1
|
Ojwach DBA, Madlala P, Gordon M, Ndung'u T, Mann JK. Vulnerable targets in HIV-1 Pol for attenuation-based vaccine design. Virology 2021; 554:1-8. [PMID: 33316731 PMCID: PMC7931244 DOI: 10.1016/j.virol.2020.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 11/24/2022]
Abstract
Identification of viral immune escape mutations that compromise HIV's ability to replicate may aid rational attenuation-based vaccine design. Previously we reported amino acids associated with altered viral replication capacity (RC) from a sequence-function analysis of 487 patient-derived RT-integrase sequences. In this study, site-directed mutagenesis experiments were performed to validate the effect of these mutations on RC. Viral reverse transcripts were measured by quantitative PCR and structural modelling was performed to gain further insight into the effect of reverse transcriptase (RT) mutations on reverse transcription. RT-integrase variants in or flanking cytotoxic T cell epitopes in the RT palm (158S), RT thumb (241I and 257V) and integrase catalytic core domain (124N) were confirmed to significantly reduce RC. RT mutants showed a delayed initiation of viral DNA synthesis. Structural models provide insight into how these attenuating RT mutations may affect amino acid interactions in the helix clamp, primer grip and catalytic site regions.
Collapse
Affiliation(s)
- Doty B A Ojwach
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Paradise Madlala
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Michelle Gordon
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA; Africa Health Research Institute, Durban, South Africa; Max Planck Institute for Infection Biology, Berlin, Germany; Division of Infection and Immunity, University College London, London, UK
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
| |
Collapse
|
2
|
Gonelli CA, Khoury G, Center RJ, Purcell DFJ. HIV-1-based Virus-like Particles that Morphologically Resemble Mature, Infectious HIV-1 Virions. Viruses 2019; 11:v11060507. [PMID: 31159488 PMCID: PMC6630479 DOI: 10.3390/v11060507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 01/04/2023] Open
Abstract
A prophylactic vaccine eliciting both broad neutralizing antibodies (bNAbs) to the HIV-1 envelope glycoprotein (Env) and strong T cell responses would be optimal for preventing HIV-1 transmissions. Replication incompetent HIV-1 virus-like particles (VLPs) offer the opportunity to present authentic-structured, virion-associated Env to elicit bNAbs, and also stimulate T cell responses. Here, we optimize our DNA vaccine plasmids as VLP expression vectors for efficient Env incorporation and budding. The original vector that was used in human trials inefficiently produced VLPs, but maximized safety by inactivating RNA genome packaging, enzyme functions that are required for integration into the host genome, and deleting accessory proteins Vif, Vpr, and Nef. These original DNA vaccine vectors generated VLPs with incomplete protease-mediated cleavage of Gag and were irregularly sized. Mutations to restore function within the defective genes revealed that several of the reverse transcriptase (RT) deletions mediated this immature phenotype. Here, we made efficient budding, protease-processed, and mature-form VLPs that resembled infectious virions by introducing alternative mutations that completely removed the RT domain, but preserved most other safety mutations. These VLPs, either expressed from DNA vectors in vivo or purified after expression in vitro, are potentially useful immunogens that can be used to elicit antibody responses that target Env on fully infectious HIV-1 virions.
Collapse
Affiliation(s)
- Christopher A Gonelli
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
| | - Georges Khoury
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
| | - Rob J Center
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
- Viral Entry and Vaccines Laboratory, Disease Elimination, Burnet Institute, Melbourne, Victoria 3004, Australia.
| | - Damian F J Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
| |
Collapse
|
3
|
Wapling J, Srivastava S, Shehu-Xhilaga M, Tachedjian G. Targeting Human Immunodeficiency Virus Type 1 Assembly, Maturation and Budding. Drug Target Insights 2017. [DOI: 10.1177/117739280700200020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Johanna Wapling
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
- Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Seema Srivastava
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
| | - Miranda Shehu-Xhilaga
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia
- Infectious Diseases Unit, Alfred Hospital, Prahran, Victoria 3181, Australia
| | - Gilda Tachedjian
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
- Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia
| |
Collapse
|
4
|
Chiang CC, Tseng YT, Huang KJ, Pan YY, Wang CT. Mutations in the HIV-1 reverse transcriptase tryptophan repeat motif affect virion maturation and Gag-Pol packaging. Virology 2011; 422:278-87. [PMID: 22104208 DOI: 10.1016/j.virol.2011.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 08/30/2011] [Accepted: 11/01/2011] [Indexed: 11/29/2022]
Abstract
Our goal was to determine the contribution of HIV-1 reverse transcriptase tryptophan repeat motif residues to virion maturation. With the exception of W402A, we found none of the single substitution mutations exerted major impacts on virus assembly or processing. However, all mutants except for W410A exhibited significant decreases in virus-associated RT, presumably a result of unstable RT mutant degradation. Mutations W398A, W401A and W406A decreased the enhancement effect of efavirenz on PR-mediated Gag processing efficiency, which is in agreement with their destabilizing RT effects. Furthermore, combined double or triple W398, W401 and W406 mutations significantly affected virus processing and Gag-Pol packaging. Further analyses suggest that inefficient PR-mediated Gag cleavage partly accounts for the virion processing defect. Our results support the idea that in addition to playing a role in RT heterodimer stabilization, the RT Trp repeat motif in the Gag-Pol context is also involved in PR activation via Gag-Pol/Gag-Pol interaction.
Collapse
Affiliation(s)
- Chien-Cheng Chiang
- Department of Medical Research and Education, Taipei Veterans General Hospital and Institute of Clinical Medicine, National Yang-Ming University School of Medicine, Taipei, Taiwan
| | | | | | | | | |
Collapse
|
5
|
Pandey N, Mishra CA, Manvar D, Upadhyay AK, Talele TT, Comollo TW, Kaushik-Basu N, Pandey VN. The glutamine side chain at position 91 on the β5a-β5b loop of human immunodeficiency virus type 1 reverse transcriptase is required for stabilizing the dNTP binding pocket. Biochemistry 2011; 50:8067-77. [PMID: 21800837 PMCID: PMC3204787 DOI: 10.1021/bi200815e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Earlier, we postulated that Gln91 of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT) stabilizes the side chain of Tyr183 via hydrogen bonding interaction between O(H) of Tyr183 and CO of Q91 [Harris, D., et al. (1998) Biochemistry 37, 9630-9640]. To test this hypothesis, we generated mutant derivatives of Gln91 and analyzed their biochemical properties. The efficiency of reverse transcription was severely impaired by nonconservative substitution of Gln with Ala, while conservative substitution of Gln with Asn resulted in an approximately 70% loss of activity, a value similar to that observed with the Y183F mutation. The loss of polymerase activity from both Q91A and Q91N was significantly improved by a Met to Val substitution at position 184. Curiously, the Q91N mutant exhibited stringency in discriminating between correct and incorrect nucleotides, suggesting its possible interaction with residues influencing the flexibility of the dNTP binding pocket. In contrast, both double mutants, Q91A/M184V and Q91N/M184V, are found to be as error prone as the wild-type enzyme. We propose a model that suggests that subtle structural changes in the region due to mutation at position 91 may influence the stability of the side chain of Tyr183 in the catalytic YMDD motif of the enzyme, thus altering the active site geometry that may interfere in substrate recognition.
