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Handa S, Reyna A, Wiryaman T, Ghosh P. Determinants of adenine-mutagenesis in diversity-generating retroelements. Nucleic Acids Res 2021; 49:1033-1045. [PMID: 33367793 PMCID: PMC7826257 DOI: 10.1093/nar/gkaa1240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 02/01/2023] Open
Abstract
Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial ‘dark matter’. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.
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Affiliation(s)
- Sumit Handa
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Andres Reyna
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Timothy Wiryaman
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
| | - Partho Ghosh
- Department of Chemistry & Biochemistry, 9500 Gilman Drive, La Jolla, CA, 92093-0375, USA
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2
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The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance. Viruses 2020; 12:v12030297. [PMID: 32182845 PMCID: PMC7150816 DOI: 10.3390/v12030297] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/31/2022] Open
Abstract
The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance, from the development of vaccines to therapeutic drugs. In addressing the crux of the issue, various attempts to estimate the mutation rate of HIV-1 resulted in a large range of 10−5–10−3 errors/bp/cycle due to the use of different types of investigation methods. In this review, we discuss the different assay methods, their findings on the mutation rates of HIV-1 and how the locations of mutations can be further analyzed for their allosteric effects to allow for new inhibitor designs. Given that HIV is one of the fastest mutating viruses, it serves as a good model for the comprehensive study of viral mutations that can give rise to a more horizontal understanding towards overall viral drug resistance as well as emerging viral diseases.
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3
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Lloyd SB, Lichtfuss M, Amarasena TH, Alcantara S, De Rose R, Tachedjian G, Alinejad-Rokny H, Venturi V, Davenport MP, Winnall WR, Kent SJ. High fidelity simian immunodeficiency virus reverse transcriptase mutants have impaired replication in vitro and in vivo. Virology 2016; 492:1-10. [PMID: 26896929 DOI: 10.1016/j.virol.2016.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 11/15/2022]
Abstract
The low fidelity of HIV replication facilitates immune and drug escape. Some reverse transcriptase (RT) inhibitor drug-resistance mutations increase RT fidelity in biochemical assays but their effect during viral replication is unclear. We investigated the effect of RT mutations K65R, Q151N and V148I on SIV replication and fidelity in vitro, along with SIV replication in pigtailed macaques. SIVmac239-K65R and SIVmac239-V148I viruses had reduced replication capacity compared to wild-type SIVmac239. Direct virus competition assays demonstrated a rank order of wild-type>K65R>V148I mutants in terms of viral fitness. In single round in vitro-replication assays, SIVmac239-K65R demonstrated significantly higher fidelity than wild-type, and rapidly reverted to wild-type following infection of macaques. In contrast, SIVmac239-Q151N was replication incompetent in vitro and in pigtailed macaques. Thus, we showed that RT mutants, and specifically the common K65R drug-resistance mutation, had impaired replication capacity and higher fidelity. These results have implications for the pathogenesis of drug-resistant HIV.
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Affiliation(s)
- Sarah B Lloyd
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Marit Lichtfuss
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Thakshila H Amarasena
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Sheilajen Alcantara
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Robert De Rose
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Gilda Tachedjian
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia; Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia; Department of Microbiology, Monash University, Clayton, Victoria 3168, Australia
| | | | - Vanessa Venturi
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Miles P Davenport
- Kirby Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - Wendy R Winnall
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Victoria 3010, Australia; Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Health, Central Clinical School, Monash University, Melbourne, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of Melbourne, Parkville, Australia.
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4
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Mutation V111I in HIV-2 reverse transcriptase increases the fitness of the nucleoside analogue-resistant K65R and Q151M viruses. J Virol 2014; 89:833-43. [PMID: 25355888 DOI: 10.1128/jvi.02259-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Infection with HIV-2 can ultimately lead to AIDS, although disease progression is much slower than with HIV-1. HIV-2 patients are mostly treated with a combination of nucleoside reverse transcriptase (RT) inhibitors (NRTIs) and protease inhibitors designed for HIV-1. Many studies have described the development of HIV-1 resistance to NRTIs and identified mutations in the polymerase domain of RT. Recent studies have shown that mutations in the connection and RNase H domains of HIV-1 RT may also contribute to resistance. However, only limited information exists regarding the resistance of HIV-2 to NRTIs. In this study, therefore, we analyzed the polymerase, connection, and RNase H domains of RT in HIV-2 patients failing NRTI-containing therapies. Besides the key resistance mutations K65R, Q151M, and M184V, we identified a novel mutation, V111I, in the polymerase domain. This mutation was significantly associated with mutations K65R and Q151M. Sequencing of the connection and RNase H domains of the HIV-2 patients did not reveal any of the mutations that were reported to contribute to NRTI resistance in HIV-1. We show that V111I does not strongly affect drug susceptibility but increases the replication capacity of the K65R and Q151M viruses. Biochemical assays demonstrate that V111I restores the polymerization defects of the K65R and Q151M viruses but negatively affects the fidelity of the HIV-2 RT enzyme. Molecular dynamics simulations were performed to analyze the structural changes mediated by V111I. This showed that V111I changed the flexibility of the 110-to-115 loop region, which may affect deoxynucleoside triphosphate (dNTP) binding and polymerase activity. IMPORTANCE Mutation V111I in the HIV-2 reverse transcriptase enzyme was identified in patients failing therapies containing nucleoside analogues. We show that the V111I change does not strongly affect the sensitivity of HIV-2 to nucleoside analogues but increases the fitness of viruses with drug resistance mutations K65R and Q151M.
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5
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Mutations in HIV-1 reverse transcriptase affect the errors made in a single cycle of viral replication. J Virol 2014; 88:7589-601. [PMID: 24760888 DOI: 10.1128/jvi.00302-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED The genetic variation in HIV-1 in patients is due to the high rate of viral replication, the high viral load, and the errors made during viral replication. Some of the mutations in reverse transcriptase (RT) that alter the deoxynucleoside triphosphate (dNTP)-binding pocket, including those that confer resistance to nucleoside/nucleotide analogs, affect dNTP selection during replication. The effects of mutations in RT on the spectrum (nature, position, and frequency) of errors made in vivo are poorly understood. We previously determined the mutation rate and the frequency of different types of mutations and identified hot spots for mutations in a lacZα (the α complementing region of lacZ) reporter gene carried by an HIV-1 vector that replicates using wild-type RT. We show here that four mutations (Y115F, M184V, M184I, and Q151M) in the dNTP-binding pocket of RT that had relatively small effects on the overall HIV-1 mutation rate (less than 3-fold compared to the wild type) significantly increased mutations at some specific positions in the lacZα reporter gene. We also show that changes in a sequence that flanks the reporter gene can affect the mutations that arise in the reporter. These data show that changes either in HIV-1 RT or in the sequence of the nucleic acid template can affect the spectrum of mutations made during viral replication. This could, by implication, affect the generation of drug-resistant mutants and immunological-escape mutants in patients. IMPORTANCE RT is the viral enzyme that converts the RNA genome of HIV into DNA. Errors made during replication allow the virus to escape from the host's immune system and to develop resistance to the available anti-HIV drugs. We show that four different mutations in RT which are known to be associated with resistance to anti-RT drugs modestly increased the overall frequency of errors made during viral replication. However, the increased errors were not uniformly distributed; the additional errors occurred at a small number of positions (hot spots). Moreover, some of the RT mutations preferentially affected the nature of the errors that were made (some RT mutations caused an increase in insertion and deletion errors; others caused an increase in substitution errors). We also show that sequence changes in a region adjacent to a target gene can affect the errors made within the target gene.
