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High-Frequency Illegitimate Strand Transfers of Nascent DNA Fragments During Reverse Transcription Result in Defective Retrovirus Genomes. J Acquir Immune Defic Syndr 2017; 72:353-62. [PMID: 26885810 DOI: 10.1097/qai.0000000000000952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Two strand transfers of nascent DNA fragments during reverse transcription are required for retrovirus replication. However, whether strand transfers occur at illegitimate sites and how this may affect retrovirus replication are not well understood. METHODS The reverse transcription was carried out with reverse transcriptases (RTs) from HIV-1, HIV-2, and murine leukemia virus. The nascent complementary DNA fragments were directly cloned without polymerase chain reaction amplification. The sequences were compared with the template sequence to determine if new sequences contained mismatched sequences caused by illegitimate strand transfers. RESULTS Among 1067 nascent reverse transcript sequences, most of them (72%) matched to the template sequences, although they randomly stopped across the RNA templates. The other 28% of them contained mismatched 3'-end sequences because of illegitimate strand transfers. Most of the illegitimate strand transfers (81%) were disassociated from RNA templates and realigned onto opposite complementary DNA strands. Up to 3 strand transfers were detected in a single sequence, whereas most of them (93%) contained 1 strand transfer. Because most of the illegitimate strand-transfer fragments were generated from templates at 2 opposite orientations, they resulted in defective viral genomes and could not be detected by previous methods. Further analysis showed that mutations at pause/disassociation sites resulted in significantly higher strand-transfer rates. Moreover, illegitimate strand-transfer rates were significantly higher for HIV-2 RT (38.2%) and murine leukemia virus RT (44.6%) than for HIV-1 RT (5.1%). CONCLUSIONS Illegitimate strand transfers frequently occur during reverse transcription and can result in a large portion of defective retrovirus genomes.
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2
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Achuthan V, Singh K, DeStefano JJ. Physiological Mg 2+ Conditions Significantly Alter the Inhibition of HIV-1 and HIV-2 Reverse Transcriptases by Nucleoside and Non-Nucleoside Inhibitors in Vitro. Biochemistry 2016; 56:33-46. [PMID: 27936595 DOI: 10.1021/acs.biochem.6b00943] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reverse transcriptases (RTs) are typically assayed in vitro with 5-10 mM Mg2+, whereas the free Mg2+ concentration in cells is much lower. Artificially high Mg2+ concentrations used in vitro can misrepresent different properties of human immunodeficiency virus (HIV) RT, including fidelity, catalysis, pausing, and RNase H activity. Here, we analyzed nucleoside (NRTIs) and non-nucleoside RT inhibitors (NNRTIs) in primer extension assays at different concentrations of free Mg2+. At low concentrations of Mg2+, NRTIs and dideoxynucleotides (AZTTP, ddCTP, ddGTP, and 3TCTP) inhibited HIV-1 and HIV-2 RT synthesis less efficiently than they did with large amounts of Mg2+, whereas inhibition by the "translocation-defective RT inhibitor" EFdA (4'-ethynyl-2-fluoro-2'-deoxyadenosine) was unaffected by Mg2+ concentrations. Steady-state kinetic analyses revealed that the reduced level of inhibition at low Mg2+ concentrations resulted from a 3-9-fold (depending on the particular nucleotide and inhibitor) less efficient incorporation (based on kcat/Km) of these NRTIs under this condition compared to incorporation of natural dNTPs. In contrast, EFdATP was incorporated with an efficiency similar to that of its analogue dATP at low Mg2+ concentrations. Unlike NRTIs, NNRTIs (nevirapine, efavirenz, and rilviripine), were approximately 4-fold (based on IC50 values) more effective at low than at high Mg2+ concentrations. Drug-resistant HIV-1 RT mutants also displayed the Mg2+-dependent difference in susceptibility to NRTIs and NNRTIs. In summary, analyzing the efficiency of inhibitors under more physiologically relevant low-Mg2+ conditions yielded results dramatically different from those from measurements using commonly employed high-Mg2+ in vitro conditions. These results also emphasize differences in Mg2+ sensitivity between the translocation inhibitor EFdATP and other NRTIs.
