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De La Torre Tarazona E, Passaes C, Moreno S, Sáez-Cirión A, Alcamí J. High concentrations of Maraviroc do not alter immunological and metabolic parameters of CD4 T cells. Sci Rep 2024; 14:13980. [PMID: 38886484 PMCID: PMC11183235 DOI: 10.1038/s41598-024-64902-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Maraviroc (MVC) is an antiretroviral drug capable of binding to CCR5 receptors and block HIV entry into target cells. Moreover, MVC can activate NF-kB pathway and induce viral transcription in HIV-infected cells, being proposed as a latency reversal agent (LRA) in HIV cure strategies. However, the evaluation of immunological and metabolic parameters induced by MVC concentrations capable of inducing HIV transcription have not been explored in depth. We cultured isolated CD4 T cells in the absence or presence of MVC, and evaluated the frequency of CD4 T cell subpopulations and activation markers levels by flow cytometry, and the oxidative and glycolytic metabolic rates of CD4 T cells using a Seahorse Analyzer. Our results indicate that a high concentration of MVC did not increase the levels of activation markers, as well as glycolytic or oxidative metabolic rates in CD4 T cells. Furthermore, MVC did not induce significant changes in the frequency and activation levels of memory cell subpopulations. Our data support a safety profile of MVC as a promising LRA candidate since it does not induce alterations of the immunological and metabolic parameters that could affect the functionality of these immune cells.
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Affiliation(s)
- Erick De La Torre Tarazona
- Infectious Diseases Department, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University Hospital Ramón y Cajal, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Caroline Passaes
- HIV, Inflammation and Persistence Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Viral Reservoirs and Immune Control Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Santiago Moreno
- Infectious Diseases Department, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), University Hospital Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Medicine, Alcalá University, Madrid, Spain
| | - Asier Sáez-Cirión
- HIV, Inflammation and Persistence Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Viral Reservoirs and Immune Control Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - José Alcamí
- AIDS Immunopathogenesis Unit, National Center of Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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2
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Gao C, Su X, Wu N, Jin C. A new mechanism of SAMHD1 inhibition of HIV-1 infection by induction of autophagy. Med Hypotheses 2022. [DOI: 10.1016/j.mehy.2022.110890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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3
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Immunometabolic Reprogramming in Response to HIV Infection Is Not Fully Normalized by Suppressive Antiretroviral Therapy. Viruses 2022; 14:v14061313. [PMID: 35746785 PMCID: PMC9228482 DOI: 10.3390/v14061313] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/25/2022] Open
Abstract
Background: HIV infection results in immunometabolic reprogramming. While we are beginning to understand how this metabolic reprogramming regulates the immune response to HIV infection, we do not currently understand the impact of ART on immunometabolism in people with HIV (PWH). Methods: Serum obtained from HIV-infected (n = 278) and geographically matched HIV seronegative control subjects (n = 300) from Rakai Uganda were used in this study. Serum was obtained before and ~2 years following the initiation of ART from HIV-infected individuals. We conducted metabolomics profiling of the serum and focused our analysis on metabolic substrates and pathways assocaited with immunometabolism. Results: HIV infection was associated with metabolic adaptations that implicated hyperactive glycolysis, enhanced formation of lactate, increased activity of the pentose phosphate pathway (PPP), decreased β-oxidation of long-chain fatty acids, increased utilization of medium-chain fatty acids, and enhanced amino acid catabolism. Following ART, serum levels of ketone bodies, carnitine, and amino acid metabolism were normalized, however glycolysis, PPP, lactate production, and β-oxidation of long-chain fatty acids remained abnormal. Conclusion: Our findings suggest that HIV infection is associated with an increased immunometabolic demand that is satisfied through the utilization of alternative energetic substrates, including fatty acids and amino acids. ART alone was insufficient to completely restore this metabolic reprogramming to HIV infection, suggesting that a sustained impairment of immunometabolism may contribute to chronic immune activation and comorbid conditions in virally suppressed PWH.
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4
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Gibson MS, Noronha-Estima C, Gama-Carvalho M. Therapeutic Metabolic Reprograming Using microRNAs: From Cancer to HIV Infection. Genes (Basel) 2022; 13:genes13020273. [PMID: 35205318 PMCID: PMC8872267 DOI: 10.3390/genes13020273] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
MicroRNAs (miRNAs) are crucial regulators of cellular processes, including metabolism. Attempts to use miRNAs as therapeutic agents are being explored in several areas, including the control of cancer progression. Recent evidence suggests fine tuning miRNA activity to reprogram tumor cell metabolism has enormous potential as an alternative treatment option. Indeed, cancer growth is known to be linked to profound metabolic changes. Likewise, the emerging field of immunometabolism is leading to a refined understanding of how immune cell proliferation and function is governed by glucose homeostasis. Different immune cell types are now known to have unique metabolic signatures that switch in response to a changing environment. T-cell subsets exhibit distinct metabolic profiles which underlie their alternative differentiation and phenotypic functions. Recent evidence shows that the susceptibility of CD4+ T-cells to HIV infection is intimately linked to their metabolic activity, with many of the metabolic features of HIV-1-infected cells resembling those found in tumor cells. In this review, we discuss the use of miRNA modulation to achieve metabolic reprogramming for cancer therapy and explore the idea that the same approach may serve as an effective mechanism to restrict HIV replication and eliminate infected cells.