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Abstract
The notoriously low fidelity of HIV-1 replication is largely responsible for the virus's rapid mutation rate, facilitating escape from immune or drug control. The error-prone activity of the viral reverse transcriptase (RT) is predicted to be the most influential mechanism for generating mutations. The low fidelity of RT has been successfully exploited by nucleoside and nucleotide analogue reverse transcriptase inhibitors (NRTIs) that halt viral replication upon incorporation. Consequently, drug-resistant strains have arisen in which the viral RT has an increased fidelity of replication, thus reducing analogue incorporation. Higher fidelity, however, impacts on viral fitness. The appearance of compensatory mutations in combination with higher fidelity NRTI resistance mutations and the subsequent reversion of NRTI-resistant mutations upon cessation of antiretroviral treatment lend support to the notion that higher fidelity exacts a fitness cost. Potential mechanisms for reduced viral fitness are a smaller pool of mutant strains available to respond to immune or drug pressure, slower rates of replication, and a limitation to the dNTP tropism of the virus. Unraveling the relationship between replication fidelity and fitness should lead to a greater understanding of the evolution and control of HIV.
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Affiliation(s)
- Sarah B. Lloyd
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
| | - Wendy R. Winnall
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia
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7
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Daddacha W, Noble E, Nguyen LA, Kennedy EM, Kim B. Effect of ribonucleotides embedded in a DNA template on HIV-1 reverse transcription kinetics and fidelity. J Biol Chem 2013; 288:12522-32. [PMID: 23479739 DOI: 10.1074/jbc.m113.458398] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HIV-1 reverse transcriptase (RT) frequently incorporates ribonucleoside triphosphates (rNTPs) during proviral DNA synthesis, particularly under the limited dNTP conditions found in macrophages. We investigated the mechanistic impacts of an rNMP embedded in DNA templates on HIV-1 RT-mediated DNA synthesis. We observed that the template-embedded rNMP induced pausing of RT and delayed DNA synthesis kinetics at low macrophage dNTP concentrations but not at high T cell dNTP concentrations. Although the binding affinity of RT to the rNMP-containing template-primer was not altered, the dNTP incorporation kinetics of RT were significantly reduced at one nucleotide upstream and downstream of the rNMP site, leading to pause sites. Finally, HIV-1 RT becomes more error-prone at rNMP sites with an elevated mismatch extension capability but not enhanced misinsertion capability. Together these data suggest that rNMPs embedded in DNA templates may influence reverse transcription kinetics and impact viral mutagenesis in macrophages.
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Affiliation(s)
- Waaqo Daddacha
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
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8
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Kennedy EM, Daddacha W, Slater R, Gavegnano C, Fromentin E, Schinazi RF, Kim B. Abundant non-canonical dUTP found in primary human macrophages drives its frequent incorporation by HIV-1 reverse transcriptase. J Biol Chem 2011; 286:25047-55. [PMID: 21454906 PMCID: PMC3137078 DOI: 10.1074/jbc.m111.234047] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 03/29/2011] [Indexed: 01/21/2023] Open
Abstract
Terminally differentiated/non-dividing macrophages contain extremely low cellular dNTP concentrations (20-40 nm), compared with activated CD4(+) T cells (2-5 μm). However, our LC-MS/MS study revealed that the non-canonical dUTP concentration (2.9 μm) is ∼60 times higher than TTP in macrophages, whereas the concentrations of dUTP and TTP in dividing human primary lymphocytes are very similar. Specifically, we evaluated the contribution of HIV-1 reverse transcriptase to proviral DNA uracilation under the physiological conditions found in HIV-1 target cells. Indeed, biochemical simulation of HIV-1 reverse transcription demonstrates that HIV-1 RT efficiently incorporates dUTP in the macrophage nucleotide pools but not in the T cell nucleotide pools. Measurement of both pre-steady state and steady state kinetic parameters of dUTP incorporation reveals minimal selectivity of HIV-1 RT for TTP over dUTP, implying that the cellular dUTP/TTP ratio determines the frequency of HIV-1 RT-mediated dUTP incorporation. The RT of another lentivirus, simian immunodeficiency virus, also displays efficient dUTP incorporation in the dNTP/dUTP pools found in macrophages but not in T cells. Finally, 2',3'-dideoxyuridine was inhibitory to HIV-1 proviral DNA synthesis in macrophages but not in T cells. The data presented demonstrates that the non-canonical dUTP was abundant relative to TTP, and efficiently incorporated during HIV-1 reverse transcription, particularly in non-dividing macrophages.
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Affiliation(s)
- Edward M. Kennedy
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642 and
| | - Waaqo Daddacha
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642 and
| | - Rebecca Slater
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642 and
| | - Christina Gavegnano
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Emilie Fromentin
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Raymond F. Schinazi
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Baek Kim
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642 and
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9
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Thermostable HIV-1 group O reverse transcriptase variants with the same fidelity as murine leukaemia virus reverse transcriptase. Biochem J 2011; 436:599-607. [DOI: 10.1042/bj20101852] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Wild-type HIV-1 group O RT (reverse transcriptase) shows increased thermostability in comparison with HIV-1 group M subtype B RT and MLV (murine leukaemia virus) RT. However, its utility in the amplification of RNA targets is limited by the reduced accuracy of lentiviral RTs compared with oncoretroviral RTs (i.e. MLV RT). The effects of the mutations K65R, R78A and K65R/V75I on the fidelity of HIV-1 group O RTs were studied using gel-based and M13mp2 lacZ forward-mutation fidelity assays. Forward-mutation assays demonstrated that mutant RTs K65R, R78A and K65R/V75I showed >9-fold increased accuracy in comparison with the wild-type enzyme and were approximately two times more faithful than the MLV RT. Compared with MLV RT, all of the tested HIV-1 group O RT variants showed decreased frameshift fidelity. However, K65R RT showed a higher tendency to introduce one-nucleotide deletions in comparison with other HIV-1 group O RT variants. R78A had a destabilizing effect on the RT, either in the presence or absence of V75I. At temperatures above 52 °C, K65R and K65R/V75I retained similar levels of DNA polymerase activity to the wild-type HIV-1 group O RT, but were more efficient than HIV-1 group M subtype B and MLV RTs. K65R, K65R/V75I and R78A RTs showed decreased misinsertion and mispair extension fidelity in comparison with the wild-type enzyme for most base pairs studied. These assays revealed that nucleotide selection is mainly governed by kpol (pol is polymerization) in the case of K65R, whereas both kpol and Kd affect nucleotide discrimination in the case of K65R/V75I.
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10
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The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error-prone as that encoded by HIV-1. J Mol Biol 2011; 407:661-72. [PMID: 21320510 DOI: 10.1016/j.jmb.2011.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 11/20/2022]
Abstract
Reverse transcriptases (RTs) encoded by a wide range of mobile retroelements have had a major impact on the structure and function of genomes. Among the most abundant elements in eukaryotes are the non long terminal repeat (LTR) retrotransposons. Here we compare the dNTP concentration requirements and error rates of the RT encoded by the non-LTR retrotransposon R2 of Bombyx mori with the well-characterized RTs of retroviruses. Surprisingly, R2 was found to have properties more similar to those of lentiviral RTs, such as human immunodeficiency virus type 1 (HIV-1), than to those of oncoretroviral RTs, such as murine leukemia virus. Like HIV-1 RT, R2 RT was able to synthesize DNA at low dNTP concentrations, suggesting that R2 is able to retrotranspose in nondividing cells. R2 RT also showed levels of misincorporation in biased dNTP pools and replication error rates in M13 lacZα forward mutation assays, similar to HIV-1 RT. Most of the R2 base substitutions in the forward mutation assay were caused by the misincorporation of dTMP. Analogous to HIV-1, the high error rate of R2 RT appears to be a result of its ability to extend mismatches once generated. We suggest that the low fidelity of R2 RT is a by-product of the flexibility of its active site/dNTP binding pocket required for the target-primed reverse transcription reaction used by R2 for retrotransposition. Finally, we discuss that in spite of the high R2 RT error rate, the long-term nucleotide substitution rate for R2 is not significantly above that associated with cellular DNA replication, based on the frequency of R2 retrotranspositions determined in natural populations.
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11
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Kennedy EM, Gavegnano C, Nguyen L, Slater R, Lucas A, Fromentin E, Schinazi RF, Kim B. Ribonucleoside triphosphates as substrate of human immunodeficiency virus type 1 reverse transcriptase in human macrophages. J Biol Chem 2010; 285:39380-91. [PMID: 20924117 PMCID: PMC2998149 DOI: 10.1074/jbc.m110.178582] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/04/2010] [Indexed: 01/04/2023] Open
Abstract
We biochemically simulated HIV-1 DNA polymerization in physiological nucleotide pools found in two HIV-1 target cell types: terminally differentiated/non-dividing macrophages and activated/dividing CD4(+) T cells. Quantitative tandem mass spectrometry shows that macrophages harbor 22-320-fold lower dNTP concentrations and a greater disparity between ribonucleoside triphosphate (rNTP) and dNTP concentrations than dividing target cells. A biochemical simulation of HIV-1 reverse transcription revealed that rNTPs are efficiently incorporated into DNA in the macrophage but not in the T cell environment. This implies that HIV-1 incorporates rNTPs during viral replication in macrophages and also predicts that rNTP chain terminators lacking a 3'-OH should inhibit HIV-1 reverse transcription in macrophages. Indeed, 3'-deoxyadenosine inhibits HIV-1 proviral DNA synthesis in human macrophages more efficiently than in CD4(+) T cells. This study reveals that the biochemical landscape of HIV-1 replication in macrophages is unique and that ribonucleoside chain terminators may be a new class of anti-HIV-1 agents specifically targeting viral macrophage infection.
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Affiliation(s)
- Edward M. Kennedy
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Christina Gavegnano
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Laura Nguyen
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Rebecca Slater
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Amanda Lucas
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Emilie Fromentin
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Raymond F. Schinazi
- the Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Veterans Affairs Medical Center, Decatur, Georgia 30033
| | - Baek Kim
- From the Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, and
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12
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Kennedy EM, Hergott C, Dewhurst S, Kim B. The mechanistic architecture of thermostable Pyrococcus furiosus family B DNA polymerase motif A and its interaction with the dNTP substrate. Biochemistry 2009; 48:11161-8. [PMID: 19817489 DOI: 10.1021/bi9010122] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Thermostable DNA polymerases isolated from archaeal organisms have not been completely characterized kinetically and require further study if we are to understand both their dNTP binding mechanism and their role within the organism. Here, we demonstrate that the thermostable family B DNA polymerase from Pyrococcus furiosus (Pfu Pol) contains sensitive determinants of both dNTP binding and replicational fidelity within the highly conserved motif A. Site-directed mutagenesis of the motif A SYLP region revealed that small shifts in side chain volume result in significant changes in the dNTP binding affinity, steady state kinetics, and fidelity of the enzyme. Mutants of Y410 show high fidelity in both misincorporation assays and forward mutation assays, but display a substantially higher K(m) than the wild type. In contrast, mutations of upstream residue L409 result in a drastically reduced affinity for the correct dNTP, a much higher efficiency of both misincorporation and mismatch extension, and substantially lower fidelity as demonstrated by a PCR-based forward mutation assay. The A408S mutant, however, displayed a significant increase in both dNTP binding affinity and fidelity. In summary, these data show that modulation of motif A can greatly shift both the steady and pre-steady state kinetics of the enzyme as well as the fidelity of Pfu Pol.
