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A sequence similar to tRNA3Lys gene is embedded in HIV-1 U3–R and promotes minus-strand transfer

Nature Structural & Molecular Biology volume 17, pages 83–89 (2010)Cite this article

Abstract

We identified a sequence embedded in the U3–R region of HIV-1 RNA that is highly complementary to human tRNA3Lys. The free energy of annealing to tRNA3Lys is significantly lower for this sequence and the primer-binding site than for other viral sequences of similar length. The only interruption in complementarity is a 29-nucleotide segment inserted where a tRNA intron would be expected. The insert contains the TATA box for viral RNA transcription. The embedded sequence includes a 9-nucleotide segment previously reported to aid minus-strand transfer by binding the primer tRNA3Lys. Reconstituting transfer in vitro, we show that including segments from the embedded sequence in the acceptor template, beyond the 9 nucleotides, further increases transfer efficiency. We propose that a gene encoding tRNA3Lys was incorporated during HIV-1 evolution and retained, largely intact, because of its roles in transcription and strand transfer.

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Figure 1: A sequence in HIV-1 U3–R complementary to tRNA3Lys.
Figure 2: Distribution of binding stabilities in kcal mol−1 of shuffled tRNA3Lys to HIV-1.
Figure 3: The tRNA gene–like sequence is well preserved in HIV-1 and SIVcpz.
Figure 4: A system for analysis of the influence of tRNA3Lys-U3 interactions during minus-strand DNA transfer.
Figure 5: Analysis of the tRNA3Lys/U3 interaction during minus-strand DNA transfer.
Figure 6: Effects of mutations within U3 on the minus-strand transfer reaction primed from tRNA3Lys and the DNA oligonucleotide.

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References

  1. Basu, V.P. et al. Strand transfer events during HIV-1 reverse transcription. Virus Res. 134, 19–38 (2008).

    Article  CAS  Google Scholar 

  2. Chen, Y., Balakrishnan, M., Roques, B.P. & Bambara, R.A. Steps of the acceptor invasion mechanism for HIV-1 minus strand strong stop transfer. J. Biol. Chem. 278, 38368–38375 (2003).

    Article  CAS  Google Scholar 

  3. Peliska, J.A. & Benkovic, S.J. Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase. Science 258, 1112–1118 (1992).

    Article  CAS  Google Scholar 

  4. Negroni, M. & Buc, H. Copy-choice recombination by reverse transcriptases: reshuffling of genetic markers mediated by RNA chaperones. Proc. Natl. Acad. Sci. USA 97, 6385–6390 (2000).

    Article  CAS  Google Scholar 

  5. Feng, Y.X. et al. The human immunodeficiency virus type 1 Gag polyprotein has nucleic acid chaperone activity: possible role in dimerization of genomic RNA and placement of tRNA on the primer binding site. J. Virol. 73, 4251–4256 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. You, J.C. & McHenry, C.S. Human immunodeficiency virus nucleocapsid protein accelerates strand transfer of the terminally redundant sequences involved in reverse transcription. J. Biol. Chem. 269, 31491–31495 (1994).

    CAS  PubMed  Google Scholar 

  7. Rodriguez-Rodriguez, L., Tsuchihashi, Z., Fuentes, G.M., Bambara, R.A. & Fay, P.J. Influence of human immunodeficiency virus nucleocapsid protein on synthesis and strand transfer by the reverse transcriptase in vitro. J. Biol. Chem. 270, 15005–15011 (1995).

    Article  CAS  Google Scholar 

  8. Brule, F. et al. In vitro evidence for the interaction of tRNA3Lys with U3 during the first strand transfer of HIV-1 reverse transcription. Nucleic Acids Res. 28, 634–640 (2000).

    Article  CAS  Google Scholar 

  9. Song, M., Balakrishnan, M., Gorelick, R.J. & Bambara, R.A. A succession of mechanisms stimulate efficient reconstituted HIV-1 minus strand strong stop DNA transfer. Biochemistry 48, 1810–1819 (2009).