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Barrett B, Nguyen DH, Xu J, Guo K, Shetty S, Jones ST, Mickens KL, Shepard C, Roers A, Behrendt R, Wu L, Kim B, Santiago ML. SAMHD1 Promotes the Antiretroviral Adaptive Immune Response in Mice Exposed to Lipopolysaccharide. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:444-453. [PMID: 34893529 DOI: 10.4049/jimmunol.2001389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 11/08/2021] [Indexed: 12/13/2022]
Abstract
SAMHD1 is a potent HIV-1 restriction factor that blocks reverse transcription in monocytes, dendritic cells and resting CD4+ T cells by decreasing intracellular dNTP pools. However, SAMHD1 may diminish innate immune sensing and Ag presentation, resulting in a weaker adaptive immune response. To date, the role of SAMHD1 on antiretroviral immunity remains unclear, as mouse SAMHD1 had no impact on murine retrovirus replication in prior in vivo studies. Here, we show that SAMHD1 significantly inhibits acute Friend retrovirus infection in mice. Pretreatment with LPS, a significant driver of inflammation during HIV-1 infection, further unmasked a role for SAMHD1 in influencing immune responses. LPS treatment in vivo doubled the intracellular dNTP levels in immune compartments of SAMHD1 knockout but not wild-type mice. SAMHD1 knockout mice exhibited higher plasma infectious viremia and proviral DNA loads than wild-type mice at 7 d postinfection (dpi), and proviral loads inversely correlated with a stronger CD8+ T cell response. SAMHD1 deficiency was also associated with weaker NK, CD4+ T and CD8+ T cell responses by 14 dpi and weaker neutralizing Ab responses by 28 dpi. Intriguingly, SAMHD1 influenced these cell-mediated immune (14 dpi) and neutralizing Ab (28 dpi) responses in male but not female mice. Our findings formally demonstrate SAMHD1 as an antiretroviral factor in vivo that could promote adaptive immune responses in a sex-dependent manner. The requirement for LPS to unravel the SAMHD1 immunological phenotype suggests that comorbidities associated with a "leaky" gut barrier may influence the antiviral function of SAMHD1 in vivo.
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Affiliation(s)
- BradleyS Barrett
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | - David H Nguyen
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Joella Xu
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Kejun Guo
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Shravida Shetty
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO
| | - Sean T Jones
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Kaylee L Mickens
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
| | - Caitlin Shepard
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA
| | - Axel Roers
- Institute for Immunology, Faculty of Medicine, Technical University Dresden, Dresden, Germany
| | - Rayk Behrendt
- Institute for Immunology, Faculty of Medicine, Technical University Dresden, Dresden, Germany
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA; and
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA.,Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, GA
| | - Mario L Santiago
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO; .,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO
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Abstract
Cytomegaloviruses (CMVs) are among the largest pathogenic viruses in mammals. To enable replication of their long double-stranded DNA genomes, CMVs induce profound changes in cell cycle regulation. A hallmark of CMV cell cycle control is the establishment of an unusual cell cycle arrest at the G1/S transition, which is characterized by the coexistence of cell cycle stimulatory and inhibitory activities. While CMVs interfere with cellular DNA synthesis and cell division, they activate S-phase-specific gene expression and nucleotide metabolism. This is facilitated by a set of CMV gene products that target master regulators of G1/S progression such as cyclin E and A kinases, Rb-E2F transcription factors, p53-p21 checkpoint proteins, the APC/C ubiquitin ligase, and the nucleotide hydrolase SAMHD1. While the major themes of cell cycle regulation are well conserved between human and murine CMVs (HCMV and MCMV), there are considerable differences at the level of viral cell cycle effectors and their mechanisms of action. Furthermore, both viruses have evolved unique mechanisms to sense the host cell cycle state and modulate the infection program accordingly. This review provides an overview of conserved and divergent features of G1/S control by MCMV and HCMV.
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7
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Andor N, Altrock PM, Jain N, Gomes AP. Tipping cancer cells over the edge: the context-dependent cost of high ploidy. Cancer Res 2021; 82:741-748. [PMID: 34785577 DOI: 10.1158/0008-5472.can-21-2794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/27/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022]
Abstract
Tetraploidy is an aneuploidy-permissive condition that can fuel tumorgenesis. The tip-over hypothesis of cytotoxic therapy-sensitivity proposes that therapy is effective if it pushes a cell's aneuploidy above a viable tipping point. But elevated aneuploidy alone may not account for this tipping point. Tissue micro-environments (TMEs) that lack sufficient resources to support tetraploid cells can explain the fitness cost of aneuploidy. Raw materials needed to generate deoxynucleotides, the building blocks of DNA, are candidate rate-limiting factors for the evolution of high-ploidy cancer cells. Understanding the resource cost of high ploidy is key to uncover its therapeutic vulnerabilities across tissue sites with versatile energy supplies.
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Affiliation(s)
- Noemi Andor
- Integrated Mathematical Oncology, Moffitt Cancer Center
| | - Philipp M Altrock
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology
| | | | - Ana P Gomes
- Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute
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8
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Liu R, Li J, Shao J, Lee JH, Qiu X, Xiao Y, Zhang B, Hao Y, Li M, Chen Q. Innate immune response orchestrates phosphoribosyl pyrophosphate synthetases to support DNA repair. Cell Metab 2021; 33:2076-2089.e9. [PMID: 34343500 DOI: 10.1016/j.cmet.2021.07.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/09/2021] [Accepted: 06/12/2021] [Indexed: 02/08/2023]
Abstract
Ionizing radiation-induced DNA damages cause genome instability and are highly cytotoxic. Deoxyribonucleotide metabolism provides building blocks for DNA repair. Nevertheless, how deoxyribonucleotide metabolism is timely regulated to coordinate with DNA repair remains elusive. Here, we show that ionizing radiation results in TBK1-mediated phosphorylation of phosphoribosyl pyrophosphate synthetase (PRPS)1/2 at T228, thereby enhancing PRPS1/2 catalytic activity and promoting deoxyribonucleotide synthesis. DNA damage-elicited activation of cGAS/STING axis and ATM-mediated PRPS1/2 S16 phosphorylation are required for PRPS1/2 T228 phosphorylation under ionizing radiation. Furthermore, T228 phosphorylation overrides allosteric regulator-mediated effects and preserves PRPS1/2 with high activity. The expression of non-phosphorylatable PRPS1/2 mutants or inhibition of cGAS/STING axis counteracts ionizing radiation-induced PRPS1/2 activation, deoxyribonucleotide synthesis, and DNA repair, and further impairs cell viability. This study highlights a novel and important mechanism underlying an innate immune response-guided deoxyribonucleotide metabolism, which supports DNA repair.
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Affiliation(s)
- Rui Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Jingyi Li
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610051, China; School of Biological Sciences and Technology, Chengdu Medical College, Chengdu 610599, China
| | - Jichun Shao
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610051, China
| | - Jong-Ho Lee
- Department of Health Sciences, The Graduate School of Dong-A University, Busan 49315, Republic of Korea; Department of Biological Sciences, Dong-A University, Busan 49315, Republic of Korea
| | - Xuemei Qiu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanxuan Xiao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Bowen Zhang
- The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, Sichuan 610051, China
| | - Yilong Hao
- Key Laboratory of Oral Biomedical Research of Zhejiang Province, and the Affiliated Hospital of Stomatology, School of Stomatology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, China
| | - Mi Li
- UTHealth Graduate School of Biomedical Sciences, Houston, TX 77225, USA
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China.
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9
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Martinat C, Cormier A, Tobaly-Tapiero J, Palmic N, Casartelli N, Mahboubi B, Coggins SA, Buchrieser J, Persaud M, Diaz-Griffero F, Espert L, Bossis G, Lesage P, Schwartz O, Kim B, Margottin-Goguet F, Saïb A, Zamborlini A. SUMOylation of SAMHD1 at Lysine 595 is required for HIV-1 restriction in non-cycling cells. Nat Commun 2021; 12:4582. [PMID: 34321470 PMCID: PMC8319325 DOI: 10.1038/s41467-021-24802-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
SAMHD1 is a cellular triphosphohydrolase (dNTPase) proposed to inhibit HIV-1 reverse transcription in non-cycling immune cells by limiting the supply of the dNTP substrates. Yet, phosphorylation of T592 downregulates SAMHD1 antiviral activity, but not its dNTPase function, implying that additional mechanisms contribute to viral restriction. Here, we show that SAMHD1 is SUMOylated on residue K595, a modification that relies on the presence of a proximal SUMO-interacting motif (SIM). Loss of K595 SUMOylation suppresses the restriction activity of SAMHD1, even in the context of the constitutively active phospho-ablative T592A mutant but has no impact on dNTP depletion. Conversely, the artificial fusion of SUMO2 to a non-SUMOylatable inactive SAMHD1 variant restores its antiviral function, a phenotype that is reversed by the phosphomimetic T592E mutation. Collectively, our observations clearly establish that lack of T592 phosphorylation cannot fully account for the restriction activity of SAMHD1. We find that SUMOylation of K595 is required to stimulate a dNTPase-independent antiviral activity in non-cycling immune cells, an effect that is antagonized by cyclin/CDK-dependent phosphorylation of T592 in cycling cells.
