Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is an essential enzyme for HIV replication which converts the single-stranded viral RNA into a double-stranded DNA, suitable for integration into the host cell genome (Telesnitsky and Goff 1997). Heterodimeric p66/p51 HIV-1 RT (Fig. 19.1) has both synthetic (DNA polymerase) and degradative activities (ribonuclease H or RNase H), located at the N- and C-terminus of its p66 subunit, respectively. During HIV-1 replication, a complicated series of protein–protein and protein–nucleic acid interactions occur, each with the potential to be targeted by a small-molecule antagonist which might be developed into a potent therapeutic agent. Given the problem of increasing resistance against anti-HIV drugs currently in clinical use and the continued need to identify new drug targets, enzymatic activities and interactions, protein folding, and disruption of nucleic-acid structure are areas where detailed studies promise to unveil novel approaches with the potential for therapeutic intervention.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Aiyar, A., D. Cobrinik, et al. (1992). “Interaction between retroviral U5 RNA and the T psi C loop of the tRNA(Trp) primer is required for efficient initiation of reverse transcription.” J Virol 66(4): 2464–72.
Aiyar, A., Z. Ge, et al. (1994). “A specific orientation of RNA secondary structures is required for initiation of reverse transcription.” J Virol 68(2): 611–8.
Amacker, M. and U. Hubscher (1998). “Chimeric HIV-1 and feline immunodeficiency virus reverse transcriptases: critical role of the p51 subunit in the structural integrity of heterodimeric lentiviral DNA polymerases.” J Mol Biol 278(4): 757–65.
Andersen, E. S., R. E. Jeeninga, et al. (2003). “Dimerization and template switching in the 5' untranslated region between various subtypes of human immunodeficiency virus type 1.” J Virol 77(5): 3020–30.
Ao, Z., X. Yao, et al. (2004). “Assessment of the role of the central DNA flap in human immunodeficiency virus type 1 replication by using a single-cycle replication system.” J Virol 78(6): 3170–7.
Arhel, N., S. Munier, et al. (2006). “Nuclear import defect of human immunodeficiency virus type 1 DNA flap mutants is not dependent on the viral strain or target cell type.” J Virol 80(20): 10262–9.
Arhel, N. J., S. Souquere-Besse, et al. (2007). “HIV-1 DNA Flap formation promotes uncoating of the pre-integration complex at the nuclear pore.” Embo J 26(12): 3025–37.
Arts, E. J., M. Ghosh, et al. (1996a). “Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication.” J Biol Chem 271(15): 9054–61.
Arts, E. J., S. R. Stetor, et al. (1996b). “Initiation of (-) strand DNA synthesis from tRNA(3Lys) on lentiviral RNAs: implications of specific HIV-1 RNA-tRNA(3Lys) interactions inhibiting primer utilization by retroviral reverse transcriptases.” Proc Natl Acad Sci USA 93(19): 10063–8.
Bahar, I., B. Erman, et al. (1999). “Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.” J Mol Biol 285(3): 1023–37.
Bajji, A. C., M. Sundaram, et al. (2002). “An RNA complex of the HIV-1 A-loop and tRNA(Lys,3) is stabilized by nucleoside modifications.” J Am Chem Soc 124(48): 14302–3.
Bar-Nahum, G., V. Epshtein, et al. (2005). “A ratchet mechanism of transcription elongation and its control.” Cell 120(2): 183–93.
Barat, C., O. Schatz, et al. (1993). “Analysis of the interactions of HIV1 replication primer tRNA(Lys,3) with nucleocapsid protein and reverse transcriptase.” J Mol Biol 231(2): 185–90.
Barraud, P., C. Gaudin, et al. (2007). “New insights into the formation of HIV-1 reverse transcription initiation complex.” Biochimie 89(10): 1204–10.
Beard, W. A., S. J. Stahl, et al. (1994). “Structure/function studies of human immunodeficiency virus type 1 reverse transcriptase. Alanine scanning mutagenesis of an alpha-helix in the thumb subdomain.” J Biol Chem 269(45): 28091–7.
Bebenek, K., W. A. Beard, et al. (1995). “Reduced frameshift fidelity and processivity of HIV-1 reverse transcriptase mutants containing alanine substitutions in helix H of the thumb subdomain.” J Biol Chem 270(33): 19516–23.
Bebenek, K., W. A. Beard, et al. (1997). “A minor groove binding track in reverse transcriptase.” Nat Struct Biol 4(3): 194–7.
Becerra, S. P., A. Kumar, et al. (1991). “Protein-protein interactions of HIV-1 reverse transcriptase: implication of central and C-terminal regions in subunit binding.” Biochemistry 30(50): 11707–19.
Beerens, N. and B. Berkhout (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): 2329–39.
Beerens, N., F. Groot, et al. (2001). “Initiation of HIV-1 reverse transcription is regulated by a primer activation signal.” J Biol Chem 276(33): 31247–56.
