Skip to main content
PMC home page
Journal of Virology logoLink to Journal of Virology
. 1997 May;71(5):4005–4015. doi: 10.1128/jvi.71.5.4005-4015.1997

Retrovirus-like end processing of the tobacco Tnt1 retrotransposon linear intermediates of replication.

F Feuerbach 1, J Drouaud 1, H Lucas 1
PMCID: PMC191553  PMID: 9094678

Abstract

The tobacco retrotransposon Tnt1 can transpose through an RNA intermediate in the heterologous host Arabidopsis thaliana. We report here the identification and characterization of extrachromosomal linear and circular DNA forms of Tnt1 in this heterologous host. Our results demonstrate that Tnt1 linear intermediates possess two extra base pairs at each end compared with Tnt1's integrated forms. Prior to integration into the host genome, the two terminal nucleotides at the 3' end of these linear intermediates are removed, as in the case of the yeast Ty3 retrotransposon and of retroviruses. Our data, together with those from recent studies of Ty3, reinforce the idea that 3' dinucleotide cleavage is not restricted to retroviral integrases and is probably a feature shared by many different retrotransposons' enzymes.

Full Text

The Full Text of this article is available as a PDF (620.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Akama K., Tanifuji S. Nucleotide sequence of a methionine initiator tRNA gene of Arabidopsis thaliana. Plant Mol Biol. 1989 Nov;13(5):599–600. doi: 10.1007/BF00027320. [DOI] [PubMed] [Google Scholar]
  2. Boeke J. D., Eichinger D., Castrillon D., Fink G. R. The Saccharomyces cerevisiae genome contains functional and nonfunctional copies of transposon Ty1. Mol Cell Biol. 1988 Apr;8(4):1432–1442. doi: 10.1128/mcb.8.4.1432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Braiterman L. T., Boeke J. D. Ty1 in vitro integration: effects of mutations in cis and in trans. Mol Cell Biol. 1994 Sep;14(9):5731–5740. doi: 10.1128/mcb.14.9.5731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brown P. O., Bowerman B., Varmus H. E., Bishop J. M. Retroviral integration: structure of the initial covalent product and its precursor, and a role for the viral IN protein. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2525–2529. doi: 10.1073/pnas.86.8.2525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bushman F. D., Craigie R. Activities of human immunodeficiency virus (HIV) integration protein in vitro: specific cleavage and integration of HIV DNA. Proc Natl Acad Sci U S A. 1991 Feb 15;88(4):1339–1343. doi: 10.1073/pnas.88.4.1339. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bushman F. D., Fujiwara T., Craigie R. Retroviral DNA integration directed by HIV integration protein in vitro. Science. 1990 Sep 28;249(4976):1555–1558. doi: 10.1126/science.2171144. [DOI] [PubMed] [Google Scholar]
  7. Canaday J., Guillemaut P., Weil J. H. The nucleotide sequences of the initiator transfer RNAs from bean cytoplasm and chloroplasts. Nucleic Acids Res. 1980 Mar 11;8(5):999–1008. doi: 10.1093/nar/8.5.999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Casacuberta J. M., Vernhettes S., Grandbastien M. A. Sequence variability within the tobacco retrotransposon Tnt1 population. EMBO J. 1995 Jun 1;14(11):2670–2678. doi: 10.1002/j.1460-2075.1995.tb07265.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chapman K. B., Byström A. S., Boeke J. D. Initiator methionine tRNA is essential for Ty1 transposition in yeast. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3236–3240. doi: 10.1073/pnas.89.8.3236. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Craigie R., Fujiwara T., Bushman F. The IN protein of Moloney murine leukemia virus processes the viral DNA ends and accomplishes their integration in vitro. Cell. 1990 Aug 24;62(4):829–837. doi: 10.1016/0092-8674(90)90126-y. [DOI] [PubMed] [Google Scholar]
  11. Eibel H., Gafner J., Stotz A., Philippsen P. Characterization of the yeast mobile element Ty1. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 2):609–617. doi: 10.1101/sqb.1981.045.01.079. [DOI] [PubMed] [Google Scholar]
  12. Eichinger D. J., Boeke J. D. A specific terminal structure is required for Ty1 transposition. Genes Dev. 1990 Mar;4(3):324–330. doi: 10.1101/gad.4.3.324. [DOI] [PubMed] [Google Scholar]
  13. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  14. Flavell A. J., Brierley C. The termini of extrachromosomal linear copia elements. Nucleic Acids Res. 1986 May 12;14(9):3659–3669. doi: 10.1093/nar/14.9.3659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Flavell A. J., Ish-Horowicz D. The origin of extrachromosomal circular copia elements. Cell. 1983 Sep;34(2):415–419. doi: 10.1016/0092-8674(83)90375-6. [DOI] [PubMed] [Google Scholar]