Collapse
Affiliation(s)
- Nootan Pandey
- Department of Biochemistry and Molecular Biology, UMD-New Jersey Medical School 185 South Orange Ave Newark, NJ 07103
| | - Chaturbhuj A. Mishra
- Department of Biochemistry and Molecular Biology, UMD-New Jersey Medical School 185 South Orange Ave Newark, NJ 07103
| | - Dinesh Manvar
- Department of Biochemistry and Molecular Biology, UMD-New Jersey Medical School 185 South Orange Ave Newark, NJ 07103
| | - Alok K. Upadhyay
- Department of Biochemistry and Molecular Biology, UMD-New Jersey Medical School 185 South Orange Ave Newark, NJ 07103
| | - Tanaji T. Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, St. John’s University, 8000 Utopia Parkway, Queens, NY 11439
| | - Thomas W. Comollo
- Department of Biochemistry and Molecular Biology, UMD-New Jersey Medical School 185 South Orange Ave Newark, NJ 07103
| | - Neerja Kaushik-Basu
- Department of Biochemistry and Molecular Biology, UMD-New Jersey Medical School 185 South Orange Ave Newark, NJ 07103
| | - Virendra N. Pandey
- Department of Biochemistry and Molecular Biology, UMD-New Jersey Medical School 185 South Orange Ave Newark, NJ 07103
| |
Collapse
|
6
|
Zhang F, Zang T, Wilson SJ, Johnson MC, Bieniasz PD. Clathrin facilitates the morphogenesis of retrovirus particles. PLoS Pathog 2011; 7:e1002119. [PMID: 21738476 PMCID: PMC3128127 DOI: 10.1371/journal.ppat.1002119] [Citation(s) in RCA: 43] [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: 02/10/2011] [Accepted: 04/29/2011] [Indexed: 12/20/2022] Open
Abstract
The morphogenesis of retroviral particles is driven by Gag and GagPol proteins that provide the major structural component and enzymatic activities required for particle assembly and maturation. In addition, a number of cellular proteins are found in retrovirus particles; some of these are important for viral replication, but many lack a known functional role. One such protein is clathrin, which is assumed to be passively incorporated into virions due to its abundance at the plasma membrane. We found that clathrin is not only exceptionally abundant in highly purified HIV-1 particles but is recruited with high specificity. In particular, the HIV-1 Pol protein was absolutely required for clathrin incorporation and point mutations in reverse transcriptase or integrase domains of Pol could abolish incorporation. Clathrin was also specifically incorporated into other retrovirus particles, including members of the lentivirus (simian immunodeficiency virus, SIVmac), gammaretrovirus (murine leukemia virus, MLV) and betaretrovirus (Mason-Pfizer monkey virus, M-PMV) genera. However, unlike HIV-1, these other retroviruses recruited clathrin primarily using peptide motifs in their respective Gag proteins that mimicked motifs found in cellular clathrin adaptors. Perturbation of clathrin incorporation into these retroviruses, via mutagenesis of viral proteins, siRNA based clathrin depletion or adaptor protein (AP180) induced clathrin sequestration, had a range of effects on the accuracy of particle morphogenesis. These effects varied according to which retrovirus was examined, and included Gag and/or Pol protein destabilization, inhibition of particle assembly and reduction in virion infectivity. For each retrovirus examined, clathrin incorporation appeared to be important for optimal replication. These data indicate that a number of retroviruses employ clathrin to facilitate the accurate morphogenesis of infectious particles. We propose a model in which clathrin contributes to the spatial organization of Gag and Pol proteins, and thereby regulates proteolytic processing of virion components during particle assembly. The assembly and maturation of infectious retroviruses is driven by two viral proteins, Gag and Pol. Additionally, a number of cellular proteins are found in retrovirus particles, many of which lack a known functional role. One such protein is clathrin, which normally mediates several physiological processes in cells and was previously thought to be only passively incorporated into virions. In this study we show that clathrin is actively, specifically and abundantly incorporated into retrovirus particles. In several cases, retroviral proteins encode peptide motifs that mimic those found in cellular adaptor proteins that are responsible for clathrin recruitment. The range of retroviruses into which clathrin is packaged includes human and simian immunodeficiency viruses as well as other murine and simian retroviruses. Manipulations that prevented clathrin incorporation into virions also caused a variety of defects in the genesis of infectious retroviruses, including viral protein destabilization, inhibition of particle assembly and release, and reduction in virion infectiousness. The precise nature of the defect varied according to which particular retrovirus was examined. Overall these studies suggest that clathrin is frequently employed by retroviruses to facilitate the accurate assembly of infectious virions.
Collapse
Affiliation(s)
- Fengwen Zhang
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America
| | - Trinity Zang
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America
| | - Sam J. Wilson
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America
| | - Marc C. Johnson
- Department of Molecular Microbiology and Immunology, M616 Medical Sciences Building, University of Missouri-Columbia, Columbia, Missouri, United States of America
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
7
|
Xu HT, Oliveira M, Quan Y, Bar-Magen T, Wainberg MA. Differential impact of the HIV-1 non-nucleoside reverse transcriptase inhibitor mutations K103N and M230L on viral replication and enzyme function. J Antimicrob Chemother 2010; 65:2291-9. [DOI: 10.1093/jac/dkq338] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
8
|
A single amino acid substitution in HIV-1 reverse transcriptase significantly reduces virion release. J Virol 2009; 84:976-82. [PMID: 19889767 DOI: 10.1128/jvi.01532-09] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 protease (PR) mediates the proteolytic processing of virus particles during or after virus budding. PR activation is thought to be triggered by appropriate Gag-Pol/Gag-Pol interaction; factors affecting this interaction either enhance or reduce PR-mediated cleavage efficiency, resulting in markedly reduced virion production or the release of inadequately processed virions. We previously showed that a Gag-Pol deletion mutation involving the reverse transcriptase tryptophan (Trp) repeat motif markedly impairs PR-mediated virus maturation and that an alanine substitution at W401 (W401A) or at both W401 and W402 (W401A/W402A) partially or almost completely negates the enhancement effect of efavirenz (a nonnucleoside reverse transcriptase inhibitor) on PR-mediated virus processing efficiency. These data suggest that the Trp repeat motif may contribute to the PR activation process. Here we demonstrate that due to enhanced Gag cleavage efficiency, W402 alanine or leucine substitution significantly reduces virus production. However, W402 replacement with phenylalanine does not significantly affect virus particle assembly or processing, but it does markedly impair viral infectivity in a single-cycle infection assay. Our results demonstrate that a single amino acid substitution at HIV-1 RT can radically affect virus assembly by enhancing Gag cleavage efficiency, suggesting that in addition to contributing to RT biological function during the early stages of virus replication, the HIV-1 RT tryptophan repeat motif in a Gag-Pol context may play an important role in suppressing the premature activation of PR during late-stage virus replication.