Beese, L. S. and T. A. Steitz (1991). “Structural basis for the 3ʹ-5ʹ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism.” Embo J 10(1): 25–33.
Ben-Artzi, H., E. Zeelon, et al. (1992a). “Double-stranded RNA-dependent RNase activity associated with human immunodeficiency virus type 1 reverse transcriptase.” Proc Natl Acad Sci USA 89(3): 927–31.
Ben-Artzi, H., E. Zeelon, et al. (1992b). “Characterization of the double stranded RNA dependent RNase activity associated with recombinant reverse transcriptases.” Nucleic Acids Res 20(19): 5115–8.
Ben-Artzi, H., J. Shemesh, et al. (1996). “Molecular analysis of the second template switch during reverse transcription of the HIV RNA template.” Biochemistry 35(32): 10549–57.
Berkhout, B., J. van Wamel, et al. (1995). “Requirements for DNA strand transfer during reverse transcription in mutant HIV-1 virions.” J Mol Biol 252(1): 59–69.
Blain, S. W. and S. P. Goff (1993). “Nuclease activities of Moloney murine leukemia virus reverse transcriptase. Mutants with altered substrate specificities.” J Biol Chem 268(31): 23585–92.
Borroto-Esoda, K. and L. R. Boone (1991). “Equine infectious anemia virus and human immunodeficiency virus DNA synthesis in vitro: characterization of the endogenous reverse transcriptase reaction.” J Virol 65(4): 1952–9.
Boyer, P. L., A. L. Ferris, 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): 472–83.
Boyer, P. L., A. L. Ferris, et al. (1992). “Cassette mutagenesis of the reverse transcriptase of human immunodeficiency virus type 1.” J Virol 66(2): 1031–9.
Brautigam, C. A. and T. A. Steitz (1998). “Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.” Curr Opin Struct Biol 8(1): 54–63.
Budihas, S. R., I. Gorshkova, et al. (2005). “Selective inhibition of HIV-1 reverse transcriptase-associated ribonuclease H activity by hydroxylated tropolones.” Nucleic Acids Res 33(4): 1249–56.
Cabodevilla, J. F., L. Odriozola, et al. (2001). “Factors affecting the dimerization of the p66 form of HIV-1 reverse transcriptase.” Eur J Biochem 268(5): 1163–72.
Carvalho, A. T., P. A. Fernandes, et al. (2006). “Molecular dynamics model of unliganded HIV-1 reverse transcriptase.” Med Chem 2(5): 491–8.
Cases-Gonzalez, C. E., M. Gutierrez-Rivas, 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): 19759–67.
Charneau, P., M. Alizon, et al. (1992). “A second origin of DNA plus-strand synthesis is required for optimal human immunodeficiency virus replication.” J Virol 66(5): 2814–20.
Charneau, P. and F. Clavel (1991). “A single-stranded gap in human immunodeficiency virus unintegrated linear DNA defined by a central copy of the polypurine tract.” J Virol 65(5): 2415–21.
Charneau, P., G. Mirambeau, et al. (1994). “HIV-1 reverse transcription. A termination step at the center of the genome.” J Mol Biol 241(5): 651–62.
Cobrinik, D., L. Soskey, et al. (1988). “A retroviral RNA secondary structure required for efficient initiation of reverse transcription.” J Virol 62(10): 3622–30.
Cowan, J. A., T. Ohyama, et al. (2000). “Metal-ion stoichiometry of the HIV-1 RT ribonuclease H domain: evidence for two mutually exclusive sites leads to new mechanistic insights on metal-mediated hydrolysis in nucleic acid biochemistry.” J Biol Inorg Chem 5(1): 67–74.
Dahlberg, M. E. and S. J. Benkovic (1991). “Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant.” Biochemistry 30(20): 4835–43.
Dardalhon, V., B. Herpers, et al. (2001). “Lentivirus-mediated gene transfer in primary T cells is enhanced by a central DNA flap.” Gene Ther 8(3): 190–8.
Das, K., S. G. Sarafianos, et al. (2007). “Crystal structures of clinically relevant Lys103Asn/ Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097.” J Mol Biol 365(1): 77–89.
Dash, C., T. S. Fisher, et al. (2006a). “Examining interactions of HIV-1 reverse transcriptase with single-stranded template nucleotides by nucleoside analog interference.” J Biol Chem 281(38): 27873–81.
Dash, C., J. P. Marino, et al. (2006b). “Examining Ty3 polypurine tract structure and function by nucleoside analog interference.” J Biol Chem 281(5): 2773–83.
Dash, C., J. W. Rausch, et al. (2004a). “Using pyrrolo-deoxycytosine to probe RNA/DNA hybrids containing the human immunodeficiency virus type-1 3ʹ polypurine tract.” Nucleic Acids Res 32(4): 1539–47.
