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Reverse Transcriptases

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Nucleic Acid Polymerases

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 30))

Abstract

Reverse transcriptases (RTs) catalyze the multi-step process that converts the single-stranded viral RNA genome to double-stranded integration-competent DNA, a process that is essential for the proliferation of retroviruses and retrotransposons. The former are released from cells as infectious particles and include human immunodeficiency virus (HIV) and hepadnaviruses such as hepatitis B virus (HBV). In contrast, retrotransposons are restricted to intracellular proliferation cycle and are very common in eukaryotic genomes. The N-terminal DNA polymerase domain of RTs structurally resembles other nucleic acid polymerases and assumes the topology of a right hand, with subdomains designated fingers, palm, and thumb. RTs exhibit low fidelity and processivity and are capable of both intra- and intermolecular strand displacement synthesis. A distinguishing feature of RTs is the presence of a C-terminal ribonuclease H (RNase H) domain in enzymes from viruses and long terminal repeat (LTR)-containing retrotransposons. The general role of this domain is sequence-independent removal of RNA from the RNA/DNA hybrid intermediates of reverse transcription, although precise cleavage is also required to mediate key steps such as (+) strand primer selection and DNA strand transfer. In LTR retroelements the RNase H domain is located immediately following the thumb subdomain, while in retroviruses an RNase H-like “connection domain” devoid of catalytic activity is followed by the catalytically competent C-terminal RNase H domain. DNA polymerase and RNase H activities are coordinated, but RNA/DNA hybrid hydrolysis is significantly slower than nucleotide incorporation. Whether this reflects simultaneous or individual active site occupancy of the nucleic acid substrate remains controversial.

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References

  • Agopian A, Depollier J et al (2007) p66 Trp24 and Phe61 are essential for accurate association of HIV-1 reverse transcriptase with primer/template. J Mol Biol 373(1):127–140

    PubMed  CAS  Google Scholar 

  • Anzai T, Takahashi H et al (2001) Sequence-specific recognition and cleavage of telomeric repeat (TTAGG)(n) by endonuclease of non-long terminal repeat retrotransposon TRAS1. Mol Cell Biol 21(1):100–108

    PubMed  CAS  Google Scholar 

  • Arion D, Sluis-Cremer N et al (2002) Mutational analysis of Tyr-501 of HIV-1 reverse transcriptase. Effects on ribonuclease H activity and inhibition of this activity by N-acylhydrazones. J Biol Chem 277(2):1370–1374

    PubMed  CAS  Google Scholar 

  • Avidan O, Meer ME et al (2002) The processivity and fidelity of DNA synthesis exhibited by the reverse transcriptase of bovine leukemia virus. Eur J Biochem 269(3):859–867

    PubMed  CAS  Google Scholar 

  • Bahar I, Erman B et al (1999) Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. J Mol Biol 285(3):1023–1037

    PubMed  CAS  Google Scholar 

  • Bakhanashvili M, Avidan O et al (1996) Mutational studies of human immunodeficiency virus type 1 reverse transcriptase: the involvement of residues 183 and 184 in the fidelity of DNA synthesis. FEBS Lett 391(3):257–262

    PubMed  CAS  Google Scholar 

  • Baltimore D (1970) RNA-dependent DNA polymerase in virions of RNA tumour viruses. Nature 226(5252):1209–1211

    PubMed  CAS  Google Scholar 

  • Beerens N, Berkhout B (2002) The tRNA primer activation signal in the human immunodeficiency virus type 1 genome is important for initiation and processive elongation of reverse transcription. J Virol 76(5):2329–2339

    PubMed  CAS  Google Scholar 

  • Ben-Artzi H, Zeelon E et al (1992) Double-stranded RNA-dependent RNase activity associated with human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci USA 89(3):927–931

    PubMed  CAS  Google Scholar 

  • Berdis AJ, Stetor SR et al (2001) Molecular mechanism of sequence-specific termination of lentiviral replication. Biochemistry 40(40):12140–12149

    PubMed  CAS  Google Scholar 

  • Bibillo A, Lener D et al (2005a) Functional roles of carboxylate residues comprising the DNA polymerase active site triad of Ty3 reverse transcriptase. Nucleic Acids Res 33(1):171–181

    PubMed  CAS  Google Scholar 

  • Bibillo A, Lener D et al (2005b) Interaction of the Ty3 reverse transcriptase thumb subdomain with template-primer. J Biol Chem 280(34):30282–30290