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Affiliation(s)
- Charlotte Martinat
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Arthur Cormier
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Joëlle Tobaly-Tapiero
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Noé Palmic
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Nicoletta Casartelli
- grid.428999.70000 0001 2353 6535Institut Pasteur, Virus and Immunity Unit, CNRS-UMR3569, Paris, France ,grid.511001.4Vaccine Research Institute, Créteil, France
| | - Bijan Mahboubi
- grid.189967.80000 0001 0941 6502Emory School of Medicine, Atlanta, USA
| | - Si’Ana A. Coggins
- grid.189967.80000 0001 0941 6502Emory School of Medicine, Atlanta, USA
| | - Julian Buchrieser
- grid.428999.70000 0001 2353 6535Institut Pasteur, Virus and Immunity Unit, CNRS-UMR3569, Paris, France ,grid.511001.4Vaccine Research Institute, Créteil, France ,grid.4991.50000 0004 1936 8948James Martin Stem Cell Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Mirjana Persaud
- grid.251993.50000000121791997Albert Einstein College of Medicine, Microbiology and Immunology, Bronx, NY USA
| | - Felipe Diaz-Griffero
- grid.251993.50000000121791997Albert Einstein College of Medicine, Microbiology and Immunology, Bronx, NY USA
| | - Lucile Espert
- grid.503217.2IRIM, University of Montpellier, UMR 9004 CNRS, Montpellier, France
| | - Guillaume Bossis
- grid.429192.50000 0004 0599 0285IGMM, Univ Montpellier, CNRS, Montpellier, France
| | - Pascale Lesage
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Olivier Schwartz
- grid.428999.70000 0001 2353 6535Institut Pasteur, Virus and Immunity Unit, CNRS-UMR3569, Paris, France ,grid.511001.4Vaccine Research Institute, Créteil, France
| | - Baek Kim
- grid.189967.80000 0001 0941 6502Emory School of Medicine, Atlanta, USA
| | | | - Ali Saïb
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Alessia Zamborlini
- INSERM U944, CNRS UMR 7212, Genomes & Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France ,grid.457334.2Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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Meissner ME, Julik EJ, Badalamenti JP, Arndt WG, Mills LJ, Mansky LM. Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing. Viruses 2021; 13:v13071338. [PMID: 34372543 PMCID: PMC8310143 DOI: 10.3390/v13071338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 01/23/2023] Open
Abstract
Human immunodeficiency virus type 2 (HIV-2) accumulates fewer mutations during replication than HIV type 1 (HIV-1). Advanced studies of HIV-2 mutagenesis, however, have historically been confounded by high background error rates in traditional next-generation sequencing techniques. In this study, we describe the adaptation of the previously described maximum-depth sequencing (MDS) technique to studies of both HIV-1 and HIV-2 for the ultra-accurate characterization of viral mutagenesis. We also present the development of a user-friendly Galaxy workflow for the bioinformatic analyses of sequencing data generated using the MDS technique, designed to improve replicability and accessibility to molecular virologists. This adapted MDS technique and analysis pipeline were validated by comparisons with previously published analyses of the frequency and spectra of mutations in HIV-1 and HIV-2 and is readily expandable to studies of viral mutation across the genomes of both viruses. Using this novel sequencing pipeline, we observed that the background error rate was reduced 100-fold over standard Illumina error rates, and 10-fold over traditional unique molecular identifier (UMI)-based sequencing. This technical advancement will allow for the exploration of novel and previously unrecognized sources of viral mutagenesis in both HIV-1 and HIV-2, which will expand our understanding of retroviral diversity and evolution.
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Affiliation(s)
- Morgan E. Meissner
- Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA;
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
| | - Emily J. Julik
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jonathan P. Badalamenti
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN 55455, USA;
| | - William G. Arndt
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lauren J. Mills
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (L.J.M.); (L.M.M.)
| | - Louis M. Mansky
- Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA;
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; (E.J.J.); (W.G.A.)
- Division of Basic Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence: (L.J.M.); (L.M.M.)