Dash, C., H. Y. Yi-Brunozzi, et al. (2004b). “Two modes of HIV-1 polypurine tract cleavage are affected by introducing locked nucleic acid analogs into the (-) DNA template.” J Biol Chem 279(35): 37095–102.
Davies, J. F., 2nd, Z. Hostomska, et al. (1991). “Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase.” Science 252(5002): 88–95.
De Rijck, J. and Z. Debyser (2006). “The central DNA flap of the human immunodeficiency virus type 1 is important for viral replication.” Biochem Biophys Res Commun 349(3): 1100–10.
Derbyshire, V., P. S. Freemont, et al. (1988). “Genetic and crystallographic studies of the 3ʹ,5ʹ-exonucleolytic site of DNA polymerase I.” Science 240(4849): 199–201.
DeStefano, J. J. (1995). “The orientation of binding of human immunodeficiency virus reverse transcriptase on nucleic acid hybrids.” Nucleic Acids Res 23(19): 3901–8.
DeStefano, J. J., R. A. Bambara, et al. (1993). “Parameters that influence the binding of human immunodeficiency virus reverse transcriptase to nucleic acid structures.” Biochemistry 32(27): 6908–15.
DeStefano, J. J., J. V. Cristofaro, et al. (2001). “Physical mapping of HIV reverse transcriptase to the 5ʹ end of RNA primers.” J Biol Chem 276(35): 32515–21.
di Marzo Veronese, F., T. D. Copeland, et al. (1986). “Characterization of highly immunogenic p66/p51 as the reverse transcriptase of HTLV-III/LAV.” Science 231(4743): 1289–91.
Ding, J., K. Das, et al. (1998). “Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution.” J Mol Biol 284(4): 1095–111.
Ding, J., K. Das, et al. (1995). “Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 A resolution.” Structure 3(4): 365–79.
Divita, G., T. Restle, et al. (1993). “Characterization of the dimerization process of HIV-1 reverse transcriptase heterodimer using intrinsic protein fluorescence.” FEBS Lett 324(2): 153–8.
Divita, G., K. Rittinger, et al. (1995). “Dimerization kinetics of HIV-1 and HIV-2 reverse transcriptase: a two step process.” J Mol Biol 245(5): 508–21.
Doublie, S., M. R. Sawaya, et al. (1999). “An open and closed case for all polymerases.” Structure 7(2): R31–5.
Dvorin, J. D., P. Bell, et al. (2002). “Reassessment of the roles of integrase and the central DNA flap in human immunodeficiency virus type 1 nuclear import.” J Virol 76(23): 12087–96.
Esnouf, R., J. Ren, et al. (1995). “Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors.” Nat Struct Biol 2(4): 303–8.
Furfine, E. S. and J. E. Reardon (1991). “Reverse transcriptase. RNase H from the human immunodeficiency virus. Relationship of the DNA polymerase and RNA hydrolysis activities.” J Biol Chem 266(1): 406–12.
Gao, H. Q., S. G. Sarafianos, et al. (2001). “RNase H cleavage of the 5ʹ end of the human immunodeficiency virus type 1 genome.” J Virol 75(23): 11874–80.
Garforth, S. J., T. W. Kim, et al. (2007). “Site-directed mutagenesis in the fingers subdomain of HIV-1 reverse transcriptase reveals a specific role for the beta3-beta4 hairpin loop in dNTP selection.” J Mol Biol 365(1): 38–49.
Ghosh, M., P. S. Jacques, et al. (1996). “Alterations to the primer grip of p66 HIV-1 reverse transcriptase and their consequences for template-primer utilization.” Biochemistry 35(26): 8553–62.
Ghosh, M., J. Williams, et al. (1997). “Mutating a conserved motif of the HIV-1 reverse transcriptase palm subdomain alters primer utilization.” Biochemistry 36(19): 5758–68.
Godet, J., H. de Rocquigny, et al. (2006). “During the early phase of HIV-1 DNA synthesis, nucleocapsid protein directs hybridization of the TAR complementary sequences via the ends of their double-stranded stem.” J Mol Biol 356(5): 1180–92.
Goel, R., W. A. Beard, et al. (1993). “Structure/function studies of HIV-1(1) reverse transcriptase: dimerization-defective mutant L289K.” Biochemistry 32(48): 13012–8.
Goldschmidt, V., J. C. Paillart, et al. (2004). “Structural variability of the initiation complex of HIV-1 reverse transcription.” J Biol Chem 279(34): 35923–31.
Golinelli, M. P. and S. H. Hughes (2003). “Secondary structure in the nucleic acid affects the rate of HIV-1 nucleocapsid-mediated strand annealing.” Biochemistry 42(27): 8153–62.
Gopalakrishnan, V., J. A. Peliska, 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): 10763–7.
Gotte, M. (2006). “Effects of nucleotides and nucleotide analogue inhibitors of HIV-1 reverse transcriptase in a ratchet model of polymerase translocation.” Curr Pharm Des 12(15): 1867–77.
Gotte, M., M. Kameoka, et al. (2001). “Analysis of efficiency and fidelity of HIV-1 (+)-strand DNA synthesis reveals a novel rate-limiting step during retroviral reverse transcription.” J Biol Chem 276(9): 6711–9.
Gotte, M., G. Maier, et al. (1998). “Localization of the active site of HIV-1 reverse transcriptase-associated RNase H domain on a DNA template using site-specific generated hydroxyl radicals.” J Biol Chem 273(17): 10139–46.
Guajardo, R. and R. Sousa (1997). “A model for the mechanism of polymerase translocation.” J Mol Biol 265(1): 8–19.
Guo, F., S. Cen, et al. (2006). “Inhibition of formula-primed reverse transcription by human APOBEC3G during human immunodeficiency virus type 1 replication.” J Virol 80(23): 11710–22.
Guo, J., T. Wu, et al. (2000). “Zinc finger structures in the human immunodeficiency virus type 1 nucleocapsid protein facilitate efficient minus- and plus-strand transfer.” J Virol 74(19): 8980–8.
Hang, J. Q., S. Rajendran, et al. (2004). “Activity of the isolated HIV RNase H domain and specific inhibition by N-hydroxyimides.” Biochem Biophys Res Commun 317(2): 321–9.
Harris, D., R. Lee, et al. (1998). “The p51 subunit of human immunodeficiency virus type 1 reverse transcriptase is essential in loading the p66 subunit on the template primer.” Biochemistry 37(17): 5903–8.
Hsiou, Y., J. Ding, 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): 853–60.
Huang, H., R. Chopra, et al. (1998). “Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.” Science 282(5394): 1669–75.
Huber, H. E. and C. C. Richardson (1990). “Processing of the primer for plus strand DNA synthesis by human immunodeficiency virus 1 reverse transcriptase.” J Biol Chem 265(18): 10565–73.
Hungnes, O., E. Tjotta, et al. (1991). “The plus strand is discontinuous in a subpopulation of unintegrated HIV-1 DNA.” Arch Virol 116(1–4): 133–41.
Hungnes, O., E. Tjotta, et al. (1992). “Mutations in the central polypurine tract of HIV-1 result in delayed replication.” Virology 190(1): 440–2.
Isel, C., C. Ehresmann, 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): 236–50.
Isel, C., R. Marquet, 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): 25269–72.
Iwatani, Y., A. E. Rosen, et al. (2003). “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(16): 14185–95.
Jacobo-Molina, A., J. Ding, 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): 6320–4.
Jacques, P. S., B. M. Wohrl, et al. (1994a). “Modulation of HIV-1 reverse transcriptase function in “selectively deleted” p66/p51 heterodimers.” J Biol Chem 269(2): 1388–93.
Jacques, P. S., B. M. Wohrl, et al. (1994b). “Mutating the “primer grip” of p66 HIV-1 reverse transcriptase implicates tryptophan-229 in template-primer utilization.” J Biol Chem 269(42): 26472–8.
Javanbakht, H., R. Halwani, et al. (2003). “The interaction between HIV-1 Gag and human lysyl-tRNA synthetase during viral assembly.” J Biol Chem 278(30): 27644–51.
Jones, F. D. and S. H. Hughes (2007). “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 360(2): 341–9.
Julias, J. G., M. J. McWilliams, et al. (2004). “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 78(23): 13315–24.
Kaminska, M., V. Shalak, et al. (2007). “Viral hijacking of mitochondrial lysyl-tRNA synthetase.” J Virol 81(1): 68–73.
Kang, S. M., J. K. Wakefield, et al. (1996). “Mutations in both the U5 region and the primer-binding site influence the selection of the tRNA used for the initiation of HIV-1 reverse transcription.” Virology 222(2): 401–14.
Kankia, B. I. and K. Musier-Forsyth (2007). “The HIV-1 central DNA flap region contains a “flapping” third strand.” Biophys Chem 127(1–2): 64–8.
Kao, H. I., J. Veeraraghavan, et al. (2004). “On the roles of Saccharomyces cerevisiae Dna2p and Flap endonuclease 1 in Okazaki fragment processing.” J Biol Chem 279(15): 15014–24.
Katayanagi, K., M. Miyagawa, et al. (1990). “Three-dimensional structure of ribonuclease H from E. coli.” Nature 347(6290): 306–9.
Kensch, O., T. Restle, et al. (2000). “Temperature-dependent equilibrium between the open and closed conformation of the p66 subunit of HIV-1 reverse transcriptase revealed by site-directed spin labelling.” J Mol Biol 301(4): 1029–39.
Khorchid, A., H. Javanbakht, et al. (2000). “Sequences within Pr160gag-pol affecting the selective packaging of primer tRNA(Lys3) into HIV-1.” J Mol Biol 299(1): 17–26.