Collapse
|
9
|
Zhang HJ, Wang YX, Wu H, Jin DY, Wen YM, Zheng BJ. The y271 and i274 amino acids in reverse transcriptase of human immunodeficiency virus-1 are critical to protein stability. PLoS One 2009; 4:e6108. [PMID: 19578544 PMCID: PMC2701634 DOI: 10.1371/journal.pone.0006108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Accepted: 06/04/2009] [Indexed: 11/19/2022] Open
Abstract
Reverse transcriptase (RT) of human immunodeficiency virus (HIV)-1 plays a key role in initiating viral replication and is an important target for developing anti-HIV drugs. Our previous study showed that two mutations (Y271A and I274A) in the turn RT (Gln(269)-Arg(277)) abrogated viral replication, but the replication capacity and RT activity was discordant. In this study, we further investigated why alanine substitutions at these two sites would affect viral replication. We found that both RT activity and RT protein were almost undetectable in viral particles of these two mutants, although the Pr160(gag-pol) mutants were properly expressed, transported and incorporated. Using protease inhibition assay, we demonstrated a correlation between the degradation of the RT mutants and the activity of viral protease. Our native gel analysis indicated that the mutations at 271 and 274 amino acids might cause conformational changes, leading to the formation of higher order oligomers instead of dimers, resulting in increased protein instability and susceptibility to viral protease. Thus, residues 271 and 274 are critical to RT stability and resistance to viral protease. The conservation of the two amino acid residues among different strains of HIV-1 lent further support to this conclusion. The knowledge gained here may prove useful in drug design.
Collapse
Affiliation(s)
- Hao-Jie Zhang
- Department of Microbiology, the University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Yong-Xiang Wang
- Key Laboratory of Medical Molecular Virology, Institute of Medical Microbiology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hao Wu
- Department of Microbiology, the University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Dong-Yan Jin
- Department of Biochemistry, the University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Yu-Mei Wen
- Key Laboratory of Medical Molecular Virology, Institute of Medical Microbiology, Shanghai Medical College, Fudan University, Shanghai, China
- * E-mail: (YMW); (BJZ)
| | - Bo-Jian Zheng
- Department of Microbiology, the University of Hong Kong, Hong Kong SAR, People's Republic of China
- * E-mail: (YMW); (BJZ)
| |
Collapse
|
10
|
Mougel M, Houzet L, Darlix JL. When is it time for reverse transcription to start and go? Retrovirology 2009; 6:24. [PMID: 19261185 PMCID: PMC2656454 DOI: 10.1186/1742-4690-6-24] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 03/04/2009] [Indexed: 11/25/2022] Open
Abstract
Upon cell infection by a retrovirus, the viral DNA polymerase, called reverse transcriptase (RT), copies the genomic RNA to generate the proviral DNA flanked by two long terminal repeats (LTR). A discovery twenty years ago demonstrated that the structural viral nucleocapsid protein (NC) encoded by Gag is an essential cofactor of reverse transcription, chaperoning RT during viral DNA synthesis. However, it is only recently that NC was found to exert a control on the timing of reverse transcription, in a spatio-temporal manner. This brief review summarizes findings on the timing of reverse transcription in wild type HIV-1 and in nucleopcapsid (NC) mutants where virions contain a large amount of newly made viral DNA. This brief review also proposes some explanations of how NC may control late reverse transcription during Gag assembly in virus producer cells.
Collapse
Affiliation(s)
- Marylène Mougel
- LaboRetro, Unité de virologie humaine INSERM U758, IFR128, ENS, 46 allée d'Italie, Lyon, France.
| | | | | |
Collapse
|
11
|
Pattyn E, Lavens D, Van der Heyden J, Verhee A, Lievens S, Lemmens I, Hallenberger S, Jochmans D, Tavernier J. MAPPIT (MAmmalian Protein–Protein Interaction Trap) as a tool to study HIV reverse transcriptase dimerization in intact human cells. J Virol Methods 2008; 153:7-15. [DOI: 10.1016/j.jviromet.2008.06.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Revised: 06/17/2008] [Accepted: 06/19/2008] [Indexed: 10/21/2022]
|
12
|
Wapling J, Srivastava S, Shehu-Xhilaga M, Tachedjian G. Targeting human immunodeficiency virus type 1 assembly, maturation and budding. Drug Target Insights 2007; 2:159-82. [PMID: 21901072 PMCID: PMC3155237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The targets for licensed drugs used for the treatment of human immunodeficiency virus type 1 (HIV-1) are confined to the viral reverse transcriptase (RT), protease (PR), and the gp41 transmembrane protein (TM). While currently approved drugs are effective in controlling HIV-1 infections, new drug targets and agents are needed due to the eventual emergence of drug resistant strains and drug toxicity. Our increased understanding of the virus life-cycle and how the virus interacts with the host cell has unveiled novel mechanisms for blocking HIV-1 replication. This review focuses on inhibitors that target the late stages of virus replication including the synthesis and trafficking of the viral polyproteins, viral assembly, maturation and budding. Novel approaches to blocking the oligomerization of viral enzymes and the interactions between viral proteins and host cell factors, including their feasibility as drug targets, are discussed.
Collapse
Affiliation(s)
- Johanna Wapling
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia,Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | - Seema Srivastava
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia
| | - Miranda Shehu-Xhilaga
- Department of Medicine, Monash University, Prahran, Victoria 3181, Australia,Infectious Diseases Unit, Alfred Hospital, Prahran, Victoria 3181, Australia
| | - Gilda Tachedjian
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Victoria, 3004, Australia,Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia,Department of Medicine, Monash University, Prahran, Victoria 3181, Australia,Correspondence: Gilda Tachedjian, Ph.D., Molecular Interactions Group, The Macfarlane Burnet Institute for Medical Research and Public Health, GPO Box 2284, Melbourne, Victoria, 3001, Australia. Tel: 61 3 9282 2256; Fax: 61 3 9282 2100;
| |
Collapse
|
13
|
Olivares I, Mulky A, Boross PI, Tözsér J, Kappes JC, López-Galíndez C, Menéndez-Arias L. HIV-1 protease dimer interface mutations that compensate for viral reverse transcriptase instability in infectious virions. J Mol Biol 2007; 372:369-81. [PMID: 17651754 PMCID: PMC2696282 DOI: 10.1016/j.jmb.2007.06.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 06/20/2007] [Accepted: 06/26/2007] [Indexed: 11/19/2022]
Abstract
Mature enzymes encoded within the human immunodeficiency virus type 1 (HIV-1) genome (protease (PR), reverse transcriptase (RT) and integrase (IN)) derive from proteolytic processing of a large polyprotein (Gag-Pol). Gag-Pol processing is catalyzed by the viral PR, which is active as a homodimer. The HIV-1 RT functions as a heterodimer (p66/p51) composed of subunits of 560 and 440 amino acid residues, respectively. Both subunits have identical amino acid sequence, but p51 lacks 120 residues that are removed by the HIV-1 PR during viral maturation. While p66 is the catalytic subunit, p51 has a primarily structural role. Amino acid substitutions affecting the stability of p66/p51 (i.e. F130W) have a deleterious effect on viral fitness. Previously, we showed that the effects of F130W are mediated by p51 and can be compensated by mutation T58S. While studying the dynamics of emergence of the compensatory mutation, we observed that mutations in the viral PR-coding region were selected in HIV clones containing the RT substitution F130W, before the imposition of T58S/F130W mutations. The PR mutations identified (G94S and T96S) improved the replication capacity of the F130W mutant virus. By using a trans-complementation assay, we demonstrate that the loss of p66/p51 heterodimer stability caused by Trp130 can be attributed to an increased susceptibility of RT to viral PR degradation. Recombinant HIV-1 PRs bearing mutations G94S or T96S showed decreased dimer stability and reduced catalytic efficiency. These results were consistent with crystallographic data showing the location of both residues in the PR dimerization interface.
