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Wang S, Sotcheff SL, Gallardo CM, Jaworski E, Torbett B, Routh A. Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa. Nucleic Acids Res 2022; 50:e41. [PMID: 35018461 PMCID: PMC9023271 DOI: 10.1093/nar/gkab1259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 11/17/2022] Open
Abstract
Adaptation of viruses to their environments occurs through the acquisition of both novel single-nucleotide variants (SNV) and recombination events including insertions, deletions, and duplications. The co-occurrence of SNVs in individual viral genomes during their evolution has been well-described. However, unlike covariation of SNVs, studying the correlation between recombination events with each other or with SNVs has been hampered by their inherent genetic complexity and a lack of bioinformatic tools. Here, we expanded our previously reported CoVaMa pipeline (v0.1) to measure linkage disequilibrium between recombination events and SNVs within both short-read and long-read sequencing datasets. We demonstrate this approach using long-read nanopore sequencing data acquired from Flock House virus (FHV) serially passaged in vitro. We found SNVs that were either correlated or anti-correlated with large genomic deletions generated by nonhomologous recombination that give rise to Defective-RNAs. We also analyzed NGS data from longitudinal HIV samples derived from a patient undergoing antiretroviral therapy who proceeded to virological failure. We found correlations between insertions in the p6Gag and mutations in Gag cleavage sites. This report confirms previous findings and provides insights on novel associations between SNVs and specific recombination events within the viral genome and their role in viral evolution.
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Affiliation(s)
- Shiyi Wang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Stephanea L Sotcheff
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Christian M Gallardo
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bruce E Torbett
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
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2
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Budding of a Retrovirus: Some Assemblies Required. Viruses 2020; 12:v12101188. [PMID: 33092109 PMCID: PMC7589157 DOI: 10.3390/v12101188] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
One of the most important steps in any viral lifecycle is the production of progeny virions. For retroviruses as well as other viruses, this step is a highly organized process that occurs with exquisite spatial and temporal specificity on the cellular plasma membrane. To facilitate this process, retroviruses encode short peptide motifs, or L domains, that hijack host factors to ensure completion of this critical step. One such cellular machinery targeted by viruses is known as the Endosomal Sorting Complex Required for Transport (ESCRTs). Typically responsible for vesicular trafficking within the cell, ESCRTs are co-opted by the retroviral Gag polyprotein to assist in viral particle assembly and release of infectious virions. This review in the Viruses Special Issue “The 11th International Retroviral Nucleocapsid and Assembly Symposium”, details recent findings that shed light on the molecular details of how ESCRTs and the ESCRT adaptor protein ALIX, facilitate retroviral dissemination at sites of viral assembly.
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3
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How HIV-1 Gag Manipulates Its Host Cell Proteins: A Focus on Interactors of the Nucleocapsid Domain. Viruses 2020; 12:v12080888. [PMID: 32823718 PMCID: PMC7471995 DOI: 10.3390/v12080888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/27/2022] Open
Abstract
The human immunodeficiency virus (HIV-1) polyprotein Gag (Group-specific antigen) plays a central role in controlling the late phase of the viral lifecycle. Considered to be only a scaffolding protein for a long time, the structural protein Gag plays determinate and specific roles in HIV-1 replication. Indeed, via its different domains, Gag orchestrates the specific encapsidation of the genomic RNA, drives the formation of the viral particle by its auto-assembly (multimerization), binds multiple viral proteins, and interacts with a large number of cellular proteins that are needed for its functions from its translation location to the plasma membrane, where newly formed virions are released. Here, we review the interactions between HIV-1 Gag and 66 cellular proteins. Notably, we describe the techniques used to evidence these interactions, the different domains of Gag involved, and the implications of these interactions in the HIV-1 replication cycle. In the final part, we focus on the interactions involving the highly conserved nucleocapsid (NC) domain of Gag and detail the functions of the NC interactants along the viral lifecycle.
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4
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Sharma S, Arunachalam PS, Menon M, Ragupathy V, Satya RV, Jebaraj J, Aralaguppe SG, Rao C, Pal S, Saravanan S, Murugavel KG, Balakrishnan P, Solomon S, Hewlett I, Ranga U. PTAP motif duplication in the p6 Gag protein confers a replication advantage on HIV-1 subtype C. J Biol Chem 2018; 293:11687-11708. [PMID: 29773649 DOI: 10.1074/jbc.m117.815829] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 04/30/2018] [Indexed: 11/06/2022] Open
Abstract
HIV-1 subtype C (HIV-1C) may duplicate longer amino acid stretches in the p6 Gag protein, leading to the creation of an additional Pro-Thr/Ser-Ala-Pro (PTAP) motif necessary for viral packaging. However, the biological significance of a duplication of the PTAP motif for HIV-1 replication and pathogenesis has not been experimentally validated. In a longitudinal study of two different clinical cohorts of select HIV-1 seropositive, drug-naive individuals from India, we found that 8 of 50 of these individuals harbored a mixed infection of viral strains discordant for the PTAP duplication. Conventional and next-generation sequencing of six primary viral quasispecies at multiple time points disclosed that in a mixed infection, the viral strains containing the PTAP duplication dominated the infection. The dominance of the double-PTAP viral strains over a genetically similar single-PTAP viral clone was confirmed in viral proliferation and pairwise competition assays. Of note, in the proximity ligation assay, double-PTAP Gag proteins exhibited a significantly enhanced interaction with the host protein tumor susceptibility gene 101 (Tsg101). Moreover, Tsg101 overexpression resulted in a biphasic effect on HIV-1C proliferation, an enhanced effect at low concentration and an inhibitory effect only at higher concentrations, unlike a uniformly inhibitory effect on subtype B strains. In summary, our results indicate that the duplication of the PTAP motif in the p6 Gag protein enhances the replication fitness of HIV-1C by engaging the Tsg101 host protein with a higher affinity. Our results have implications for HIV-1 pathogenesis, especially of HIV-1C.
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Affiliation(s)
- Shilpee Sharma
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Prabhu S Arunachalam
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Malini Menon
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Viswanath Ragupathy
- the Laboratory of Molecular Virology, Division of Emerging and Transmission Transmitted Diseases, Office of Blood Review and Research, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | | | - Joshua Jebaraj
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | | | - Chaitra Rao
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Sreshtha Pal
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India
| | - Shanmugam Saravanan
- the Y. R. Gaitonde Centre for AIDS Research and Education, Chennai 600113, India
| | | | | | - Suniti Solomon
- the Y. R. Gaitonde Centre for AIDS Research and Education, Chennai 600113, India
| | - Indira Hewlett
- the Laboratory of Molecular Virology, Division of Emerging and Transmission Transmitted Diseases, Office of Blood Review and Research, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | - Udaykumar Ranga
- From the Jawaharlal Nehru Centre for Advanced Scientific Research, HIV-AIDS Laboratory, Bengaluru 56006, India,
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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
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6
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Abstract
UNLABELLED HIV-1 assembles at the plasma membrane of virus-producing cells as an immature, noninfectious particle. Processing of the Gag and Gag-Pol polyproteins by the viral protease (PR) activates the viral enzymes and results in dramatic structural rearrangements within the virion--termed maturation--that are a prerequisite for infectivity. Despite its fundamental importance for viral replication, little is currently known about the regulation of proteolysis and about the dynamics and structural intermediates of maturation. This is due mainly to the fact that HIV-1 release and maturation occur asynchronously both at the level of individual cells and at the level of particle release from a single cell. Here, we report a method to synchronize HIV-1 proteolysis in vitro based on protease inhibitor (PI) washout from purified immature virions, thereby temporally uncoupling virus assembly and maturation. Drug washout resulted in the induction of proteolysis with cleavage efficiencies correlating with the off-rate of the respective PR-PI complex. Proteolysis of Gag was nearly complete and yielded the correct products with an optimal half-life (t(1/2)) of ~5 h, but viral infectivity was not recovered. Failure to gain infectivity following PI washout may be explained by the observed formation of aberrant viral capsids and/or by pronounced defects in processing of the reverse transcriptase (RT) heterodimer associated with a lack of RT activity. Based on our results, we hypothesize that both the polyprotein processing dynamics and the tight temporal coupling of immature particle assembly and PR activation are essential for correct polyprotein processing and morphological maturation and thus for HIV-1 infectivity. IMPORTANCE Cleavage of the Gag and Gag-Pol HIV-1 polyproteins into their functional subunits by the viral protease activates the viral enzymes and causes major structural rearrangements essential for HIV-1 infectivity. This proteolytic maturation occurs concomitant with virus release, and investigation of its dynamics is hampered by the fact that virus populations in tissue culture contain particles at all stages of assembly and maturation. Here, we developed an inhibitor washout strategy to synchronize activation of protease in wild-type virus. We demonstrated that nearly complete Gag processing and resolution of the immature virus architecture are accomplished under optimized conditions. Nevertheless, most of the resulting particles displayed irregular morphologies, Gag-Pol processing was not faithfully reconstituted, and infectivity was not recovered. These data show that HIV-1 maturation is sensitive to the dynamics of processing and also that a tight temporal link between virus assembly and PR activation is required for correct polyprotein processing.