Klarmann, G. J., B. M. Eisenhauer, 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): 2118–26.
Klarmann, G. J., B. M. Eisenhauer, et al. (2004). “Site- and subunit-specific incorporation of unnatural amino acids into HIV-1 reverse transcriptase.” Protein Expr Purif 38(1): 37–44.
Kleiman, L., R. Halwani, et al. (2004). “The selective packaging and annealing of primer tRNALys3 in HIV-1.” Curr HIV Res 2(2): 163–75.
Kohlstaedt, L. A., J. Wang, et al. (1992). “Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor.” Science 256(5065): 1783–90.
Kovaleski, B. J., R. Kennedy, et al. (2006). “In vitro characterization of the interaction between HIV-1 Gag and human lysyl-tRNA synthetase.” J Biol Chem 281(28): 19449–56.
Kvaratskhelia, M., S. R. Budihas, et al. (2002). “Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase.” J Biol Chem 277(19): 16689–96.
Lanchy, J. M., C. Ehresmann, et al. (1996). “Binding and kinetic properties of HIV-1 reverse transcriptase markedly differ during initiation and elongation of reverse transcription.” Embo J 15(24): 7178–87.
Landick, R. (2004). “Active-site dynamics in RNA polymerases.” Cell 116(3): 351–3.
Lavigne, M. and H. Buc (1999). “Compression of the DNA minor groove is responsible for termination of DNA synthesis by HIV-1 reverse transcriptase.” J Mol Biol 285(3): 977–95.
Lavigne, M., L. Polomack, et al. (2001). “DNA synthesis by HIV-1 reverse transcriptase at the central termination site: a kinetic study.” J Biol Chem 276(33): 31429–38.
Lavigne, M., P. Roux, et al. (1997). “DNA curvature controls termination of plus strand DNA synthesis at the centre of HIV-1 genome.” J Mol Biol 266(3): 507–24.
Le Grice, S. F. (2003). ““In the beginning”: initiation of minus strand DNA synthesis in retroviruses and LTR-containing retrotransposons.” Biochemistry 42(49): 14349–55.
Le Grice, S. F., T. Naas, et al. (1991). “Subunit-selective mutagenesis indicates minimal polymerase activity in heterodimer-associated p51 HIV-1 reverse transcriptase.” Embo J 10(12): 3905–11.
Lener, D., S. R. Budihas, et al. (2002). “Mutating conserved residues in the ribonuclease H domain of Ty3 reverse transcriptase affects specialized cleavage events.” J Biol Chem 277(29): 26486–95.
Levin, J. G., J. Guo, et al. (2005). “Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism.” Prog Nucleic Acid Res Mol Biol 80: 217–86.
Liang, C., X. Li, et al. (1997). “The importance of the A-rich loop in human immunodeficiency virus type 1 reverse transcription and infectivity.” J Virol 71(8): 5750–7.
Limon, A., N. Nakajima, et al. (2002). “Wild-type levels of nuclear localization and human immunodeficiency virus type 1 replication in the absence of the central DNA flap.” J Virol 76(23): 12078–86.
Liu, H. W., G. Cosa, et al. (2005). “Single-molecule FRET studies of important intermediates in the nucleocapsid-protein-chaperoned minus-strand transfer step in HIV-1 reverse transcription.” Biophys J 89(5): 3470–9.
Liu, H. W., Y. Zeng, et al. (2007). “Insights on the role of nucleic acid/protein interactions in chaperoned nucleic acid rearrangements of HIV-1 reverse transcription.” Proc Natl Acad Sci USA 104(13): 5261–7.
Lowe, D. M., A. Aitken, et al. (1988). “HIV-1 reverse transcriptase: crystallization and analysis of domain structure by limited proteolysis.” Biochemistry 27(25): 8884–9.
Luo, G. X. and J. Taylor (1990). “Template switching by reverse transcriptase during DNA synthesis.” J Virol 64(9): 4321–8.
Ma, J. B., Y. R. Yuan, et al. (2005). “Structural basis for 5ʹ-end-specific recognition of guide RNA by the A. fulgidus Piwi protein.” Nature 434(7033): 666–70.
Majumdar, C., J. Abbotts, et al. (1988). “Studies on the mechanism of human immunodeficiency virus reverse transcriptase. Steady-state kinetics, processivity, and polynucleotide inhibition.” J Biol Chem 263(30): 15657–65.
Mak, J. and L. Kleiman (1997). “Primer tRNAs for reverse transcription.” J Virol 71(11): 8087–95.
Marchand, B., E. P. Tchesnokov, 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): 3337–46.
Marquet, R., C. Isel, et al. (1995). “tRNAs as primer of reverse transcriptases.” Biochimie 77(1–2): 113–24.