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Affiliation(s)
- Edward M Kennedy
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
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13
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Menéndez-Arias L. Mutation rates and intrinsic fidelity of retroviral reverse transcriptases. Viruses 2009; 1:1137-65. [PMID: 21994586 PMCID: PMC3185545 DOI: 10.3390/v1031137] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Revised: 12/03/2009] [Accepted: 12/03/2009] [Indexed: 11/27/2022] Open
Abstract
Retroviruses are RNA viruses that replicate through a DNA intermediate, in a process catalyzed by the viral reverse transcriptase (RT). Although cellular polymerases and host factors contribute to retroviral mutagenesis, the RT errors play a major role in retroviral mutation. RT mutations that affect the accuracy of the viral polymerase have been identified by in vitro analysis of the fidelity of DNA synthesis, by using enzymological (gel-based) and genetic assays (e.g., M13mp2 lacZ forward mutation assays). For several amino acid substitutions, these observations have been confirmed in cell culture using viral vectors. This review provides an update on studies leading to the identification of the major components of the fidelity center in retroviral RTs.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" [Consejo Superior de Investigaciones Científicas (CSIC) & Universidad Autónoma de Madrid], Campus de Cantoblanco, 28049 Madrid, Spain; E-Mail: ; Tel.: +34 91 196 4494
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14
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Increased Thermostability and Fidelity of DNA Synthesis of Wild-Type and Mutant HIV-1 Group O Reverse Transcriptases. J Mol Biol 2009; 392:872-84. [DOI: 10.1016/j.jmb.2009.07.081] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/24/2009] [Accepted: 07/28/2009] [Indexed: 11/18/2022]
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15
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Skasko M, Diamond TL, Kim B. Mechanistic variations among reverse transcriptases of simian immunodeficiency virus variants isolated from African green monkeys. Biochemistry 2009; 48:5389-95. [PMID: 19408961 DOI: 10.1021/bi900346m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we report enzymatic variations among the reverse transcriptases (RTs) of five simian immunodeficiency virus (SIV) strains, Sab-1, 155-4, Gri-1, 9063-2, and Tan-1, which were isolated from four different species of naturally infected African green monkeys living in different regions across Africa. First, Sab-1 RT exhibits the most efficient dNTP incorporation efficiency at low dNTP concentrations, whereas the other four SIVagm RT proteins display different levels of reduced polymerase activity at low dNTP concentrations. Tan-1 RT exhibited the most restricted dNTP incorporation efficiency. Indeed, the pre-steady state analysis revealed that Sab-1 RT displays tight dNTP binding affinity (K(d) approximately 1-5 microM), comparable to values observed for NL4-3 and HXB2 HIV-1 RTs, whereas the dNTP binding affinity of Tan-1 RT is 6.2, approximately 34.8-fold lower than that of Sab-1 RT. Second, Tan-1 RT fidelity was significantly higher than that of Sab-1 RT. Indeed, Tan-1 RT enzymatically mimics oncoretroviral murine leukemia virus RT which is characterized by its low dNTP binding affinity and high fidelity. This study reports that simultaneous changes in dNTP binding affinity and fidelity of RTs appear to occur among natural SIV variants isolated from African green monkeys.
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Affiliation(s)
- Mark Skasko
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 672, Rochester, New York 14642, USA
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16
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Jamburuthugoda VK, Santos-Velazquez JM, Skasko M, Operario DJ, Purohit V, Chugh P, Szymanski EA, Wedekind JE, Bambara RA, Kim B. Reduced dNTP binding affinity of 3TC-resistant M184I HIV-1 reverse transcriptase variants responsible for viral infection failure in macrophage. J Biol Chem 2008; 283:9206-16. [PMID: 18218633 PMCID: PMC2431026 DOI: 10.1074/jbc.m710149200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Revised: 01/18/2008] [Indexed: 11/06/2022] Open
Abstract
We characterized HIV-1 reverse transcriptase (RT) variants either with or without the (-)-2',3'-deoxy-3'-thiacytidine-resistant M184I mutation isolated from a single HIV-1 infected patient. First, unlike variants with wild-type M184, M184I RT variants displayed significantly reduced DNA polymerase activity at low dNTP concentrations, which is indicative of reduced dNTP binding affinity. Second, the M184I variant displayed a approximately 10- to 13-fold reduction in dNTP binding affinity, compared with the Met-184 variant. However, the k(pol) values of these two RTs were similar. Third, unlike HIV-1 vectors with wild-type RT, the HIV-1 vector harboring M184I RT failed to transduce cell types containing low dNTP concentrations, such as human macrophage, likely due to the reduced DNA polymerization activity of the M184I RT under low cellular dNTP concentration conditions. Finally, we compared the binary complex structures of wild-type and M184I RTs. The Ile mutation at position 184 with a longer and more rigid beta-branched side chain, which was previously known to alter the RT-template interaction, also appears to deform the shape of the dNTP binding pocket. This can restrict ground state dNTP binding and lead to inefficient DNA synthesis particularly at low dNTP concentrations, ultimately contributing to viral replication failure in macrophage and instability in vivo of the M184I mutation.
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Affiliation(s)
- Varuni K Jamburuthugoda
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
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17
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Howell CA, Kondratick CM, Washington MT. Substitution of a residue contacting the triphosphate moiety of the incoming nucleotide increases the fidelity of yeast DNA polymerase zeta. Nucleic Acids Res 2008; 36:1731-40. [PMID: 18263611 PMCID: PMC2275142 DOI: 10.1093/nar/gkn023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA polymerase zeta (pol zeta), which is required for DNA damage-induced mutagenesis, functions in the error-prone replication of a wide range of DNA lesions. During this process, pol zeta extends from nucleotides incorporated opposite template lesions by other polymerases. Unlike classical polymerases, pol zeta efficiently extends from primer-terminal base pairs containing mismatches or lesions, and it synthesizes DNA with moderate fidelity. Here we describe genetic and biochemical studies of three yeast pol zeta mutant proteins containing substitutions of highly conserved amino acid residues that contact the triphosphate moiety of the incoming nucleotide. The R1057A and K1086A proteins do not complement the rev3Delta mutation, and these proteins have significantly reduced polymerase activity relative to the wild-type protein. In contrast, the K1061A protein partially complements the rev3Delta mutation and has nearly normal polymerase activity. Interestingly, the K1061A protein has increased fidelity relative to wild-type pol zeta and is somewhat less efficient at extending from mismatched primer-terminal base pairs. These findings have important implications both for the evolutionary divergence of pol zeta from classical polymerases and for the mechanism by which this enzyme accommodates distortions in the DNA caused by mismatches and lesions.
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Affiliation(s)
- Craig A Howell
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, USA
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18
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Boyer PL, Stenbak CR, Hoberman D, Linial ML, Hughes SH. In vitro fidelity of the prototype primate foamy virus (PFV) RT compared to HIV-1 RT. Virology 2007; 367:253-64. [PMID: 17631930 PMCID: PMC2720797 DOI: 10.1016/j.virol.2007.05.034] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 01/22/2007] [Accepted: 05/14/2007] [Indexed: 01/30/2023]
Abstract
We compared the in vitro fidelity of wild-type human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT) and the prototype foamy virus (PFV) RT. Both enzymes had similar error rates for single nucleotide substitutions; however, PFV RT did not appear to make errors at specific hotspots, like HIV-1 RT. In addition, PFV RT made more deletions and insertions than HIV-1 RT. Although the majority of the missense errors made by HIV-1 RT and PFV RT are different, relatively few of the mutations caused by either enzyme can be explained by a misalignment/slippage mechanism. We suggest that the higher polymerase activity of PFV RT could contribute to the ability of the enzyme to jump to the same or a different template.