    PubMed  CAS  Google Scholar 

  • Boutabout M, Wilhelm M et al (2001) DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1. Nucleic Acids Res 29(11):2217–2222

    PubMed  CAS  Google Scholar 

  • Boyer PL, Ferris AL et al (1992a) Cassette mutagenesis of the reverse transcriptase of human immunodeficiency virus type 1. J Virol 66(2):1031–1039

    PubMed  CAS  Google Scholar 

  • Boyer PL, Ferris AL et al (1992b) Mutational analysis of the fingers domain of human immunodeficiency virus type 1 reverse transcriptase. J Virol 66(12):7533–7537

    PubMed  CAS  Google Scholar 

  • Boyer PL, Ferris AL et al (1994) Mutational analysis of the fingers and palm subdomains of human immunodeficiency virus type-1 (HIV-1) reverse transcriptase. J Mol Biol 243(3):472–483

    PubMed  CAS  Google Scholar 

  • Broccoli S, Rallu F et al (2004) Effects of RNA polymerase modifications on transcription-induced negative supercoiling and associated R-loop formation. Mol Microbiol 52(6):1769–1779

    PubMed  CAS  Google Scholar 

  • Brown JA, Suo Z (2011) Unlocking the sugar “steric gate” of DNA polymerases. Biochemistry 50(7):1135–1142

    PubMed  CAS  Google Scholar 

  • Cases-Gonzalez CE, Gutierrez-Rivas M et al (2000) Coupling ribose selection to fidelity of DNA synthesis. The role of Tyr-115 of human immunodeficiency virus type 1 reverse transcriptase. J Biol Chem 275(26):19759–19767

    PubMed  CAS  Google Scholar 

  • Cen S, Khorchid A et al (2001) Incorporation of lysyl-tRNA synthetase into human immunodeficiency virus type 1. J Virol 75(11):5043–5048

    PubMed  CAS  Google Scholar 

  • Charneau P, Alizon M et al (1992) A second origin of DNA plus-strand synthesis is required for optimal human immunodeficiency virus replication. J Virol 66(5):2814–2820

    PubMed  CAS  Google Scholar 

  • Christensen S, Pont-Kingdon G et al (2000) Target specificity of the endonuclease from the Xenopus laevis non-long terminal repeat retrotransposon, Tx1L. Mol Cell Biol 20(4):1219–1226

    PubMed  CAS  Google Scholar 

  • Christensen SM, Ye J et al (2006) RNA from the 5′ end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site. Proc Natl Acad Sci USA 103(47):17602–17607

    PubMed  CAS  Google Scholar 

  • Cordaux R, Batzer MA (2009) The impact of retrotransposons on human genome evolution. Nat Rev Genet 10(10):691–703

    PubMed  CAS  Google Scholar 

  • Cost GJ, Feng Q et al (2002) Human L1 element target-primed reverse transcription in vitro. EMBO J 21(21):5899–5910

    PubMed  CAS  Google Scholar 

  • Cote ML, Roth MJ (2008) Murine leukemia virus reverse transcriptase: structural comparison with HIV-1 reverse transcriptase. Virus Res 134(1–2):186–202

    PubMed  CAS  Google Scholar 

  • Das D, Georgiadis MM (2004) The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus. Structure 12(5):819–829

    PubMed  CAS  Google Scholar 

  • Delviks-Frankenberry KA, Nikolenko GN et al (2008) HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision. Proc Natl Acad Sci USA 105(31):10943–10948

    PubMed  CAS  Google Scholar 

  • DeStefano JJ, Cristofaro JV et al (2001) Physical mapping of HIV reverse transcriptase to the 5′ end of RNA primers. J Biol Chem 276(35):32515–32521

    PubMed  CAS  Google Scholar 

  • Eickbush TH, Jamburuthugoda VK (2008) The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 134(1–2):221–234

    PubMed  CAS  Google Scholar 

  • Evans DB, Brawn K et al (1991) A recombinant ribonuclease H domain of HIV-1 reverse transcriptase that is enzymatically active. J Biol Chem 266(31):20583–20585

    PubMed  CAS  Google Scholar 

  • Fabris D, Marino JP et al (2009) Revisiting plus-strand DNA synthesis in retroviruses and long terminal repeat retrotransposons: dynamics of enzyme: substrate interactions. Viruses 1(3):657–677