Martin-Hernandez, A. M., E. Domingo, et al. (1996). “Human immunodeficiency virus type 1 reverse transcriptase: role of Tyr115 in deoxynucleotide binding and misinsertion fidelity of DNA synthesis.” Embo J 15(16): 4434–42.
McWilliams, M. J., J. G. Julias, et al. (2003). “Mutations in the 5ʹ end of the human immunodeficiency virus type 1 polypurine tract affect RNase H cleavage specificity and virus titer.” J Virol 77(20): 11150–7.
Menendez-Arias, L., A. Abraha, et al. (2001). “Functional characterization of chimeric reverse transcriptases with polypeptide subunits of highly divergent HIV-1 group M and O strains.” J Biol Chem 276(29): 27470–9.
Miles, L. R., B. E. Agresta, et al. (2005). “Effect of polypurine tract (PPT) mutations on human immunodeficiency virus type 1 replication: a virus with a completely randomized PPT retains low infectivity.” J Virol 79(11): 6859–67.
Miller, J. T., A. Khvorova, et al. (2004). “Synthetic tRNALys,3 as the replication primer for the HIV-1HXB2 and HIV-1Mal genomes.” Nucleic Acids Res 32(15): 4687–95.
Molling, K., D. P. Bolognesi, et al. (1971). “Association of viral reverse transcriptase with an enzyme degrading the RNA moiety of RNA-DNA hybrids.” Nat New Biol 234(51): 240–3.
Mulky, A., S. G. Sarafianos, et al. (2005). “Identification of amino acid residues in the human immunodeficiency virus type-1 reverse transcriptase tryptophan-repeat motif that are required for subunit interaction using infectious virions.” J Mol Biol 349(4): 673–84.
Muller, B., T. Restle, et al. (1989). “Co-expression of the subunits of the heterodimer of HIV-1 reverse transcriptase in Escherichia coli.” J Biol Chem 264(24): 13975–8.
Ni, N., W. Xu, et al. (2007). “Importance of A-loop complementarity with tRNAHis anticodon for continued selection of tRNAHis as the HIV reverse transcription primer.” Virol J 4: 4.
Nowotny, M., S. A. Gaidamakov, et al. (2005). “Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.” Cell 121(7): 1005–16.
Nowotny, M. and W. Yang (2006). “Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release.” Embo J 25(9): 1924–33.
Ooms, M., D. Cupac, et al. (2007). “The availability of the primer activation signal (PAS) affects the efficiency of HIV-1 reverse transcription initiation.” Nucleic Acids Res 35(5): 1649–59.
Operario, D. J., M. Balakrishnan, et al. (2006). “Reduced dNTP interaction of human immunodeficiency virus type 1 reverse transcriptase promotes strand transfer.” J Biol Chem 281(43): 32113–21.
Palaniappan, C., M. Wisniewski, et al. (1997). “Mutations within the primer grip region of HIV-1 reverse transcriptase result in loss of RNase H function.” J Biol Chem 272(17): 11157–64.
Peliska, J. A. and S. J. Benkovic (1992). “Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase.” Science 258(5085): 1112–8.
Powell, M. D., M. Ghosh, et al. (1997). “Alanine-scanning mutations in the “primer grip” of p66 HIV-1 reverse transcriptase result in selective loss of RNA priming activity.” J Biol Chem 272(20): 13262–9.
Powell, M. D. and J. G. Levin (1996). “Sequence and structural determinants required for priming of plus-strand DNA synthesis by the human immunodeficiency virus type 1 polypurine tract.” J Virol 70(8): 5288–96.
Pullen, K. A., A. J. Rattray, et al. (1993). “The sequence features important for plus strand priming by human immunodeficiency virus type 1 reverse transcriptase.” J Biol Chem 268(9): 6221–7.
Rausch, J. W. and S. F. Le Grice (2007). “Purine analog substitution of the HIV-1 polypurine tract primer defines regions controlling initiation of plus-strand DNA synthesis.” Nucleic Acids Res 35(1): 256–68.
Rausch, J. W., J. Qu, et al. (2003). “Hydrolysis of RNA/DNA hybrids containing nonpolar pyrimidine isosteres defines regions essential for HIV type 1 polypurine tract selection.” Proc Natl Acad Sci USA 100(20): 11279–84.
Restle, T., B. Muller, et al. (1990). “Dimerization of human immunodeficiency virus type 1 reverse transcriptase. A target for chemotherapeutic intervention.” J Biol Chem 265(16): 8986–8.
Restle, T., B. Muller, et al. (1992). “RNase H activity of HIV reverse transcriptases is confined exclusively to the dimeric forms.” FEBS Lett 300(1): 97–100.
Rice, P. A. and T. A. Baker (2001). “Comparative architecture of transposase and integrase complexes.” Nat Struct Biol 8(5): 302–7.