Collapse
Affiliation(s)
- Isabel Olivares
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Alok Mulky
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Peter I. Boross
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Debrecen, H-4012 Hungary
| | - József Tözsér
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, University of Debrecen, Debrecen, H-4012 Hungary
| | - John C. Kappes
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
- Research Service, Birmingham Veterans Affairs Medical Center, Birmingham, Alabama 35233, USA
| | - Cecilio López-Galíndez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas – Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid, Spain
- E-mail address of the corresponding author:
| |
Collapse
|
14
|
Mulky A, Vu BC, Conway JA, Hughes SH, Kappes JC. Analysis of amino acids in the beta7-beta8 loop of human immunodeficiency virus type 1 reverse transcriptase for their role in virus replication. J Mol Biol 2006; 365:1368-78. [PMID: 17141805 DOI: 10.1016/j.jmb.2006.10.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 10/19/2006] [Accepted: 10/25/2006] [Indexed: 11/25/2022]
Abstract
The HIV-1 p51/p66 reverse transcriptase (RT) heterodimer interface comprises, in part, intermolecular interaction of the loop region between beta-strands 7 and 8 (beta7-beta8 loop) in the p51 fingers subdomain with the p66 palm subdomain. In this study, for the first time in the context of infectious HIV-1 particles, we analyzed the contribution of amino acid residues (S134, I135, N136, N137, T139 and P140) in the beta7-beta8 loop for RT heterodimerization, enzymatic activity, and virus infectivity. Mutating asparagine 136 to alanine (N136A) reduced viral infectivity and enzyme activity dramatically. The N136A mutation appeared to destabilize the RT heterodimer and render both the p66 and p51 subunits susceptible to aberrant cleavage by the viral protease. Subunit-specific mutagenesis demonstrated that the presence of the N136A mutation in the p51 subunit alone was sufficient to cause degradation of RT within the virus particle. Alanine mutation at other residues of the beta7-beta8 loop did not affect either RT stability or virus infectivity significantly. None of the beta7-beta8 loop alanine mutations affected the sensitivity of virus to inhibition by NNRTIs. In the context of infectious virions, our results indicate a critical role of the p51 N136 residue within the beta7-beta8 loop for RT heterodimer stability and function. These findings suggest the interface comprising N136 in p51 and interacting residues in p66 as a possible target for rational drug design.
Collapse
Affiliation(s)
- Alok Mulky
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | | | | | | |
Collapse
|
15
|
Mescalchin A, Wünsche W, Laufer SD, Grohmann D, Restle T, Sczakiel G. Specific binding of a hexanucleotide to HIV-1 reverse transcriptase: a novel class of bioactive molecules. Nucleic Acids Res 2006; 34:5631-7. [PMID: 17038335 PMCID: PMC1635251 DOI: 10.1093/nar/gkl533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Short oligonucleotides below 8–10 nt in length adopt relatively simple structures. Accordingly, they represent interesting and so far unexplored lead compounds as molecular tools and, potentially, for drug development as a rational improvement of efficacy seem to be less complex than for other classes of longer oligomeric nucleic acid. As a ‘proof of concept’, we describe the highly specific binding of the hexanucleotide UCGUGU (Hex-S3) to human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) as a model target. Ultraviolet (UV) cross-linking studies and competition experiments with primer/template substrates and a RT-directed aptamer suggest site-specific binding of Hex-S3 to the large subunit (p66) of the viral enzyme. The affinity of 5.3 μM is related to hexanucleotide-specific suppression of HIV-1 replication in human cells by up to three orders of magnitude indicating that Hex-S3 exerts specific and biologically relevant activity. Experimental evidence described here further suggests a systematic hexamer array-based search for new tools for molecular biology and novel lead compounds in nucleic acid-based drug development.
Collapse
Affiliation(s)
- Alessandra Mescalchin
- Kompetenzzentrum Drug Design and Target MonitoringMaria-Göppert-Strasse 1, D-23538 Lübeck, Germany
- Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein and ZMSB, Universität zu LübeckRatzeburger Allee 160, D-23538 Lübeck, Germany
| | - Winfried Wünsche
- Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein and ZMSB, Universität zu LübeckRatzeburger Allee 160, D-23538 Lübeck, Germany
| | - Sandra D. Laufer
- Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein and ZMSB, Universität zu LübeckRatzeburger Allee 160, D-23538 Lübeck, Germany
| | - Dina Grohmann
- Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein and ZMSB, Universität zu LübeckRatzeburger Allee 160, D-23538 Lübeck, Germany
| | - Tobias Restle
- Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein and ZMSB, Universität zu LübeckRatzeburger Allee 160, D-23538 Lübeck, Germany
| | - Georg Sczakiel
- Kompetenzzentrum Drug Design and Target MonitoringMaria-Göppert-Strasse 1, D-23538 Lübeck, Germany
- Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein and ZMSB, Universität zu LübeckRatzeburger Allee 160, D-23538 Lübeck, Germany
- To whom correspondence should be addressed. Tel: +49 451 500 2731l; Fax: +49 451 500 2729;
| |
Collapse
|
16
|
Dash C, Fisher TS, Prasad VR, Le Grice SFJ. Examining interactions of HIV-1 reverse transcriptase with single-stranded template nucleotides by nucleoside analog interference. J Biol Chem 2006; 281:27873-81. [PMID: 16867979 DOI: 10.1074/jbc.m603970200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Crystallographic studies have implicated several residues of the p66 fingers subdomain of human immunodeficiency virus type-1 reverse transcriptase in contacting the single-stranded template overhang immediately ahead of the DNA polymerase catalytic center. This interaction presumably assists in inducing the appropriate geometry on the template base for efficient and accurate incorporation of the incoming dNTP. To investigate this, we introduced nucleoside analogs either individually or in tandem into the DNA template ahead of the catalytic center and investigated whether they induce pausing of the replication machinery before serving as the template base. Analogs included abasic tetrahydrofuran linkages, neutralizing methylphosphonate linkages, and conformationally locked nucleosides. In addition, several Phe-61 mutants were included in our analysis, based on previous data indicating that altering this residue affects both strand displacement synthesis and the fidelity of DNA synthesis. We demonstrate here that altering the topology of the template strand two nucleotides ahead of the catalytic center can interrupt DNA synthesis. Mutating Phe-61 to either Ala or Leu accentuates this defect, whereas replacement with an aromatic residue (Trp) allows the mutant enzyme to bypass the template analogs with relative ease.