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Affiliation(s)
- Paul L. Boyer
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702
| | | | - David Hoberman
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702
| | - Maxine L. Linial
- Division of Basic Sciences A3-015, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - Stephen H. Hughes
- HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, Maryland 21702
- Corresponding author. Fax: +1 301 846-6966. E-mail address:
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19
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Smith RA, Anderson DJ, Preston BD. Hypersusceptibility to substrate analogs conferred by mutations in human immunodeficiency virus type 1 reverse transcriptase. J Virol 2006; 80:7169-78. [PMID: 16809322 PMCID: PMC1489025 DOI: 10.1128/jvi.00322-06] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Accepted: 04/29/2006] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) contains four structural motifs (A, B, C, and D) that are conserved in polymerases from diverse organisms. Motif B interacts with the incoming nucleotide, the template strand, and key active-site residues from other motifs, suggesting that motif B is an important determinant of substrate specificity. To examine the functional role of this region, we performed "random scanning mutagenesis" of 11 motif B residues and screened replication-competent mutants for altered substrate analog sensitivity in culture. Single amino acid replacements throughout the targeted region conferred resistance to lamivudine and/or hypersusceptibility to zidovudine (AZT). Substitutions at residue Q151 increased the sensitivity of HIV-1 to multiple nucleoside analogs, and a subset of these Q151 variants was also hypersusceptible to the pyrophosphate analog phosphonoformic acid (PFA). Other AZT-hypersusceptible mutants were resistant to PFA and are therefore phenotypically similar to PFA-resistant variants selected in vitro and in infected patients. Collectively, these data show that specific amino acid replacements in motif B confer broad-spectrum hypersusceptibility to substrate analog inhibitors. Our results suggest that motif B influences RT-deoxynucleoside triphosphate interactions at multiple steps in the catalytic cycle of polymerization.
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Affiliation(s)
- Robert A Smith
- Department of Pathology, University of Washington, K-084 HSB, Box 357705, 1959 NE Pacific St., Seattle, 98195, USA.
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20
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Jamburuthugoda VK, Chugh P, Kim B. Modification of human immunodeficiency virus type 1 reverse transcriptase to target cells with elevated cellular dNTP concentrations. J Biol Chem 2006; 281:13388-13395. [PMID: 16497663 DOI: 10.1074/jbc.m600291200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retroviruses and DNA viruses utilize cellular dNTPs as substrates for their DNA polymerases during viral replication in infected cells. However, because of S phase-dependent dNTP biosynthesis, the availability of cellular dNTPs significantly varies among cell types (e.g. dividing versus nondividing cells and normal versus tumor cells). Here we tested whether alterations in the dNTP utilization efficiency and dNTP binding affinity of viral DNA polymerases can switch viral infection specificity to cell types with different dNTP concentrations. We employed an HIV-1 reverse transcriptase (RT) mutant (Q151N), which is catalytically active only at high dNTP concentrations because of its reduced dNTP binding affinity. Indeed, the modified HIV-1 vector harboring the Q151N mutant RT preferentially transduced tumor cells containing higher cellular dNTP concentrations than primary cells (e.g. human lung fibroblasts (HLFs) and human keratinocytes). Although the wild type HIV-1 vector transduced both HLFs and tumor cells, the Q151N vector failed to transduce HLFs and keratinocytes but efficiently transduced tumor cells. Pretreatment of HLFs with deoxynucleosides, which increase cellular dNTP pools, enabled the mutant vector to transduce HLFs, suggesting that the transduction failure of the RT mutant vector to primary cells is because of inefficient reverse transcription in low cellular dNTP environments. We also observed that the Q151N vector expressing herpes simplex virus-thymidine kinase renders tumor cells sensitive to gancyclovir. This study validates a novel strategy in which modifications of viral DNA polymerases in various vector systems allow the delivery of target genes exclusively to tumor cells exploiting elevated cellular dNTP concentration as a tumor cell-specific host factor.
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Affiliation(s)
- Varuni K Jamburuthugoda
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
| | - Pauline Chugh
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642
| | - Baek Kim
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642.
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21
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Cases-González C, Menéndez-Arias L. Nucleotide specificity of HIV-1 reverse transcriptases with amino acid substitutions affecting Ala-114. Biochem J 2005; 387:221-9. [PMID: 15548134 PMCID: PMC1134950 DOI: 10.1042/bj20041056] [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: 11/17/2022]
Abstract
Ala-114, together with Asp-113, Tyr-115 and Gln-151, form the pocket that accommodates the 3'-OH of the incoming dNTP in the HIV-1 RT (reverse transcriptase). Four mutant RTs having serine, glycine, threonine or valine instead of Ala-114 were obtained by site-directed mutagenesis. While mutants A114S and A114G retained significant DNA polymerase activity, A114T and A114V showed very low catalytic efficiency in nucleotide incorporation assays, due to their high apparent K(m) values for dNTP. Discrimination between AZTTP (3'-azido-3'-deoxythymidine triphosphate) and dTTP was not significantly affected by mutations A114S and A114G in assays carried out with heteropolymeric template/primers. However, both mutants showed decreased susceptibility to AZTTP when poly(rA)/(dT)16 was used as substrate. Steady-state kinetic analysis of the incorporation of ddNTPs compared with dNTPs showed that substituting glycine for Ala-114 produced a 5-6-fold increase in the RT's ability to discriminate against ddNTPs (including the physiologically relevant metabolites of zalcitabine and didanosine), a result that was confirmed in primer-extension assays. In contrast, A114S and A114V showed wild-type ddNTP/dNTP discrimination efficiencies. Discrimination against ribonucleotides was not affected by mutations at position 114. Misinsertion and mispair extension fidelity assays as well as determinations of G-->A mutation frequencies using a lacZ complementation assay showed that, unlike Tyr-115 or Gln-151 mutants, the fidelity of HIV-1 RT was not largely affected by substitutions of Ala-114. The role of the side-chain of Ala-114 in ddNTP/dNTP discrimination appears to be determined by its participation in van der Waals interactions with the ribose moiety of the incoming nucleotide.
