang,, and H. L. Levin. 1999. Nup124p is a nuclear pore factor of Schizosaccharomyces pombe that is important for nuclear import and activity of retrotransposon Tf1. Mol. Cell. Biol. 19:57685784.
7. Bannister, A. J.,, E. A. Miska,, D. Gorlich,, and T. Kouzarides. 2000. Acetylation of importin-alpha nuclear import factors by CBP/p300. Curr. Biol. 10:467470.
8. Batistoni, R.,, I. Nardi,, L. Rebecchi,, M. Nardone,, and A. Demartis. 1991. A centromeric satelliteDNAin the European plethodontid salamanders (amphibia, urodela). Genome 34: 10071012.
9. Beeman, R. W.,, M. S. Thomson,, J. M. Clark,, M. A. DeCamillis,, S. J. Brown,, and R. E. Denell. 1996. Woot, an active gypsy-class retrotransposon in the flour beetle, Tribolium castaneum, is associated with a recent mutation. Genetics 143:417426.
10. Belcourt, M. F.,, and P. J. Farabaugh. 1990. Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell 62:339352.
11. Bennetzen, J. L. 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251269.
12. Blain, S. W.,, and S. P. Goff. 1993. Nuclease activities of Moloney murine leukemia virus reverse transcriptase. Mutants with altered substrate specificities. J. Biol. Chem. 268: 2358523592.
13. Boeke, J. D.,, T. Eickbush,, S. B. Sandmeyer,, and D. F. Voytas,. 1998. Metaviridae in virus taxonomy, p. 359367. In F. A. Murphy (ed.), Virus Taxonomy: ICTV VIIth Report. Springer-Verlag, New York, N.Y..
14. Boeke, J. D.,, and J. P. Stoye. 1997. Retrotransposons, Endogenous Retroviruses, and the Evolution of Retroelements. Cold Spring Harbor Laboratory Press, Plainview, N.Y..
15. Bowen, N. J.,, and J. F. McDonald. 1999. Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral- like elements. Genome Res. 9:924935.
16. Britten, R. J.,, T. J. McCormack,, T. L. Mears,, and E. H. Davidson. 1995. Gypsy/Ty3-class retrotransposons integrated in the DNA of herring, tunicate, and echinoderms. J. Mol. Evol. 40:1324.
17. Cambareri, E. B.,, R. Aisner,, and J. Carbon. 1998. Structure of the chromosome VII centromere region in Neurospora crassa: degenerate transposons and simple repeats. Mol. Cell. Biol. 18:54655477.
18. Carrington, J. C.,, K. D. Kasschau,, S. K. Mahajan,, and M. C. Schaad. 1996. Cell-to-cell and long-distance transport of viruses in plants. Plant Cell. 8:16691681.
19. Chalker, D. L.,, and S. B. Sandmeyer. 1990. Transfer RNA genes are genomic targets for de novo transposition of Ty3. Genetics 126:837850.
20. Chalvet, F.,, L. Teysset,, C. Terzian,, N. Prud’homme,, P. Santamaria,, A. Bucheton,, and A. Pelisson. 1999. Proviral amplification of the Gypsy endogenous retrovirus of Drosophila melanogaster involves env-independent invasion of the female germline. EMBO J. 18:26592669.
21. Chapman, K. B.,, A. S. Bystrom,, and J. D. Boeke. 1992. Initiator methionine tRNA is essential for Ty1 transposition in yeast. Proc. Natl. Acad. Sci. USA 89:32363240.
22. Chavanne, F.,, D. X. Zhang,, M. F. Liaud,, and R. Cerff. 1998. Structure and evolution of Cyclops: a novel giant retrotransposon of the Ty3/Gypsy family highly amplified in pea and other legume species. Plant Mol. Biol. 37:363375.
23. Cobrinik, D.,, A. Aiyar,, Z. Ge,, M. Katzman,, H. Huang,, and J. Leis. 1991. Overlapping retrovirus U5 sequence elements are required for efficient integration and initiation of reverse transcription. J. Virol. 65:38643872.