Collapse
Affiliation(s)
- Chandravanu Dash
- Resistance Mechanisms Laboratory, HIV Drug Resistance Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702, USA
| | | | | | | |
Collapse
|
17
|
Mulky A, Kappes JC. Analysis of human immunodeficiency virus type 1 reverse transcriptase subunit structure/function in the context of infectious virions and human target cells. Antimicrob Agents Chemother 2005; 49:3762-9. [PMID: 16127051 PMCID: PMC1195396 DOI: 10.1128/aac.49.9.3762-3769.2005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The reverse transcriptase (RT) of all retroviruses is required for synthesis of the viral DNA genome. The human immunodeficiency virus type 1 (HIV-1) RT exists as a heterodimer made up of 51-kDa and 66-kDa subunits. The crystal structure and in vitro biochemical analyses indicate that the p66 subunit of RT is primarily responsible for the enzyme's polymerase and RNase H activities. Since both the p51 and p66 subunits are generated from the same coding region, as part of the Pr160(Gag-Pol) precursor protein, there are inherent limitations for studying subunit-specific function with intact provirus in a virologically relevant context. Our lab has recently described a novel system for studying the RT heterodimer (p51/p66) wherein a LTR-vpr-p51-IRES-p66 expression cassette provided in trans to an RT-deleted HIV-1 genome allows precise molecular analysis of the RT heterodimer. In this report, we describe in detail the specific approaches, alternative strategies, and pitfalls that may affect the application of this novel assay for analyzing RT subunit structure/function in infectious virions and human target cells. The ability to study HIV-1 RT subunit structure/function in a physiologically relevant context will advance our understanding of both RT and the process of reverse transcription. The study of antiretroviral drugs in a subunit-specific virologic context should provide new insights into drug resistance and viral fitness. Finally, we anticipate that this approach will help elucidate determinants that mediate p51-p66 subunit interactions, which is essential for structure-based drug design targeting RT heterodimerization.
Collapse
Affiliation(s)
- Alok Mulky
- University of Alabama at Birmingham, Department of Microbiology, LHRB 613, 701 South 19th Street, Birmingham, AL 35294, USA
| | | |
Collapse
|
18
|
Wapling J, Moore KL, Sonza S, Mak J, Tachedjian G. Mutations that abrogate human immunodeficiency virus type 1 reverse transcriptase dimerization affect maturation of the reverse transcriptase heterodimer. J Virol 2005; 79:10247-57. [PMID: 16051818 PMCID: PMC1182633 DOI: 10.1128/jvi.79.16.10247-10257.2005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The specific impact of mutations that abrogate human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) dimerization on virus replication is not known, as mutations shown previously to inhibit RT dimerization also impact Gag-Pol stability, resulting in pleiotropic effects on HIV-1 replication. We have previously characterized mutations at codon 401 in the HIV-1 RT tryptophan repeat motif that abrogate RT dimerization in vitro, leading to a loss in polymerase activity. The introduction of the RT dimerization-inhibiting mutations W401L and W401A into HIV-1 resulted in the formation of noninfectious viruses with reduced levels of both virion-associated and intracellular RT activity compared to the wild-type virus and the W401F mutant, which does not inhibit RT dimerization in vitro. Steady-state levels of the p66 and p51 RT subunits in viral lysates of the W401L and W401A mutants were reduced, but no significant decrease in Gag-Pol was observed compared to the wild type. In contrast, there was a decrease in processing of p66 to p51 in cell lysates for the dimerization-defective mutants compared to the wild type. The treatment of transfected cells with indinavir suggested that the HIV-1 protease contributed to the degradation of virion-associated RT subunits. These data demonstrate that mutations near the RT dimer interface that abrogate RT dimerization in vitro result in the production of replication-impaired viruses without detectable effects on Gag-Pol stability or virion incorporation. The inhibition of RT activity is most likely due to a defect in RT maturation, suggesting that RT dimerization represents a valid drug target for chemotherapeutic intervention.
Collapse
Affiliation(s)
- Johanna Wapling
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, 85 Commercial Road, GPO Box 2284, Melbourne, Victoria 3001, Australia
| | | | | | | | | |
Collapse
|
19
|
Buxton P, Tachedjian G, Mak J. Analysis of the contribution of reverse transcriptase and integrase proteins to retroviral RNA dimer conformation. J Virol 2005; 79:6338-48. [PMID: 15858017 PMCID: PMC1091692 DOI: 10.1128/jvi.79.10.6338-6348.2005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
All retroviruses contain two copies of genomic RNA that are linked noncovalently. The dimeric RNA of human immunodeficiency virus type 1 (HIV-1) undergoes rearrangement during virion maturation, whereby the dimeric RNA genome assumes a more stable conformation. Previously, we have shown that the packaging of the HIV-1 polymerase (Pol) proteins reverse transcriptase (RT) and integrase (IN) is essential for the generation of the mature RNA dimer conformation. Analysis of HIV-1 mutants that are defective in processing of Pol showed that these mutant virions contained altered dimeric RNA conformation, indicating that the mature RNA dimer conformation in HIV-1 requires the correct proteolytic processing of Pol. The HIV-1 Pol proteins are multimeric in their mature enzymatically active forms; RT forms a heterodimer, and IN appears to form a homotetramer. Using RT and IN multimerization defective mutants, we have found that dimeric RNA from these mutant virions has the same stability and conformation as wild-type RNA dimers, showing that the mature enzymatically active RT and IN proteins are dispensable for the generation of mature RNA dimer conformation. This also indicated that formation of the mature RNA dimer structure occurs prior to RT or IN maturation. We have also investigated the requirement of Pol for RNA dimerization in both Mason-Pfizer monkey virus (M-PMV) and Moloney murine leukemia virus (MoMuLV) and found that in contrast to HIV-1, Pol is dispensable for RNA dimer maturation in M-PMV and MoMuLV, demonstrating that the requirement of Pol in retroviral RNA dimer maturation is not conserved among all retroviruses.
