Phylogenetic evidence for Ty1-copia-like endogenous retroviruses in plant genomes

Genetica

Volumn 107, Issue 1-3, 1999, Pages 87-93

  Laten, Howard M ^a  

^a LOYOLA UNIVERSITY CHICAGO   (United States)

Author keywords

Arabidopsis; Envelope; Retrotransposon; Reverse transcriptase; Soybean

Indexed keywords

ANIMALIA; ARABIDOPSIS; GLYCINE MAX; LYCOPERSICON ESCULENTUM; MAMMALIA; UNIDENTIFIED RETROVIRUS; ZEA MAYS;

ARTICLE; CLASSIFICATION; ENDOGENOUS RETROVIRUS; GENETICS; GENOME; OPEN READING FRAME; PHYLOGENY; PLANT; RETROPOSON; VIROLOGY;

ENDOGENOUS RETROVIRUSES; GENOME, PLANT; OPEN READING FRAMES; PHYLOGENY; PLANTS; RETROELEMENTS;

EID: 0033287379     PISSN: 00166707     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1003901009861     Document Type: Article

References (44)

1. Altschul, S.F., T.L. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller & D.J. Lipman, 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Bennetzen, J.L., 1996. The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol. 4: 347-353.
3. Bhattacharyya, M.K., R.A. Gonzales, M. Kraft & R.I. Buzzell, 1997. A copia-like retrotransposon Tgmr closely linked to the Rps-k allele that confers race-specific resistance of soybean to Phytophthora sojae. Plant Mol. Biol. 34: 255-264.
4. Bi, Y.-A. & H.M. Laten, 1996. Sequence analysis of a cDNA containing the gag and prot regions of the soybean retrovirus-like element, SIRE-1. Plant Mol. Biol. 30: 1315-1319.
5. Boeke, J.D., T. Eickbush, S.B. Sandmeyer & D.F. Voytas, 1999. Metaviridae, In Virus Taxonomy: ICTV VIIth Report, edited by M.H.V van Regenmortel, C.M. Fauquet, D.H.L. Bishop, E.B. Carstens, M.K. Estes, S.M. Lemon, J. Maniloff, M.S. Mayo, D.J. McGeoch, C.R. Pringle & R.B. Wickner. Academic Press, NY, in press.
6. Boeke, J.D. & J.P. Stoye, 1997. Retrotransposons, endogenous retroviruses, and the evolution of retroelements, pp. 343-436 in Retroviruses, edited by J.M. Coffin, S.H. Hughes & H.E. Varmus. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
7. Britten, R.J., 1995. Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 92: 599-601.
8. Britten, R.J., T.J. McCormack, T.L. Mears & E.H. Davidson, 1995. Gypsy/Ty3-class retrotransposons integrated in the DNA of herring, tunicate, and echinoderms. J. Mol. Evol. 40: 13-24.
9. Brunt, A.A., K. Crabtree, M.J. Dallwitz, A.J. Gibbs, L. Watson & E.J. Zurcher (eds.), 1997. Plant Viruses Online: Descriptions and Lists from the VIDE Database, Version 16.
10. Bureau, T.E., S.E. White & S.R. Wessler, 1994. Transduction of a cellular gene by a plant retroelement. Cell 77: 479-480.
11. Carrington, J.C., K.D. Kasschau, S.K. Mahajan & M.C. Schaad, 1996. Cell-to-cell and long-distance transport of viruses in plants. Plant Cell 8: 1669-1681.
12. Coffin, J.M., 1993. Reverse transcriptase and evolution, pp. 445-479 in Reverse Transcriptase, edited by A.M. Skalka & S.P. Goff. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
13. Ding, B., 1998. Intercellular protein trafficking through plasmodesmata. Plant Mol. Biol. 38: 279-310.
14. Doolittle, R.F. & D.-F. Feng, 1992. Tracing the origin of retroviruses. Curr. Top. Microbiol. Immunol. 176: 195-211.
15. Eickbush, T.H., 1994. Origin and evolutionary relationships of retroelements, pp. 121-157 in The Evolutionary Biology of Viruses, edited by S.S. Morse. Raven Press, NY.
16. Felder, H., A. Herzceg, Y. deChastonay, P. Aeby, H. Tobler & F. Muller, 1994. Tas, a retrotransposon from the parasitic nematode Ascaris lumbricoides. Gene 149: 219-225.
17. 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.
18. Flavell, A.J. & D.B. Smith, 1992. A Ty1-copia group retrotransposon sequence in a vertebrate. Mol. Gen. Genet. 233: 322-326.