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Qi H, Zhao K, Xu F, Zhang X, Zhang Z, Yang L, Li C, Liang X, Guo W, Chen S, Liu Z, Zhang W, Yu XF. HIV-1 diversity, drug-resistant mutations, and viral evolution among high-risk individuals in phase II HIV vaccine trial sites in southern China. PLoS One 2013; 8:e68656. [PMID: 23869225 PMCID: PMC3711821 DOI: 10.1371/journal.pone.0068656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 06/03/2013] [Indexed: 11/21/2022] Open
Abstract
HIV-1 prevalence in Guangxi, China, has been growing since 1996, when the first case was reported. Over half of HIV-1 positive patients in Guangxi Province were injecting drug users (IDUs), possibly because of the province’s location near drug-trafficking routes. Since a phase II HIV vaccine trial is ongoing there, a current characterization of the subtypes of HIV-1 among IDUs in Guangxi would provide critical information for future HIV vaccine trials, as well as further control and prevention of HIV-1 transmission. Thus, we conducted a molecular epidemiological investigation of HIV-1 samples from 2008–2010 among IDUs in multiple cities in Guangxi Province. Our results, based on the gag/pol fragment, indicated a very high proportion (78.47%) of HIV-1 CRF08_BC recombinants, some CRF01_AE (15.38%) recombinants, and a low proportion of CRF07_BC (6.15%) recombinants among the IDUs. The high proportion of CRF08 HIV-1 strains among recent IDUs matches the vaccine candidate constructs. However, future vaccine development should also incorporate CRF01-targeted vaccine candidates. Distinct Env sequence evolution patterns were observed for CRF08_BC and CRF01_AE, indicating that different local selection pressures have been exerted on these two HIV-1 subtypes. Unique drug-resistant mutations were also detected, and our data indicate that HIV treatment programs should consider pre-existing drug-resistant mutations.
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Affiliation(s)
- Haiyan Qi
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ke Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Fei Xu
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xuzhao Zhang
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zhiyong Zhang
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Li Yang
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Chunling Li
- School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Xu Liang
- Centers for Disease Control and Prevention, Baise, Guangxi, China
| | - Weigui Guo
- Centers for Disease Control and Prevention, Beihai, Guangxi, China
| | - Shihai Chen
- Centers for Disease Control and Prevention, Nanning, Guangxi, China
| | - Zhihao Liu
- Centers for Disease Control and Prevention, Baise, Guangxi, China
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiao-Fang Yu
- Cancer Institute, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, Jilin, China
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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8
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Aspects of HIV-1 assembly that promote primer tRNALys3 annealing to viral RNA. Virus Res 2012; 169:340-8. [DOI: 10.1016/j.virusres.2012.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 05/25/2012] [Accepted: 06/01/2012] [Indexed: 01/30/2023]
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9
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Abstract
HIV infection of macrophages is a critically important component of viral pathogenesis and progression to AIDS. Although the virus follows the same life cycle in macrophages and T lymphocytes, several aspects of the virus-host relationship are unique to macrophage infection. Examples of these are the long-term persistence of productive infection, sustained by the absence of cell death, and the ability of progeny virus to bud into and accumulate in endocytic compartments designated multivesicular bodies (MVBs). Recently, the hypothesis that viral exploitation of the macrophage endocytic machinery is responsible for perpetuating the chronic state of infection unique to this cell type has been challenged in several independent studies employing a variety of experimental strategies. This review examines the evidence supporting and refuting the canonical hypothesis and highlights recently identified cellular factors that may contribute to the unique aspects of the HIV-macrophage interaction.
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Affiliation(s)
- Carol A Carter
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA.
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10
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Ojesina AI, Chaplin B, Sankalé JL, Murphy R, Idigbe E, Adewole I, Ekong E, Idoko J, Kanki PJ. Interplay of reverse transcriptase inhibitor therapy and gag p6 diversity in HIV type 1 subtype G and CRF02_AG. AIDS Res Hum Retroviruses 2008; 24:1167-74. [PMID: 18729771 DOI: 10.1089/aid.2007.0308] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract The gag p6 region of HIV-1 has various nonsubstitutionary mutations, including insertions, duplications, deletions, and premature stop codons. Studies have linked gag p6 mutations to reduced susceptibility to antiretroviral therapy in HIV-1 subtype B. This study examined the relationship between antiretroviral therapy and gag p6 diversity in HIV-1 CRF02_AG and subtype G. p6 data were generated for secondary analyses following Viroseq genotyping of pol gene sequences in plasma samples from HIV-1-infected Nigerians on reverse transcriptase inhibitor therapy, with virologic failure (repeat VL > 2000 copies/ml). p6 sequence chromatograms were available for 40 CRF02_AG and 43 subtype G-infected individuals. Subjects who had not received their supply of antiretroviral drugs for at least 2 months prior to the plasma sampling were classified as nonadherent. p6 sequences from therapy-adherent individuals had more nonsubstitutionary mutations than sequences from drug-naive individuals (p = 0.0005). The P5L/T mutation was inversely correlated with the presence of K27Q/N in p6, with each mutation being more prominent in subtype G and CRF02_AG, respectively. The data also suggested that P5L/T may be a compensatory mutation for the loss of an essential phosphorylation site in p6. In addition, there was an inverse association between P5L/T mutations in p6 and thymidine analog mutations in reverse transcriptase (p = 0.0001), and drug nonadherence was associated with an 8-fold lower risk of having a nonsubstitutionary mutation in p6 (95% CI = 1.27-52.57). Our data suggest that antiretroviral therapy influences gag p6 diversity, but further studies are needed to clarify these observations.