    PubMed  CAS  Google Scholar 

  • Fuentes GM, Rodriguez-Rodriguez L et al (1996) Strand displacement synthesis of the long terminal repeats by HIV reverse transcriptase. J Biol Chem 271(4):1966–1971

    PubMed  CAS  Google Scholar 

  • Furfine ES, Reardon JE (1991a) Human immunodeficiency virus reverse transcriptase ribonuclease H: specificity of tRNA(Lys3)-primer excision. Biochemistry 30(29):7041–7046

    PubMed  CAS  Google Scholar 

  • Furfine ES, Reardon JE (1991b) Reverse transcriptase. RNase H from the human immunodeficiency virus. Relationship of the DNA polymerase and RNA hydrolysis activities. J Biol Chem 266(1):406–412

    PubMed  CAS  Google Scholar 

  • Gabriel A, Boeke JD (1991) Reverse transcriptase encoded by a retrotransposon from the trypanosomatid Crithidia fasciculata. Proc Natl Acad Sci USA 88(21):9794–9798

    PubMed  CAS  Google Scholar 

  • Gao G, Orlova M et al (1997) Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection. Proc Natl Acad Sci USA 94(2):407–411

    PubMed  CAS  Google Scholar 

  • Gao HQ, Boyer PL et al (1998) Effects of mutations in the polymerase domain on the polymerase, RNase H and strand transfer activities of human immunodeficiency virus type 1 reverse transcriptase. J Mol Biol 277(3):559–572

    PubMed  CAS  Google Scholar 

  • Gopalakrishnan V, Peliska JA et al (1992) Human immunodeficiency virus type 1 reverse transcriptase: spatial and temporal relationship between the polymerase and RNase H activities. Proc Natl Acad Sci USA 89(22):10763–10767

    PubMed  CAS  Google Scholar 

  • Gu J, Villanueva RA et al (2001) Substitution of Asp114 or Arg116 in the fingers domain of moloney murine leukemia virus reverse transcriptase affects interactions with the template-primer resulting in decreased processivity. J Mol Biol 305(2):341–359

    PubMed  CAS  Google Scholar 

  • Haruki M, Noguchi E et al (1997) Kinetic and stoichiometric analysis for the binding of Escherichia coli ribonuclease HI to RNA-DNA hybrids using surface plasmon resonance. J Biol Chem 272(35):22015–22022

    PubMed  CAS  Google Scholar 

  • Herschhorn A, Hizi A (2010) Retroviral reverse transcriptases. Cell Mol Life Sci 67(16):2717–2747

    PubMed  CAS  Google Scholar 

  • Himmel DM, Maegley KA et al (2009) Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site. Structure 17(12):1625–1635

    PubMed  CAS  Google Scholar 

  • Hostomsky Z, Hostomska Z et al (1991) Reconstitution in vitro of RNase H activity by using purified N-terminal and C-terminal domains of human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci USA 88(4):1148–1152

    PubMed  CAS  Google Scholar 

  • Hostomsky Z, Hughes SH et al (1994) Redesignation of the RNase D activity associated with retroviral reverse transcriptase as RNase H. J Virol 68(3):1970–1971

    PubMed  CAS  Google Scholar 

  • Hsiou Y, Ding J et al (1996) Structure of unliganded HIV-1 reverse transcriptase at 2.7 A resolution: implications of conformational changes for polymerization and inhibition mechanisms. Structure 4(7):853–860

    PubMed  CAS  Google Scholar 

  • Huang H, Chopra R et al (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282(5394):1669–1675

    PubMed  CAS  Google Scholar 

  • Huber HE, McCoy JM et al (1989) Human immunodeficiency virus 1 reverse transcriptase. Template binding, processivity, strand displacement synthesis, and template switching. J Biol Chem 264(8):4669–4678

    PubMed  CAS  Google Scholar 

  • Hungnes O, Tjotta E et al (1991) The plus strand is discontinuous in a subpopulation of unintegrated HIV-1 DNA. Arch Virol 116(1–4):133–141

    PubMed  CAS  Google Scholar 

  • Ilina T, Parniak MA (2008) Inhibitors of HIV-1 reverse transcriptase. Adv Pharmacol 56:121–167

    PubMed  CAS  Google Scholar 

  • Isel C, Marquet R et al (1993) Modified nucleotides of tRNA(3Lys) modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription. J Biol Chem 268(34):25269–25272

    PubMed  CAS  Google Scholar 

  • Isel C, Ehresmann C et al (1995) Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer). J Mol Biol 247(2):236–250