    Article  CAS  Google Scholar 

  10. Aiyar, A., Cobrinik, D., Ge, Z., Kung, H.J. & Leis, J. Interaction between retroviral U5 RNA and the T psi C loop of the tRNATrp primer is required for efficient initiation of reverse transcription. J. Virol. 66, 2464–2472 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Isel, C., Marquet, R., Keith, G., Ehresmann, C. & Ehresmann, B. Modified nucleotides of tRNA(3Lys) modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription. J. Biol. Chem. 268, 25269–25272 (1993).

    CAS  PubMed  Google Scholar 

  12. Zhang, Z., Kang, S.M., Li, Y. & Morrow, C.D. Genetic analysis of the U5-PBS of a novel HIV-1 reveals multiple interactions between the tRNA and RNA genome required for initiation of reverse transcription. RNA 4, 394–406 (1998).

    Article  CAS  Google Scholar 

  13. Iwatani, Y., Rosen, A.E., Guo, J., Musier-Forsyth, K. & Levin, J.G. Efficient initiation of HIV-1 reverse transcription in vitro. Requirement for RNA sequences downstream of the primer binding site abrogated by nucleocapsid protein-dependent primer-template interactions. J. Biol. Chem. 278, 14185–14195 (2003).

    Article  CAS  Google Scholar 

  14. Beerens, N., Groot, F. & Berkhout, B. Initiation of HIV-1 reverse transcription is regulated by a primer activation signal. J. Biol. Chem. 276, 31247–31256 (2001).

    Article  CAS  Google Scholar 

  15. Berkhout, B. & Schoneveld, I. Secondary structure of the HIV-2 leader RNA comprising the tRNA-primer binding site. Nucleic Acids Res. 21, 1171–1178 (1993).

    Article  CAS  Google Scholar 

  16. Friant, S., Heyman, T., Wilhelm, M.L. & Wilhelm, F.X. Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon. Nucleic Acids Res. 24, 441–449 (1996).

    Article  CAS  Google Scholar 

  17. Kleiman, L. tRNA(Lys3): the primer tRNA for reverse transcription in HIV-1. IUBMB Life 53, 107–114 (2002).

    Article  CAS  Google Scholar 

  18. Mathews, D.H., Burkard, M.E., Freier, S.M., Wyatt, J.R. & Turner, D.H. Predicting oligonucleotide affinity to nucleic acid targets. RNA 5, 1458–1469 (1999).

    Article  CAS  Google Scholar 

  19. Mathews, D.H. et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101, 7287–7292 (2004).

    Article  CAS  Google Scholar 

  20. Peeters, M. et al. Isolation and partial characterization of an HIV-related virus occurring naturally in chimpanzees in Gabon. AIDS 3, 625–630 (1989).

    Article  CAS  Google Scholar 

  21. Hirsch, V.M., Olmsted, R.A., Murphey-Corb, M., Purcell, R.H. & Johnson, P.R. An African primate lentivirus (SIVsm) closely related to HIV-2. Nature 339, 389–392 (1989).

    Article  CAS  Google Scholar 

  22. Tebit, D.M., Nankya, I., Arts, E.J. & Gao, Y. HIV diversity, recombination and disease progression: how does fitness “fit” into the puzzle? AIDS Rev. 9, 75–87 (2007).

    PubMed  Google Scholar 

  23. Goudsmit, J. Beyond SIV and HIV: the cat connection. in Viral Sex: The Nature of AIDS Ch. 8, 127–142 (Oxford University Press US, New York, 1997).

  24. Gifford, R.J. et al. A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc. Natl. Acad. Sci. USA 105, 20362–20367 (2008).

    Article  CAS  Google Scholar 

  25. Chen, Y., Balakrishnan, M., Roques, B.P., Fay, P.J. & Bambara, R.A. Mechanism of minus strand strong stop transfer in HIV-1 reverse transcription. J. Biol. Chem. 278, 8006–8017 (2003).

    Article  CAS  Google Scholar 

  26. Guo, J., Henderson, L.E., Bess, J., Kane, B. & Levin, J.G. Human immunodeficiency virus type 1 nucleocapsid protein promotes efficient strand transfer and specific viral DNA synthesis by inhibiting TAR-dependent self-priming from minus-strand strong-stop DNA. J. Virol. 71, 5178–5188 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Pereira, L.A., Bentley, K., Peeters, A., Churchill, M.J. & Deacon, N.J. A compilation of cellular transcription factor interactions with the HIV-1 LTR promoter. Nucleic Acids Res. 28, 663–668 (2000).