Collapse
Affiliation(s)
- Penelope Buxton
- The Macfarlane Burnet Institute for Medical Research and Public Health, Cnr Punt & Commercial Rds, Melbourne, Victoria, Australia 3004.
| | | | | |
Collapse
|
20
|
Mulky A, Sarafianos SG, Jia Y, Arnold E, Kappes JC. 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 2005; 349:673-84. [PMID: 15893326 DOI: 10.1016/j.jmb.2005.03.057] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2005] [Revised: 03/17/2005] [Accepted: 03/21/2005] [Indexed: 10/25/2022]
Abstract
The human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT) functions as a heterodimer (p51/p66), which makes disruption of subunit interactions a possible target for antiviral drug design. Our understanding of subunit interface interactions has been limited by the lack of virus-based approaches for studying the heterodimer. Therefore, we developed a novel subunit-specific mutagenesis approach that enables precise molecular analysis of the heterodimer in the context of infectious HIV-1 particles. Here, we analyzed the contributions of amino acid residues comprising the Trp-motif to RT subunit interaction and function. Our results reveal important inter- and intra-subunit interactions of residues in the Trp-motif. A tryptophan cluster in p51 (W398, W402, W406, W414), proximal to the interface, was found to be important for p51/p66 interaction and stability. At the dimer interface, residues W401, Y405 and N363 in p51 and W410 in p66 mediate inter-subunit interactions. The W401 residue is critical for RT dimerization, exerting distinct effects in p51 and p66. Our analysis of the RT heterodimerization enhancing non-nucleoside RT inhibitor (NNRTI), efavirenz, indicates that the effects of drugs on RT dimer stability can be examined in human cells. Thus, we provide the first description of subunit-specific molecular interactions that affect RT heterodimer function and virus infection in vivo. Moreover, with heightened interest in novel RT inhibitors that affect dimerization, we demonstrate the ability to assess the effects of RT inhibitors on subunit interactions in a physiologically relevant context.
Collapse
Affiliation(s)
- Alok Mulky
- Department of Microbiology, University of Alabama at Birmingham, AL 35294, USA
| | | | | | | | | |
Collapse
|
21
|
Derebail SS, DeStefano JJ. Mechanistic analysis of pause site-dependent and -independent recombinogenic strand transfer from structurally diverse regions of the HIV genome. J Biol Chem 2004; 279:47446-54. [PMID: 15342633 DOI: 10.1074/jbc.m408927200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retroviral recombinants are generated by strand transfers occurring within internal regions of the viral genome and are a major source of genetic variability. Strand transfer has been linked to "pausing" occurring at secondary structures during synthesis by reverse transcriptase. Yet, weakly structured templates lacking strong pause sites also undergo efficient transfer. In this report, transfer crossover sites on high and low structured templates from the gag-pol frameshift region (GagPol) and the env (Env) regions, respectively, were determined by using a reconstituted in vitro strand transfer assay. The assay tested transfers occurring between a donor and acceptor template over a 150-nucleotide homologous region. The majority of crossovers were in a small 23-nucleotide region near a major pause site on GagPol, clearly indicating a pause-driven mechanism. In contrast, on Env, transfers were more dispersed clustering toward the end of the homologous region. Slowing down polymerization on Env by decreasing the dNTP concentration resulted in crossovers shifting toward the beginning of the homologous region. Removal of a small 38-nucleotide region at the 3'-end of the Env acceptor had a large effect on the level of strand transfer despite very few crossovers mapping to this region. This implicated this part of the acceptor in transfers occurring at downstream positions. For Env the results support a mechanism where the acceptor rapidly binds nascent DNA, then "zippers" downstream catching up with the donor-DNA hybrid and displacing the donor. Such a mechanism may be important to recombination in low structure regions of the HIV genome.
Collapse
MESH Headings
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Fusion Proteins, gag-pol/genetics
- Genes, env
- Genome, Viral
- HIV-1/genetics
- Humans
- Models, Genetic
- Nucleic Acid Conformation
- Nucleic Acid Hybridization
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombination, Genetic
Collapse
Affiliation(s)
- Suchitra S Derebail
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland 20742, USA
| | | |
Collapse
|
22
|
Dash C, Yi-Brunozzi HY, Le Grice SFJ. Two modes of HIV-1 polypurine tract cleavage are affected by introducing locked nucleic acid analogs into the (-) DNA template. J Biol Chem 2004; 279:37095-102. [PMID: 15220330 DOI: 10.1074/jbc.m403306200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Unusual base-pairing in a co-crystal of reverse transcriptase (RT) and a human immunodeficiency virus type 1 (HIV-1) polypurine tract (PPT)-containing RNA/DNA hybrid suggests local nucleic acid flexibility mediates selection of the plus-strand primer. Structural elements of HIV-1 RT potentially participating in recognition of this duplex include the thumb subdomain and the ribonuclease H (RNase H) primer grip, the latter comprising elements of the connection subdomain and RNase H domain. To investigate how stabilizing HIV-1 PPT structure influences its recognition, we modified the (-) DNA template by inserting overlapping locked nucleic acid (LNA) doublets and triplets. Modified RNA/DNA hybrids were evaluated for cleavage at the PPT/U3 junction. Altered specificity was observed when the homopolymeric dA.rU tract immediately 5' of the PPT was modified, whereas PPT/U3 cleavage was lost after substitutions in the adjacent dT.rA tract. In contrast, the "unzipped" portion of the PPT was moderately insensitive to LNA insertions. Although a portion of the dC.rG and neighboring dT.rA tract were minimally affected by LNA insertion, RNase H activity was highly sensitive to altering the junction between these structural elements. Using 3'-end-labeled PPT RNA primers, we also identified novel cleavage sites ahead (+5/+6) of the PPT/U3 junction. Differential cleavage at the PPT/U3 junction and U3 + 5/+6 site in response to LNA-induced template modification suggests two binding modes for HIV-1 RT, both of which may be controlled by the interaction of its thumb subdomain (potentially via the minor groove binding track) at either site of the unzipped region.
Collapse
Affiliation(s)
- Chandravanu Dash
- Resistance Mechanisms Laboratory, HIV Drug Resistance Program, NCI-Frederick, National Institutes of Health, Frederick, MD 21702, USA
| | | | | |
Collapse
|
23
|
Cases-González CE, Menéndez-Arias L. Increased G-->A transition frequencies displayed by primer grip mutants of human immunodeficiency virus type 1 reverse transcriptase. J Virol 2004; 78:1012-9. [PMID: 14694133 PMCID: PMC368828 DOI: 10.1128/jvi.78.2.1012-1019.2004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A genetic screen based on the blue-white beta-galactosidase complementation assay designed to detect G-->A mutations arising during RNA-dependent DNA synthesis was used to compare the fidelity of mutant human immunodeficiency virus type 1 reverse transcriptases (RTs) with the mutations M230L and M230I with the wild-type enzyme, in the presence of biased deoxynucleoside triphosphate (dNTP) pools. The mutant RTs with the M230L and M230I changes were found to be 20 to 70 times less faithful than the wild-type RT in the presence of low [dCTP]/[dTTP] ratios but showed similar fidelity in assays carried out with equimolar concentrations of each nucleotide. Biased dNTP pools led to short tandem repeat deletions in the target sequence, which were also detectable with the assay. However, deletion frequencies were similar for all of the RTs tested. The reported data suggest that RT pausing due to the low dNTP levels available in the RT reaction mixture facilitates strand transfer, in a process that is not necessarily mediated by nucleotide misinsertion.