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11
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Dilmore C, DeStefano JJ. HIV Reverse Transcriptase Pre-Steady-State Kinetic Analysis of Chain Terminators and Translocation Inhibitors Reveals Interactions between Magnesium and Nucleotide 3'-OH. ACS OMEGA 2021; 6:14621-14628. [PMID: 34124485 PMCID: PMC8190884 DOI: 10.1021/acsomega.1c01742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/12/2021] [Indexed: 05/06/2023]
Abstract
Deoxythymidine triphosphate analogues with various 3' substituents in the sugar ring (-OH (dTTP)), -H, -N3, -NH2, -F, -O-CH3, no group (2',3'-didehydro-2',3'-dideoxythymidine triphosphate (d4TTP)), and those retaining the 3'-OH but with 4' additions (4'-C-methyl, 4'-C-ethyl) or sugar ring modifications (d-carba dTTP) were evaluated using pre-steady-state kinetics in low (0.5 mM) and high (6 mM) Mg2+ with HIV reverse transcriptase (RT). Analogues showed diminished observed incorporation rate constants (k obs) compared to dTTP ranging from about 2-fold (3'-H, -N3, and d4TTP with high Mg2+) to >10-fold (3'-NH2 and 3'-F with low Mg2+), while 3'-O-CH3 dTTP incorporated much slower than other analogues. Illustrating the importance of interactions between Mg2+ and the 3'-OH, k obs using 5 μM dTTP and 0.5 mM Mg2+ was only modestly slower (1.6-fold) than with 6 mM Mg2+, while analogues with 3' alterations incorporated 2.8-5.1-fold slower in 0.5 mM Mg2+. In contrast, 4'-C-methyl and d-carba dTTP, which retain the 3'-OH, were not significantly affected by Mg2+. Consistent with these results, analogues with 3' modifications were better inhibitors in 6 versus 0.5 mM Mg2+. Equilibrium dissociation constant (K D) and maximum incorporation rate (k pol) determinations for dTTP and analogues lacking a 3'-OH indicated that low Mg2+ caused a several-fold greater reduction in k pol with the analogues but did not significantly affect K D, results consistent with a role for 3'-OH/Mg2+ interactions in catalysis rather than nucleotide binding. Overall, results emphasize the importance of previously unreported interactions between Mg2+ and the 3'-OH of the incoming nucleotide and suggest that inhibitors with 3'-OH groups may have advantages in low free Mg2+ in physiological settings.
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Affiliation(s)
- Christopher
R. Dilmore
- Cell
Biology and Molecular Genetics, 3130 Bioscience Research
Building, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffrey J. DeStefano
- Cell
Biology and Molecular Genetics, 3130 Bioscience Research
Building, University of Maryland, College Park, Maryland 20742, United States
- Maryland
Pathogen Research Institute, College
Park, Maryland 20742, United States
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12
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Veenhuis RT, Abreu CM, Shirk EN, Gama L, Clements JE. HIV replication and latency in monocytes and macrophages. Semin Immunol 2021; 51:101472. [PMID: 33648815 PMCID: PMC10171083 DOI: 10.1016/j.smim.2021.101472] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 02/20/2021] [Indexed: 12/13/2022]
Abstract
The relevance of monocyte and macrophage reservoirs in virally suppressed people with HIV (vsPWH) has previously been debatable. Macrophages were assumed to have a moderate life span and lack self-renewing potential. However, recent studies have challenged this dogma and now suggest an important role of these cell as long-lived HIV reservoirs. Lentiviruses have a long-documented association with macrophages and abundant evidence exists that macrophages are important target cells for HIV in vivo. A critical understanding of HIV infection, replication, and latency in macrophages is needed in order to determine the appropriate method of measuring and eliminating this cellular reservoir. This review provides a brief discussion of the biology and acute and chronic infection of monocytes and macrophages, with a more substantial focus on replication, latency and measurement of the reservoir in cells of myeloid origin.
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Affiliation(s)
- Rebecca T Veenhuis
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Celina M Abreu
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Erin N Shirk
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lucio Gama
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Vaccine Research Center, NIAID, NIH, Bethesda, MD, United States
| | - Janice E Clements
- Department of Molecular and Comparative Biology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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13
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Coggins SA, Mahboubi B, Schinazi RF, Kim B. Mechanistic cross-talk between DNA/RNA polymerase enzyme kinetics and nucleotide substrate availability in cells: Implications for polymerase inhibitor discovery. J Biol Chem 2020; 295:13432-13443. [PMID: 32737197 PMCID: PMC7521635 DOI: 10.1074/jbc.rev120.013746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/31/2020] [Indexed: 01/01/2023] Open
Abstract
Enzyme kinetic analysis reveals a dynamic relationship between enzymes and their substrates. Overall enzyme activity can be controlled by both protein expression and various cellular regulatory systems. Interestingly, the availability and concentrations of intracellular substrates can constantly change, depending on conditions and cell types. Here, we review previously reported enzyme kinetic parameters of cellular and viral DNA and RNA polymerases with respect to cellular levels of their nucleotide substrates. This broad perspective exposes a remarkable co-evolution scenario of DNA polymerase enzyme kinetics with dNTP levels that can vastly change, depending on cell proliferation profiles. Similarly, RNA polymerases display much higher Km values than DNA polymerases, possibly due to millimolar range rNTP concentrations found in cells (compared with micromolar range dNTP levels). Polymerases are commonly targeted by nucleotide analog inhibitors for the treatments of various human diseases, such as cancers and viral pathogens. Because these inhibitors compete against natural cellular nucleotides, the efficacy of each inhibitor can be affected by varying cellular nucleotide levels in their target cells. Overall, both kinetic discrepancy between DNA and RNA polymerases and cellular concentration discrepancy between dNTPs and rNTPs present pharmacological and mechanistic considerations for therapeutic discovery.