  16. Friesen P. D., Nissen M. S. Gene organization and transcription of TED, a lepidopteran retrotransposon integrated within the baculovirus genome. Mol Cell Biol. 1990 Jun;10(6):3067–3077. doi: 10.1128/mcb.10.6.3067. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Fujiwara T., Mizuuchi K. Retroviral DNA integration: structure of an integration intermediate. Cell. 1988 Aug 12;54(4):497–504. doi: 10.1016/0092-8674(88)90071-2. [DOI] [PubMed] [Google Scholar]
  18. Ghosh H. P., Ghosh K., Simsek M., RajBhandary U. L. Nucleotide sequence of wheat germ cytoplasmic initiator methionine transfer ribonucleic acid. Nucleic Acids Res. 1982 May 25;10(10):3241–3247. doi: 10.1093/nar/10.10.3241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Gilboa E., Mitra S. W., Goff S., Baltimore D. A detailed model of reverse transcription and tests of crucial aspects. Cell. 1979 Sep;18(1):93–100. doi: 10.1016/0092-8674(79)90357-x. [DOI] [PubMed] [Google Scholar]
  20. Goff S. P. Genetics of retroviral integration. Annu Rev Genet. 1992;26:527–544. doi: 10.1146/annurev.ge.26.120192.002523. [DOI] [PubMed] [Google Scholar]
  21. Grandbastien M. A., Audeon C., Casacuberta J. M., Grappin P., Lucas H., Moreau C., Pouteau S. Functional analysis of the tobacco Tnt1 retrotransposon. Genetica. 1994;93(1-3):181–189. doi: 10.1007/BF01435250. [DOI] [PubMed] [Google Scholar]
  22. Grandbastien M. A., Spielmann A., Caboche M. Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature. 1989 Jan 26;337(6205):376–380. doi: 10.1038/337376a0. [DOI] [PubMed] [Google Scholar]
  23. Hirochika H., Otsuki H. Extrachromosomal circular forms of the tobacco retrotransposon Tto1. Gene. 1995 Nov 20;165(2):229–232. doi: 10.1016/0378-1119(95)00581-p. [DOI] [PubMed] [Google Scholar]
  24. Hong T., Drlica K., Pinter A., Murphy E. Circular DNA of human immunodeficiency virus: analysis of circle junction nucleotide sequences. J Virol. 1991 Jan;65(1):551–555. doi: 10.1128/jvi.65.1.551-555.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Katz R. A., Skalka A. M. The retroviral enzymes. Annu Rev Biochem. 1994;63:133–173. doi: 10.1146/annurev.bi.63.070194.001025. [DOI] [PubMed] [Google Scholar]
  26. Katzman M., Katz R. A., Skalka A. M., Leis J. The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration. J Virol. 1989 Dec;63(12):5319–5327. doi: 10.1128/jvi.63.12.5319-5327.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kere J., Nagaraja R., Mumm S., Ciccodicola A., D'Urso M., Schlessinger D. Mapping human chromosomes by walking with sequence-tagged sites from end fragments of yeast artificial chromosome inserts. Genomics. 1992 Oct;14(2):241–248. doi: 10.1016/s0888-7543(05)80212-5. [DOI] [PubMed] [Google Scholar]
  28. Kiesewetter S., Ott G., Sprinzl M. The role of modified purine 64 in initiator/elongator discrimination of tRNA(iMet) from yeast and wheat germ. Nucleic Acids Res. 1990 Aug 25;18(16):4677–4682. doi: 10.1093/nar/18.16.4677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Kikuchi Y., Ando Y., Shiba T. Unusual priming mechanism of RNA-directed DNA synthesis in copia retrovirus-like particles of Drosophila. 1986 Oct 30-Nov 5Nature. 323(6091):824–826. doi: 10.1038/323824a0. [DOI] [PubMed] [Google Scholar]
  30. Kim A., Terzian C., Santamaria P., Pélisson A., Purd'homme N., Bucheton A. Retroviruses in invertebrates: the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1285–1289. doi: 10.1073/pnas.91.4.1285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Kirchner J., Sandmeyer S. B. Ty3 integrase mutants defective in reverse transcription or 3'-end processing of extrachromosomal Ty3 DNA. J Virol. 1996 Jul;70(7):4737–4747. doi: 10.1128/jvi.70.7.4737-4747.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Lauermann V., Nam K., Trambley J., Boeke J. D. Plus-strand strong-stop DNA synthesis in retrotransposon Ty1. J Virol. 1995 Dec;69(12):7845–7850. doi: 10.1128/jvi.69.12.7845-7850.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Levin H. L. A novel mechanism of self-primed reverse transcription defines a new family of retroelements. Mol Cell Biol. 1995 Jun;15(6):3310–3317. doi: 10.1128/mcb.15.6.3310. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Lucas H., Feuerbach F., Kunert K., Grandbastien M. A., Caboche M. RNA-mediated transposition of the tobacco retrotransposon Tnt1 in Arabidopsis thaliana. EMBO J. 1995 May 15;14(10):2364–2373. doi: 10.1002/j.1460-2075.1995.tb07231.