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Affiliation(s)
- Akinyemi I. Ojesina
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts 02115
| | - Beth Chaplin
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts 02115
| | - Jean-Louis Sankalé
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts 02115
| | | | | | - Isaac Adewole
- University College Hospital, Ibadan, Oyo State, Nigeria
| | - Ernest Ekong
- APIN Plus/Harvard PEPFAR Program, Lagos, Nigeria
| | - John Idoko
- Jos University Teaching Hospital, Jos, Plateau State, Nigeria
| | - Phyllis J. Kanki
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts 02115
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Nikolaitchik OA, Gorelick RJ, Leavitt MG, Pathak VK, Hu WS. Functional complementation of nucleocapsid and late domain PTAP mutants of human immunodeficiency virus type 1 during replication. Virology 2008; 375:539-49. [PMID: 18353416 DOI: 10.1016/j.virol.2008.02.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Revised: 01/02/2008] [Accepted: 02/21/2008] [Indexed: 01/16/2023]
Abstract
During human immunodeficiency virus type 1 (HIV-1) assembly, the nucleocapsid (NC) and the PTAP motif in p6 of Gag play important roles in RNA encapsidation and virus release, respectively. We have previously demonstrated that functional complementation occurs between an NC mutant and a PTAP mutant to rescue viral replication. In this report, we examined the amounts of functional NC and PTAP motif that are required during virus replication. When NC and PTAP mutants were coexpressed at 5:1, 5:5, and 1:5 ratios, virus titers were rescued at 5%, 51%, and 86% of the wild-type level, respectively. These results indicate that HIV-1 requires a small amount of functional PTAP motif but far more functional NC to complete efficient replication. Further analyses reveal that RNA packaging can be significantly rescued in viruses containing a small amount of functional NC. However, most of the NC proteins must be functional to generate the wild-type level of R-U5 DNA product. Once the R-U5 product is generated, viruses containing half of the functional NC can complete reverse transcription and DNA integration at near-wild-type efficiency. These results define the quantitative requirements of NC and p6 during HIV-1 replication and provide insights into the requirement for the development of anti-HIV strategies using NC and p6 as targets.
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12
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Dykes C, Demeter LM. Clinical significance of human immunodeficiency virus type 1 replication fitness. Clin Microbiol Rev 2007; 20:550-78. [PMID: 17934074 PMCID: PMC2176046 DOI: 10.1128/cmr.00017-07] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The relative fitness of a variant, according to population genetics theory, is that variant's relative contribution to successive generations. Most drug-resistant human immunodeficiency virus type 1 (HIV-1) variants have reduced replication fitness, but at least some of these deficits can be compensated for by the accumulation of second-site mutations. HIV-1 replication fitness also appears to influence the likelihood of a drug-resistant mutant emerging during treatment failure and is postulated to influence clinical outcomes. A variety of assays are available to measure HIV-1 replication fitness in cell culture; however, there is no agreement regarding which assays best correlate with clinical outcomes. A major limitation is that there is no high-throughput assay that incorporates an internal reference strain as a control and utilizes intact virus isolates. Some retrospective studies have demonstrated statistically significant correlations between HIV-1 replication fitness and clinical outcomes in some patient populations. However, different studies disagree as to which clinical outcomes are most closely associated with fitness. This may be in part due to assay design, sample size limitations, and differences in patient populations. In addition, the strength of the correlations between fitness and clinical outcomes is modest, suggesting that, at present, it would be difficult to utilize these assays for clinical management.
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Affiliation(s)
- Carrie Dykes
- Infectious Diseases Division, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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13
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Mirambeau G, Lyonnais S, Coulaud D, Hameau L, Lafosse S, Jeusset J, Borde I, Reboud-Ravaux M, Restle T, Gorelick RJ, Le Cam E. HIV-1 protease and reverse transcriptase control the architecture of their nucleocapsid partner. PLoS One 2007; 2:e669. [PMID: 17712401 PMCID: PMC1940317 DOI: 10.1371/journal.pone.0000669] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Accepted: 06/18/2007] [Indexed: 11/18/2022] Open
Abstract
The HIV-1 nucleocapsid is formed during protease (PR)-directed viral maturation, and is transformed into pre-integration complexes following reverse transcription in the cytoplasm of the infected cell. Here, we report a detailed transmission electron microscopy analysis of the impact of HIV-1 PR and reverse transcriptase (RT) on nucleocapsid plasticity, using in vitro reconstitutions. After binding to nucleic acids, NCp15, a proteolytic intermediate of nucleocapsid protein (NC), was processed at its C-terminus by PR, yielding premature NC (NCp9) followed by mature NC (NCp7), through the consecutive removal of p6 and p1. This allowed NC co-aggregation with its single-stranded nucleic-acid substrate. Examination of these co-aggregates for the ability of RT to catalyse reverse transcription showed an effective synthesis of double-stranded DNA that, remarkably, escaped from the aggregates more efficiently with NCp7 than with NCp9. These data offer a compelling explanation for results from previous virological studies that focused on i) Gag processing leading to nucleocapsid condensation, and ii) the disappearance of NCp7 from the HIV-1 pre-integration complexes. We propose that HIV-1 PR and RT, by controlling the nucleocapsid architecture during the steps of condensation and dismantling, engage in a successive nucleoprotein-remodelling process that spatiotemporally coordinates the pre-integration steps of HIV-1. Finally we suggest that nucleoprotein remodelling mechanisms are common features developed by mobile genetic elements to ensure successful replication.
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Affiliation(s)
- Gilles Mirambeau
- Laboratoire de Microscopie Moléculaire, UMR 8126: Interactions moléculaires et cancer, CNRS, Université Paris Sud-Institut de Cancérologie Gustave Roussy, Villejuif, France
- Division de Biochimie, UFR des Sciences de la Vie, Université Pierre et Marie Curie-Paris, Paris, France
- * To whom correspondence should be addressed. E-mail: (GM); (ELC)
| | - Sébastien Lyonnais
- Laboratoire de Microscopie Moléculaire, UMR 8126: Interactions moléculaires et cancer, CNRS, Université Paris Sud-Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Dominique Coulaud
- Laboratoire de Microscopie Moléculaire, UMR 8126: Interactions moléculaires et cancer, CNRS, Université Paris Sud-Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Laurence Hameau
- Laboratoire de Microscopie Moléculaire, UMR 8126: Interactions moléculaires et cancer, CNRS, Université Paris Sud-Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Sophie Lafosse
- Laboratoire de Microscopie Moléculaire, UMR 8126: Interactions moléculaires et cancer, CNRS, Université Paris Sud-Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Josette Jeusset
- Laboratoire de Microscopie Moléculaire, UMR 8126: Interactions moléculaires et cancer, CNRS, Université Paris Sud-Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Isabelle Borde
- Laboratoire Biologie et Multimedia, Université Pierre et Marie Curie-Paris, Paris, France
| | - Michèle Reboud-Ravaux
- Laboratoire d'Enzymologie Moléculaire et Fonctionnelle, CNRS FRE 2852, Institut Jacques Monod, CNRS-Université Pierre et Marie Curie-Paris, Paris, France
| | - Tobias Restle
- Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein and ZMSB, Lübeck, Germany
| | - Robert J. Gorelick
- AIDS Vaccine Program, Basic Research Program, Science Applications International Corporation at Frederick, The National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Eric Le Cam
- Laboratoire de Microscopie Moléculaire, UMR 8126: Interactions moléculaires et cancer, CNRS, Université Paris Sud-Institut de Cancérologie Gustave Roussy, Villejuif, France
- * To whom correspondence should be addressed. E-mail: (GM); (ELC)
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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.
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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;
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15
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Neumann G, Ebihara H, Takada A, Noda T, Kobasa D, Jasenosky LD, Watanabe S, Kim JH, Feldmann H, Kawaoka Y. Ebola virus VP40 late domains are not essential for viral replication in cell culture. J Virol 2005; 79:10300-7. [PMID: 16051823 PMCID: PMC1182630 DOI: 10.1128/jvi.79.16.10300-10307.2005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ebola virus particle formation and budding are mediated by the VP40 protein, which possesses overlapping PTAP and PPXY late domain motifs (7-PTAPPXY-13). These late domain motifs have also been found in the Gag proteins of retroviruses and the matrix proteins of rhabdo- and arenaviruses. While in vitro studies suggest a critical role for late domain motifs in the budding of these viruses, including Ebola virus, it remains unclear as to whether the VP40 late domains play a role in Ebola virus replication. Alteration of both late domain motifs drastically reduced VP40 particle formation in vitro. However, using reverse genetics, we were able to generate recombinant Ebola virus containing mutations in either or both of the late domains. Viruses containing mutations in one or both of their late domain motifs were attenuated by one log unit. Transmission and scanning electron microscopy did not reveal appreciable differences between the mutant and wild-type viruses released from infected cells. These findings indicate that the Ebola VP40 late domain motifs enhance virus replication but are not absolutely required for virus replication in cell culture.