Collapse
Affiliation(s)
- Clara E Cases-González
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | | |
Collapse
|
24
|
Isaguliants MG, Belikov SV, Starodubova ES, Gizatullin RZ, Rollman E, Zuber B, Zuber AK, Grishchenko OIA, Rytting AS, Källander CFR, Kochetkov SN, Karpov VL, Wahren B. Mutations conferring drug resistance affect eukaryotic expression of HIV type 1 reverse transcriptase. AIDS Res Hum Retroviruses 2004; 20:191-201. [PMID: 15018707 DOI: 10.1089/088922204773004914] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mutations in reverse transcriptase (RT) confer high levels of HIV resistance to drugs. However, while conferring drug resistance, they can lower viral replication capacity (fitness). The molecular mechanisms behind remain largely unknown. The aim of the study was to characterize the effect of drug-resistance mutations on HIV RT expression. Genes encoding AZT-resistant RTs with single or combined mutations D67N, K70R, T215F, and K219Q, and RTs derived from drug-resistant HIV-1 strains were designed and expressed in a variety of eukaryotic cells. Expression in transiently transfected cells was assessed by Western blotting and immunofluorescent staining with RT-specific antibodies. To compare the levels of expression, mutated RT genes were microinjected into the nucleus of the oocytes of Xenopus laevis. Expression of RT was quantified by sandwich ELISA. Relative stability of RTs was assessed by pulse-chase experiments. Xenopus oocytes microinjected with the genes expressed 2-50 pg of RT mutants per cell. The level of RT expression decreased with accumulation of drug-resistance mutations. Pulse-chase experiments demonstrated that poor expression of DR-RTs was due to proteolytic instability. Instability could be attributed to additional cleavage sites predicted to appear in the vicinity of resistance mutations. Accumulation of drug-resistance mutations appears to affect the level of eukaryotic expression of HIV-1 RT by inducing proteolytic instability. Low RT levels might be one of the determinants of impaired replication fitness of drug-resistant HIV-1 strains.
Collapse
|
25
|
Menéndez-Arias L. Molecular basis of fidelity of DNA synthesis and nucleotide specificity of retroviral reverse transcriptases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2003; 71:91-147. [PMID: 12102562 DOI: 10.1016/s0079-6603(02)71042-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Reverse transcription involves the conversion of viral genomic RNAinto proviral double-stranded DNA that integrates into the host cell genome. Cellular DNA polymerases replicate the integrated viral DNA and RNA polymerase II transcribes the proviral DNA into RNA genomes that are packaged into virions. Although mutations can be introduced at any of these replication steps, reverse transcriptase (RT) errors play a major role in retroviral mutation. This review summarizes our current knowledge on fidelity of reverse transcriptases. Estimates of retroviral mutation rates or fidelity of retroviral RTs are discussed in the context of the different techniques used for this purpose (i.e., retroviral vectors replicated in culture, misinsertion and mispair extension fidelity assay, etc.). In vitro fidelity assays provide information on the RT's accuracy during the elongation reaction of DNA synthesis. In addition, other steps such as initiation of reverse transcription, or strand transfer, and factors including viral proteins such as Vpr [in the case of the human immunodeficiency virus type 1 (HIV-1)] have been shown to influence fidelity. A comprehensive description of the effect of amino acid substitutions on the fidelity of HIV-1 RT is presented. Published data point to certain dNTP-binding residues, as well as to various amino acids involved in interactions with the template or the primer strand, and to residues in the minor groove-binding track as major components of the fidelity center of retroviral RTs. Implications of these studies include the design of novel therapeutic strategies leading to virus extinction, by increasing the viral mutation rate beyond a tolerable threshold.
Collapse
Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Spain
| |
Collapse
|
26
|
Sluis-Cremer N, Tachedjian G. Modulation of the oligomeric structures of HIV-1 retroviral enzymes by synthetic peptides and small molecules. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:5103-11. [PMID: 12392542 DOI: 10.1046/j.1432-1033.2002.03216.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The efficacy of antiretroviral agents approved for the treatment of HIV-1 infection is limited by the virus's ability to develop resistance. As such there is an urgent need for new ways of thinking about anti-HIV drug development, and accordingly novel viral and cellular targets critical to HIV-1 replication need to be explored and exploited. The retroviral RNA genome encodes for three enzymes essential for viral replication: HIV-1 protease (PR), HIV-1 reverse transcriptase (RT) and HIV-1 integrase (IN). The enzymatic functioning of each of these enzymes is entirely dependent on their oligomeric structures, suggesting that inhibition of subunit-subunit assembly or modulation of their quaternary structures provide alternative targets for HIV-1 inhibition. This review discusses the recent advances in the design and/or identification of synthetic peptides and small molecules that specifically target the subunit-subunit interfaces of these retroviral enzymes, resulting in the inactivation of their enzymatic functioning.
Collapse
Affiliation(s)
- Nicolas Sluis-Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh, PA 15261, USA.
| | | |
Collapse
|
27
|
Chaloin L, Lehmann MJ, Sczakiel G, Restle T. Endogenous expression of a high-affinity pseudoknot RNA aptamer suppresses replication of HIV-1. Nucleic Acids Res 2002; 30:4001-8. [PMID: 12235384 PMCID: PMC137107 DOI: 10.1093/nar/gkf522] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aptamers, small oligonucleotides derived from an in vitro evolution process called SELEX, are promising therapeutic and diagnostic agents. Although very effective in vitro, only a few examples are available showing their potential in vivo. We have analyzed the effect of a well characterized pseudoknot RNA aptamer selected for tight binding to human immunodeficiency virus (HIV) type 1 reverse transcriptase on HIV replication. Transient intracellular expression of a chimeric RNA consisting of the human initiator tRNA(Met) (tRNA(Meti))/aptamer sequence in human 293T cells showed inhibition of HIV particle release by >75% when the cells were co-transfected with proviral HIV-1 DNA. Subsequent virus production of human T-lymphoid C8166 cells, infected with viral particles derived from co-transfected 293T cells, was again reduced by >75% as compared with the control. As the observed effects are additive, in this model for virus spread, the total reduction of HIV particle formation by transient intracellular expression of the pseudoknot RNA aptamer amounts to >95%. Low-dose HIV infection of human T cells stably expressing the aptamer did not show any virus replication over a period of 35 days. This is the first example of an RNA aptamer selected against a viral enzyme target to show powerful antiviral activity in HIV-1-permissive human T-lymphoid cell lines.