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Affiliation(s)
- Si'Ana A Coggins
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Bijan Mahboubi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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14
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Abstract
Antiretroviral therapies efficiently block HIV-1 replication but need to be maintained for life. Moreover, chronic inflammation is a hallmark of HIV-1 infection that persists despite treatment. There is, therefore, an urgent need to better understand the mechanisms driving HIV-1 pathogenesis and to identify new targets for therapeutic intervention. In the past few years, the decisive role of cellular metabolism in the fate and activity of immune cells has been uncovered, as well as its impact on the outcome of infectious diseases. Emerging evidence suggests that immunometabolism has a key role in HIV-1 pathogenesis. The metabolic pathways of CD4+ T cells and macrophages determine their susceptibility to infection, the persistence of infected cells and the establishment of latency. Immunometabolism also shapes immune responses against HIV-1, and cell metabolic products are key drivers of inflammation during infection. In this Review, we summarize current knowledge of the links between HIV-1 infection and immunometabolism, and we discuss the potential opportunities and challenges for therapeutic interventions.
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15
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Benayas B, Sastre I, López-Martín S, Oo A, Kim B, Bullido MJ, Aldudo J, Yáñez-Mó M. Tetraspanin CD81 regulates HSV-1 infection. Med Microbiol Immunol 2020; 209:489-498. [PMID: 32500359 PMCID: PMC7271138 DOI: 10.1007/s00430-020-00684-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/27/2020] [Indexed: 02/08/2023]
Abstract
Different members of the tetraspanin superfamily have been described to regulate different virus infectious cycles at several stages: viral entry, viral replication or virion exit or infectivity. In addition, tetraspanin CD81 regulates HIV reverse transcription through its association with the dNTP hydrolase SAMHD1. Here we aimed at analysing the role of CD81 in Herpes simplex virus 1 infectivity using a neuroblastoma cell model. For this purpose, we generated a CD81 KO cell line using the CRISPR/Cas9 technology. Despite being CD81 a plasma membrane protein, CD81 KO cells showed no defects in viral entry nor in the expression of early protein markers. In contrast, glycoprotein B and C, which require viral DNA replication for their expression, were significantly reduced in CD81 KO infected cells. Indeed, HSV-1 DNA replication and the formation of new infectious particles were severely compromised in CD81 KO cells. We could not detect significant changes in SAMHD1 total expression levels, but a relocalization into endosomal structures was observed in CD81 KO cells. In summary, CD81 KO cells showed impaired viral DNA replication and produced greatly diminished viral titers.
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Affiliation(s)
- Beatriz Benayas
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), 28006, Madrid, Spain
| | - Isabel Sastre
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain
- Centro de Investigacion Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Soraya López-Martín
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), 28006, Madrid, Spain
| | - Adrian Oo
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Drug Discovery, Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Maria J Bullido
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain
- Centro de Investigacion Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Instituto de Investigación Sanitaria "Hospital la Paz" (IdIPaz), Madrid, Spain
| | - Jesús Aldudo
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain.
- Centro de Investigacion Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
- Instituto de Investigación Sanitaria "Hospital la Paz" (IdIPaz), Madrid, Spain.
| | - María Yáñez-Mó
- Centro de Biología Molecular, "Severo Ochoa" (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049, Madrid, Spain.
- Centro de Biología Molecular Severo Ochoa, Instituto de Investigación Sanitaria La Princesa (IIS-IP), 28006, Madrid, Spain.
- Departamento de Bioquímica y Biología Molecular, UAM, Centro de Biología Molecular Severo Ochoa, Lab 412, C/Nicolás Cabrera, 1, 28049, Madrid, Spain.