Rittinger, K., G. Divita, et al. (1995). “Human immunodeficiency virus reverse transcriptase substrate-induced conformational changes and the mechanism of inhibition by nonnucleoside inhibitors.” Proc Natl Acad Sci USA 92(17): 8046–9.
Robson, N. D. and A. Telesnitsky (2000). “Selection of optimal polypurine tract region sequences during Moloney murine leukemia virus replication.” J Virol 74(22): 10293–303.
Rodgers, D. W., S. J. Gamblin, et al. (1995). “The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1.” Proc Natl Acad Sci USA 92(4): 1222–6.
Rodriguez-Barrios, F., C. Perez, et al. (2001). “Identification of a putative binding site for [2ʹ,5ʹ-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3ʹ-spiro-5''- (4''-amino-1'',2''-oxathiole-2'',2''-dioxide)thymine (TSAO) derivatives at the p51-p66 interface of HIV-1 reverse transcriptase.” J Med Chem 44(12): 1853–65.
Rothwell, P. J., S. Berger, et al. (2003). “Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes.” Proc Natl Acad Sci USA 100(4): 1655–60.
Rumbaugh, J. A., G. M. Fuentes, et al. (1998). “Processing of an HIV replication intermediate by the human DNA replication enzyme FEN1.” J Biol Chem 273(44): 28740–5.
Sarafianos, S. G., K. Das, et al. (1999). “Touching the heart of HIV-1 drug resistance: the fingers close down on the dNTP at the polymerase active site.” Chem Biol 6(5): R137–46.
Sarafianos, S. G., K. Das, et al. (2001). “Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.” Embo J 20(6): 1449–61.
Schultz, S. J., M. Zhang, et al. (2006). “Sequence, distance, and accessibility are determinants of 5ʹ-end-directed cleavages by retroviral RNases H.” J Biol Chem 281(4): 1943–55.
Shaw-Reid, C. A., V. Munshi, et al. (2003). “Inhibition of HIV-1 ribonuclease H by a novel diketo acid, 4-[5-(benzoylamino)thien-2-yl]-2,4-dioxobutanoic acid.” J Biol Chem 278(5): 2777–80.
Sirven, A., F. Pflumio, et al. (2000). “The human immunodeficiency virus type-1 central DNA flap is a crucial determinant for lentiviral vector nuclear import and gene transduction of human hematopoietic stem cells.” Blood 96(13): 4103–10.
Smith, C. M., J. S. Smith, et al. (1999). “RNase H requirements for the second strand transfer reaction of human immunodeficiency virus type 1 reverse transcription.” J Virol 73(8): 6573–81.
Song, J. J., S. K. Smith, et al. (2004). “Crystal structure of Argonaute and its implications for RISC slicer activity.” Science 305(5689): 1434–7.
Song, M., M. Balakrishnan, et al. (2006). “Stimulation of HIV-1 minus strand strong stop DNA transfer by genomic sequences 3ʹ of the primer binding site.” J Biol Chem 281(34): 24227–35.
Spence, R. A., W. M. Kati, et al. (1995). “Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors.” Science 267(5200): 988–93.
Srivastava, S., N. Sluis-Cremer, et al. (2006). “Dimerization of human immunodeficiency virus type 1 reverse transcriptase as an antiviral target.” Curr Pharm Des 12(15): 1879–94.
Steitz, T. A. (1993). “DNA- and RNA-dependent DNA polymerases.” Curr Opin Struct Biol 3: 31–38.
Steitz, T. A. (1998). “A mechanism for all polymerases.” Nature 391(6664): 231–2.
Steitz, T. A. (1999). “DNA polymerases: structural diversity and common mechanisms.” J Biol Chem 274(25): 17395–8.
Steitz, T. A. (2004). “The structural basis of the transition from initiation to elongation phases of transcription, as well as translocation and strand separation, by T7 RNA polymerase.” Curr Opin Struct Biol 14(1): 4–9.
Steitz, T. A., S. J. Smerdon, et al. (1994). “A unified polymerase mechanism for nonhomologous DNA and RNA polymerases.” Science 266(5193): 2022–5.
Steitz, T. A. and J. A. Steitz (1993). “A general two-metal-ion mechanism for catalytic RNA.” Proc Natl Acad Sci USA 90(14): 6498–502.
Steitz, T. A. and Y. W. Yin (2004). “Accuracy, lesion bypass, strand displacement and translocation by DNA polymerases.” Philos Trans R Soc Lond B Biol Sci 359(1441): 17–23.
Stetor, S. R., J. W. Rausch, et al. (1999). “Characterization of (+) strand initiation and termination sequences located at the center of the equine infectious anemia virus genome.” Biochemistry 38(12): 3656–67.
Tachedjian, G., H. E. Aronson, et al. (2003). “Role of residues in the tryptophan repeat motif for HIV-1 reverse transcriptase dimerization.” J Mol Biol 326(2): 381–96.