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Affiliation(s)
- Clara E. Cases-González
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas – Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Luis Menéndez-Arias
- Centro de Biología Molecular “Severo Ochoa”, Consejo Superior de Investigaciones Científicas – Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- To whom correspondence should be addressed (email )
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22
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Operario DJ, Reynolds HM, Kim B. Comparison of DNA polymerase activities between recombinant feline immunodeficiency and leukemia virus reverse transcriptases. Virology 2005; 335:106-21. [PMID: 15823610 DOI: 10.1016/j.virol.2005.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2004] [Revised: 12/22/2004] [Accepted: 02/11/2005] [Indexed: 11/29/2022]
Abstract
In this study, we present enzymatic differences found between recombinant RTs derived from feline leukemia virus and feline immunodeficiency virus. Firstly, FIV RT showed low steady state K(m) values for dNTPs compared to FeLV RT. Consistent with this, FIV RT synthesized DNA more efficiently than FeLV RT at low dNTP concentrations. We observed similar concentration-dependent activity differences between other lentiviral (HIV-1 and SIV) and non-lentiviral (MuLV and AMV) RTs. Second, FeLV RT showed less efficient misincorporation with biased dNTP pools and mismatch primer extension capabilities, compared to FIV RT. In M13mp2 lacZalpha forward mutation assays, FeLV RT displayed approximately 11-fold higher fidelity than FIV RT. Finally, FeLV RT was less sensitive to 3TCTP and ddATP than FIV RT. This study represents the comprehensive enzymatic characterization of RTs from a lentivirus and a non-lentivirus retrovirus from the same host species. The data presented here support enzymatic divergences seen among retroviral RTs.
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Affiliation(s)
- Darwin J Operario
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Avenue, Box 672, Rochester, NY 14642, USA
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23
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Skasko M, Weiss KK, Reynolds HM, Jamburuthugoda V, Lee K, Kim B. Mechanistic differences in RNA-dependent DNA polymerization and fidelity between murine leukemia virus and HIV-1 reverse transcriptases. J Biol Chem 2005; 280:12190-200. [PMID: 15644314 PMCID: PMC1752212 DOI: 10.1074/jbc.m412859200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We compared the mechanistic and kinetic properties of murine leukemia virus (MuLV) and human immunodeficiency virus type 1 (HIV-1) reverse transcriptases (RTs) during RNA-dependent DNA polymerization and mutation synthesis using pre-steady-state kinetic analysis. First, MuLV RT showed 6.5-121.6-fold lower binding affinity (K(d)) to deoxynucleotide triphosphate (dNTP) substrates than HIV-1 RT, although the two RTs have similar incorporation rates (k(pol)). Second, compared with HIV-1 RT, MuLV RT showed dramatic reduction during multiple dNTP incorporations at low dNTP concentrations. Presumably, due to its low dNTP binding affinity, the dNTP binding step becomes rate-limiting in the multiple rounds of the dNTP incorporation by MuLV RT, especially at low dNTP concentrations. Third, similar fold differences between MuLV and HIV-1 RTs in the K(d) and k(pol) values to correct and incorrect dNTPs were observed. This indicates that these two RT proteins have similar misinsertion fidelities. Fourth, these two RT proteins have different mechanistic capabilities regarding mismatch extension. MuLV RT has a 3.1-fold lower mismatch extension fidelity, compared with HIV-1 RT. Finally, MuLV RT has a 3.8-fold lower binding affinity to mismatched template/primer (T/P) substrate compared with HIV-1 RT. Our data suggest that the active site of MuLV RT has an intrinsically low dNTP binding affinity, compared with HIV-1 RT. In addition, instead of the misinsertion step, the mismatch extension step, which varies between MuLV and HIV-1 RTs, contributes to their fidelity differences. The implications of these kinetic differences between MuLV and HIV-1 RTs on viral cell type specificity and mutagenesis are discussed.
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Affiliation(s)
- Mark Skasko
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York 14642, USA
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24
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Nikolenko GN, Svarovskaia ES, Delviks KA, Pathak VK. Antiretroviral drug resistance mutations in human immunodeficiency virus type 1 reverse transcriptase increase template-switching frequency. J Virol 2004; 78:8761-70. [PMID: 15280484 PMCID: PMC479068 DOI: 10.1128/jvi.78.16.8761-8770.2004] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Template-switching events during reverse transcription are necessary for completion of retroviral replication and recombination. Structural determinants of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) that influence its template-switching frequency are not known. To identify determinants of HIV-1 RT that affect the frequency of template switching, we developed an in vivo assay in which RT template-switching events during viral replication resulted in functional reconstitution of the green fluorescent protein gene. A survey of single amino acid substitutions near the polymerase active site or deoxynucleoside triphosphate-binding site of HIV-1 RT indicated that several substitutions increased the rate of RT template switching. Several mutations associated with resistance to antiviral nucleoside analogs (K65R, L74V, E89G, Q151N, and M184I) dramatically increased RT template-switching frequencies by two- to sixfold in a single replication cycle. In contrast, substitutions in the RNase H domain (H539N, D549N) decreased the frequency of RT template switching by twofold. Depletion of intracellular nucleotide pools by hydroxyurea treatment of cells used as targets for infection resulted in a 1.8-fold increase in the frequency of RT template switching. These results indicate that the dynamic steady state between polymerase and RNase H activities is an important determinant of HIV-1 RT template switching and establish that HIV-1 recombination occurs by the previously described dynamic copy choice mechanism. These results also indicate that mutations conferring resistance to antiviral drugs can increase the frequency of RT template switching and may influence the rate of retroviral recombination and viral evolution.
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Affiliation(s)
- Galina N Nikolenko
- HIV Drug Resistance Program, NCI-Frederick, Bldg. 535, Rm. 334, Frederick, MD 21702, USA
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25
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Smith RA, Anderson DJ, Preston BD. Purifying Selection Masks the Mutational Flexibility of HIV-1 Reverse Transcriptase. J Biol Chem 2004; 279:26726-34. [PMID: 15014075 DOI: 10.1074/jbc.m314038200] [Citation(s) in RCA: 13] [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
DNA and RNA polymerases share a core architecture composed of three structurally conserved motifs: A, B, and C. Although the amino acid sequences of these motifs are highly conserved between closely related organisms, variation across broader evolutionary distances suggests that only a few residues in each motif are indispensable for polymerase function. To test this, we constructed libraries of human immunodeficiency virus type-1 (HIV-1) containing random single amino acid replacements in motif B of reverse transcriptase (RT), and we used selection in culture to assess RT function. Despite the nearly absolute constancy of motif B in vivo, virus replicating in culture tolerated a range of conservative and nonconservative substitutions at 10 of the 11 amino acid positions examined. These included residues that are invariant across all retroviral subfamilies and highly conversed in diverse retroelements. Several mutants retained wild type infectivity, and serial passage experiments revealed replacements that were neutral or even beneficial to viral fitness. In addition, a number of the selected variants exhibited altered susceptibility to the nucleoside analog inhibitors AZT and 3TC. Taken together, these data indicate that HIV-1 tolerates a range of substitutions at conserved RT residues and that selection against slightly deleterious mutations (purifying selection) in vivo masks a large repertoire of viable phenotypic variants. This mutational flexibility likely contributes to HIV-1 evolution in response to changing selection pressures in infected individuals.
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Affiliation(s)
- Robert A Smith
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
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26
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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: 12] [Impact Index Per Article: 0.6] [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.