    Article  CAS  Google Scholar 

  28. Rana, T.M. & Jeang, K.T. Biochemical and functional interactions between HIV-1 Tat protein and TAR RNA. Arch. Biochem. Biophys. 365, 175–185 (1999).

    Article  CAS  Google Scholar 

  29. Naghavi, M.H., Schwartz, S., Sonnerborg, A. & Vahlne, A. Long terminal repeat promoter/enhancer activity of different subtypes of HIV type 1. AIDS Res. Hum. Retroviruses 15, 1293–1303 (1999).

    Article  CAS  Google Scholar 

  30. Ramirez de Arellano, E., Martin, C., Soriano, V., Alcami, J. & Holguin, A. Genetic analysis of the long terminal repeat (LTR) promoter region in HIV-1-infected individuals with different rates of disease progression. Virus Genes 34, 111–116 (2007).

    Article  CAS  Google Scholar 

  31. Lowe, T.M. & Eddy, S.R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).

    Article  CAS  Google Scholar 

  32. Carpenter, M.A. & O'Brien, S.J. Coadaptation and immunodeficiency virus: lessons from the Felidae. Curr. Opin. Genet. Dev. 5, 739–745 (1995).

    Article  CAS  Google Scholar 

  33. Halpern, C.C., Hayward, W.S. & Hanafusa, H. Characterization of some isolates of newly recovered avian sarcoma virus. J. Virol. 29, 91–101 (1979).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Temin, H.M. Origin of retroviruses from cellular moveable genetic elements. Cell 21, 599–600 (1980).

    Article  CAS  Google Scholar 

  35. Malik, H.S. & Eickbush, T.H. Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res. 11, 1187–1197 (2001).

    Article  CAS  Google Scholar 

  36. Eickbush, T.H. Origin and evolutionary relationships of retroelements. in The Evolutionary Biology of Viruses (ed. Morse, S.S.) 121–157 (Raven Press., New York, 1994).

  37. Eickbush, T.H. & Malik, H.S. Origins and evolution of retrotransposons. in Mobile DNA II (eds. Craig, N.L., Craigie, R., Gellert, M. & Lambowitz, A.M.) 1111–1144 (American Society of Microbiology Press, Washington, DC, 2002).

  38. Hansen, L.J., Chalker, D.L., Orlinsky, K.J. & Sandmeyer, S.B. Ty3 GAG3 and POL3 genes encode the components of intracellular particles. J. Virol. 66, 1414–1424 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Kim, A. et al. Retroviruses in invertebrates: the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 91, 1285–1289 (1994).

    Article  CAS  Google Scholar 

  40. Llorens, C., Fares, M.A. & Moya, A. Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis. BMC Evol. Biol. 8, 276 (2008).

    Article  Google Scholar 

  41. Boeke, J.D. & Devine, S.E. Yeast retrotransposons: finding a nice quiet neighborhood. Cell 93, 1087–1089 (1998).

    Article  CAS  Google Scholar 

  42. Szafranski, K. et al. Non-LTR retrotransposons with unique integration preferences downstream of Dictyostelium discoideum tRNA genes. Mol. Gen. Genet. 262, 772–780 (1999).

    Article  CAS  Google Scholar 

  43. Paolella, G., Lucero, M.A., Murphy, M.H. & Baralle, F.E. The Alu family repeat promoter has a tRNA-like bipartite structure. EMBO J. 2, 691–696 (1983).

    Article  CAS  Google Scholar 

  44. Lawrence, C.B., McDonnell, D.P. & Ramsey, W.J. Analysis of repetitive sequence elements containing tRNA-like sequences. Nucleic Acids Res. 13, 4239–4252 (1985).

    Article  CAS  Google Scholar 

  45. Bertling, W.M. Full length L1 retroposons contain tRNA-like sequences near the 5′ termini–hypothesis on the replication mechanism of retroposons. J. Theor. Biol. 138, 185–194 (1989).