Collapse
Affiliation(s)
- Laurent Chaloin
- Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto Hahn Strasse 11, 44227 Dortmund, Germany
| | | | | | | |
Collapse
|
28
|
Gutiérrez-Rivas M, Menéndez-Arias L. A mutation in the primer grip region of HIV-1 reverse transcriptase that confers reduced fidelity of DNA synthesis. Nucleic Acids Res 2001; 29:4963-72. [PMID: 11812826 PMCID: PMC97574 DOI: 10.1093/nar/29.24.4963] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A compensatory mutation (M230I) in the primer grip of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) restores the replication capacity of virus having a Y115W mutation in their RT coding region. The Y115W substitution impairs DNA polymerase activity and produces an enzyme with a lower fidelity of DNA synthesis. Gel-based fidelity assays with the double mutant Y115W/M230I revealed that the M230I substitution increased the accuracy of mutant Y115W. Y115W/M230I showed wild-type misinsertion fidelity in assays performed with DNA/DNA templates. However, when present alone, M230I conferred reduced fidelity as determined in misinsertion and mispair extension fidelity assays, as well as in primer extension assays carried out with three dNTPs. The mutant M230I showed a 3.3-16-fold increase in misinsertion efficiency for G, C and T opposite T, compared with the wild-type enzyme. Its fidelity was not influenced by nucleotide substitutions in the template/primer around the incorporation site. However, its accuracy was apparently affected by the structure of the 5'-overhang of the template strand. Unlike wild-type HIV-1 RT, nucleotide selectivity of mutant M230I at dT:dG, dT:dC and dT:dT mispairs was almost exclusively dependent on the K(m) values for correct and incorrect dNTPs, a characteristic that has not been described for other low fidelity mutants of HIV-1 RT.
Collapse
Affiliation(s)
- M Gutiérrez-Rivas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | | |
Collapse
|
29
|
Bleiber G, Munoz M, Ciuffi A, Meylan P, Telenti A. Individual contributions of mutant protease and reverse transcriptase to viral infectivity, replication, and protein maturation of antiretroviral drug-resistant human immunodeficiency virus type 1. J Virol 2001; 75:3291-300. [PMID: 11238855 PMCID: PMC114122 DOI: 10.1128/jvi.75.7.3291-3300.2001] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) variants resistant to protease (PR) and reverse transcriptase (RT) inhibitors may display impaired infectivity and replication capacity. The individual contributions of mutated HIV-1 PR and RT to infectivity, replication, RT activity, and protein maturation (herein referred to as "fitness") in recombinant viruses were investigated by separately cloning PR, RT, and PR-RT cassettes from drug-resistant mutant viral isolates into the wild-type NL4-3 background. Both mutant PR and RT contributed to measurable deficits in fitness of viral constructs. In peripheral blood mononuclear cells, replication rates (means +/- standard deviations) of RT recombinants were 72.5% +/- 27.3% and replication rates of PR recombinants were 60.5% +/- 33.6% of the rates of NL4-3. PR mutant deficits were enhanced in CEM T cells, with relative replication rates of PR recombinants decreasing to 15.8% +/- 23.5% of NL4-3 replication rates. Cloning of the cognate RT improved fitness of some PR mutant clones. For a multidrug-resistant virus transmitted through sexual contact, RT constructs displayed a marked infectivity and replication deficit and diminished packaging of Pol proteins (RT content in virions diminished by 56.3% +/- 10.7%, and integrase content diminished by 23.3% +/- 18.4%), a novel mechanism for a decreased-fitness phenotype. Despite the identified impairment of recombinant clones, fitness of two of the three drug-resistant isolates was comparable to that of wild-type, susceptible viruses, suggestive of extensive compensation by genomic regions away from PR and RT. Only limited reversion of mutated positions to wild-type amino acids was observed for the native isolates over 100 viral replication cycles in the absence of drug selective pressure. These data underscore the complex relationship between PR and RT adaptive changes and viral evolution in antiretroviral drug-resistant HIV-1.
Collapse
Affiliation(s)
- G Bleiber
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | | | | | | | | |
Collapse
|
30
|
Olivares I, Sánchez-Merino V, Martínez MA, Domingo E, López-Galíndez C, Menéndez-Arias L. Second-site reversion of a human immunodeficiency virus type 1 reverse transcriptase mutant that restores enzyme function and replication capacity. J Virol 1999; 73:6293-8. [PMID: 10400720 PMCID: PMC112707 DOI: 10.1128/jvi.73.8.6293-6298.1999] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nonconservative substitutions for Tyr-115 in the reverse transcriptase (RT) of human immunodeficiency virus type 1 (HIV-1) lead to enzymes displaying lower affinity for deoxynucleoside triphosphates (dNTPs) (A. M. Martín-Hernández, E. Domingo, and L. Menéndez-Arias, EMBO J. 15:4434-4442, 1996). Several mutations at this position (Y115W, Y115L, Y115A, and Y115D) were introduced in an infectious HIV-1 clone, and the replicative capacity of the mutant viruses was monitored. Y115W was the only mutant able to replicate in MT-4 cells, albeit very poorly. Nucleotide sequence analysis of the progeny virus recovered from supernatants of four independent transfection experiments showed that the Y115W mutation was maintained. However, in all cases an additional substitution in the primer grip of the RT (M230I) emerged when the virus increased its replication capacity. Using recombinant HIV-1 RT, we demonstrate that M230I mitigates the polymerase activity defect of the Y115W mutant, by increasing the dNTP binding affinity of the enzyme. The second-site suppressor effects observed were mediated by mutations in the 66-kDa subunit of the RT, as demonstrated with chimeric heterodimers. Examination of available crystal structures of HIV-1 RT suggests a possible mechanism for restoration of enzyme activity by the second-site revertant.
Collapse
Affiliation(s)
- I Olivares
- Centro Nacional de Biología Fundamental, Instituto de Salud Carlos III, 28220 Majadahonda (Madrid), Spain
| | | | | | | | | | | |
Collapse
|
31
|
Dufour E, Reinbolt J, Castroviejo M, Ehresmann B, Litvak S, Tarrago-Litvak L, Andreola ML. Cross-linking localization of a HIV-1 reverse transcriptase peptide involved in the binding of primer tRNALys3. J Mol Biol 1999; 285:1339-46. [PMID: 9917377 DOI: 10.1006/jmbi.1998.2430] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) initiates the synthesis of DNA from the 3' end of its specific primer, tRNALys3. The regions of tRNALys3 in close contact with RT are well known, while a precise knowledge of the RT regions interacting with tRNALys3 is not yet available. To address this question we cross-linked the heterodimeric p66/p51 RT to tRNALys3 using cis-aquahydroxydiammino-platinum. Ribonucleoprotein complexes of molecular masses higher than the p66 subunit were obtained. After RNase A digestion of the RT-tRNA complex, a labeled oligoribonucleotide (ORN) was mainly found associated to the p66 subunit. This labeled p66-ORN complex was then proteolyzed with Staphylococcus aureus V8 protease. A highly purified radioactive peptide was obtained after two chromatographic purification steps. Its N-terminal sequence corresponded with amino acid residues 241VQPI244. Using the crystallographic structure of HIV-1 RT, this peptide was localized at the beta14-sheet end, near to the hairpin formed by beta12 and beta13-sheets ("primer grip") and the alphaH-helix. The so called "VQPI peptide" is in the border of the thumb and the palm subdomains of the p66 subunit. This study palliates the absence of a three- dimensional structure of the RT-tRNA complex and led to a peptide in interaction with tRNALys3 present in all HIV-1 RT isolates.
Collapse
Affiliation(s)
- E Dufour
- IFR 66 Pathologies Infectieuses, CNRS-Université Victor Segalen Bordeaux 2, EP-630, 1, rue Camille Saint Saëns, Bordeaux Cedex, 33077, France
| | | | | | | | | | | | | |
Collapse
|