24. Cobrinik, D.,, L. Soskey,, and J. Leis. 1988. A retroviral RNA secondary structure required for efficient initiation of reverse transcription. J. Virol. 62:36223630.
25.. Dang, V. D.,, M. J. Benedik,, K. Ekwall,, J. Choi,, R. C. Allshire,, and H. L. Levin. 1999. A new member of the sin3 family of corepressors is essential for cell viability and required for retroelement propagation in fission yeast. Mol. Cell. Biol. 19:23512365.
26. Diolez, A.,, F. Marches,, D. Fortini,, and Y. Brygoo. 1995. Boty, a long-terminal-repeat retroelement in the phytopathogenic fungus Botrytis cinerea. Appl. Environ. Microbiol. 61: 103108.
27. Dobinson, K. F.,, R. E. Harris,, and J. E. Hamer. 1993. Grasshopper, a long terminal repeat (LTR) retroelement in the phytopathogenic fungus Magnaporthe grisea. Mol. Plant-Microbe Interact. 6:114126.
28. Doolittle, R. F.,, D. F. Feng,, M. S. Johnson,, and M. A. Mc- Clure. 1989. Origins and evolutionary relationships of retroviruses. Q. Rev. Biol. 64:130.
29. Eickbush, T. H. (ed.). 1994. The Evolutionary Biology of Viruses. Raven Press, New York, N.Y..
30. Elgar, G.,, M. S. Clark,, S. Meek,, S. Smith,, S. Warner,, Y. J. K. Edwards,, N. Bouchireb,, A. Cottage,, G. S. H. Yeo,, Y. Umrania,, G. Williams,, and S. Brenner. 1999. Generation and analysis of 25 Mb of genomic DNA from the pufferfish Fugu rubripes by sequence scanning. Genome Res. 9:960971.
31. Evgen’ev, M. B.,, V. G. Corces,, and D. H. Lankenau. 1992. Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses. J. Mol. Biol. 225:917924.
32. Farman, M. L.,, Y. Tosa,, N. Nitta,, and S. A. Leong. 1996. MAGGY, a retrotransposon in the genome of the rice blast fungus Magnaporthe grisea. Mol. Gen. Genet. 251:665674.
33. Felsenstein, K.,, and S. Goff. 1988. Expression of the gag-pol fusion protein of Moloney murine leukemia virus without gag protein does not induce viron formation or proteolytic processing. J. Virol. 62:21792182.
34. Flavell, A. J. 1981. Did retroviruses evolve from transposable elements? Nature 289:1011.
35. Fouchier, R.,, B. Meyer,, J. Simon,, U. Fischer,, A. Albright,, F. Gonzá lez-Scarano,, and M. Malim. 1998. Interaction of the human immunodeficiency virus type 1 Vpr protein with the nuclear pore complex. J. Virol. 72:60046013.
36. Friesen, P. D.,, and M. S. Nissen. 1990. Gene organization and transcription of TED, a lepidopteran retrotransposon integrated within the baculovirus genome. Mol. Cell. Biol. 10: 30673077.
37. Gallay, P.,, V. Stitt,, C. Mundy,, M. Oettinger,, and D. Trono. 1996. Role of the karyopherin pathway in human immunodeficiency virus type 1 nuclear import. J. Virol. 70:10271032.
38. Grandbastien, M. A.,, A. Spielmann,, and M. Caboche. 1989. Tnt1, a mobile retroviral-like element of tobacco isolated by plant cell genetics. Nature 337:376380.
39. Hahnenberger, K. M.,, M. P. Baum,, C. M. Polizzi,, J. Carbon,, and L. Clarke. 1989. Construction of functional artificial minichromosomes in the fission yeast. Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. USA 86:577581.
40. Hajek, K.,, and P. D. Friesen. 1998. Proteolytic processing and assembly of gag and gag-pol proteins of TED, a baculovirusassociated retrotransposon of the gypsy family. J. Virol. 72:87188724.
41.. Hansen, L. J.,, and S. B. Sandmeyer. 1990. Characterization of a transpositionally active Ty3 element and identification of the Ty3 integrase protein. J. Virol. 64:25992607.