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Sharma B, Kaushik N, Upadhyay A, Tripathi S, Singh K, Pandey VN. A positively charged side chain at position 154 on the beta8-alphaE loop of HIV-1 RT is required for stable ternary complex formation. Nucleic Acids Res 2003; 31:5167-74. [PMID: 12930968 PMCID: PMC212807 DOI: 10.1093/nar/gkg708] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Lys154 is the only positively charged residue located in the VLPQGWK motif on the beta8-alphaE loop at the junction of the fingers and palm subdomains of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). Some of the conserved residues in this motif are critical for RT function, while others have been shown to confer nucleoside drug resistance and fidelity to the enzyme. In order to understand the functional implication of this positively charged residue, we carried out site-directed mutagenesis at position 154 and biochemically characterized the mutant enzymes. Mutants carrying negatively charged side chains (K154D and K154E) were severely impaired in their polymerase function, while those with hydrophobic side chains (K154A and K154I) were moderately affected. Analysis of the binary complexes formed by these mutants revealed that all the mutant derivatives retained their ability to form an enzyme template primer (E-TP) binary complex similar to the wild-type enzyme. In contrast, their ability to form stable E-TP-dNTP ternary complexes varied greatly and was dependent on the nature of the side chain at position 154. The conservative Lys-->Arg mutant was not affected in its ability to form a stable ternary complex, while those carrying non-polar or negatively charged side chains were significantly impaired. The apparent K(d [dNTP]) values for these non-conservative mutants were approximately 16- to 400-fold higher than the wild-type enzyme, indicating that a positively charged side chain at position 154 may be required for efficient formation of a stable ternary complex. Interestingly, all the mutant derivatives of Lys154 were completely resistant to a nucleoside analog inhibitor, 3'-dideoxy 3'-thiacytidine (3TC), implying that Lys154 may play a role in conferring 3TC sensitivity to HIV-1 RT. These findings are discussed in the context of the binary and ternary complex crystal structures of HIV-1 RT.
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Affiliation(s)
- Bechan Sharma
- Department of Biochemistry and Molecular Biology, Center for the Study of Emerging and Re-Emerging Pathogens, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
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28
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Diamond TL, Souroullas G, Weiss KK, Lee KY, Bambara RA, Dewhurst S, Kim B. Mechanistic understanding of an altered fidelity simian immunodeficiency virus reverse transcriptase mutation, V148I, identified in a pig-tailed macaque. J Biol Chem 2003; 278:29913-24. [PMID: 12740369 DOI: 10.1074/jbc.m211754200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have recently reported that the reverse transcriptase (RT) of SIVMNE 170 (170), which is a representative viral clone of the late symptomatic phase of infection with the parental strain, SIVMNE CL8 (CL8), has a largely increased fidelity, compared with the CL8 RT. In the present study, we analyzed the mechanistic alterations of the high fidelity 170 RT variant. First, we found that among several 170 RT mutations, only one, V148I, is solely responsible for the fidelity increase over the CL8 RT. This V148I mutation lies near the Gln-151 residue that we recently found is important to the low fidelity of RT and the binding of incoming dNTPs. Second, we compared dNTP binding affinity (Kd) and catalysis (kpol) of the CL8 RT and the CL8-V148I RT using pre-steady state kinetic analysis. In this experiment, the high fidelity CL8-V148I RT has largely decreased binding to both correct and incorrect dNTP without altering kpol. The fidelity increase imparted by the V148I mutation is likely because of the major reduction seen in RT binding to dNTPs. This parallels our findings with the Q151N mutant. Third, site-directed mutagenesis targeting amino acid residue 148 has revealed that a valine amino acid at this position is essential to RT infidelity. Based on these findings, we discuss possible structural impacts of residue 148 (and mutations at this site) on the interaction of RT with incoming dNTPs and infer how alterations in these properties may relate to viral replication and fitness.
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Affiliation(s)
- Tracy L Diamond
- Department of Microbiology and Immunology, University of Rochester, New York, 14642, USA
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29
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Mansky LM, Le Rouzic E, Benichou S, Gajary LC. Influence of reverse transcriptase variants, drugs, and Vpr on human immunodeficiency virus type 1 mutant frequencies. J Virol 2003; 77:2071-80. [PMID: 12525642 PMCID: PMC140916 DOI: 10.1128/jvi.77.3.2071-2080.2003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The evolution of drug resistance is a major complication of human immunodeficiency virus type 1 (HIV-1) chemotherapy. HIV-1 reverse transcriptase (RT) is a major target of antiretroviral therapy and ultimately the target of drug resistance mutations. Previous studies have indicated that drug-resistant HIV-1 RTs can alter HIV-1 mutant frequencies. In this study, we have tested a panel of HIV-1 RT variants for their ability to influence virus mutant frequencies. The RT variants tested included drug-resistant RT variants as well as other variants analyzed in enzyme fidelity studies with the lacZalpha gene as a mutation target and/or implicated as being important for enzyme fidelity by structural studies. Combinations of mutations that alone had a statistically significant influence on virus mutant frequencies resulted in different mutant frequency phenotypes. Furthermore, when virus replication occurred in the presence of drugs [e.g., 3'-azido-3'-deoxythymidine, (-)2/,3'-dideoxy-3'-thiacytidine, hydroxyurea, thymidine, or thioguanine] with selected RT variants, virus mutant frequencies increased. Similarly, Vpr variants deficient for binding to the uracil DNA glycosylase repair enzyme were observed to influence HIV-1 virus mutant frequencies when tested alone or in combination with RT variants. In summary, these observations indicate that HIV-1 mutant frequencies can significantly change by single amino acid substitutions in RT and that these effects can be altered by additional mutations in RT, by drugs, and/or by expression of Vpr variants. Such altered virus mutant frequencies could impact HIV-1 dynamics and evolution in small population sizes.
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Affiliation(s)
- Louis M Mansky
- Department of Molecular Virology, Immunology, and Medical Genetics, Center for Retrovirus Research, Comprehensive Cancer Center, Ohio State University Medical Center, Columbus, Ohio 43210, USA.