    PubMed  CAS  Google Scholar 

  • Isel C, Keith G et al (1998) Mutational analysis of the tRNA3Lys/HIV-1 RNA (primer/template) complex. Nucleic Acids Res 26(5):1198–1204

    PubMed  CAS  Google Scholar 

  • Isel C, Westhof E et al (1999) Structural basis for the specificity of the initiation of HIV-1 reverse transcription. EMBO J 18(4):1038–1048

    PubMed  CAS  Google Scholar 

  • Ivanov VA, Melnikov AA et al (1991) Authentic reverse transcriptase is coded by jockey, a mobile Drosophila element related to mammalian LINEs. EMBO J 10(9):2489–2495

    PubMed  CAS  Google Scholar 

  • Jacobo-Molina A, Ding J et al (1993) Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA. Proc Natl Acad Sci USA 90(13):6320–6324

    PubMed  CAS  Google Scholar 

  • Julias JG, McWilliams MJ et al (2002) Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specificity of RNase H cleavage in vivo. Proc Natl Acad Sci USA 99(14):9515–9520

    PubMed  CAS  Google Scholar 

  • Julias JG, McWilliams MJ et al (2003) Mutation of amino acids in the connection domain of human immunodeficiency virus type 1 reverse transcriptase that contact the template-primer affects RNase H activity. J Virol 77(15):8548–8554

    PubMed  CAS  Google Scholar 

  • Kanaya S, Katsuda-Nakai C et al (1991) Importance of the positive charge cluster in Escherichia coli ribonuclease HI for the effective binding of the substrate. J Biol Chem 266(18):11621–11627

    PubMed  CAS  Google Scholar 

  • Kati WM, Johnson KA et al (1992) Mechanism and fidelity of HIV reverse transcriptase. J Biol Chem 267(36):25988–25997

    PubMed  CAS  Google Scholar 

  • Kaushik N, Rege N et al (1996) Biochemical analysis of catalytically crucial aspartate mutants of human immunodeficiency virus type 1 reverse transcriptase. Biochemistry 35(36):11536–11546

    PubMed  CAS  Google Scholar 

  • Kaushik N, Chowdhury K et al (2000) Valine of the YVDD motif of moloney murine leukemia virus reverse transcriptase: role in the fidelity of DNA synthesis. Biochemistry 39(17):5155–5165

    PubMed  CAS  Google Scholar 

  • Keck JL, Marqusee S (1995) Substitution of a highly basic helix/loop sequence into the RNase H domain of human immunodeficiency virus reverse transcriptase restores its Mn(2+)-dependent RNase H activity. Proc Natl Acad Sci USA 92(7):2740–2744

    PubMed  CAS  Google Scholar 

  • Keck JL, Marqusee S (1996) The putative substrate recognition loop of Escherichia coli ribonuclease H is not essential for activity. J Biol Chem 271(33):19883–19887

    PubMed  CAS  Google Scholar 

  • Kelleher CD, Champoux JJ (1998) Characterization of RNA strand displacement synthesis by Moloney murine leukemia virus reverse transcriptase. J Biol Chem 273(16):9976–9986

    PubMed  CAS  Google Scholar 

  • Kim JK, Palaniappan C et al (1997) Evidence for a unique mechanism of strand transfer from the transactivation response region of HIV-1. J Biol Chem 272(27):16769–16777

    PubMed  CAS  Google Scholar 

  • Kim B, Ayran JC et al (1999) New human immunodeficiency virus, type 1 reverse transcriptase (HIV-1 RT) mutants with increased fidelity of DNA synthesis. Accuracy, template binding, and processivity. J Biol Chem 274(39):27666–27673

    PubMed  CAS  Google Scholar 

  • Klarmann GJ, Eisenhauer BM et al (2007) Investigating the “steric gate” of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase by targeted insertion of unnatural amino acids. Biochemistry 46(8):2118–2126

    PubMed  CAS  Google Scholar 

  • Kohlstaedt LA, Wang J et al (1992) Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256(5065):1783–1790

    PubMed  CAS  Google Scholar 

  • Krug MS, Berger SL (1989) Ribonuclease H activities associated with viral reverse transcriptases are endonucleases. Proc Natl Acad Sci USA 86(10):3539–3543

    PubMed  CAS  Google Scholar 

  • Kurzynska-Kokorniak A, Jamburuthugoda VK et al (2007) DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon. J Mol Biol 374(2):322–333

