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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References
Basu, V.P. et al. Strand transfer events during HIV-1 reverse transcription. Virus Res. 134, 19–38 (2008).
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).
Peliska, J.A. & Benkovic, S.J. Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase. Science 258, 1112–1118 (1992).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Kleiman, L. tRNA(Lys3): the primer tRNA for reverse transcription in HIV-1. IUBMB Life 53, 107–114 (2002).
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).
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).
Peeters, M. et al. Isolation and partial characterization of an HIV-related virus occurring naturally in chimpanzees in Gabon. AIDS 3, 625–630 (1989).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Carpenter, M.A. & O'Brien, S.J. Coadaptation and immunodeficiency virus: lessons from the Felidae. Curr. Opin. Genet. Dev. 5, 739–745 (1995).
Halpern, C.C., Hayward, W.S. & Hanafusa, H. Characterization of some isolates of newly recovered avian sarcoma virus. J. Virol. 29, 91–101 (1979).
Temin, H.M. Origin of retroviruses from cellular moveable genetic elements. Cell 21, 599–600 (1980).
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).
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).
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).
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).
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).
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).
Boeke, J.D. & Devine, S.E. Yeast retrotransposons: finding a nice quiet neighborhood. Cell 93, 1087–1089 (1998).
Szafranski, K. et al. Non-LTR retrotransposons with unique integration preferences downstream of Dictyostelium discoideum tRNA genes. Mol. Gen. Genet. 262, 772–780 (1999).
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).
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).
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).
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).
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).
Geiduschek, E.P. & Tocchini-Valentini, G.P. Transcription by RNA polymerase III. Annu. Rev. Biochem. 57, 873–914 (1988).
Oliviero, S. & Monaci, P. RNA polymerase III promoter elements enhance transcription of RNA polymerase II genes. Nucleic Acids Res. 16, 1285–1293 (1988).
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).
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).
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).
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).
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).
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).
Rehmsmeier, M., Steffen, P., Hochsmann, M. & Giegerich, R. Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507–1517 (2004).
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).
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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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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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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DOI: https://doi.org/10.1038/nsmb.1687
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