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16
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Meshesha M, Esadze A, Cui J, Churgulia N, Sahu SK, Stivers JT. Deficient uracil base excision repair leads to persistent dUMP in HIV proviruses during infection of monocytes and macrophages. PLoS One 2020; 15:e0235012. [PMID: 32663205 PMCID: PMC7360050 DOI: 10.1371/journal.pone.0235012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/05/2020] [Indexed: 11/19/2022] Open
Abstract
Non-dividing cells of the myeloid lineage such as monocytes and macrophages are target cells of HIV that have low dNTP pool concentrations and elevated levels of dUTP, which leads to frequent incorporation of dUMP opposite to A during reverse transcription ("uracilation"). One factor determining the fate of dUMP in proviral DNA is the host cell uracil base excision repair (UBER) system. Here we explore the relative UBER capacity of monocytes (MC) and monocyte-derived macrophages (MDM) and the fate of integrated uracilated viruses in both cell types to understand the implications of viral dUMP on HIV diversification and infectivity. We find that the kinetics for MC infection is compatible with their lifetime in vivo and their near absence of hUNG2 activity is consistent with the retention of viral dUMP at high levels at least until differentiation into macrophages, where UBER becomes possible. Overexpression of human uracil DNA glycosylase in MDM prior to infection resulted in rapid removal of dUMP from HIV cDNA and near complete depletion of dUMP-containing viral copies. This finding establishes that the low hUNG2 expression level in these cells limits UBER but that hUNG2 is restrictive against uracilated viruses. In contrast, overexpression of hUNG2 after viral integration did not accelerate the excision of uracils, suggesting that they may poorly accessible in the context of chromatin. We found that viral DNA molecules with incorporated dUMP contained unique (+) strand transversion mutations that were not observed when dUMP was absent (G→T, T→A, T→G, A→C). These observations and other considerations suggest that dUMP introduces errors predominantly during (-) strand synthesis when the template is RNA. Overall, the likelihood of producing a functional virus from in vitro infection of MC is about 50-fold and 300-fold reduced as compared to MDM and activated T cells. The results implicate viral dUMP incorporation in MC and MDM as a potential viral diversification and restriction pathway during human HIV infection.
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Affiliation(s)
- Mesfin Meshesha
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Alexandre Esadze
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Junru Cui
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Natela Churgulia
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Sushil Kumar Sahu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - James T. Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
- * E-mail:
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17
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Zhang Z, Zheng L, Yu Y, Wu J, Yang F, Xu Y, Guo Q, Wu X, Cao S, Cao L, Song X. Involvement of SAMHD1 in dNTP homeostasis and the maintenance of genomic integrity and oncotherapy (Review). Int J Oncol 2020; 56:879-888. [PMID: 32319570 DOI: 10.3892/ijo.2020.4988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/07/2020] [Indexed: 11/06/2022] Open
Abstract
Sterile alpha motif and histidine/aspartic acid domain‑containing protein 1 (SAMHD1), the only deoxynucleotide triphosphate (dNTP) hydrolase in eukaryotes, plays a crucial role in regulating the dynamic balance and ratio of cellular dNTP pools. Furthermore, SAMHD1 has been reported to be involved in the pathological process of several diseases. Homozygous SAMHD1 mutations have been identified in immune system disorders, such as autoimmune disease Aicardi‑Goutières syndrome (AGS), whose primary pathogenesis is associated with the abnormal accumulation and disproportion of dNTPs. SAMHD1 is also considered to be an intrinsic virus‑restriction factor by suppressing the viral infection process, including reverse transcription, replication, packaging and transmission. In addition, SAMHD1 has been shown to promote genome integrity during homologous recombination following DNA damage, thus being considered a promising candidate for oncotherapy applications. The present review summarizes the molecular mechanisms of SAMHD1 regarding the regulation of dNTP homeostasis and DNA damage response. Additionally, its potential effects on tumorigenesis and oncotherapy are reported.
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Affiliation(s)
- Zhou Zhang
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Lixia Zheng
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yang Yu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Jinying Wu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Fan Yang
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yingxi Xu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Qiqiang Guo
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Xuan Wu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Sunrun Cao
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Liu Cao
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Xiaoyu Song
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
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18
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Metabolomic Analysis of Influenza A Virus A/WSN/1933 (H1N1) Infected A549 Cells during First Cycle of Viral Replication. Viruses 2019; 11:v11111007. [PMID: 31683654 PMCID: PMC6893833 DOI: 10.3390/v11111007] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022] Open
Abstract
Influenza A virus (IAV) has developed strategies to utilize host metabolites which, after identification and isolation, can be used to discover the value of immunometabolism. During this study, to mimic the metabolic processes of influenza virus infection in human cells, we infect A549 cells with H1N1 (WSN) influenza virus and explore the metabolites with altered levels during the first cycle of influenza virus infection using ultra-high-pressure liquid chromatography-quadrupole time-of-flight mass spectrometer (UHPLC-Q-TOF MS) technology. We annotate the metabolites using MetaboAnalyst and the Kyoto Encyclopedia of Genes and Genomes pathway analyses, which reveal that IAV regulates the abundance of the metabolic products of host cells during early infection to provide the energy and metabolites required to efficiently complete its own life cycle. These metabolites are correlated with the tricarboxylic acid (TCA) cycle and mainly are involved in purine, lipid, and glutathione metabolisms. Concurrently, the metabolites interact with signal receptors in A549 cells to participate in cellular energy metabolism signaling pathways. Metabonomic analyses have revealed that, in the first cycle, the virus not only hijacks cell metabolism for its own replication, but also affects innate immunity, indicating a need for further study of the complex relationship between IAV and host cells.