42. Harada, F.,, G. G. Peters,, and J. E. Dahlberg. 1979. The primer tRNA for Moloney murine leukemia virus DNA synthesis. Nucleotide sequence and aminoacylation of tRNAPro. J. Biol. Chem. 254:1097910985.
43. Harada, F.,, R. C. Sawyer,, and J. E. Dahlberg. 1975. A primer ribonucleic acid for initiation of in vitro Rous sarcoma virus deoxyribonucleic acid synthesis. J. Biol. Chem. 250: 34873497.
44. Hizi, A.,, L. E. Henderson,, T. D. Copeland,, R. C. Sowder,, C. V. Hixson,, and S. Oroszlan. 1987. Characterization of mouse mammary tumor virus gag-pro gene products and the ribosomal frameshift site by protein sequencing. Proc. Natl. Acad. Sci. USA 84:70417045.
45. Hoff, E. F.,, H. L. Levin,, and J. D. Boeke. 1998. Schizosaccharomyces pombe retrotransposon Tf2 mobilizes primarily through homologous cDNA recombination. Mol. Cell. Biol. 18:68396852.
46. Hostomsky, Z.,, S. H. Hughes,, S. P. Goff,, and S. F. Le Grice. 1994. Redesignation of the RNase D activity associated with retroviral reverse transcriptase as RNase H. J. Virol. 68:19701971.
47. Inouye, S.,, K. Saigo,, K. Yamada,, and Y. Kuchino. 1986. Identification and nucleotide sequence determination of a potential primer tRNA for reverse transcription of a Drosophila retrotransposon, 297. Nucleic Acids Res. 14:30313043.
48. Jacks, T.,, M. D. Power,, F. R. Masiarz,, P. A. Luciw,, P. J. Barr,, and H. E. Varmus. 1988. Characterization of ribosomal frameshifting in HIV-1 gag-pol expression. Nature 331: 280283.
49. Jacks, T.,, and H. E. Varmus. 1985. Expression of the Rous sarcoma virus pol gene by ribosomal frameshifting. Science 230:12371242.
50. Jenkins, Y.,, M. McEntee,, K. Weis,, and W. C. Greene. 1998. Characterization of HIV-1 vpr nuclear import: analysis of signals and pathways. J. Cell Biol. 143:875885.
51. Jiang, M.,, J. Mak,, A. Ladha,, E. Cohen,, M. Klein,, B. Rovinski,, and L. Kleiman. 1993. Identification of tRNAs incorporated into wild-type and mutant human immunodeficiency virus type 1. J. Virol. 67:32463253.
52. Kikuchi, Y.,, Y. Ando,, and T. Shiba. 1986. Unusual priming mechanism of RNA-directed DNA synthesis in copia retrovirus- like particles of Drosophila. Nature 323:824826.
53. Kim, A.,, C. Terzian,, P. Santamaria,, A. Pelisson,, N. Prudhomme,, and A. Bucheton. 1994. Retroviruses in invertebrates: the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 91:12851289.
54. Kim, J. M.,, S. Vanguri,, J. D. Boeke,, A. Gabriel,, and D. F. Voytas. 1998. Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8:464478.
55. Kumar, A. 1998. The evolution of plant retroviruses: moving to green pastures. Trends Plant Sci. 3:371374.
56. Kumekawa, N.,, H. Ohtsubo,, T. Horiuchi,, and E. Ohtsubo. 1999. Identification and characterization of novel retrotransposons of the gypsy type in rice. Mol. Gen. Genet. 260: 593602.
57. Laten, H. M.,, A. Majumdar,, and E. A. Gaucher. 1998. SIRE- 1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein. Proc. Natl. Acad. Sci. USA 95: 68976902.
58. Leblanc, P.,, S. Desset,, B. Dastugue,, and C. Vaury. 1997. Invertebrate retroviruses: ZAM a new candidate in D. melanogaster. EMBO J. 16:75217531.
59. Leis, J.,, A. Aiyar,, and D. Cobrinik,. 1993. Regulation of initiation of reverse transcription of retroviruses, p. 3347. In A. Skalka, and S. Goff (ed.), Reverse Transcriptase. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y..