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Affiliation(s)
- Vasudevan Achuthan
- Cell Biology and Molecular Genetics, University of Maryland , College Park, Maryland 20742, United States.,Maryland Pathogen Research Institute , College Park, Maryland 20742, United States
| | - Kamlendra Singh
- Christopher S. Bond Life Sciences Center, University of Missouri , Columbia, Missouri 65211, United States.,Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine , Columbia, Missouri 65211, United States
| | - Jeffrey J DeStefano
- Cell Biology and Molecular Genetics, University of Maryland , College Park, Maryland 20742, United States.,Maryland Pathogen Research Institute , College Park, Maryland 20742, United States
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3
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Beach LB, Rawson JM, Kim B, Patterson SE, Mansky LM. Novel inhibitors of human immunodeficiency virus type 2 infectivity. J Gen Virol 2014; 95:2778-2783. [PMID: 25103850 DOI: 10.1099/vir.0.069864-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human immunodeficiency virus type 2 (HIV-2) infects about two million people worldwide. HIV-2 has fewer treatment options than HIV-1, yet may evolve drug resistance more quickly. We have analysed several novel drugs for anti-HIV-2 activity. It was observed that 5-azacytidine, clofarabine, gemcitabine and resveratrol have potent anti-HIV-2 activity. The EC50 values for 5-azacytidine, clofarabine and resveratrol were found to be significantly lower with HIV-2 than with HIV-1. A time-of-addition assay was used to analyse the ability of these drugs to interfere with HIV-2 replication. Reverse transcription was the likely target for antiretroviral activity. Taken together, several novel drugs have been discovered to have activity against HIV-2. Based upon their known activities, these drugs may elicit enhanced HIV-2 mutagenesis and therefore be useful for inducing HIV-2 lethal mutagenesis. In addition, the data are consistent with HIV-2 reverse transcriptase being more sensitive than HIV-1 reverse transcriptase to dNTP pool alterations.
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Affiliation(s)
- Lauren B Beach
- Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonathan M Rawson
- Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Steven E Patterson
- Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Louis M Mansky
- Center for Drug Design, University of Minnesota, Minneapolis, MN 55455, USA.,Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA.,Department of Microbiology, University of Minnesota, Minneapolis, MN 55455, USA
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4
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Lahouassa H, Daddacha W, Hofmann H, Ayinde D, Logue EC, Dragin L, Bloch N, Maudet C, Bertrand M, Gramberg T, Pancino G, Priet S, Canard B, Laguette N, Benkirane M, Transy C, Landau NR, Kim B, Margottin-Goguet F. SAMHD1 restricts the replication of human immunodeficiency virus type 1 by depleting the intracellular pool of deoxynucleoside triphosphates. Nat Immunol 2012; 13:223-228. [PMID: 22327569 PMCID: PMC3771401 DOI: 10.1038/ni.2236] [Citation(s) in RCA: 657] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 01/13/2012] [Indexed: 02/06/2023]
Abstract
SAMHD1 restricts the infection of dendritic and other myeloid cells by human immunodeficiency virus type 1 (HIV-1), but in lentiviruses of the simian immunodeficiency virus of sooty mangabey (SIVsm)-HIV-2 lineage, SAMHD1 is counteracted by the virion-packaged accessory protein Vpx. Here we found that SAMHD1 restricted infection by hydrolyzing intracellular deoxynucleoside triphosphates (dNTPs), lowering their concentrations to below those required for the synthesis of the viral DNA by reverse transcriptase (RT). SAMHD1-mediated restriction was alleviated by the addition of exogenous deoxynucleosides. An HIV-1 with a mutant RT with low affinity for dNTPs was particularly sensitive to SAMHD1-mediated restriction. Vpx prevented the SAMHD1-mediated decrease in dNTP concentration and induced the degradation of human and rhesus macaque SAMHD1 but had no effect on mouse SAMHD1. Nucleotide-pool depletion could be a general mechanism for protecting cells from infectious agents that replicate through a DNA intermediate.
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Affiliation(s)
- Hichem Lahouassa
- Inserm, U1016, Institut Cochin, 27 rue du faubourg St Jacques, Bat G. Roussy, 75014 Paris France
- Cnrs, UMR8104, Paris, France
- Univ Paris Descartes, Paris, France
| | - Waaqo Daddacha
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Henning Hofmann
- New York University School of Medicine, Microbiology Department, 550 First Ave., New York, NY 10016, USA
| | - Diana Ayinde
- Inserm, U1016, Institut Cochin, 27 rue du faubourg St Jacques, Bat G. Roussy, 75014 Paris France
- Cnrs, UMR8104, Paris, France
- Univ Paris Descartes, Paris, France
| | - Eric C. Logue
- New York University School of Medicine, Microbiology Department, 550 First Ave., New York, NY 10016, USA
| | - Loïc Dragin
- Inserm, U1016, Institut Cochin, 27 rue du faubourg St Jacques, Bat G. Roussy, 75014 Paris France
- Cnrs, UMR8104, Paris, France
- Univ Paris Descartes, Paris, France
| | - Nicolin Bloch
- New York University School of Medicine, Microbiology Department, 550 First Ave., New York, NY 10016, USA
| | - Claire Maudet
- Inserm, U1016, Institut Cochin, 27 rue du faubourg St Jacques, Bat G. Roussy, 75014 Paris France
- Cnrs, UMR8104, Paris, France
- Univ Paris Descartes, Paris, France
| | - Matthieu Bertrand
- Inserm, U1016, Institut Cochin, 27 rue du faubourg St Jacques, Bat G. Roussy, 75014 Paris France
- Cnrs, UMR8104, Paris, France
- Univ Paris Descartes, Paris, France
| | - Thomas Gramberg
- Virologisches Institut, Klinische und Molekulare Virologie, Universitat Erlangen-Nurnberg, 91054 Erlangen
| | - Gianfranco Pancino
- Institut Pasteur, Unité de Régulation des Infections Rétrovirales, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Stéphane Priet
- Laboratoire d’Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS-Universitéd’Aix-Marseille, 13288 Marseille cedex 09, France
| | - Bruno Canard
- Laboratoire d’Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS-Universitéd’Aix-Marseille, 13288 Marseille cedex 09, France
| | - Nadine Laguette
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, CNRS UPR1142, Montpellier 34000, France
| | - Monsef Benkirane
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, CNRS UPR1142, Montpellier 34000, France
| | - Catherine Transy
- Inserm, U1016, Institut Cochin, 27 rue du faubourg St Jacques, Bat G. Roussy, 75014 Paris France
- Cnrs, UMR8104, Paris, France
- Univ Paris Descartes, Paris, France
| | - Nathaniel R. Landau
- New York University School of Medicine, Microbiology Department, 550 First Ave., New York, NY 10016, USA
| | - Baek Kim
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Florence Margottin-Goguet
- Inserm, U1016, Institut Cochin, 27 rue du faubourg St Jacques, Bat G. Roussy, 75014 Paris France
- Cnrs, UMR8104, Paris, France
- Univ Paris Descartes, Paris, France
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5
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Post K, Kankia B, Gopalakrishnan S, Yang V, Cramer E, Saladores P, Gorelick RJ, Guo J, Musier-Forsyth K, Levin JG. Fidelity of plus-strand priming requires the nucleic acid chaperone activity of HIV-1 nucleocapsid protein. Nucleic Acids Res 2009; 37:1755-66. [PMID: 19158189 PMCID: PMC2665208 DOI: 10.1093/nar/gkn1045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During minus-strand DNA synthesis, RNase H degrades viral RNA sequences, generating potential plus-strand DNA primers. However, selection of the 3' polypurine tract (PPT) as the exclusive primer is required for formation of viral DNA with the correct 5'-end and for subsequent integration. Here we show a new function for the nucleic acid chaperone activity of HIV-1 nucleocapsid protein (NC) in reverse transcription: blocking mispriming by non-PPT RNAs. Three representative 20-nt RNAs from the PPT region were tested for primer extension. Each primer had activity in the absence of NC, but less than the PPT. NC reduced priming by these RNAs to essentially base-line level, whereas PPT priming was unaffected. RNase H cleavage and zinc coordination by NC were required for maximal inhibition of mispriming. Biophysical properties, including thermal stability, helical structure and reverse transcriptase (RT) binding affinity, showed significant differences between PPT and non-PPT duplexes and the trends were generally correlated with the biochemical data. Binding studies in reactions with both NC and RT ruled out a competition binding model to explain NC's observed effects on mispriming efficiency. Taken together, these results demonstrate that NC chaperone activity has a major role in ensuring the fidelity of plus-strand priming.