Tan, C. K., J. Zhang, et al. (1991). “Functional characterization of RNA-dependent DNA polymerase and RNase H activities of a recombinant HIV reverse transcriptase.” Biochemistry 30(10): 2651–5.
Tantillo, C., J. Ding, et al. (1994). “Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase. Implications for mechanisms of drug inhibition and resistance.” J Mol Biol 243(3): 369–87.
Telesnitsky, A. and S. P. Goff (1997). Reverse Transcriptase and the Generation of Retroviral DNA. Retroviruses. J. M. Coffin, S. H. Hughes and H. E. Varmus. Plainview, Cold Spring Harbor Laboratory Press: 121–160.
Temiakov, D., V. Patlan, et al. (2004). “Structural basis for substrate selection by t7 RNA polymerase.” Cell 116(3): 381–91.
Tisdale, M., T. Schulze, 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.
Tisne, C., B. P. Roques, et al. (2004). “The annealing mechanism of HIV-1 reverse transcription primer onto the viral genome.” J Biol Chem 279(5): 3588–95.
Van Maele, B., J. De Rijck, et al. (2003). “Impact of the central polypurine tract on the kinetics of human immunodeficiency virus type 1 vector transduction.” J Virol 77(8): 4685–94.
van Wamel, J. L. and B. Berkhout (1998). “The first strand transfer during HIV-1 reverse transcription can occur either intramolecularly or intermolecularly.” Virology 244(2): 245–51.
Wang, J., S. J. Smerdon, et al. (1994). “Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer.” Proc Natl Acad Sci USA 91(15): 7242–6.
Whitwam, T., M. Peretz, et al. (2001). “Identification of a central DNA flap in feline immunodeficiency virus.” J Virol 75(19): 9407–14.
Wisniewski, M., Y. Chen, et al. (2002). “Substrate requirements for secondary cleavage by HIV-1 reverse transcriptase RNase H.” J Biol Chem 277(32): 28400–10.
Wisniewski, M., C. Palaniappan, et al. (1999). “Mutations in the primer grip region of HIV reverse transcriptase can increase replication fidelity.” J Biol Chem 274(40): 28175–84.
Wohrl, B. M., K. J. Howard, et al. (1994). “Alternative modes of polymerization distinguish the subunits of equine infectious anemia virus reverse transcriptase.” J Biol Chem 269(11): 8541–8.
Wohrl, B. M., R. Krebs, et al. (1999). “Refined model for primer/template binding by HIV-1 reverse transcriptase: pre-steady-state kinetic analyses of primer/template binding and nucleotide incorporation events distinguish between different binding modes depending on the nature of the nucleic acid substrate.” J Mol Biol 292(2): 333–44.
Wohrl, B. M., R. Krebs, et al. (1997). “Kinetic analysis of four HIV-1 reverse transcriptase enzymes mutated in the primer grip region of p66. Implications for DNA synthesis and dimerization.” J Biol Chem 272(28): 17581–7.
Xiong, Y. and T. H. Eickbush (1990). “Origin and evolution of retroelements based upon their reverse transcriptase sequences.” Embo J 9(10): 3353–62.
Yang, W., J. Y. Lee, et al. (2006). “Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.” Mol Cell 22(1): 5–13.
Yi-Brunozzi, H. Y. and S. F. Le Grice (2005). “Investigating HIV-1 polypurine tract geometry via targeted insertion of abasic lesions in the (-)-DNA template and (+)-RNA primer.” J Biol Chem 280(20): 20154–62.
Yin, Y. W. and T. A. Steitz (2004). “The structural mechanism of translocation and helicase activity in T7 RNA polymerase.” Cell 116(3): 393–404.
You, J. C. and C. S. McHenry (1994). “Human immunodeficiency virus nucleocapsid protein accelerates strand transfer of the terminally redundant sequences involved in reverse transcription.” J Biol Chem 269(50): 31491–5.
Yuan, Y. R., Y. Pei, et al. (2005). “Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage.” Mol Cell 19(3): 405–19.
Zennou, V., C. Petit, et al. (2000). “HIV-1 genome nuclear import is mediated by a central DNA flap.” Cell 101(2): 173–85.
Zennou, V., C. Serguera, et al. (2001). “The HIV-1 DNA flap stimulates HIV vector-mediated cell transduction in the brain.” Nat Biotechnol 19(5): 446–50.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Wendeler, M., Miller, J.T., Le Grice, S.F. (2009). Human Immunodeficiency Virus Reverse Transcriptase. In: Raney, K., Gotte, M., Cameron, C. (eds) Viral Genome Replication. Springer, Boston, MA. https://doi.org/10.1007/b135974_19
Download citation
DOI: https://doi.org/10.1007/b135974_19
Published:
Publisher Name: Springer, Boston, MA
Print ISBN: 978-0-387-89425-6
Online ISBN: 978-0-387-89456-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)