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Affiliation(s)
- Gabriele Neumann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 2015 Linden Dr., Madison, WI 53706, USA
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16
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Paulus C, Ludwig C, Wagner R. Contribution of the Gag-Pol transframe domain p6* and its coding sequence to morphogenesis and replication of human immunodeficiency virus type 1. Virology 2005; 330:271-83. [PMID: 15527852 DOI: 10.1016/j.virol.2004.09.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Revised: 08/19/2004] [Accepted: 09/13/2004] [Indexed: 10/26/2022]
Abstract
The human immunodeficiency virus type-1 (HIV-1) transframe domain p6* is located between the nucleocapsid protein (NC) and the protease (PR) within the Gag-Pol precursor. This flexible, 68-amino-acid HIV-1 p6* domain has been suggested to negatively interfere with HIV PR activity in vitro proposing a contribution of either the C-terminal p6* tetrapeptide, internal cryptic PR cleavage sites, or a zymogen-related mechanism to a regulated PR activation. To assess these hypotheses in the viral context, a series of recombinant HX10-based provirus constructs has been established with clustered amino acid substitutions throughout the entire p6* coding sequence. Comparative analysis of the mutant proviral clones in different cell culture systems revealed that mutations within the well-conserved amino-terminal p6* region modified the Gag/Gag-Pol ratio and thus resulted in the release of viruses with impaired infectivity. Clustered amino acid substitutions destroying (i) the predicted cryptic PR cleavage sites or (ii) homologies to the pepsinogen propeptide did not influence viral replication in cell culture, whereas substitutions of the carboxyl-terminal p6* residues 62 to 68 altering proper release of the mature PR from the Gag-Pol precursor drastically reduced viral infectivity. Thus, the critical contribution of p6* and overlapping cis-acting sequence elements to timely regulated virus maturation and infectivity is closely linked to precise ribosomal frameshifting and proper N-terminal release of the viral PR from the Gag-Pol precursor, clearly disproving the hypothesis that sequence motifs in the central part of p6* modulate PR activation and viral infectivity.
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Affiliation(s)
- Christina Paulus
- Institute of Medical Microbiology and Hygiene, D-93053 Regensburg, Germany
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17
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Marlowe N, Flys T, Hackett J, Schumaker M, Jackson JB, Eshleman SH. Analysis of insertions and deletions in the gag p6 region of diverse HIV type 1 strains. AIDS Res Hum Retroviruses 2004; 20:1119-25. [PMID: 15585104 DOI: 10.1089/aid.2004.20.1119] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sequence variation in the gag p6 region in subtype B HIV-1 has been associated with changes in viral replication capacity and antiretroviral drug susceptibility. We examined sequence variation in the HIV-1 gag p6 region using plasma samples from 22 individuals with non-subtype B HIV-1 infection [subtypes A, C, D, F, and G, and circulating recombinant forms (CRFs) CRF01-AE and CRF02_AG]. An additional 105 gag sequences from the Los Alamos National Laboratory database were also analyzed. Extensive length variation was observed in the p6 gag region. Specific patterns of insertions and deletions were observed in different subtypes and CRFs, and no two subtypes or CRFs had the same general pattern. PTAP duplications were more common in subtype C than other strains (3 of 14 in subtype C vs. 2 of 113 in other strains, p = 0.004), and KQE duplications were seen only in subtype B. Further studies are needed to determine whether such genotypic differences influence viral replication capacity, antiretroviral drug susceptibility, or other phenotypic properties of these strains.
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18
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Hemonnot B, Cartier C, Gay B, Rebuffat S, Bardy M, Devaux C, Boyer V, Briant L. The host cell MAP kinase ERK-2 regulates viral assembly and release by phosphorylating the p6gag protein of HIV-1. J Biol Chem 2004; 279:32426-34. [PMID: 15155723 DOI: 10.1074/jbc.m313137200] [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: 11/06/2022] Open
Abstract
The host cell MAP kinase ERK-2 incorporated within human immunodeficiency virus type 1 particles plays a critical role in virus infectivity by phosphorylating viral proteins. Recently, a fraction of the virus incorporated late (L) domain-containing p6(gag) protein, which has an essential function in the release of viral particles from the cell surface, was reported to be phosphorylated by an unknown virus-associated cellular protein kinase (Muller, B., Patschinsky, T., and Krausslich, H. G. (2002) J. Virol. 76, 1015-1024). The present study demonstrates the contribution of the MAP kinase ERK-2 in p6(gag) phosphorylation. According to mutational analysis, a single ERK-2-phosphorylated threonine residue, belonging to a highly conserved phosphorylation MAP kinase consensus site, was identified at position 23 within p6(gag). Substitution by an alanine of the Thr(23) phosphorylable residue within the pNL4.3 molecular clone was found to decrease viral release from various cell types. As observed from electron microscopy experiments, most virions produced from this molecular clone remained incompletely separated from the host cell membrane with an immature morphology and displayed a reduced infectivity in single round infection experiments. Analysis of protein processing by Western blotting experiments revealed an incomplete Pr55(gag) maturation and a reduction in the virion-associated reverse transcriptase proteins was observed that was not related to differences in intracellular viral protein expression. Altogether, these data suggest that phosphorylation of p6(gag) protein by virus-associated ERK-2 is involved in the budding stage of HIV-1 life cycle.
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MESH Headings
- Alanine/chemistry
- Amino Acid Sequence
- Blotting, Western
- Cell Line
- DNA Mutational Analysis
- Electrophoresis, Gel, Two-Dimensional
- Electrophoresis, Polyacrylamide Gel
- Gene Products, gag/chemistry
- Gene Products, gag/metabolism
- Glutathione Transferase/metabolism
- HIV-1/metabolism
- Humans
- Microscopy, Electron
- Mitogen-Activated Protein Kinase 1/metabolism
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Phosphorylation
- Plasmids/metabolism
- Protein Binding
- Protein Structure, Tertiary
- RNA, Small Interfering/metabolism
- Sequence Homology, Amino Acid
- Threonine/chemistry
- Transfection
- Virion/metabolism
- Viruses/metabolism
- gag Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Bénédicte Hemonnot
- Laboratoire Infections Rétrovirales et Signalisation Cellulaire, Centre National pour la Recherche Scientifique, UMR 5121-Université Montpellier 1, Institut de Biologie, 4 Boulevard Henri IV, CS89508, 34960 Montpellier cedex 2, France
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19
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Bleiber G, Peters S, Martinez R, Cmarko D, Meylan P, Telenti A. The central region of human immunodeficiency virus type 1 p6 protein (Gag residues S14-I31) is dispensable for the virus in vitro. J Gen Virol 2004; 85:921-927. [PMID: 15039534 DOI: 10.1099/vir.0.19576-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The human immunodeficiency virus type 1 p6 region encodes p6(Gag) and the transframe p6(Pol) protein. The Gag frame encodes an N-terminal late assembly L domain and a C-terminal Vpr binding domain. In the Pol frame, substitution at a C-terminal motif decreases protease autocleavage. The role of the highly polymorphic central region of p6, comprising amino acids S14-I31 (p6(Gag)) and R20-D39 (p6(Pol)), is unclear. Analysis of this central region demonstrated that 35 % of p6(Gag) appears to be dispensable for virus propagation in vitro and smaller deletion and insertion polymorphisms can be tolerated in vivo. Extensive Pol deletion (deltaR20-D39, 42 % of p6(Pol)) did not alter protease autocleavage.