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Affiliation(s)
- Klara Post
- Laboratory of Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Hizi A, Herschhorn A. Retroviral reverse transcriptases (other than those of HIV-1 and murine leukemia virus): a comparison of their molecular and biochemical properties. Virus Res 2008; 134:203-20. [PMID: 18291546 DOI: 10.1016/j.virusres.2007.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 12/16/2007] [Accepted: 12/17/2007] [Indexed: 10/22/2022]
Abstract
This chapter reviews most of the biochemical data on reverse transcriptases (RTs) of retroviruses, other than those of HIV-1 and murine leukemia virus (MLV) that are covered in detail in other reviews of this special edition devoted to reverse transcriptases. The various RTs mentioned are grouped according to their retroviral origins and include the RTs of the alpharetroviruses, lentiviruses (both primate, other than HIV-1, and non-primate lentiviruses), betaretroviruses, deltaretroviruses and spumaretroviruses. For each RT group, the processing, molecular organization as well as the enzymatic activities and biochemical properties are described. Several RTs function as dimers, primarily as heterodimers, while the others are active as monomeric proteins. The comparisons between the diverse properties of the various RTs show the common traits that characterize the RTs from all retroviral subfamilies. In addition, the unique features of the specific RTs groups are also discussed.
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Affiliation(s)
- Amnon Hizi
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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7
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Strand transfer events during HIV-1 reverse transcription. Virus Res 2008; 134:19-38. [PMID: 18279992 DOI: 10.1016/j.virusres.2007.12.017] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 12/19/2007] [Accepted: 12/20/2007] [Indexed: 11/20/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) and other retroviruses replicate through reverse transcription, a process in which the single stranded RNA of the viral genome is converted to a double stranded DNA. The virally encoded reverse transcriptase (RT) mediates reverse transcription through DNA polymerase and RNase H activities. Conversion of the plus strand RNA to plus/minus strand RNA/DNA hybrid involves a transfer of the growing DNA strand from one site on the genomic RNA to another. This is called minus strong-stop DNA transfer. Later synthesis of the second or plus DNA strand involves a second strand transfer, involving a similar mechanism as the minus strand transfer. A basic feature of the strand transfer mechanism is the use of the RT RNase H to remove segments of the RNA template strand from the growing DNA strand, freeing a single stranded region to anneal to the second site. Viral nucleocapsid protein (NC) functions to promote transfer by facilitating this strand exchange process. Two copies of the RNA genomes, sometimes non-identical, are co-packaged in the genomes of retroviruses. The properties of the reverse transcriptase allow a transfer of the growing DNA strand between these genomes to occur occasionally at any point during reverse transcription, producing recombinant viral progeny. Recombination promotes structural diversity of the virus that helps it to survive host immunity and drug therapy. Recombination strand transfer can be forced by a break in the template, or can occur at sites where folding structure of the template pauses the RT, allowing a concentration of RNase H cleavages that promote transfers. Transfer can be a simple one-step process, or can proceed by a complex multi-step invasion mechanism. In this latter process, the second RNA template interacts with the growing DNA strand well behind the DNA 3'-terminus. The newly formed RNA-DNA hybrid expands by branch migration and eventually catches the elongating DNA primer 3'-terminus to complete the transfer. Transfers are also promoted by interactions between the two RNA templates, which accelerate transfer by a proximity effect. Other details of the role of strand transfers in reverse transcription and the biochemical features of the transfer reaction are discussed.
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8
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Dat NT, Bae K, Wamiru A, McMahon JB, Le Grice SFJ, Bona M, Beutler JA, Kim YH. A dimeric lactone from Ardisia japonica with inhibitory activity for HIV-1 and HIV-2 ribonuclease H. JOURNAL OF NATURAL PRODUCTS 2007; 70:839-41. [PMID: 17397219 DOI: 10.1021/np060359m] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A new dimeric lactone, ardimerin digallate (1), was isolated from the whole plants of Ardisia japonica, along with six known constituents. The structure of 1 was established on the basis of spectroscopic analysis including 1D- and 2D-NMR techniques. Compound 1 inhibited HIV-1 and HIV-2 RNase H in vitro with IC50 values of 1.5 and 1.1 microM, respectively.
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Affiliation(s)
- Nguyen Tien Dat
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Korea
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9
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Held DM, Kissel JD, Thacker SJ, Michalowski D, Saran D, Ji J, Hardy RW, Rossi JJ, Burke DH. Cross-clade inhibition of recombinant human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus SIVcpz reverse transcriptases by RNA pseudoknot aptamers. J Virol 2007; 81:5375-84. [PMID: 17329328 PMCID: PMC1900219 DOI: 10.1128/jvi.01923-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reverse transcriptase (RT) remains a primary target in therapies directed at human immunodeficiency virus type 1 (HIV-1). RNA aptamers that bind RT from HIV-1 subtype B have been shown to protect human cells from infection and to reduce viral infectivity, but little is known about the sensitivity of the inhibition to amino sequence variations of the RT target. Therefore, we assembled a panel of 10 recombinant RTs from phylogenetically diverse lentiviral isolates (including strains of HIV-1, simian immunodeficiency virus SIVcpz, and HIV-2). After validating the panel by measuring enzymatic activities and inhibition by small-molecule drugs, dose-response curves for each enzyme were established for four pseudoknot RNA aptamers representing two structural subfamilies. All four aptamers potently inhibited RTs from multiple HIV-1 subtypes. For aptamers carrying family 1 pseudoknots, natural resistance was essentially all-or-none and correlated with the identity of the amino acid at position 277. In contrast, natural resistance to aptamers carrying the family 2 pseudoknots was much more heterogeneous, both in degree (gradation of 50% inhibitory concentrations) and in distribution across clades. Site-directed and subunit-specific mutagenesis identified a common R/K polymorphism within the p66 subunit as a primary determinant of resistance to family 1, but not family 2, pseudoknot aptamers. RNA structural diversity therefore translates into a nonoverlapping spectrum of mutations that confer resistance, likely due to differences in atomic-level contacts with RT.
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Affiliation(s)
- Daniel M Held
- Department of Molecular Microbiology & Immunology and Department of Biochemistry, University of Missouri School of Medicine, Columbia, Missouri 65211, USA
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10
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Chen J, Powell D, Hu WS. High frequency of genetic recombination is a common feature of primate lentivirus replication. J Virol 2006; 80:9651-8. [PMID: 16973569 PMCID: PMC1617242 DOI: 10.1128/jvi.00936-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent studies indicate that human immunodeficiency virus type 1 (HIV-1) recombines at exceedingly high rates, approximately 1 order of magnitude more frequently than simple gammaretroviruses such as murine leukemia virus and spleen necrosis virus. We hypothesize that this high frequency of genetic recombination is a common feature of primate lentiviruses. Alternatively, it is possible that HIV-1 is unique among primate lentiviruses in possessing high recombination rates. Among other primate lentiviruses, only the molecular mechanisms of HIV-2 replication have been extensively studied. There are reported differences between the replication mechanisms of HIV-1 and those of HIV-2, such as preferences for RNA packaging in cis and properties of reverse transcriptase and RNase H activities. These biological disparities could lead to differences in recombination rates between the two viruses. Currently, HIV-1 is the only primate lentivirus in which recombination rates have been measured. To test our hypothesis, we established recombination systems to measure the recombination rates of two other primate lentiviruses, HIV-2 and simian immunodeficiency virus from African green monkeys (SIVagm), in one round of viral replication. We determined that, for markers separated by 588, 288, and 90 bp, HIV-2 recombined at rates of 7.4%, 5.5%, and 2.4%, respectively, whereas SIVagm recombined at rates of 7.8%, 5.6%, and 2.7%, respectively. These high recombination rates are within the same range as the previously measured HIV-1 recombination rates. Taken together, our results indicate that HIV-1, HIV-2, and SIVagm all possess high recombination frequencies; hence, the high recombination potential is most likely a common feature of primate lentivirus replication.
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Affiliation(s)
- Jianbo Chen
- HIV Drug Resistance Program, NCI-Frederick, P.O. Box B, Building 535, Room 336, Frederick, MD 21702, USA
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11
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Boyer PL, Sarafianos SG, Clark PK, Arnold E, Hughes SH. Why do HIV-1 and HIV-2 use different pathways to develop AZT resistance? PLoS Pathog 2006; 2:e10. [PMID: 16485036 PMCID: PMC1364504 DOI: 10.1371/journal.ppat.0020010] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Accepted: 01/10/2006] [Indexed: 11/18/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) develops resistance to all available drugs, including the nucleoside analog reverse transcriptase inhibitors (NRTIs) such as AZT. ATP-mediated excision underlies the most common form of HIV-1 resistance to AZT. However, clinical data suggest that when HIV-2 is challenged with AZT, it usually accumulates resistance mutations that cause AZT resistance by reduced incorporation of AZTTP rather than selective excision of AZTMP. We compared the properties of HIV-1 and HIV-2 reverse transcriptase (RT) in vitro. Although both RTs have similar levels of polymerase activity, HIV-1 RT more readily incorporates, and is more susceptible to, inhibition by AZTTP than is HIV-2 RT. Differences in the region around the polymerase active site could explain why HIV-2 RT incorporates AZTTP less efficiently than HIV-1 RT. HIV-1 RT is markedly more efficient at carrying out the excision reaction with ATP as the pyrophosphate donor than is HIV-2 RT. This suggests that HIV-1 RT has a better nascent ATP binding site than HIV-2 RT, making it easier for HIV-1 RT to develop a more effective ATP binding site by mutation. A comparison of HIV-1 and HIV-2 RT shows that there are numerous differences in the putative ATP binding sites that could explain why HIV-1 RT binds ATP more effectively. HIV-1 RT incorporates AZTTP more efficiently than does HIV-2 RT. However, HIV-1 RT is more efficient at ATP-mediated excision of AZTMP than is HIV-2 RT. Mutations in HIV-1 RT conferring AZT resistance tend to increase the efficiency of the ATP-mediated excision pathway, while mutations in HIV-2 RT conferring AZT resistance tend to increase the level of AZTTP exclusion from the polymerase active site. Thus, each RT usually chooses the pathway best suited to extend the properties of the respective wild-type enzymes.
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Affiliation(s)
- Paul L Boyer
- HIV Drug Resistance Program, NCI-Frederick, Frederick, Maryland, United States of America
| | - Stefan G Sarafianos
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Patrick K Clark
- Basic Research Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, United States of America
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, United States of America
| | - Stephen H Hughes
- HIV Drug Resistance Program, NCI-Frederick, Frederick, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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12
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Levin JG, Guo J, Rouzina I, Musier-Forsyth K. Nucleic acid chaperone activity of HIV-1 nucleocapsid protein: critical role in reverse transcription and molecular mechanism. ACTA ACUST UNITED AC 2006; 80:217-86. [PMID: 16164976 DOI: 10.1016/s0079-6603(05)80006-6] [Citation(s) in RCA: 256] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Judith G Levin
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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13
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Colson P, Henry M, Tivoli N, Gallais H, Gastaut JA, Moreau J, Tamalet C. Polymorphism and drug-selected mutations in the reverse transcriptase gene of HIV-2 from patients living in southeastern France. J Med Virol 2005; 75:381-90. [PMID: 15648062 DOI: 10.1002/jmv.20296] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Few data are available about the susceptibility and the genotypic resistance pattern of human immunodeficiency virus type 2 (HIV-2) to nucleoside reverse transcriptase inhibitors (NRTIs). The HIV-2 reverse transcriptase (RT) gene from 25 HIV-2-infected patients followed-up in Marseilles and the surrounding area was analyzed. The aims of this study were to characterize the polymorphism of HIV-2 RT in the absence of drug, to determine whether it naturally harbors codons associated with drug-resistance in HIV-1, and to identify mutations emerging under NRTI-selective pressure. Fourteen patients had never undergone antiretroviral therapy and 11 received NRTI. Seventy sequences were analyzed. In untreated patients, 12 spots of high natural polymorphism (at positions 10, 11, 20, 43, 104, 121, 135, 162, 176, 180, 200, and 227) were observed; 4 of them were specific of HIV-2 (10, 176, 180, 227). Moreover, results showed four positions that could be associated with natural resistance to NRTI (75I, 118I, 219E, and perhaps 215S), in addition to those described previously for non-nucleoside reverse transcriptase inhibitors (NNRTIs) (181I, 188L, 190A). In HIV-2-infected patients receiving NRTI-containing therapies, specific genotypic patterns were observed with a high frequency of mutation Q151M (in 45% of patients) often associated with 70R, 115F, 214L, and/or 223R, which might compose an HIV-2 multi-NRTI resistance complex. Four newly or rarely described NRTI-selected mutations were observed: I5V, K35R, F214L, and K223R. As in HIV-1, substitution M184V was found in 3TC-treated patients. In conclusion, these findings highlight the need for specific guidelines for determining genotypic resistance and treatment of HIV-2.
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Affiliation(s)
- Philippe Colson
- Féedération Hospitalière de Microbiologie Clinique et d'Hygiène, Laboratoire de Virologie, Centre Hospitalo-Universitaire Timone, Faculté de Médecine, Université de la Méditerranée, Marseille, France
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Chan KC, Budihas SR, Le Grice SFJ, Parniak MA, Crouch RJ, Gaidamakov SA, Isaaq HJ, Wamiru A, McMahon JB, Beutler JA. A capillary electrophoretic assay for ribonuclease H activity. Anal Biochem 2005; 331:296-302. [PMID: 15265735 DOI: 10.1016/j.ab.2004.05.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Indexed: 11/21/2022]
Abstract
A capillary electrophoretic assay was developed to measure the ribonuclease (RNase) H activity of human immunodeficiency virus (HIV) type 1 reverse transcriptase. Cleavage of a fluorescein-labeled RNA-DNA heteroduplex was monitored by capillary electrophoresis. This new assay was used as a secondary assay to confirm hits from a high-throughput screening program. Since autofluorescent compounds in samples migrated differently from both substrate and product in most cases, the assay was extremely robust for assaying enzymatic inhibition of such samples, in contrast to a simple well-based approach. The assay was broadly applicable to other RNases H, specifically those from human, Escherichia coli, and HIV-2, although product profiles varied for each enzyme.
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Affiliation(s)
- King C Chan
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick, Inc., Center for Cancer Research, NCI at Frederick, Frederick, MD 21702, USA
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