    PubMed  CAS  Google Scholar 

  • Kvaratskhelia M, Budihas SR et al (2002) Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase. J Biol Chem 277(19):16689–16696

    PubMed  CAS  Google Scholar 

  • Lampson BC, Inouye M et al (2005) Retrons, msDNA, and the bacterial genome. Cytogenet Genome Res 110(1–4):491–499

    PubMed  CAS  Google Scholar 

  • Lander ES, Linton LM et al (2001) Initial sequencing and analysis of the human genome. Nature 409(6822):860–921

    PubMed  CAS  Google Scholar 

  • Lapkouski M, Tian L et al (2013) Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation. Nat Struct Mol Biol 20(2):230–236

    PubMed  CAS  Google Scholar 

  • Le Grice SF (2003) “In the beginning”: initiation of minus strand DNA synthesis in retroviruses and LTR-containing retrotransposons. Biochemistry 42(49):14349–14355

    PubMed  Google Scholar 

  • Lener D, Budihas SR et al (2002) Mutating conserved residues in the ribonuclease H domain of Ty3 reverse transcriptase affects specialized cleavage events. J Biol Chem 277(29):26486–26495

    PubMed  CAS  Google Scholar 

  • Lewi P, Heeres J et al (2012) Reverse transcriptase inhibitors as microbicides. Curr HIV Res 10(1):27–35

    PubMed  CAS  Google Scholar 

  • Lin JH, Levin HL (1997) A complex structure in the mRNA of Tf1 is recognized and cleaved to generate the primer of reverse transcription. Genes Dev 11(2):270–285

    PubMed  CAS  Google Scholar 

  • Luan DD, Korman MH et al (1993) Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 72(4):595–605

    PubMed  CAS  Google Scholar 

  • Malik HS, Eickbush TH (2001) Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Genome Res 11(7):1187–1197

    PubMed  CAS  Google Scholar 

  • Mandal D, Dash C et al (2006) Analysis of HIV-1 replication block due to substitutions at F61 residue of reverse transcriptase reveals additional defects involving the RNase H function. Nucleic Acids Res 34(10):2853–2863

    PubMed  CAS  Google Scholar 

  • Marchand B, Tchesnokov EP et al (2007) The pyrophosphate analogue foscarnet traps the pre-translocational state of HIV-1 reverse transcriptase in a Brownian ratchet model of polymerase translocation. J Biol Chem 282(5):3337–3346

    PubMed  CAS  Google Scholar 

  • Mathias SL, Scott AF et al (1991) Reverse transcriptase encoded by a human transposable element. Science 254(5039):1808–1810

    PubMed  CAS  Google Scholar 

  • McWilliams MJ, Julias JG et al (2006) Combining mutations in HIV-1 reverse transcriptase with mutations in the HIV-1 polypurine tract affects RNase H cleavages involved in PPT utilization. Virology 348(2):378–388

    PubMed  CAS  Google Scholar 

  • Miller HI, Riggs AD et al (1973) Ribonuclease H (hybrid) in Escherichia coli. Identification and characterization. J Biol Chem 248(7):2621–2624

    PubMed  CAS  Google Scholar 

  • Mizrahi V, Usdin MT et al (1990) Site-directed mutagenesis of the conserved Asp-443 and Asp-498 carboxy-terminal residues of HIV-1 reverse transcriptase. Nucleic Acids Res 18(18):5359–5363

    PubMed  CAS  Google Scholar 

  • Mizrahi V, Brooksbank RL et al (1994) Mutagenesis of the conserved aspartic acid 443, glutamic acid 478, asparagine 494, and aspartic acid 498 residues in the ribonuclease H domain of p66/p51 human immunodeficiency virus type I reverse transcriptase. Expression and biochemical analysis. J Biol Chem 269(30):19245–19249

    PubMed  CAS  Google Scholar 

  • Moelling K (1974) Characterization of reverse transcriptase and RNase H from friend-murine leukemia virus. Virology 62(1):46–59

    PubMed  CAS  Google Scholar 

  • Nowak E, Potrzebowski W et al (2013) Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res 41(6):3874–3887

    PubMed  CAS  Google Scholar 

  • Nowotny M, Yang W (2006) Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release. EMBO J 25(9):1924–1933

    PubMed  CAS  Google Scholar 

  • Nowotny M, Gaidamakov SA et al (2005) Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell 121(7):1005–1016