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Affiliation(s)
- Gabriela Bleiber
- Division of Infectious Diseases, University of Lausanne, Lausanne, Switzerland
| | - Solange Peters
- Division of Infectious Diseases, University of Lausanne, Lausanne, Switzerland
| | - Raquel Martinez
- Division of Infectious Diseases, University of Lausanne, Lausanne, Switzerland
| | - Dusan Cmarko
- University Hospital, and Center of Electron Microscopy, University of Lausanne, Lausanne, Switzerland
| | - Pascal Meylan
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- Division of Infectious Diseases, University of Lausanne, Lausanne, Switzerland
| | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- Division of Infectious Diseases, University of Lausanne, Lausanne, Switzerland
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20
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Cen S, Niu M, Saadatmand J, Guo F, Huang Y, Nabel GJ, Kleiman L. Incorporation of pol into human immunodeficiency virus type 1 Gag virus-like particles occurs independently of the upstream Gag domain in Gag-pol. J Virol 2004; 78:1042-9. [PMID: 14694138 PMCID: PMC368740 DOI: 10.1128/jvi.78.2.1042-1049.2004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By using particle-associated reverse transcriptase (RT) activity as an assay for Pol incorporation into human immunodeficiency virus type 1 (HIV-1) Gag virus-like particles (VLPs), it has been found that truncated, protease-negative, Gag-Pol missing cis Gag sequences is still incorporated into Gag VLPs, albeit at significantly reduced levels (10 to 20% of the level of wild-type Gag-Pol). In this work, we have directly measured the incorporation of truncated Gag-Pol species into Gag VLPs and have found that truncated Gag-Pol that is missing all sequences upstream of RT is still incorporated into Gag VLPs at levels approximating 70% of that achieved by wild-type Gag-Pol. Neither protease nor integrase regions in Pol are required for its incorporation, implying an interaction between Gag and RT sequences in the Pol protein. While the incorporation of Gag-Pol into Gag VLPs is reduced 12-fold by the replacement of the nucleocapsid within Gag with a leucine zipper motif, this mutation does not affect Pol incorporation. However, the deletion of p6 in Gag reduces Pol incorporation into Gag VLPs four- to fivefold. Pol shows the same ability as Gag-Pol to selectively package tRNA(Lys) into Gag VLPs, and primer tRNA(3)(Lys) is found annealed to the viral genomic RNA. These data suggest that after the initial separation of Gag from Pol during cleavage of Gag-Pol by viral protease, the Pol species still retains the capacity to bind to both Gag and tRNA(3)(Lys), which may be required for Pol and tRNA(3)(Lys) to be retained in the assembling virion until budding is completed.
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Affiliation(s)
- Shan Cen
- Lady Davis Institute for Medical Research and McGill AIDS Centre, Jewish General Hospital, McGill University, Montreal, Quebec, Canada H3T 1E2
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21
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Abstract
Human immunodeficiency virus type 1 (HIV-1) encodes a PTAP motif within the p6 domain of Gag that recruits Tsg101 and associated factors to facilitate virion budding. In this study, we use trans-complementation assays to demonstrate that the PTAP motif acts synergistically with additional p6 sequences to mediate the formation of infectious extracellular HIV-1 virions. These studies suggest that Tsg101 recruitment is necessary but not sufficient to account for late-budding activity exhibited by HIV-1 p6.
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22
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Adamson CS, Davies A, Soneoka Y, Nermut M, Mitrophanous K, Jones IM. A block in virus-like particle maturation following assembly of murine leukaemia virus in insect cells. Virology 2003; 314:488-96. [PMID: 14554078 DOI: 10.1016/s0042-6822(03)00485-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Expression of the murine leukaemia virus (MLV) major Gag antigen p65(Gag) using the baculovirus expression system leads to efficient assembly and release of virus-like particles (VLP) representative of immature MLV. Expression of p180(Gag-Pol), facilitated normally in mammalian cells by readthrough of the p65(Gag) termination codon, also occurs efficiently in insect cells to provide a source of the MLV protease and a pattern of p65(Gag) processing similar to that observed in mammalian cells. VLP release from p180(Gag-Pol)-expressing cells however remains essentially immature with disproportionate levels of the uncleaved p65(Gag) precursor when compared to the intracellular Gag profile. Changing the p65(Gag) termination codon altered the level of p65(Gag) and p180(Gag-Pol) within expressing cells but did not alter the pattern of released VLP, which remained immature. Coexpression of p65(Gag) with a fixed readthrough p180(Gag-Pol) also led to only immature VLP release despite high intracellular protease levels. Our data suggest a mechanism that preferentially selects uncleaved p65(Gag) for the assembly of MLV in this heterologous expression system and implies that, in addition to their relative levels, active sorting of the correct p65(Gag) and p180(Gag-Pol) ratios may occur in producer cells.
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Affiliation(s)
- Catherine S Adamson
- School of Animal and Microbial Sciences, The University of Reading, Reading, RD6 6AJ, UK.
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23
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Whitehurst N, Chappey C, Petropoulos C, Parkin N, Gamarnik A. Polymorphisms in p1-p6/p6* of HIV type 1 can delay protease autoprocessing and increase drug susceptibility. AIDS Res Hum Retroviruses 2003; 19:779-84. [PMID: 14585208 DOI: 10.1089/088922203769232575] [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
Maturation of infectious human immunodeficiency virus type 1 (HIV-1) particles requires proteolytic cleavage of structural polyproteins by viral protease. Inhibition of protease is a powerful tool for the treatment of HIV infection. Using a well-established phenotypic drug susceptibility assay, we found that sequences outside of the protease gene can modulate the susceptibility to protease inhibitors (PIs). Chimeric viruses carrying p1-p6/p6* sequences from patient isolates in the context of an NL4-3 molecular clone exhibited increased PI susceptibility. Furthermore, this phenotype was associated with a delay in protease autoprocessing in virions and a reduction in replication capacity. We propose that the interplay between protease and the C terminus of Gag is critical for proper protease activity and mismatches between these regions can reduce viral replication and increase drug susceptibility.
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Affiliation(s)
- N Whitehurst
- ViroLogic, South San Francisco, California 94080, USA
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24
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Maguire MF, Guinea R, Griffin P, Macmanus S, Elston RC, Wolfram J, Richards N, Hanlon MH, Porter DJT, Wrin T, Parkin N, Tisdale M, Furfine E, Petropoulos C, Snowden BW, Kleim JP. Changes in human immunodeficiency virus type 1 Gag at positions L449 and P453 are linked to I50V protease mutants in vivo and cause reduction of sensitivity to amprenavir and improved viral fitness in vitro. J Virol 2002; 76:7398-406. [PMID: 12097552 PMCID: PMC136352 DOI: 10.1128/jvi.76.15.7398-7406.2002] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.6] [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) Gag protease cleavage sites (CS) undergo sequence changes during the development of resistance to several protease inhibitors (PIs). We have analyzed the association of sequence variation at the p7/p1 and p1/p6 CS in conjunction with amprenavir (APV)-specific protease mutations following PI combination therapy with APV. Querying a central resistance data repository resulted in the detection of significant associations (P < 0.001) between the presence of APV protease signature mutations and Gag L449F (p1/p6 LP1'F) and P453L (p1/p6 PP5'L) CS changes. In population-based sequence analyses the I50V mutant was invariably linked to either L449F or P453L. Clonal analysis revealed that both CS mutations were never present in the same genome. Sequential plasma samples from one patient revealed a transition from I50V M46L P453L viruses at early time points to I50V M46I L449F viruses in later samples. Various combinations of the protease and Gag mutations were introduced into the HXB2 laboratory strain of HIV-1. In both single- and multiple-cycle assay systems and in the context of I50V, the L449F and P453L changes consistently increased the 50% inhibitory concentration of APV, while the CS changes alone had no measurable effect on inhibitor sensitivity. The decreased in vitro fitness of the I50V mutant was only partially improved by addition of either CS change (I50V M46I L449F mutant replicative capacity approximately 16% of that of wild-type virus). Western blot analysis of Pr55 Gag precursor cleavage products from infected-cell cultures indicated accumulation of uncleaved Gag p1-p6 in all I50V viruses without coexisting CS changes. Purified I50V protease catalyzed cleavage of decapeptides incorporating the L449F or P453L change 10-fold and 22-fold more efficiently than cleavage of the wild-type substrate, respectively. HIV-1 protease CS changes are selected during PI therapy and can have effects on both viral fitness and phenotypic resistance to PIs.