    Article  CAS  Google Scholar 

  46. Bak, A.L. & Jorgensen, A.L. RNA polymerase III control regions in retrovirus LTR, Alu-type repetitive DNA, and papovavirus. J. Theor. Biol. 108, 339–348 (1984).

    Article  CAS  Google Scholar 

  47. Frenkel, F.E., Chaley, M.B., Korotkov, E.V. & Skryabin, K.G. Evolution of tRNA-like sequences and genome variability. Gene 335, 57–71 (2004).

    Article  CAS  Google Scholar 

  48. Geiduschek, E.P. & Tocchini-Valentini, G.P. Transcription by RNA polymerase III. Annu. Rev. Biochem. 57, 873–914 (1988).

    Article  CAS  Google Scholar 

  49. Oliviero, S. & Monaci, P. RNA polymerase III promoter elements enhance transcription of RNA polymerase II genes. Nucleic Acids Res. 16, 1285–1293 (1988).

    Article  CAS  Google Scholar 

  50. Kirchner, J., Connolly, C.M. & Sandmeyer, S.B. Requirement of RNA polymerase III transcription factors for in vitro position-specific integration of a retroviruslike element. Science 267, 1488–1491 (1995).

    Article  CAS  Google Scholar 

  51. Siol, O. et al. Role of RNA polymerase III transcription factors in the selection of integration sites by the dictyostelium non-long terminal repeat retrotransposon TRE5-A. Mol. Cell. Biol. 26, 8242–8251 (2006).

    Article  CAS  Google Scholar 

  52. Stevens, S.W. & Griffith, J.D. Human immunodeficiency virus type 1 may preferentially integrate into chromatin occupied by L1Hs repetitive elements. Proc. Natl. Acad. Sci. USA 91, 5557–5561 (1994).

    Article  CAS  Google Scholar 

  53. Stevens, S.W. & Griffith, J.D. Sequence analysis of the human DNA flanking sites of human immunodeficiency virus type 1 integration. J. Virol. 70, 6459–6462 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Noma, K., Cam, H.P., Maraia, R.J. & Grewal, S.I. A role for TFIIIC transcription factor complex in genome organization. Cell 125, 859–872 (2006).

    Article  CAS  Google Scholar 

  55. Roda, R.H. et al. Role of the reverse transcriptase, nucleocapsid protein, and template structure in the two-step transfer mechanism in retroviral recombination. J. Biol. Chem. 278, 31536–31546 (2003).

    Article  CAS  Google Scholar 

  56. Rehmsmeier, M., Steffen, P., Hochsmann, M. & Giegerich, R. Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507–1517 (2004).

    Article  CAS  Google Scholar 

  57. Notredame, C., Higgins, D.G. & Heringa, J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217 (2000).

    Article  CAS  Google Scholar 

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Acknowledgements

This work was supported by the US National Institutes of Health research grants GM049573 (to R.A.B.) and GM076485 (to D.H.M.). We received additional support from the Rochester Developmental Center for AIDS Research (NIH P30-AI78498). We are grateful to R.J. Gorelick for NC used in these studies. We thank T.H. Eickbush, H. Smith, L. Balakrishnan and students of the Bambara laboratory group for helpful comments.

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  1. Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA

    Dorota Piekna-Przybylska, Laura DiChiacchio, David H Mathews & Robert A Bambara

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  1. Dorota Piekna-Przybylska
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  2. Laura DiChiacchio
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  3. David H Mathews
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Contributions

R.A.B., D.P.-P. and D.H.M. designed the project; D.P.-P. identified the intron, performed sequence alignment, designed and performed biochemical experiments, and wrote the manuscript; L.D. and D.H.M. performed computational analysis of virus genomes for hybridization with tRNA3Lys; and R.A.B. edited the manuscript.

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Correspondence to Robert A Bambara.

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Piekna-Przybylska, D., DiChiacchio, L., Mathews, D. et al. A sequence similar to tRNA3Lys gene is embedded in HIV-1 U3–R and promotes minus-strand transfer. Nat Struct Mol Biol 17, 83–89 (2010). https://doi.org/10.1038/nsmb.1687

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