60. Lerat, E.,, and P. Capy. 1999. Retrotransposons and retroviruses: analysis of the envelope gene. Mol. Biol. Evol. 16: 11981207.
61. Lerch, R. A.,, and P. D. Friesen. 1992. The baculovirus-integrated retrotransposon TED encodes Gag and Pol proteins that assemble into virus-like particles with reverse-transcriptase. J. Virol. 66:15901601.
62. Levin, H. L. 1995. A novel mechanism of self-primed reverse transcription defines a new family of retroelements. Mol. Cell. Biol. 15:33103317.
63. Levin, H. L. 1996. An unusual mechanism of self-primed reverse transcription requires the RNase H domain of reverse transcriptase to cleave an RNA duplex. Mol. Cell. Biol. 16: 56455654.
64. Levin, H. L.,, and J. D. Boeke. 1992. Demonstration of retrotransposition of the Tf1 element in fission yeast. EMBO J. 11:11451153.
65. Levin, H. L.,, D. C. Weaver,, and J. D. Boeke. 1993. Novel gene expression mechanism in a fission yeast retroelement: Tf1 proteins are derived from a single primary translation product. EMBO J. 12:48854895. (Erratum, 15:1494, 1994.)
66. Levin, H. L.,, D. C. Weaver,, and J. D. Boeke. 1990. Two related families of retrotransposons from Schizosaccharomyces pombe. Mol. Cell. Biol. 10:67916798.
67. Lin, J. H.,, and H. L. Levin. 1997. A complex structure in the mRNA of Tf1 is recognized and cleaved to generate the primer of reverse transcription. Genes Dev. 11:270285.
68. Lin, J. H.,, and H. L. Levin. 1998. Reverse transcription of a self-primed retrotransposon requires an RNA structure similar to the U5-IRstem-loop of retroviruses. Mol. Cell. Biol. 18:68596869.
69. Lin, J. H.,, and H. L. Levin. 1997. Self-primed reverse transcription is a mechanism shared by several LTR-containing retrotransposons [letter]. RNA 3:952953.
70. Malik, H. S.,, and T. H. Eickbush. 1999. Modular evolution of the integrase domain in the Ty3/Gypsy class of LTRretrotransposons. J. Virol. 73:51865190.
71. Malik, H. S.,, S. Henikoff,, and T. H. Eickbush. 2000. Poised for contagion: evolutionary origins of the infectious abilities of invertebrate retroviruses. Genome Res. 10:13071318.
72. Marlor, R. L.,, S. M. Parkhurst,, and V. G. Corces. 1986. The Drosophila melanogaster gypsy transposable element encodes putative gene products homologous to retroviral proteins. Mol. Cell. Biol. 6:11291134.
73. Marracci, S.,, R. Batistoni,, G. Pesole,, L. Citti,, and I. Nardi. 1996. Gypsy/Ty3-like elements in the genome of the terrestrial salamander Hydromantes (Amphibia, Urodela). J. Mol. Evol. 43:584593.
74. Martinez-Izquierdo, J. A.,, J. Garcia-Martinez,, and C. M. Vicient. 1997. What makes Grande1 retrotransposon different? Genetica 100:1528.
75. McClure, M. A. 1991. Evolution of retroposons by acquisition or deletion of retrovirus-like genes. Mol. Biol. Evol. 8: 835856.
76. McHale, M. T.,, I. N. Roberts,, S. M. Noble,, C. Beaumont,, M. P. Whitehead,, D. Seth,, and R. P. Oliver. 1992. Cft-I: an Ltr-retrotransposon in Cladosporium fulvum, a fungal pathogen of tomato. Mol. Gen. Genet. 233:337347.
77. Miller, D. W.,, and L. K. Miller. 1982. A virus mutant with an insertion of a copia-like transposable element. Nature 299: 562564.
78. Miller, J. T.,, F. G. Dong,, S. A. Jackson,, J. Song,, and J. M. Jiang. 1998. Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics 150: 16151623.
79. Miller, K.,, C. Lynch,, J. Martin,, E. Herniou,, and M. Tristem. 1999. Identification of multiple gypsy LTR-retrotransposon lineages in vertebrate genomes. J. Mol. Evol. 49:358366.
80. Moore, M.,, and P. Sharp. 1992. Site-specific modification of pre-mRNA: the 2′-hydroxyl groups at the splice sites. Science 256:992997.
81. Nardi, I.,, F. Andronico,, S. Delucchini,, and R. Batistoni. 1986. Cytogenetics of the European plethodontid salamanders of the genus Hydromantes (amphibia, urodela). Chromosoma 94:377388.
82. Neuveglise, C.,, J. Sarfati,, J. P. Latge,, and S. Paris. 1996. Afut1, a retrotransposon-like element from Aspergillus fumigatus. Nucleic Acids Res. 24:14281434.
83. Ozers, M. S.,, and P. D. Friesen. 1996. The Env-like open reading frame of the baculovirus-integrated retrotransposon TED encodes a retrovirus-like envelope protein. Virology 226:252259.
84. Panet, A.,, W. A. Haseltine,, D. Baltimore,, G. Peters,, F. Harada,, and J. E. Dahlberg. 1975. Specific binding of tryptophan tRNA to avian myeloblastosis virus RNA-dependent DNA polymerase (reverse transcriptase). Proc. Natl. Acad. Sci. USA 72:25352539.
85. Pelissier, T.,, S. Tutois,, S. Tourmente,, J. M. Deragon,, and G. Picard. 1996. DNA regions flanking the major Arabidopsis thaliana satellite are principally enriched in Athila retroelement sequences. Genetica 97:141151.
86. Peters, G.,, F. Harada,, J. E. Dahlberg,, A. Panet,, W. A. Haseltine,, and D. Baltimore. 1977. Low-molecular-weight RNAs of Moloney murine leukemia virus: identification of the primer for RNA-directed DNA synthesis. J. Virol. 21: 10311041.
87. Peters, G. G.,, and C. Glover. 1980. Low-molecular-weight RNAs and initiation of RNA-directedDNAsynthesis in avian reticuloendotheliosis virus. J. Virol. 33:708716.
88. Peterson-Burch, B. D.,, D. A. Wright,, H. M. Laten,, and D. F. Voytas. 2000. Retroviruses in plants? Trends Genet. 16: 151152.
89. Poch, O.,, I. Sauvaget,, M. Delarue,, and N. Tordo. 1989. Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J. 8:38673874.
90. Poulet, F. M.,, P. R. Bower,, and J. W. Casey,. 1994. Retroviruses of fish, reptiles, and molluscs, p. 138. In J. A. Levy (ed.), The Retroviridae, vol. 3. Plenum Press, New York, N.Y.
91. Poulter, R.,, and M. Butler. 1998. A retrotransposon family from the pufferfish (fugu) Fugu rubripes. Gene 215:241249.
92. Presting, G. G.,, L. Malysheva,, J. Fuchs,, and I. Z. Schubert. 1998. A TY3/GYPSY retrotransposon-like sequence localizes to the centromeric regions of cereal chromosomes. Plant J. 16:721728.
93. Ratner, L.,, W. Haseltine,, R. Patarca,, K. J. Livak,, B. Starcich,, S. F. Josephs,, E. R. Doran,, J. A. Rafalski,, E. A. Whitehorn,, K. Baumeister, et al. 1985. Complete nucleotide sequence of the AIDS virus, HTLV-III. Nature 313:277284.
94. Saigo, K.,, W. Kugimiya,, Y. Matsuo,, S. Inouye,, K. Yoshioka,, and S. Yuki. 1984. Identification of the coding sequence for a reverse transcriptase-like enzyme in a transposable genetic element in Drosophila melanogaster. Nature 312:659661.
95. Sanmiguel, P.,, and J. L. Bennetzen. 1998. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. 82:3744.
96. SanMiguel, P.,, B. S. Gaut,, A. Tikhonov,, Y. Nakajima,, and J. L. Bennetzen. 1998. The paleontology of intergene retrotransposons of maize. Nature Genetics 20:4345.
97. SanMiguel, P.,, A. Tikhonov,, Y. K. Jin,, N. Motchoulskaia,, D. Zakharov,, A. Melake-Berhan,, P. S. Springer,, K. J. Edwards,, M. Lee,, Z. Avramova,, and J. L. Bennetzen. 1996. Nested retrotransposons in the intergenic regions of the maize genome. Science 274:765768.