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Affiliation(s)
- Michael F Maguire
- Department of Clinical Virology, GlaxoSmithKline Research and Development, Stevenage SG1 2NY, United Kingdom
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25
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Robinson LH, Gale CV, Kleim JP. Inclusion of full length human immunodeficiency virus type 1 (HIV-1) gag sequences in viral recombinants applied to drug susceptibility phenotyping. J Virol Methods 2002; 104:147-60. [PMID: 12088824 DOI: 10.1016/s0166-0934(02)00059-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Drug susceptibility phenotyping of recombinant clinical human immunodeficiency virus type 1 (HIV-1) isolates has been used widely to quantitatively assess viral resistance to antiretroviral agents. A novel method is described for HIV-1 drug susceptibility phenotyping. Recombinant virus that contains the entire HIV-1 Gag, protease (PR) and reverse transcriptase (RT) coding regions is generated from plasma of HIV-1 infected subjects, thus allowing the in vitro investigation of effects caused by all protein-coding sequence elements upstream from the drug targets on: (i) drug susceptibility; and (ii) viral replicative capacity. Mutations known to cause retarded viral growth kinetics (RT M184V and PR I50V) were introduced and analyzed in parallel using both the new Five Prime HIV assay (FPH) and a standard recombinant virus assay (RVA). The M184V and I50V mutants produced up to 4.8- and 5.9-fold higher p24 antigen levels, respectively, with the FPH when compared to the cultures containing RVA-derived viruses. The reduced number of homologous recombination events necessary to generate replication-competent provirus with the FPH is the most likely explanation for these findings. Long range RT-PCR products were generated from plasma of HIV-1 infected subjects and HIV-1 LTR sequences were added using one-step PCR-mediated recombination. FPH-recombinants generated from two patients with previous HIV PR and RT inhibitor therapy showed lower drug susceptibilities than mutants established in parallel by RVA, and relative in vitro replication of the FPH recombinant derived from one of these subjects was enhanced compared to the corresponding RVA mutant. Although there were changes from the HIV-1 subtype B consensus sequence in amino acids flanking the Gag p17/p24, p24/p2 or p2/p7 PR cleavage sites, none were within the 10 amino acids immediately flanking the sites. These data suggest that determinants of drug susceptibility may be encoded in Gag upstream of the p7/p1 and p1/p6 regions, and that some phenotyping assays may therefore be underdetermining the reduction of drug susceptibility in some viral isolates.
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Affiliation(s)
- Laurence H Robinson
- Clinical Virology and Surrogates Unit, GlaxoSmithKline Research and Development, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK
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26
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Affiliation(s)
- Eric O Freed
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0460, USA.
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27
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Müller B, Patschinsky T, Kräusslich HG. The late-domain-containing protein p6 is the predominant phosphoprotein of human immunodeficiency virus type 1 particles. J Virol 2002; 76:1015-24. [PMID: 11773377 PMCID: PMC135845 DOI: 10.1128/jvi.76.3.1015-1024.2002] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Gag-derived protein p6 of human immunodeficiency virus type 1 (HIV-1) plays a crucial role in the release of virions from the membranes of infected cells. It is presumed that p6 and functionally related proteins from other viruses act as adapters, recruiting cellular factors to the budding site. This interaction is mediated by so-called late domains within the viral proteins. Previous studies had suggested that virus release from the plasma membrane shares elements with the cellular endocytosis machinery. Since protein phosphorylation is known to be a regulatory mechanism in these processes, we have investigated the phosphorylation of HIV-1 structural proteins. Here we show that p6 is the major phosphoprotein of HIV-1 particles. After metabolic labeling of infected cells with [ortho-32P]phosphate, we found that phosphorylated p6 from infected cells and from virus particles consisted of several forms, suggesting differential phosphorylation at multiple sites. Apparently, phosphorylation occurred shortly before or after the release of p6 from Gag and involved only a minor fraction of the total virion-associated p6 molecules. Phosphoamino acid analysis indicated phosphorylation at Ser and Thr, as well as a trace of Tyr phosphorylation, supporting the conclusion that multiple phosphorylation events do occur. In vitro experiments using purified virus revealed that endogenous or exogenously added p6 was efficiently phosphorylated by virion-associated cellular kinase(s). Inhibition experiments suggested that a cyclin-dependent kinase or a related kinase, most likely ERK2, was involved in p6 phosphorylation by virion-associated enzymes.
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Affiliation(s)
- Barbara Müller
- Abteilung Virologie, Universitätsklinikum Heidelberg, D-69120 Heidelberg, Germany.
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28
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Brumme ZL, Chan KJ, Dong WWY, Wynhoven B, Mo T, Hogg RS, Montaner JSG, O'Shaughnessy MV, Harrigan PR. Prevalence and clinical implications of insertions in the HIV-1 p6 Gag N-terminal region in drug-naive individuals initiating antiretroviral therapy. Antivir Ther 2002. [DOI: 10.1177/135965350300800202] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We assessed the prevalence and clinical impact of insertions within the HIV-1 p6Gag proline-rich (PTAP) region on initial antiretroviral therapy response in 461 HIV-infected, drug-naive individuals initiating therapy in British Columbia, Canada between June 1996 and August 1998. HIV p6Gag insertions were detected by nested RT-PCR of extracted patient plasma followed by direct DNA sequencing. Insertions were observed in 70 of 423 successfully genotyped samples (16.5%). HIV p6Gag insertions were significantly associated with a lower baseline CD4 cell count (P<<0.05) and the presence of basic amino acids at key positions in the HIV envelope V3 loop linked to a syncytium-inducing phenotype (P<<0.05). After adjusting for baseline factors, no effect of HIV p6Gag insertions was observed on time to virological success (pVL ≤500 copies/ml), virological failure (subsequent confirmed pVL ≥500 copies/ml) or immunological failure (confirmed CD4 count below baseline), as evaluated by Kaplan-Meier methods and Cox proportional hazard regression (P>0.1). The data suggest that HIV p6Gag insertions are not exclusively related to drug resistance and may not influence response to antiretroviral therapy, but may be linked to sequence variations in the HIV envelope.