    PubMed  CAS  Google Scholar 

  • Nowotny M, Gaidamakov SA et al (2007) Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription. Mol Cell 28(2):264–276

    PubMed  CAS  Google Scholar 

  • Ortiz TP, Marshall JA et al (2005) Stepping statistics of single HIV-1 reverse transcriptase molecules during DNA polymerization. J Phys Chem B 109(33):16127–16131

    PubMed  CAS  Google Scholar 

  • Oude Essink BB, Back NK et al (1997) Increased polymerase fidelity of the 3TC-resistant variants of HIV-1 reverse transcriptase. Nucleic Acids Res 25(16):3212–3217

    PubMed  CAS  Google Scholar 

  • Palaniappan C, Fuentes GM et al (1996) Helix structure and ends of RNA/DNA hybrids direct the cleavage specificity of HIV-1 reverse transcriptase RNase H. J Biol Chem 271(4):2063–2070

    PubMed  CAS  Google Scholar 

  • Pandey VN, Kaushik N et al (1996) Role of methionine 184 of human immunodeficiency virus type-1 reverse transcriptase in the polymerase function and fidelity of DNA synthesis. Biochemistry 35(7):2168–2179

    PubMed  CAS  Google Scholar 

  • Pandey M, Patel S et al (2004) Insights into the role of an active site aspartate in Ty1 reverse transcriptase polymerization. J Biol Chem 279(46):47840–47848

    PubMed  CAS  Google Scholar 

  • Paulson BA, Zhang M et al (2007) Substitution of alanine for tyrosine-64 in the fingers subdomain of M-MuLV reverse transcriptase impairs strand displacement synthesis and blocks viral replication in vivo. Virology 366(2):361–376

    PubMed  CAS  Google Scholar 

  • Perach M, Hizi A (1999) Catalytic features of the recombinant reverse transcriptase of bovine leukemia virus expressed in bacteria. Virology 259(1):176–189

    PubMed  CAS  Google Scholar 

  • Powell MD, Beard WA et al (1999) Residues in the alphaH and alphaI helices of the HIV-1 reverse transcriptase thumb subdomain required for the specificity of RNase H-catalyzed removal of the polypurine tract primer. J Biol Chem 274(28):19885–19893

    PubMed  CAS  Google Scholar 

  • Preston BD, Poiesz BJ et al (1988) Fidelity of HIV-1 reverse transcriptase. Science 242(4882):1168–1171

    PubMed  CAS  Google Scholar 

  • Pullen KA, Ishimoto LK et al (1992) Incomplete removal of the RNA primer for minus-strand DNA synthesis by human immunodeficiency virus type 1 reverse transcriptase. J Virol 66(1):367–373

    PubMed  CAS  Google Scholar 

  • Pyatkov KI, Arkhipova IR et al (2004) Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements. Proc Natl Acad Sci USA 101(41):14719–14724

    PubMed  CAS  Google Scholar 

  • Radzio J, Sluis-Cremer N (2011) Subunit-specific mutational analysis of residue N348 in HIV-1 reverse transcriptase. Retrovirology 8:69

    PubMed  CAS  Google Scholar 

  • Rausch JW, Le Grice SF (2004) ‘Binding, bending and bonding’: polypurine tract-primed initiation of plus-strand DNA synthesis in human immunodeficiency virus. Int J Biochem Cell Biol 36(9):1752–1766

    PubMed  CAS  Google Scholar 

  • Rausch JW, Lener D et al (2002) Altering the RNase H primer grip of human immunodeficiency virus reverse transcriptase modifies cleavage specificity. Biochemistry 41(15):4856–4865

    PubMed  CAS  Google Scholar 

  • Reardon JE (1992) Human immunodeficiency virus reverse transcriptase: steady-state and pre-steady-state kinetics of nucleotide incorporation. Biochemistry 31(18):4473–4479

    PubMed  CAS  Google Scholar 

  • Reijns MA, Rabe B et al (2012) Enzymatic removal of ribonucleotides from DNA is essential for mammalian genome integrity and development. Cell 149(5):1008–1022

    PubMed  CAS  Google Scholar 

  • Roberts JD, Bebenek K et al (1988) The accuracy of reverse transcriptase from HIV-1. Science 242(4882):1171–1173

    PubMed  CAS  Google Scholar 

  • Roberts JD, Preston BD et al (1989) Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro. Mol Cell Biol 9(2):469–476