19. Flavell, A.J., D.B. Smith & A. Kumar, 1992. Extreme heterogeneity of Ty1-copia group retrotransposons in plants. Mol. Gen. Genet. 231: 233-242.
20. Goldbach, R. & D. Peters, 1996. Molecular and biological aspects of tospoviruses, pp. 129-157 in The Bunyaviridae, edited by R.M. Elliott. Plenum Press, NY.
21. Inouye, S., S. Yuki & K. Saigo, 1986. Complete nucleotide sequence and genome organization of a Drosophila transposable genetic element, 297. Eur. J. Biochem. 154: 417-425.
22. Jin, Y.-K. & J.L. Bennetzen, 1994. Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bs1 retroelement in maize. Plant Cell 6: 1177-1186.
23. Kim, A., C. Terzian, P. Santamaria, A. Pelisson, N. Prud'homme & 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.
24. Kumar, A., 1996. The adventures of the Ty1-copia family of retrotransposons in plants. Trends Genet. 12: 41-43.
25. Kumar, A., 1998. The evolution of plant retroviruses: moving to greener pastures. Trends Plant Sci. 3: 371-374.
26. Laten, H.M. & R.O. Morris, 1993. SIRE-1, a long interspersed repetitive DNA element from soybean with weak sequence similarity to retrotransposons: initial characterization and partial sequence. Gene 133: 153-159.
27. Laten, H.M., A. Majumdar & 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: 6897-6902.
28. Leblanc, P., S. Deswset, B. Dastugue & C. Vaury, 1997. Invertebrate retroviruses - Zam, a new candidate in D. melanogaster. EMBO J. 16: 7521-7531.
29. Lerat, E. & P. Capy, 1999. Retrotransposons and retroviruses: Analysis of the envelope gene. Mol. Biol. Evol. 16: 1198-1207.
30. Mumford, R.A., I. Barker & K.R. Wood, 1996. The biology of tospoviruses. Ann. Appl. Biol. 128: 159-183.
31. Nault, L.R., 1994. Transmission biology, vector specificity and evolution of planthopper-transmitted plant viruses, pp.429-448 in Planthoppers: Their Ecology and Management, edited by R.F. Denno & T.J. Perfect. Chapman and Hall, NY.
32. Ozers, M.S. & P.D. Friesen, 1996. The Env-like open reading frame of the baculovirus-integrated retrotransposon TED encodes a retrovirus-like envelope protein. Virology 226: 252-259.
33. Pardue, M.L., N. Danilevskaya, K. Lowenhaupt, F. Slot & K.L. Traverse, 1996. Drosophila telomeres: new views on chromosome evolution. Trends Genet. 12: 48-52.
34. Patience, C., D.A. Wilkenson & R.A. Weiss, 1997. Our retroviral heritage. Trends Genet. 13: 116-120.
35. Peterson-Burch, B.D., D.A. Wright, H.M. Laten & D.F. Voytas, 2000. Retroviruses in Plants? Trends Genet. 16: 151-152.
36. Petropoulos, C., 1997. Retroviral taxonomy, protein structures, sequences, and genetic maps, pp. 757-805 in Retroviruses, edited by J.M. Coffin, S.H. Hughes & H.E. Varmus, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
37. Saigo, K., W. Kugimiya, Y. Matsuo, S. Inouye, K. Yoshioka & S. Yuki, 1984. Identification of the coding sequence for a reverse transcriptase-like enzyme in a transposable genetic element in Drosophila melanogaster. Nature 312: 659-661.
38. 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.
39. Song, S.U., T. Gerasimova, M. Kurkulos, J.D. Boeke & V.G. Corces, 1994. An Env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus. Genes Dev. 8: 2046-2057.
40. Suoniemi, A., J. Tanskanen & A.H. Schulman, 1998. Gypsy-like retrotransposons are widespread in the plant kingdom. Plant J. 13, 699-705.
41. Tanda, S., J.L. Mullor & V.G. Corces, 1994. The Drosophila tom retrotransposon encodes an envelope protein. Mol. Cell. Biol. 14: 5392-5401.
42. Temin, H.M., 1992. Origin and general nature of retroviruses, pp. 1-18 in The Retroviridae, Vol 1, edited by J.A. Levy. Plenum Press, NY.
43. 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.
44. Wright, D.A. & 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: 703-715.