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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.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco, Spain
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Entin-Meer M, Sevilya Z, Hizi A. The role of phenylalanine-119 of the reverse transcriptase of mouse mammary tumour virus in DNA synthesis, ribose selection and drug resistance. Biochem J 2002; 367:381-91. [PMID: 12097136 PMCID: PMC1222887 DOI: 10.1042/bj20020712] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2002] [Revised: 06/25/2002] [Accepted: 07/03/2002] [Indexed: 12/16/2022]
Abstract
Phe-119 in the reverse transcriptase (RT) of mouse mammary tumour virus (MMTV) is homologous with Tyr-115 in HIV type 1 (HIV-1) RT and to Phe-155 in murine leukaemia virus (MLV) RT. By mutating these residues in HIV-1 and MLV RTs (which are strict DNA polymerases) the enzymes were shown to function also as RNA polymerases. Owing to the uniqueness of MMTV as a type B retrovirus, we have generated a Phe-119-Val mutant of MMTV RT to study the involvement of this residue in affecting the catalytic features of this RT. The data presented here show that the mutant MMTV RT can incorporate both deoxyribonucleosides and ribonucleosides while copying either RNA or DNA. In addition, this mutant RT shows resistance to nucleoside analogues and an enhanced fidelity of DNA synthesis; all relative to the wild-type enzyme. The Phe-119-Val mutant is also different from the wild-type enzyme in its preference for most template primers tested and in its ability to synthesize DNA under non-processive and processive conditions. Overall, it is likely that the aromatic side chain of Phe-119 is located at the dNTP-binding site of MMTV RT and thus might be part of a putative "steric gate" that prevents the incorporation of nucleoside triphosphates. Since the only three-dimensional structures of RTs published so far are those of HIV-1 and MLV, it is likely that MMTV RT folds quite similarly to these RTs.
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Affiliation(s)
- Michal Entin-Meer
- Department of Cell Biology and Histology, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Huang KJ, Alter GM, Wooley DP. The reverse transcriptase sequence of human immunodeficiency virus type 1 is under positive evolutionary selection within the central nervous system. J Neurovirol 2002; 8:281-94. [PMID: 12161813 DOI: 10.1080/13550280290100716] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) enters the central nervous system (CNS) during the acute phase of infection and causes AIDS-related encephalitis and dementia in 30% of individuals. Previous studies show that HIV-1 sequences derived from the CNS of infected patients, including the sequence encoding reverse transcriptase (RT), are genetically distinct from sequences in other tissues. The hypothesis of the current study is that the RT sequence of HIV-1 is under positive selection within the CNS. Multiple alignments of non-CNS-derived and CNS-derived HIV-1 RT sequences were constructed using the ClustalW 1.8 program. The multiple alignments were analyzed with the Synonymous/Nonsynonymous Analysis Program. Codon positions 122-125, 135-149, and 166-212 of the CNS-derived RT sequences underwent a greater accumulation of nonsynonymous than synonymous substitutions, which was markedly different from the analysis results of the non-CNS-derived RT sequences. These residues are located in the finger and palm subdomains of the RT protein structure, which encodes the polymerase active site. The analysis of CNS-derived partial-length RT sequences that encompass these regions yielded similar results. A comparison of CNS-derived RT sequences to a non-CNS-derived RT consensus sequence revealed that a majority of the nonsynonymous substitutions resulted in a specific amino acid replacement. These results indicate that reverse transcriptase is under positive selection within the CNS. The amino acid replacements were visualized on a three-dimensional structure of HIV-1 RT using the Sybyl software suite. The protein structure analysis revealed that the amino acid replacements observed among the CNS-derived sequences occurred in areas of known structural and functional significance.
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Affiliation(s)
- Kelly J Huang
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, Ohio 45435, USA
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Weiss KK, Bambara RA, Kim B. Mechanistic role of residue Gln151 in error prone DNA synthesis by human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT). Pre-steady state kinetic study of the Q151N HIV-1 RT mutant with increased fidelity. J Biol Chem 2002; 277:22662-9. [PMID: 11927582 DOI: 10.1074/jbc.m200202200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It has previously been reported that mutations in the Gln(151) residue of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) greatly enhance RT fidelity. In this study, we employed pre-steady state kinetic assays to elucidate the mechanistic role of residue Gln(151) in highly error prone DNA synthesis by HIV-1 RT. Using our Q151N high fidelity mutant, which is structurally altered in its ability to interact with the 3'-OH on the sugar moiety of the incoming deoxynucleotide triphosphate (dNTP), we examined how this change in RT-dNTP interaction affects HIV-1 RT fidelity. First, we found the binding affinity (K(D)) of wild type and Q151N RT proteins to different template/primers to be similar. These results indicate that the Gln(151) residue is not involved in the formation of the binary complex (RT.template/primer) during DNA polymerization. We also found that by changing residue 151 from a Gln-->Asn, the maximum rate of dNTP incorporation (k(pol)) for both correct and incorrect dNTPs was not affected. In contrast, the ability of the Q151N mutant to bind both correct and incorrect dNTPs (K(d)) was diminished. The Q151N mutant was 120-fold less efficient at binding correct dNTP than wild type RT, and its decrease in binding was such that we were unable to measure the actual binding affinity of Q151N for incorrect dNTPs. Presumably, the fidelity increase observed during the steady state is explained by this defect in Q151N binding to incorrect dNTP. In wild type RT, residue Gln(151) is important for tight binding of incorrect dNTPs and may contribute to the low fidelity nature of HIV-1 RT. Since the Q151N mutation also alters RT binding to correct dNTPs, the wild type Gln(151) residue may play an important role in efficient binding of RT to correct dNTPs. Our findings suggest that residue Gln(151) is an important element for the execution of both highly error prone and efficient DNA synthesis by HIV-1 RT.
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Affiliation(s)
- Kellie K Weiss
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York 14642, USA
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Diamond TL, Kimata J, Kim B. Identification of a simian immunodeficiency virus reverse transcriptase variant with enhanced replicational fidelity in the late stage of viral infection. J Biol Chem 2001; 276:23624-31. [PMID: 11325971 DOI: 10.1074/jbc.m102496200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Genomic hypermutation of human and simian immunodeficiency viruses (HIV and SIV) enables these viruses to adapt and escape from various types of anti-viral selection by altering the molecular properties of viral gene products. In this study, we examined whether the biochemical and catalytic properties of SIV DNA polymerases (reverse transcriptases; RT) can change during the course of viral infection. For this test, we analyzed RTs obtained from two SIV clones, SIVMNE CL8 and SIVMNE 170. SIVMNE 170 was isolated during the late symptomatic phase of infection with the parental strain, SIVMNE CL8. We found these two RTs have identical DNA polymerase specific activities and kinetics with three different DNA and RNA templates. In addition, the processivity of these two SIV RT proteins were also similar. However, as demonstrated by a misincorporation assay, the SIVMNE 170 RT showed much higher fidelity than SIVMNE CL8. The fidelity difference between these two SIV RTs was also confirmed by a steady state kinetic fidelity assay. These findings suggest that the fidelity of lentiviral RTs may change during the course of viral infection, possibly in response to alterations of host anti-viral immune capability. In addition, our sequence analysis of these two RT genes proposes possible structural strategies that the virus may employ to alter RT fidelity.
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Affiliation(s)
- T L Diamond
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York 14642 and the Department of Virology and Immunology, Southwest Foundation for Biomedical Research, San Antonio, Texas 78245-0549
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