    PubMed  CAS  Google Scholar 

  • Rodgers DW, Gamblin SJ et al (1995) The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1. Proc Natl Acad Sci USA 92(4):1222–1226

    PubMed  CAS  Google Scholar 

  • Roth MJ, Tanese N et al (1985) Purification and characterization of murine retroviral reverse transcriptase expressed in Escherichia coli. J Biol Chem 260(16):9326–9335

    PubMed  CAS  Google Scholar 

  • SanMiguel P, Gaut BS et al (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20(1):43–45

    PubMed  CAS  Google Scholar 

  • Sarafianos SG, Das K et al (2001) Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. EMBO J 20(6):1449–1461

    PubMed  CAS  Google Scholar 

  • Schatz O, Cromme FV et al (1989) Point mutations in conserved amino acid residues within the C-terminal domain of HIV-1 reverse transcriptase specifically repress RNase H function. FEBS Lett 257(2):311–314

    PubMed  CAS  Google Scholar 

  • Schultz SJ, Champoux JJ (1996) RNase H domain of Moloney murine leukemia virus reverse transcriptase retains activity but requires the polymerase domain for specificity. J Virol 70(12):8630–8638

    PubMed  CAS  Google Scholar 

  • Schultz SJ, Champoux JJ (2008) RNase H activity: structure, specificity, and function in reverse transcription. Virus Res 134(1–2):86–103

    PubMed  CAS  Google Scholar 

  • Schultz SJ, Zhang M et al (2004) Recognition of internal cleavage sites by retroviral RNases H. J Mol Biol 344(3):635–652

    PubMed  CAS  Google Scholar 

  • Simon DM, Zimmerly S (2008) A diversity of uncharacterized reverse transcriptases in bacteria. Nucleic Acids Res 36(22):7219–7229

    PubMed  CAS  Google Scholar 

  • Smith JS, Roth MJ (1993) Purification and characterization of an active human immunodeficiency virus type 1 RNase H domain. J Virol 67(7):4037–4049

    PubMed  CAS  Google Scholar 

  • Smith JS, Gritsman K et al (1994) Contributions of DNA polymerase subdomains to the RNase H activity of human immunodeficiency virus type 1 reverse transcriptase. J Virol 68(9):5721–5729

    PubMed  CAS  Google Scholar 

  • Stahl SJ, Kaufman JD et al (1994) Construction of an enzymatically active ribonuclease H domain of human immunodeficiency virus type 1 reverse transcriptase. Protein Eng 7(9):1103–1108

    PubMed  CAS  Google Scholar 

  • Steitz TA (1998) A mechanism for all polymerases. Nature 391(6664):231–232

    PubMed  CAS  Google Scholar 

  • Steitz TA, Steitz JA (1993) A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90(14):6498–6502

    PubMed  CAS  Google Scholar 

  • Stetor SR, Rausch JW et al (1999) Characterization of (+) strand initiation and termination sequences located at the center of the equine infectious anemia virus genome. Biochemistry 38(12):3656–3667

    PubMed  CAS  Google Scholar 

  • Tanese N, Goff SP (1988) Domain structure of the Moloney murine leukemia virus reverse transcriptase: mutational analysis and separate expression of the DNA polymerase and RNase H activities. Proc Natl Acad Sci USA 85(6):1777–1781

    PubMed  CAS  Google Scholar 

  • Telesnitsky A, Goff SP (1997) Reverse transcriptase and the generation of retroviral DNA. In: Coffin JM, Hughes SH, Varmus HE (eds) Retroviruses. Cold Spring Harbor Laboratory, Ney York

    Google Scholar 

  • Telesnitsky A, Blain SW et al (1992) Defects in Moloney murine leukemia virus replication caused by a reverse transcriptase mutation modeled on the structure of Escherichia coli RNase H. J Virol 66(2):615–622

    PubMed  CAS  Google Scholar 

  • Temin HM, Mizutani S (1970) RNA-dependent DNA polymerase in virions of Rous sarcoma virus. Nature 226(5252):1211–1213

    PubMed  CAS  Google Scholar 

  • Tisdale M, Schulze T et al (1991) Mutations within the RNase H domain of human immunodeficiency virus type 1 reverse transcriptase abolish virus infectivity. J Gen Virol 72(Pt 1):59–66

    PubMed  CAS  Google Scholar 

  • Turner KB, Brinson RG et al (2008) Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands. Nucleic Acids Res 36(8):2799–2810