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Marlor R. L., Parkhurst S. M., Corces V. G. The Drosophila melanogaster gypsy transposable element encodes putative gene products homologous to retroviral proteins. Mol Cell Biol. 1986 Apr;6(4):1129–1134. doi: 10.1128/mcb.6.4.1129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Mhiri C., Morel J. B., Vernhettes S., Casacuberta J. M., Lucas H., Grandbastien M. A. The promoter of the tobacco Tnt1 retrotransposon is induced by wounding and by abiotic stress. Plant Mol Biol. 1997 Jan;33(2):257–266. doi: 10.1023/a:1005727132202. [DOI] [PubMed] [Google Scholar]
  37. Moore S. P., Garfinkel D. J. Expression and partial purification of enzymatically active recombinant Ty1 integrase in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1843–1847. doi: 10.1073/pnas.91.5.1843. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Moore S. P., Powers M., Garfinkel D. J. Substrate specificity of Ty1 integrase. J Virol. 1995 Aug;69(8):4683–4692. doi: 10.1128/jvi.69.8.4683-4692.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Preston B. D. Error-prone retrotransposition: rime of the ancient mutators. Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7427–7431. doi: 10.1073/pnas.93.15.7427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Ratner L., Haseltine W., Patarca R., Livak K. J., Starcich B., Josephs S. F., Doran E. R., Rafalski J. A., Whitehorn E. A., Baumeister K. Complete nucleotide sequence of the AIDS virus, HTLV-III. Nature. 1985 Jan 24;313(6000):277–284. doi: 10.1038/313277a0. [DOI] [PubMed] [Google Scholar]
  41. Roth M. J., Schwartzberg P. L., Goff S. P. Structure of the termini of DNA intermediates in the integration of retroviral DNA: dependence on IN function and terminal DNA sequence. Cell. 1989 Jul 14;58(1):47–54. doi: 10.1016/0092-8674(89)90401-7. [DOI] [PubMed] [Google Scholar]
  42. Saigo K., Kugimiya W., Matsuo Y., Inouye S., Yoshioka K., Yuki S. Identification of the coding sequence for a reverse transcriptase-like enzyme in a transposable genetic element in Drosophila melanogaster. Nature. 1984 Dec 13;312(5995):659–661. doi: 10.1038/312659a0. [DOI] [PubMed] [Google Scholar]
  43. Smith J. S., Kim S. Y., Roth M. J. Analysis of long terminal repeat circle junctions of human immunodeficiency virus type 1. J Virol. 1990 Dec;64(12):6286–6290. doi: 10.1128/jvi.64.12.6286-6290.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Tanda S., Mullor J. L., Corces V. G. The Drosophila tom retrotransposon encodes an envelope protein. Mol Cell Biol. 1994 Aug;14(8):5392–5401. doi: 10.1128/mcb.14.8.5392. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Taylor J. M., Hsu T. W., Yeater C., Mason W. S. Synthesis and integration of avian sarcoma virus DNA. Cold Spring Harb Symp Quant Biol. 1980;44(Pt 2):1091–1096. doi: 10.1101/sqb.1980.044.01.117. [DOI] [PubMed] [Google Scholar]
  46. Vink C., Plasterk R. H. The human immunodeficiency virus integrase protein. Trends Genet. 1993 Dec;9(12):433–438. doi: 10.1016/0168-9525(93)90107-s. [DOI] [PubMed] [Google Scholar]
  47. Vora A. C., Fitzgerald M. L., Grandgenett D. P. Removal of 3'-OH-terminal nucleotides from blunt-ended long terminal repeat termini by the avian retrovirus integration protein. J Virol. 1990 Nov;64(11):5656–5659. doi: 10.1128/jvi.64.11.5656-5659.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Wain-Hobson S., Sonigo P., Danos O., Cole S., Alizon M. Nucleotide sequence of the AIDS virus, LAV. Cell. 1985 Jan;40(1):9–17. doi: 10.1016/0092-8674(85)90303-4. [DOI] [PubMed] [Google Scholar]
  49. Whitcomb J. M., Hughes S. H. The sequence of human immunodeficiency virus type 2 circle junction suggests that integration protein cleaves the ends of linear DNA asymmetrically. J Virol. 1991 Jul;65(7):3906–3910. doi: 10.1128/jvi.65.7.3906-3910.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Whitcomb J. M., Kumar R., Hughes S. H. Sequence of the circle junction of human immunodeficiency virus type 1: implications for reverse transcription and integration. J Virol. 1990 Oct;64(10):4903–4906. doi: 10.1128/jvi.64.10.4903-4906.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. van den Ent F. M., Vink C., Plasterk R. H. DNA substrate requirements for different activities of the human immunodeficiency virus type 1 integrase protein. J Virol. 1994 Dec;68(12):7825–7832. doi: 10.1128/jvi.68.12.7825-7832.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES