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Thomas JA, Shatzer TL, Gorelick RJ. Blocking premature reverse transcription fails to rescue the HIV-1 nucleocapsid-mutant replication defect. Retrovirology 2011; 8:46. [PMID: 21682883 PMCID: PMC3141651 DOI: 10.1186/1742-4690-8-46] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 06/17/2011] [Indexed: 02/06/2023] Open
Abstract
Background The nucleocapsid (NC) protein of HIV-1 is critical for viral replication. Mutational analyses have demonstrated its involvement in viral assembly, genome packaging, budding, maturation, reverse transcription, and integration. We previously reported that two conservative NC mutations, His23Cys and His44Cys, cause premature reverse transcription such that mutant virions contain approximately 1,000-fold more DNA than wild-type virus, and are replication defective. In addition, both mutants show a specific defect in integration after infection. Results In the present study we investigated whether blocking premature reverse transcription would relieve the infectivity defects, which we successfully performed by transfecting proviral plasmids into cells cultured in the presence of high levels of reverse transcriptase inhibitors. After subsequent removal of the inhibitors, the resulting viruses showed no significant difference in single-round infective titer compared to viruses where premature reverse transcription did occur; there was no rescue of the infectivity defects in the NC mutants upon reverse transcriptase inhibitor treatment. Surprisingly, time-course endogenous reverse transcription assays demonstrated that the kinetics for both the NC mutants were essentially identical to wild-type when premature reverse transcription was blocked. In contrast, after infection of CD4+ HeLa cells, it was observed that while the prevention of premature reverse transcription in the NC mutants resulted in lower quantities of initial reverse transcripts, the kinetics of reverse transcription were not restored to that of untreated wild-type HIV-1. Conclusions Premature reverse transcription is not the cause of the replication defect but is an independent side-effect of the NC mutations.
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Affiliation(s)
- James A Thomas
- AIDS and Cancer Virus Program, SAIC-Frederick, Inc,, NCI at Frederick, Frederick, MD 21702, USA
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2
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Warrilow D, Warren K, Harrich D. Strand transfer and elongation of HIV-1 reverse transcription is facilitated by cell factors in vitro. PLoS One 2010; 5:e13229. [PMID: 20949087 PMCID: PMC2950853 DOI: 10.1371/journal.pone.0013229] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 09/16/2010] [Indexed: 11/19/2022] Open
Abstract
Recent work suggests a role for multiple host factors in facilitating HIV-1 reverse transcription. Previously, we identified a cellular activity which increases the efficiency of HIV-1 reverse transcription in vitro. Here, we describe aspects of the activity which shed light on its function. The cellular factor did not affect synthesis of strong-stop DNA but did improve downstream DNA synthesis. The stimulatory activity was isolated by gel filtration in a single fraction of the exclusion volume. Velocity-gradient purified HIV-1, which was free of detectable RNase activity, showed poor reverse transcription efficiency but was strongly stimulated by partially purified cell proteins. Hence, the cell factor(s) did not inactivate an RNase activity that might degrade the viral genomic RNA and block completion of reverse transcription. Instead, the cell factor(s) enhanced first strand transfer and synthesis of late reverse transcription suggesting it stabilized the reverse transcription complex. The factor did not affect lysis of HIV-1 by Triton X-100 in the endogenous reverse transcription (ERT) system, and ERT reactions with HIV-1 containing capsid mutations, which varied the biochemical stability of viral core structures and impeded reverse transcription in cells, showed no difference in the ability to be stimulated by the cell factor(s) suggesting a lack of involvement of the capsid in the in vitro assay. In addition, reverse transcription products were found to be resistant to exogenous DNase I activity when the active fraction was present in the ERT assay. These results indicate that the cell factor(s) may improve reverse transcription by facilitating DNA strand transfer and DNA synthesis. It also had a protective function for the reverse transcription products, but it is unclear if this is related to improved DNA synthesis.
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Affiliation(s)
- David Warrilow
- Division of Immunology and Infectious Disease, Queensland Institute of Medical Research, Brisbane, Australia
- Griffith Medical Research College, A Joint Program of Griffith University and the Queensland Institute of Medical Research, Herston, Australia
| | - Kylie Warren
- Division of Immunology and Infectious Disease, Queensland Institute of Medical Research, Brisbane, Australia
- School of Natural Sciences, University of Western Sydney, Hawkesbury, Australia
| | - David Harrich
- Division of Immunology and Infectious Disease, Queensland Institute of Medical Research, Brisbane, Australia
- Griffith Medical Research College, A Joint Program of Griffith University and the Queensland Institute of Medical Research, Herston, Australia
- * E-mail: .
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3
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Bouchonnet F, Dam E, Mammano F, de Soultrait V, Henneré G, Benech H, Clavel F, Hance AJ. Quantification of the effects on viral DNA synthesis of reverse transcriptase mutations conferring human immunodeficiency virus type 1 resistance to nucleoside analogues. J Virol 2005; 79:812-22. [PMID: 15613309 PMCID: PMC538537 DOI: 10.1128/jvi.79.2.812-822.2005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human immunodeficiency virus type I (HIV-1) reverse transcriptase (RT) resistance mutations reduce the susceptibility of the virus to nucleoside analogues but may also impair viral DNA synthesis. To further characterize the effect of nucleoside analogue resistance mutations on the efficiency and kinetics of HIV-1 DNA synthesis and to evaluate the impact of the depletion of deoxynucleoside triphosphates (dNTP) on this process, DNA synthesis was evaluated by allowing DNA synthesis to proceed with natural HIV-1 templates and primers, either within permeabilized viral particles or in newly infected cells, and quantifying the products by real-time PCR. Three recombinant viruses derived from three pNL4-3 molecular clones expressing mutations associated with resistance to zidovudine: a clone expressing RT mutation M184V, a clone expressing mutations M41L plus T215Y (M41L+T215Y), and clinical isolate BV34 (carrying seven resistance mutations). Following infection of P4 cells, the BV34 mutant, but not viruses expressing the M184V mutation or M41L+T215Y, exhibited a defect in DNA synthesis. Importantly, however, for mutants carrying the M184V mutation or M41L+T215Y mutations, a defect could be detected by using target cells in which dATP pools had been reduced by pretreatment with hydroxyurea. Based on these observations, we developed a recombinant-virus assay to assess the effects of hydroxyurea pretreatment on infectivity of viruses carrying plasma-derived RT sequences from patients with nucleoside resistance. Using this assay, we found that many, but not all, viruses carrying RT resistance mutations display an increased sensitivity to hydroxyurea, suggesting that the impact of RT resistance mutations on viral replication may be more profound in cell populations characterized by smaller dNTP pools.
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Affiliation(s)
- Francine Bouchonnet
- INSERM U.552, Hôpital Bichat-Claude Bernard, 46, rue Henri Huchard, 750918 Paris, France
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4
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Takahashi H, Sawa H, Hasegawa H, Shoya Y, Sata T, Hall WW, Nagashima K, Kurata T. Topoisomerase I and ATP activate cDNA synthesis of human immunodeficiency virus type 1. Biochem Biophys Res Commun 2002; 294:509-17. [PMID: 12051740 DOI: 10.1016/s0006-291x(02)00503-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Replication of human immunodeficiency virus type 1 (HIV-1) is regulated at reverse transcription. Cellular topoisomerase I has been reported to be carried into HIV-1 virions and enhance cDNA synthesis in vitro, suggesting that topoisomerase I expressed in virus producer cells regulates reverse transcription. Here, by employing both indicator cell assay and endogenous reverse transcription (ERT) assay, we show that topoisomerase I and adenosine triphosphate (ATP) enhanced cDNA synthesis of HIV-1. In addition, topoisomerase I mutants, R488A and K532A, lacking enzymatic activity, attenuated the efficiency of cDNA synthesis and resulted in inhibition of the infectivity of HIV-1, suggesting that the activity of topoisomerase I lacking in these mutants is indispensable for the cDNA synthesis in the HIV-1 replication process. Furthermore, ATP could dissociate topoisomerase I from the topoisomerase I-RNA complex and enhance cDNA synthesis in vitro. These findings suggest that cellular topoisomerase I and ATP play a pivotal role in the synthesis of cDNA of HIV-1.
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Affiliation(s)
- Hidehiro Takahashi
- Department of Pathology, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan.
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5
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Gaillard RK, Barnard J, Lopez V, Hodges P, Bourne E, Johnson L, Allen MI, Condreay P, Miller WH, Condreay LD. Kinetic analysis of wild-type and YMDD mutant hepatitis B virus polymerases and effects of deoxyribonucleotide concentrations on polymerase activity. Antimicrob Agents Chemother 2002; 46:1005-13. [PMID: 11897582 PMCID: PMC127103 DOI: 10.1128/aac.46.4.1005-1013.2002] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mutations in the YMDD motif of the hepatitis B virus (HBV) DNA polymerase result in reduced susceptibility of HBV to inhibition by lamivudine, at a cost in replication fitness. The mechanisms underlying the effects of YMDD mutations on replication fitness were investigated using both a cell-based viral replication system and an in vitro enzyme assay to examine wild-type (wt) and YMDD-mutant polymerases. We calculated the affinities of wt and YMDD-mutant polymerases for each natural deoxyribonucleoside triphosphate (dNTP) and determined the intracellular concentrations of each dNTP in HepG2 cells under conditions that support HBV replication. In addition, inhibition constants for lamivudine triphosphate were determined for wt and YMDD-mutant polymerases. Relative to wt HBV polymerase, each of the YMDD-mutant polymerases showed increased apparent K(m) values for the natural dNTP substrates, indicating decreased affinities for these substrates, as well as increased K(i) values for lamivudine triphosphate, indicating decreased affinity for the drug. The effect of the differences in apparent K(m) values between YMDD-mutant polymerase and wt HBV polymerase could be masked by high levels of dNTP substrates (>20 microM). However, assays using dNTP concentrations equivalent to those measured in HepG2 cells under physiological conditions showed decreased enzymatic activity of YMDD-mutant polymerases relative to wt polymerase. Therefore, the decrease in replication fitness of YMDD-mutant HBV strains results from the lower affinities (increased K(m) values) of the YMDD-mutant polymerases for the natural dNTP substrates and physiological intracellular concentrations of dNTPs that are limiting for the replication of YMDD-mutant HBV strains.
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Affiliation(s)
- Richard K Gaillard
- Department of Virology, GlaxoSmithKline, Research Triangle Park, North Carolina 27709, USA.
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Takahashi H, Iwata T, Kitagawa Y, Shoya Y, Takahashi RH, Nagashima K, Kurata T. Monoclonal antibodies against topoisomerase I suppressed DNA relaxation and HIV-1 cDNA synthesis. Hybridoma (Larchmt) 2000; 19:331-4. [PMID: 11001406 DOI: 10.1089/027245700429882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) virion is known to carry a number of cellular components including cellular topoisomerase I. Previously, we have demonstrated that topoisomerase I enhances HIV-1 cDNA synthesis in reverse transcription (RT) assays in vitro. In the present study, we have produced six monoclonal antibodies (MAbs) against human topoisomerase I. The MAbs suppressed nicking/closing of supercoiled DNA and cDNA synthesis in an endogenous reverse transcription (ERT) assay using a detergent-disrupted HIV-1 virion. Thus, the results suggest that topoisomerase I plays an important role in RNA-directed DNA polymerization.
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Affiliation(s)
- H Takahashi
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan.
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Simm M, Pekarskaya O, Volsky DJ. Synthesis of full-length viral DNA in CD4-positive membrane vesicles exposed to HIV-1. A model for studies of early stages of the hiv-1 life cycle. J Biol Chem 1996; 271:28266-70. [PMID: 8910445 DOI: 10.1074/jbc.271.45.28266] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
CD4-positive membrane vesicles (MV) were isolated under isotonic conditions from human T lymphoblastoid cells MT-2 and CEM and tested for their ability to support reverse transcription of viral RNA upon exposure to human immunodeficiency virus, type 1 (HIV-1). MV contained cytoplasms as confirmed by the presence of mitochondrial DNA but were devoid of chromosomal DNA. Virus binding and vesicle lysis assays revealed that 4-19% (depending upon virus dose) of MV-bound HIV-1 entered the vesicles. HIV-1 internalized in MV was able to initiate and complete viral DNA synthesis as determined by the detection of products of reverse transcription using polymerase chain reaction amplification of viral DNA using regions present in early (strong stop) transcripts and full-length double-stranded molecules. Viral DNA was undetectable in MV exposed to HIV-1 at 0 degrees C, in MV exposed to UV-inactivated virus at 37 degrees C, or after exposure to intact virus at 37 degrees C in the presence of reverse transcriptase inhibitors 2',3'-dideoxycytidine and a tetrahydroimidazo[4,5,1-jk](1,4)-benzodiazepin-2-(1H)-thione derivative, indicating that viral DNA detected in HIV-1-exposed MV was synthesized de novo. Kinetic studies revealed that HIV-1 DNA synthesis in MV was very rapid; full-length viral DNA was detected within 15 min of exposure at 37 degrees C, and the DNA levels increased 90-fold after 1 h and declined thereafter. Strong stop viral DNA was 10-fold more abundant than full-length DNA after 1 h at 37 degrees C, indicating that 10% of input viral genomes are fully transcribed in MV within this time frame. This system preserves the critical features of intact CD4-bearing cells to permit studies of HIV-1 entry, uncoating, and reverse transcription of viral RNA.
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Affiliation(s)
- M Simm
- Molecular Virology Laboratory, St. Luke's-Roosevelt Hospital Center and College of Physicians & Surgeons, Columbia University, New York, New York 10019, USA.
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8
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Quan Y, Gu Z, Li X, Li Z, Morrow CD, Wainberg MA. Endogenous reverse transcription assays reveal high-level resistance to the triphosphate of (-)2'-dideoxy-3'-thiacytidine by mutated M184V human immunodeficiency virus type 1. J Virol 1996; 70:5642-5. [PMID: 8764080 PMCID: PMC190526 DOI: 10.1128/jvi.70.8.5642-5645.1996] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Kinetic analysis showed that the Ki values and the Ki/Km ratios for mutated, recombinant M184V human immunodeficiency virus type 1 reverse transcriptase (RT) for (-)2'-dideoxy-3'-thiacytidine triphosphate (3TCTP) were 35-fold higher than the equivalent values for wild-type RT but only about twice as high as the equivalent values for each of the triphosphates of ddC (ddCTP) and ddA (ddATP). Fully endogenous RT assays showed that viruses containing the M184V substitution were highly resistant to 3TCTP, with an increase in the 50% inhibitory concentration of 250-fold in comparison with wild-type recombinant virus.
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Affiliation(s)
- Y Quan
- McGill University AIDS Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
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Krogstad P, Chen IS, Canon J, Rey O. Quantitative analysis of the endogenous reverse transcriptase reactions of HIV type 1 variants with decreased susceptibility to azidothymidine and nevirapine. AIDS Res Hum Retroviruses 1996; 12:977-83. [PMID: 8827213 DOI: 10.1089/aid.1996.12.977] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
A large number of nucleoside analog and nonnucleoside inhibitors of HIV-1 reverse transcriptase (RT) have been developed for clinical use. Data confirm that resistant variants of HIV-1 rapidly emerge in response to the selective pressure of treatment with these agents. Detection of drug resistance generally involves detection of specific mutations in the viral genome or demonstrating a failure of the drug to suppress virus replication in culture. We have developed a PCR-based method to quantitatively examine HIV-1 DNA synthesis in vitro in endogenous reverse transcription reactions and tested it as a method to detect resistance to RT inhibitors. Under certain conditions, we were able to distinguish HIV strains with high-level resistance to azidothymidine triphosphate inhibition from sensitive strains. This method was quite useful as an assay to detect resistance to nevirapine, a nonnucleoside RT inhibitor; in reconstruction experiments, nevirapine-resistant virus was detectable when it represented 10 to 25% of the total amount of virus present in reaction mixtures. These data are examined in the light of current models of the mechanisms of action of nucleoside nonnucleoside RT inhibitors. This assay may be useful for detecting the emergence of drug-resistant HIV-1 variants during therapy.
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Affiliation(s)
- P Krogstad
- Department of Pediatrics, University of California at Los Angeles, School of Medicine 90095, USA
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Wilson JE, Porter DJ, Reardon JE. Inhibition of viral polymerases by chain-terminating substrates: a kinetic analysis. Methods Enzymol 1996; 275:398-424. [PMID: 9026652 DOI: 10.1016/s0076-6879(96)75024-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- J E Wilson
- Division of Biochemistry, Burroughs Wellcome Co., Research Triangle Park, North Carolina 27709, USA
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11
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Affiliation(s)
- J Eberle
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universitat, Munchen, Germany
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12
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Bouck J, Fu XD, Skalka AM, Katz RA. Genetic selection for balanced retroviral splicing: novel regulation involving the second step can be mediated by transitions in the polypyrimidine tract. Mol Cell Biol 1995; 15:2663-71. [PMID: 7739546 PMCID: PMC230496 DOI: 10.1128/mcb.15.5.2663] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Incomplete splicing is essential for retroviral replication; and in simple retroviruses, splicing regulation appears to occur entirely in cis. Our previous studies, using avian sarcoma virus, indicated that weak splicing signals allow transcripts to escape the splicing pathway. We also isolated a series of avian sarcoma virus mutants in which env mRNA splicing was regulated by mechanisms distinct from those of the wild-type virus. In vitro splicing experiments with one such mutant (insertion suppressor 1 [IS1]) revealed that exon 1 and lariat-exon 2 intermediates were produced (step 1) but the exons were not efficiently ligated (step 2). In this work, we have studied the mechanism of this second-step block as well as its biological relevance. Our results show that the second-step block can be overcome by extending the polypyrimidine tract, and this causes an oversplicing defect in vivo. The requirement for regulated splicing was exploited to isolate new suppressor mutations that restored viral growth by down-regulating splicing. One suppressor consisted of a single U-to-C transition in the polypyrimidine tract; a second included this same change as well as an additional U-to-C transition within a uridine stretch in the polypyrimidine tract. These suppressor mutations affected primarily the second step of splicing in vitro. These results support a specific role for the polypyrimidine tract in the second step of splicing and confirm that, in a biological system, uridines and cytosines are not functionally equivalent within the polypyrimidine tract. Unlike the wild-type virus, the second-step mutants displayed significant levels of lariat-exon 2 in vivo, suggesting a role for splicing intermediates in regulation. Our results indicate that splicing regulation can involve wither the first or second step.
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Affiliation(s)
- J Bouck
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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