Viral Reverse Transcriptases Show Selective High Affinity Binding to DNA-DNA Primer-templates That Resemble the Polypurine Tract

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2012 Aug 1

PMID 22848574

Citations 5

Authors

Gauri R Nair

Chandravanu Dash

Stuart F J Le Grice

Jeffrey J DeStefano

Affiliations

Soon will be listed here.

Abstract

Previous results using a SELEX (Systematic Evolution of Ligands by Exponential Enrichment)-based approach that selected DNA primer-template duplexes binding with high affinity to HIV reverse transcriptase (RT) showed that primers mimicking the 3' end, and in particular the six nt terminal G tract, of the RNA polypurine tract (PPT; HIV PPT: 5'-AAAAGAAAAGGGGGG-3') were preferentially selected. In this report, two viral (Moloney murine leukemia virus (MuLV) and avian myeloblastosis virus (AMV)) and one retrotransposon (Ty3) RTs were used for selection. Like HIV RT, both viral RTs selected duplexes with primer strands mimicking the G tract at the PPT 3' end (AMV PPT: 5'-AGGGAGGGGGA-3'; MuLV PPT: 5'-AGAAAAAGGGGGG-3'). In contrast, Ty3, whose PPT lacks a G tract (5'-GAGAGAGAGGAA-3') showed no selective binding to any duplex sequences. Experiments were also conducted with DNA duplexes (termed DNA PPTs) mimicking the RNA PPT-DNA duplex of each virus and a control duplex with a random DNA sequence. Retroviral RTs bound with high affinity to all viral DNA PPT constructs, with HIV and MuLV RTs showing comparable binding to the counterpart DNA PPT duplexes and reduced affinity to the AMV DNA PPT. AMV RT showed similar behavior with a modest preference for its own DNA PPT. Ty3 RT showed no preferential binding for its own or any other DNA PPT and viral RTs bound the Ty3 DNA PPT with relatively low affinity. In contrast, binding affinity of HIV RT to duplexes containing the HIV RNA PPT was less dependent on the G tract, which is known to be pivotal for efficient extension. We hypothesize that the G tract on the RNA PPT helps shift the binding orientation of RT to the 3' end of the PPT where extension can occur.

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References

Patel P, Ding J, Tantillo C, Clark Jr A, Raag R, Nanni R . Insights into DNA polymerization mechanisms from structure and function analysis of HIV-1 reverse transcriptase. Biochemistry. 1995; 34(16):5351-63. DOI: 10.1021/bi00016a006. View

McClure M . Evolution of retroposons by acquisition or deletion of retrovirus-like genes. Mol Biol Evol. 1991; 8(6):835-56. DOI: 10.1093/oxfordjournals.molbev.a040686. View

Jacob D, DeStefano J . A new role for HIV nucleocapsid protein in modulating the specificity of plus strand priming. Virology. 2008; 378(2):385-96. PMC: 2607142. DOI: 10.1016/j.virol.2008.06.002. View

Destefano J . The orientation of binding of human immunodeficiency virus reverse transcriptase on nucleic acid hybrids. Nucleic Acids Res. 1995; 23(19):3901-8. PMC: 307308. DOI: 10.1093/nar/23.19.3901. View

Robson N, Telesnitsky A . Selection of optimal polypurine tract region sequences during Moloney murine leukemia virus replication. J Virol. 2000; 74(22):10293-303. PMC: 110903. DOI: 10.1128/jvi.74.22.10293-10303.2000. View

Xiong Y, Eickbush T . Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990; 9(10):3353-62. PMC: 552073. DOI: 10.1002/j.1460-2075.1990.tb07536.x. View

Schneider D, Feigon J, Hostomsky Z, Gold L . High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry. 1995; 34(29):9599-610. DOI: 10.1021/bi00029a037. View

Gorshkova I, Rausch J, Le Grice S, Crouch R . HIV-1 reverse transcriptase interaction with model RNA-DNA duplexes. Anal Biochem. 2001; 291(2):198-206. DOI: 10.1006/abio.2001.5053. View

Schatz O, Cromme F, Le Grice S . Point mutations in conserved amino acid residues within the C-terminal domain of HIV-1 reverse transcriptase specifically repress RNase H function. FEBS Lett. 1989; 257(2):311-4. DOI: 10.1016/0014-5793(89)81559-5. View

10.

Zennou V, Petit C, Guetard D, Nerhbass U, Montagnier L, Charneau P . HIV-1 genome nuclear import is mediated by a central DNA flap. Cell. 2000; 101(2):173-85. DOI: 10.1016/S0092-8674(00)80828-4. View

11.

Kvaratskhelia M, Budihas S, Le Grice S . Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase. J Biol Chem. 2002; 277(19):16689-96. DOI: 10.1074/jbc.M109914200. View

12.

Julias J, McWilliams M, Sarafianos S, Alvord W, Arnold E, Hughes S . Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage. J Virol. 2004; 78(23):13315-24. PMC: 524982. DOI: 10.1128/JVI.78.23.13315-13324.2004. View

13.

Jones F, Hughes S . In vitro analysis of the effects of mutations in the G-tract of the human immunodeficiency virus type 1 polypurine tract on RNase H cleavage specificity. Virology. 2006; 360(2):341-9. DOI: 10.1016/j.virol.2006.10.008. View

14.

Arhel N, Souquere-Besse S, Charneau P . Wild-type and central DNA flap defective HIV-1 lentiviral vector genomes: intracellular visualization at ultrastructural resolution levels. Retrovirology. 2006; 3:38. PMC: 1538615. DOI: 10.1186/1742-4690-3-38. View

15.

Rausch J, Le Grice S . 'Binding, bending and bonding': polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus. Int J Biochem Cell Biol. 2004; 36(9):1752-66. DOI: 10.1016/j.biocel.2004.02.016. View

16.

Turner K, Yi-Brunozzi H, Brinson R, Marino J, Fabris D, Le Grice S . SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids. RNA. 2009; 15(8):1605-13. PMC: 2714758. DOI: 10.1261/rna.1615409. View

17.

Peliska J, Benkovic S . Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase. Science. 1992; 258(5085):1112-8. DOI: 10.1126/science.1279806. View

18.

Skasko M, Kim B . Compensatory role of human immunodeficiency virus central polypurine tract sequence in kinetically disrupted reverse transcription. J Virol. 2008; 82(15):7716-20. PMC: 2493349. DOI: 10.1128/JVI.00120-08. View

19.

Oh J, Chang K, Alvord W, Hughes S . Alternate polypurine tracts affect rous sarcoma virus integration in vivo. J Virol. 2006; 80(20):10281-4. PMC: 1617299. DOI: 10.1128/JVI.00361-06. View

20.

Powell M, LEVIN J . Sequence and structural determinants required for priming of plus-strand DNA synthesis by the human immunodeficiency virus type 1 polypurine tract. J Virol. 1996; 70(8):5288-96. PMC: 190486. DOI: 10.1128/JVI.70.8.5288-5296.1996. View