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Affiliation(s)
- Zabrina L Brumme
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Keith J Chan
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Winnie WY Dong
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Brian Wynhoven
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Theresa Mo
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Robert S Hogg
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Julio SG Montaner
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Canada
| | - Michael V O'Shaughnessy
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Canada
| | - P Richard Harrigan
- BC Centre for Excellence in HIV/AIDS, St Paul's Hospital, Vancouver, British Columbia, Canada
- Faculty of Medicine, University of British Columbia, Canada
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Demirov DG, Orenstein JM, Freed EO. The late domain of human immunodeficiency virus type 1 p6 promotes virus release in a cell type-dependent manner. J Virol 2002; 76:105-17. [PMID: 11739676 PMCID: PMC135729 DOI: 10.1128/jvi.76.1.105-117.2002] [Citation(s) in RCA: 167] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The p6 domain of human immunodeficiency virus type 1 (HIV-1) is located at the C terminus of the Gag precursor protein Pr55(Gag). Previous studies indicated that p6 plays a critical role in HIV-1 particle budding from virus-expressing HeLa cells. In this study, we performed a detailed mutational analysis of the N terminus of p6 to map the sequences required for efficient virus release. We observed that the highly conserved P-T/S-A-P motif located near the N terminus of p6 is remarkably sensitive to change; even conservative mutations in this sequence imposed profound virus release defects in HeLa cells. In contrast, single and double amino acid substitutions outside the P-T/S-A-P motif had no significant effect on particle release. The introduction of stop codons one or two residues beyond the P-T/S-A-P motif markedly impaired virion release, whereas truncation four residues beyond P-T/S-A-P had no effect on particle production in HeLa cells. By examining the effects of p6 mutation in biological and biochemical analyses and by electron microscopy, we defined the role of p6 in particle release and virus replication in a panel of T-cell and adherent cell lines and in primary lymphocytes and monocyte-derived macrophages. We demonstrated that the effects of p6 mutation on virus replication are markedly cell type dependent. Intriguingly, even in T-cell lines and primary lymphocytes in which p6 mutations block virus replication, these changes had little or no effect on particle release. However, p6-mutant particles produced in T-cell lines and primary lymphocytes exhibited a defect in virion-virion detachment, resulting in the production of tethered chains of virions. Virus release in monocyte-derived macrophages was markedly inhibited by p6 mutation. To examine further the cell type-specific virus release defect in HeLa versus T cells, transient heterokaryons were produced between HeLa cells and the Jurkat T-cell line. These heterokaryons display a T-cell-like phenotype with respect to the requirement for p6 in particle release. The results described here define the role of p6 in virus replication in a wide range of cell types and reveal a strong cell type-dependent requirement for p6 in virus particle budding.
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Affiliation(s)
- Dimiter G Demirov
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0460, USA
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Guan Y, Diallo K, Detorio M, Whitney JB, Liang C, Wainberg MA. Partial restoration of replication of simian immunodeficiency virus by point mutations in either the dimerization initiation site (DIS) or Gag region after deletion mutagenesis within the DIS. J Virol 2001; 75:11920-3. [PMID: 11689677 PMCID: PMC114782 DOI: 10.1128/jvi.75.23.11920-11923.2001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used the simian immunodeficiency virus (SIV) molecular clone SIVmac239 to generate a deletion construct, termed SD2, in which we eliminated 22 nucleotides at positions +398 to +418 within the putative dimerization initiation site (DIS) stem. This SD2 deletion severely impaired viral replication, due to adverse effects on the packaging of viral genomic RNA, the processing of Gag proteins, and viral protein patterns. However, long-term culture of SD2 in either C8166 or CEMx174 cells resulted in restoration of replication capacity, due to two different sets of three compensatory point mutations, located within both the DIS and Gag regions. In the case of C8166 cells, both a K197R and a E49K mutation were identified within the capsid (CA) protein and the p6 protein of Gag, respectively, while the other point mutation (A423G) was found within the putative DIS loop. In the case of CEMx174 cells, two compensatory mutations were present within the viral nucleocapsid (NC) protein, E18G and Q31K, in addition to the same A423G substitution as observed with C8166 cells. A set of all three mutations was required in each case for restoration of replication capacity, and either set of mutations could be substituted for the other in both the C8166 and CEMx174 cell lines.
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Affiliation(s)
- Y Guan
- McGill AIDS Center, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
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Wang JJ, Sandefur S, Spearman P, Chiou CT, Chiang PH, Ratner L. Tracking the assembly pathway of human immunodeficiency virus type 1 Gag deletion mutants by immunogold labeling. Appl Immunohistochem Mol Morphol 2001; 9:371-9. [PMID: 11759066 DOI: 10.1097/00129039-200112000-00014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The Pr55gag gene product of human immunodeficiency virus type 1 (HIV-1) is sufficient to direct the formation of retrovirus-like particles (RVLPs). Recent biochemical evidence has indicated the presence of Gag intermediates in the cytoplasm; however, the Gag assembly process into RVLPs remains incompletely defined. The authors present here the subcellular localization of Gag mutant proteins in BSC40 and Jurkat cells by immunoelectron microscopy (IEM). The full Gag/Pol and Gag precursors, a C-terminal deletion mutant lacking a portion of nucleocapsid (NC), and all p6Gag gave rise to similar levels of RVLPs at the cell surface. A C-terminal deletion of all NC and p6Gag abrogated particle formation, whereas p24 was found in patches at the cell surface. Deletion of matrix (MA) sequences from Gag resulted in intracellular particles, and myristylation was not required for particle formation in the context of the MA deletion. Matrix expression was enhanced with Gag/Pol or Env coexpression as determined by semiquantitative IEM. p24 protein was targeted at vacuolar and mitochondrial membranes, but not at Golgi cisternae. In addition, aggregations of Gag intermediates and RVLPs in the cytoplasm, rough endoplasmic reticulum, cisternae, and mitochondria were noted. These results provide defined in situ evidence that HIV-1 particle assembly occurs in the cytosol in addition to budding at most intracellular membranes.
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Affiliation(s)
- J J Wang
- Department and Institute of Biology and Anatomy, National Defense Medical Center, Taipei, Taiwan, ROC.
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Peters S, Muñoz M, Yerly S, Sanchez-Merino V, Lopez-Galindez C, Perrin L, Larder B, Cmarko D, Fakan S, Meylan P, Telenti A. Resistance to nucleoside analog reverse transcriptase inhibitors mediated by human immunodeficiency virus type 1 p6 protein. J Virol 2001; 75:9644-53. [PMID: 11559796 PMCID: PMC114535 DOI: 10.1128/jvi.75.20.9644-9653.2001] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Resistance of human immunodeficiency virus type 1 (HIV-1) to antiretroviral agents results from target gene mutation within the pol gene, which encodes the viral protease, reverse transcriptase (RT), and integrase. We speculated that mutations in genes other that the drug target could lead to drug resistance. For this purpose, the p1-p6(gag)-p6(pol) region of HIV-1, placed immediately upstream of pol, was analyzed. This region has the potential to alter Pol through frameshift regulation (p1), through improved packaging of viral enzymes (p6(Gag)), or by changes in activation of the viral protease (p6(Pol)). Duplication of the proline-rich p6(Gag) PTAP motif, necessary for late viral cycle activities, was identified in plasma virus from 47 of 222 (21.2%) patients treated with nucleoside analog RT inhibitor (NRTI) antiretroviral therapy but was identified very rarely from drug-naïve individuals. Molecular clones carrying a 3-amino-acid duplication, APPAPP (transframe duplication SPTSPT in p6(Pol)), displayed a delay in protein maturation; however, they packaged a 34% excess of RT and exhibited a marked competitive growth advantage in the presence of NRTIs. This phenotype is reminiscent of the inoculum effect described in bacteriology, where a larger input, or a greater infectivity of an organism with a wild-type antimicrobial target, leads to escape from drug pressure and a higher MIC in vitro. Though the mechanism by which the PTAP region participates in viral maturation is not known, duplication of this proline-rich motif could improve assembly and packaging at membrane locations, resulting in the observed phenotype of increased infectivity and drug resistance.