98. Sentry, J. W.,, and D. R. Smyth. 1985. A family of repeated sequences dispersed through the genome of lilium henryi. Chromosoma 92:149155.
99. Smyth, D. R.,, P. Kalitsis,, J. L. Joseph,, and J. W. Sentry. 1989. Plant retrotransposon from lilium henryi is related to Ty3 of yeast and the gypsy group of drosophila. Proc. Nat. Acad. Sci. USA 86:50155019.
100. Song, S. U.,, T. Gerasimova,, M. Kurkulos,, J. D. Boeke,, and V. G. Corces. 1994. An env-like protein encoded by a drosophila retroelement: evidence that gypsy is an infectious retrovirus. Genes Dev. 8:20462057.
101. Springer, M.,, E. Davidson,, and R. Birtten. 1991. Retrovirallike element in a marine invertebrate. Proc. Natl. Acad. Sci. USA 88:84018404.
102. Sun, X. P.,, J. Wahlstrom,, and G. Karpen. 1997. Molecular structure of a functional Drosophila centromere. Cell 91: 10071019.
103. Tarchini, R.,, P. Biddle,, R. Wineland,, S. Tingey,, and A. Rafalski. 2000. The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell. 12:381391.
104. Temin, H. M. 1980. Origin of retroviruses from cellular moveable genetic elements. Cell 21:599600.
105. Teysset, L.,, J. C. Burns,, H. Shike,, B. L. Sullivan,, A. Bucheton,, and C. Terzian. 1998. A moloney murine leukemia virusbased retroviral vector pseudotyped by the insect retroviral gypsy envelope can infect Drosophila cells. J. Virol. 72: 853856.
106. Tikhonov, A. P.,, P. J. SanMiguel,, Y. Nakajima,, N. M. Gorenstein,, J. L. Bennetzen,, and Z. Avramova. 1999. Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc. Nat. Acad. Sci. USA 96:74097414.
107. Tristem, M.,, P. Kabat,, E. Herniou,, A. Karpas,, and F. Hill. 1995. Easel, a gypsy LTR-retrotransposon in the Salmonidae. Mol. Gen. Genet. 249:229236.
108. Vodicka, M. A.,, D. M. Koepp,, P. A. Silver,, and M. Emerman. 1998. HIV-1 Vpr interacts with the nuclear transport pathway to promote macrophage infection. Genes Dev. 12: 175185.
109. Weaver, D. C.,, G. V. Shpakovski,, E. Caputo,, H. L. Levin,, and J. D. Boeke. 1993. Sequence analysis of closely related retrotransposon families from fission yeast. Gene 131: 135139.
110. Webster, T. A.,, R. Patarca,, R. H. Lathrop,, and T. F. Smith. 1989. Potential structural motifs for reverse transcriptases. Mol. Biol. Evol. 6:317320.
111. Wright, D. A.,, and D. F. Voytas. 1998. Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins. Genetics 149:703715.
112. Xiong, Y.,, and T. H. Eickbush. 1990. Origin and evolution of retroelements based on their reverse transcriptase sequences. EMBO J. 9:33533362.
113. Xu, H.,, and J. D. Boeke. 1990. Host genes that influence transposition in yeast: the abundance of a rare tRNA regulates Ty1 transposition frequency. Proc. Natl. Acad. Sci. USA 87:83608364.
114. Yuki, S.,, S. Inouye,, S. Ishimaru,, and K. Saigo. 1986. Nucleotide sequence characterization of a Drosophila retrotransposon, 412 element. Eur. J. Biochem. 158:403410.
115. Zou, S.,, N. Ke,, J. M. Kim,, and D. F. Voytas. 1996. The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes Dev. 10:634645.

Tables

Generic image for table
Table 1

Ty3/gypsy transposons

Citation: Levin H. 2002. Newly Identified Retrotransposons of the Ty3/gypsy Class in Fungi, Plants, and Vertebrates, p 684-702. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch28

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error