    PubMed  CAS  Google Scholar 

  • Uzun O, Gabriel A (2001) A Ty1 reverse transcriptase active-site aspartate mutation blocks transposition but not polymerization. J Virol 75(14):6337–6347

    PubMed  CAS  Google Scholar 

  • Wahba L, Amon JD et al (2011) RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability. Mol Cell 44(6):978–988

    PubMed  CAS  Google Scholar 

  • Wainberg MA, Drosopoulos WC et al (1996) Enhanced fidelity of 3TC-selected mutant HIV-1 reverse transcriptase. Science 271(5253):1282–1285

    PubMed  CAS  Google Scholar 

  • Werner S, Wohrl BM (2000) Asymmetric subunit organization of heterodimeric Rous sarcoma virus reverse transcriptase alphabeta: localization of the polymerase and RNase H active sites in the alpha subunit. J Virol 74(7):3245–3252

    PubMed  CAS  Google Scholar 

  • Whiting SH, Champoux JJ (1998) Properties of strand displacement synthesis by Moloney murine leukemia virus reverse transcriptase: mechanistic implications. J Mol Biol 278(3):559–577

    PubMed  CAS  Google Scholar 

  • Whitwam T, Peretz M et al (2001) Identification of a central DNA flap in feline immunodeficiency virus. J Virol 75(19):9407–9414

    PubMed  CAS  Google Scholar 

  • Wilhelm M, Boutabout M et al (2000) Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase-RNase H domain exhibits polymerase and RNase H activities. Biochem J 348(Pt 2):337–342

    PubMed  CAS  Google Scholar 

  • Winshell J, Champoux JJ (2001) Structural alterations in the DNA ahead of the primer terminus during displacement synthesis by reverse transcriptases. J Mol Biol 306(5):931–943

    PubMed  CAS  Google Scholar 

  • Wisniewski M, Balakrishnan M et al (2000a) The sequential mechanism of HIV reverse transcriptase RNase H. J Biol Chem 275(48):37664–37671

    PubMed  CAS  Google Scholar 

  • Wisniewski M, Balakrishnan M et al (2000b) Unique progressive cleavage mechanism of HIV reverse transcriptase RNase H. Proc Natl Acad Sci USA 97(22):11978–11983

    PubMed  CAS  Google Scholar 

  • Wisniewski M, Chen Y et al (2002) Substrate requirements for secondary cleavage by HIV-1 reverse transcriptase RNase H. J Biol Chem 277(32):28400–28410

    PubMed  CAS  Google Scholar 

  • Xiong Y, Eickbush TH (1988) Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol Biol Evol 5(6):675–690

    PubMed  CAS  Google Scholar 

  • Xiong Y, Eickbush TH (1990) Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J 9(10):3353–3362

    PubMed  CAS  Google Scholar 

  • Yang W, Lee JY et al (2006) Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol Cell 22(1):5–13

    PubMed  CAS  Google Scholar 

  • Yu SF, Baldwin DN et al (1996) Human foamy virus replication: a pathway distinct from that of retroviruses and hepadnaviruses. Science 271(5255):1579–1582

    PubMed  CAS  Google Scholar 

  • Zhan X, Crouch RJ (1997) The isolated RNase H domain of murine leukemia virus reverse transcriptase. Retention of activity with concomitant loss of specificity. J Biol Chem 272(35):22023–22029

    PubMed  CAS  Google Scholar 

  • Zhou D, Chung S et al (2012) Crystal structures of the reverse transcriptase-associated ribonuclease H domain of xenotropic murine leukemia-virus related virus. J Struct Biol 177(3):638–645

    PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA

    Stuart F. J. Le Grice

  2. Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena Street, 02-109, Warsaw, Poland

    Marcin Nowotny

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  1. Stuart F. J. Le Grice
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  2. Marcin Nowotny
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Correspondence to Stuart F. J. Le Grice or Marcin Nowotny .

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Editors and Affiliations

  1. Dept. of Biochem. and Mol. Biology, The Pennsylvania State University, University Park, Pennsylvania, USA

    Katsuhiko S. Murakami

  2. Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

    Michael A. Trakselis

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Grice, S.F.J.L., Nowotny, M. (2014). Reverse Transcriptases. In: Murakami, K., Trakselis, M. (eds) Nucleic Acid Polymerases. Nucleic Acids and Molecular Biology, vol 30. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39796-7_8

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