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Affiliation(s)
- S Peters
- Division of Infectious Diseases, University Hospital, Lausanne, Switzerland
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Reichert M, Winnicka A, Willems L, Kettmann R, Cantor GH. Role of the proline-rich motif of bovine leukemia virus transmembrane protein gp30 in viral load and pathogenicity in sheep. J Virol 2001; 75:8082-9. [PMID: 11483753 PMCID: PMC115052 DOI: 10.1128/jvi.75.17.8082-8089.2001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2001] [Accepted: 06/01/2001] [Indexed: 11/20/2022] Open
Abstract
The cytoplasmic tail of bovine leukemia virus (BLV) transmembrane protein gp30 has multiple amino acid motifs that mimic those present in signaling proteins associated with B-cell and T-cell receptors. The proline-rich motif of gp30, PX(2)PX(4-5)P, is analogous to the recognition site of Src homology 3 (SH3) domains of signaling molecules. Using site-directed mutagenesis of an infectious molecular clone of BLV, point mutations were introduced which changed three of the prolines of the motif to alanines. The influence of these mutations on the pathogenicity of BLV was studied in sheep which received either (i) plasmid DNA with provirus containing proline-to-alanine mutations (pppBLV), (ii) plasmid DNA with wild-type provirus (wtBLV), or (iii) transfection reagent alone. Although all of the BLV-injected animals seroconverted at approximately the same time, viral loads at later time points were high in five of five of the wtBLV group and two of five of the pppBLV group but low in three of five of the pppBLV group, as determined by semiquantitative PCR. Viral expression was lower in the pppBLV-transfected sheep, as measured by p24 antigen enzyme-linked immunosorbent assay in cultured cells, and serologic titers were lower. Thirty-one months after transfection, four of four wtBLV-transfected sheep had died of leukemia and lymphoma, and all five of the pppBLV-transfected sheep were clinically healthy and had normal peripheral blood lymphocyte counts. These data indicate that the proline-rich motif of gp30 is not required for viral infectivity but is important for high viral load in vivo, suggesting that SH3-mediated gp30 interactions are critical for viral pathogenesis following infection. Absence of interactions with the proline-rich motif may prevent or delay tumorigenesis in sheep.
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Affiliation(s)
- M Reichert
- National Veterinary Research Institute, Pulawy, Warsaw, Poland.
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VerPlank L, Bouamr F, LaGrassa TJ, Agresta B, Kikonyogo A, Leis J, Carter CA. Tsg101, a homologue of ubiquitin-conjugating (E2) enzymes, binds the L domain in HIV type 1 Pr55(Gag). Proc Natl Acad Sci U S A 2001; 98:7724-9. [PMID: 11427703 PMCID: PMC35409 DOI: 10.1073/pnas.131059198] [Citation(s) in RCA: 484] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2001] [Indexed: 01/20/2023] Open
Abstract
Ubiquitination appears to be involved in virus particle release from infected cells. Free ubiquitin (Ub), as well as Ub covalently bound to a small fraction of p6 Gag, is detected in mature HIV particles. Here we report that the p6 region in the Pr55(Gag) structural precursor polyprotein binds to Tsg101, a putative Ub regulator that is involved in trafficking of plasma membrane-associated proteins. Tsg101 was found to interact with Gag in (i) a yeast two-hybrid assay, (ii) in vitro coimmunoprecipitation by using purified Pr55(Gag) and rabbit reticulocyte lysate-synthesized Tsg101, and (iii) in vivo in the cytoplasm of COS cells transfected with gag. The PTAPP motif [or late (L) domain] within p6, which is required for release of mature virus from the plasma membrane, was the determinant for binding Pr55(Gag). The N-terminal region in Tsg101, which is homologous to the Ubc4 class of Ub-conjugating (E2) enzymes, was the determinant of interaction with p6. Mutation of Tyr-110 in Tsg101, present in place of the active-site Cys that binds Ub in E2 enzymes, and other residues unique to Tsg101, impaired p6 interaction, indicating that features that distinguish Tsg101 from active E2 enzymes were important for binding the viral protein. The results link L-domain function in HIV to the Ub machinery and a specific component of the cellular trafficking apparatus.
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Affiliation(s)
- L VerPlank
- Department of Molecular Genetics and Microbiology, State University of New York, Stony Brook, NY 11794-5222, USA
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Kaufmann GR, Suzuki K, Cunningham P, Mukaide M, Kondo M, Imai M, Zaunders J, Cooper DA. Impact of HIV type 1 protease, reverse transcriptase, cleavage site, and p6 mutations on the virological response to quadruple therapy with saquinavir, ritonavir, and two nucleoside analogs. AIDS Res Hum Retroviruses 2001; 17:487-97. [PMID: 11350662 DOI: 10.1089/08892220151126526] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Abstract
Genotype alterations of HIV-1 protease, reverse transcriptase, cleavage sites p7/p1 and p1/p6, as well as p6(gag) and transframe protein p6* were studied in an observational cohort of 42 individuals who received antiretroviral therapy consisting of saquinavir, ritonavir, and two nucleoside analogs. In a multivariate logistic regression analysis, the prior protease inhibitor experience (odds ratio, 6.20; 95% CI, 1.22-31.38) and the presence of primary protease mutations (odds ratio, 9.99; 95% CI, 1.05-94.72) were independently associated with virological failure. Moreover, a trend was observed in that individuals with N-terminal amino acid insertions in the proline-rich motif of the p6(gag) protein were less likely to experience virological failure (OR, 0.17; 95% CI, 0.02-1.35; p = 0.09). In contrast, the presence of secondary protease, reverse transcriptase, or cleavage site mutations was not independently associated with treatment failure. However, mutations at cleavage site p7/p1 (p = 0.01) and C-terminal p6* mutations (p = 0.02) were both associated with primary protease mutations. In conclusion, the presence of primary protease mutations was the most important predictor of the subsequent virological response. Moreover, there is some evidence that insertions in the proline-rich area of the p6(gag) protein may affect the virological response. The relationship between mutations of cleavage sites or C-terminal p6* residues and protease mutations suggests that these alterations may serve a compensatory role, increasing viral fitness.
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Affiliation(s)
- G R Kaufmann
- National Centre in HIV Epidemiology and Clinical Research, Sydney NSW 2010, Australia
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Abstract
Our previous biochemical studies of HIV-1 and MuLV virions isolated and identified mature Gag products, HIV-1 p6(Gag) and MuLV p12(Gag), that were conjugated to a single ubiquitin. To study the importance of the monoubiquitination of Gag, a series of lysine to arginine mutants were constructed that eliminated ubiquitination at one or both of the lysines in HIV-1(NL4-3) p6(Gag) and both lysines in Moloney MuLV p12(Gag). HPLC and immunoblot analysis of the HIV-1 mutants demonstrated that either of the lysines in p6(Gag), K27 or K33, could be monoubiquitinated. However, infectivity assays showed that monoubiquitination of HIV-1 p6(Gag) or MuLV p12(Gag) is not required for viral replication in vitro. Pulse-chase radiolabeling of HIV-1-producing cells revealed that monoubiquitination of p6(Gag) does not affect the short-term release of virus from the cell, the maturation of Pr55(Gag), or the sensitivity of these processes to proteasome inhibitors. Experiments with protease-deficient HIV-1 showed that Pr55(Gag) can be monoubiquitinated, suggesting that p6(Gag) is first modified as a domain within Gag. Examination of the proteins inside an HIV-1 mutant found that free ubiquitin was incorporated into the virions in the absence of the lysines in p6(Gag), showing that the ubiquitin inside the virus is not initially brought in as a p6(Gag) conjugate. Although our results establish that monoubiquitination of p6(Gag) and p12(Gag) is not required for viral replication in vitro, this modification may be a by-product of interactions between Gag and cellular proteins during assembly and budding.
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Affiliation(s)
- D E Ott
- AIDS Vaccine Program, SAIC Frederick, National Cancer Institute, Frederick, Maryland 21702-1201, USA.
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