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19
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Coggins SA, Holler JM, Kimata JT, Kim DH, Schinazi RF, Kim B. Efficient pre-catalytic conformational change of reverse transcriptases from SAMHD1 non-counteracting primate lentiviruses during dNTP incorporation. Virology 2019; 537:36-44. [PMID: 31442614 DOI: 10.1016/j.virol.2019.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/10/2019] [Accepted: 08/12/2019] [Indexed: 10/26/2022]
Abstract
Unlike HIV-1, HIV-2 and some SIV strains replicate at high dNTP concentrations even in macrophages due to their accessory proteins, Vpx or Vpr, that target SAMHD1 dNTPase for proteasomal degradation. We previously reported that HIV-1 reverse transcriptase (RT) efficiently synthesizes DNA even at low dNTP concentrations because HIV-1 RT displays faster pre-steady state kpol values than SAMHD1 counteracting lentiviral RTs. Here, since the kpol step consists of two sequential sub-steps post dNTP binding, conformational change and chemistry, we investigated which of the two sub-steps RTs from SAMHD1 non-counteracting viruses accelerate in order to complete reverse transcription in the limited dNTP pools found in macrophages. Our study demonstrates that RTs of SAMHD1 non-counteracting lentiviruses have a faster conformational change rate during dNTP incorporation, supporting that these lentiviruses may have evolved to harbor RTs that can efficiently execute the conformational change step in order to circumvent SAMHD1 restriction and dNTP depletion in macrophages.
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Affiliation(s)
- Si'Ana A Coggins
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Jessica M Holler
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Jason T Kimata
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, 77030, Texas, USA
| | - Dong-Hyun Kim
- College of Pharmacy, Kyung Hee University, Seoul, 04427, South Korea
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA; College of Pharmacy, Kyung Hee University, Seoul, 04427, South Korea; Children's Healthcare of Atlanta, Atlanta, 30322, USA.
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20
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Patra KK, Bhattacharya A, Bhattacharya S. Molecular dynamics investigation of a redox switch in the anti-HIV protein SAMHD1. Proteins 2019; 87:748-759. [PMID: 31017331 DOI: 10.1002/prot.25701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 12/17/2022]
Abstract
HIV-1 is restricted in macrophages and certain quiescent myeloid cells due to a "Scorched Earth" dNTP starvation strategy attributed to the sterile alpha motif and HD domain protein-SAMHD1. Active SAMHD1 tetramers are assembled by GTP-Mg+2-dNTP cross bridges and cleave the triphosphate groups of dNTPs at a K m of ~10 μM, which is consistent with dNTP concentrations in cycling cells, but far higher than the equivalent concentration in quiescent cells. Given the substantial disparity between the dNTP concentrations required to activate SAMHD1 tetramers (~10 μM) and the dNTP concentrations in noncycling cells (~10 nM), the possibility of alternate enzymatically active forms of SAMHD1, including monomers remains open. In particular, the possibility of redox regulation of such monomers is also an open question. There have been experimental studies on the regulation of SAMHD1 by Glutathione driven redox reactions recently. Therefore, in this work, we have performed all-atom molecular dynamics simulations to study the dynamics of monomeric SAMHD1 constructs in the context of the three redox-susceptible Cysteine residues and compared them to monomers assembled within a tetramer. Our results indicate that assembly into a tetramer causes ordering of the catalytic core and increased solvent accessibility of the Catalytic Site. We have also found that glutathionylation of surface exposed C522 causes long range allosteric disruptions extending into the protein core. Finally, we see evidence suggesting a transient interaction between C522 and C341. Such a disulfide linkage has been hypothesized by experimental models, but has never been observed in crystal structures before.
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Affiliation(s)
- Kajwal Kumar Patra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Akash Bhattacharya
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Swati Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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21
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Valle-Casuso JC, Angin M, Volant S, Passaes C, Monceaux V, Mikhailova A, Bourdic K, Avettand-Fenoel V, Boufassa F, Sitbon M, Lambotte O, Thoulouze MI, Müller-Trutwin M, Chomont N, Sáez-Cirión A. Cellular Metabolism Is a Major Determinant of HIV-1 Reservoir Seeding in CD4 + T Cells and Offers an Opportunity to Tackle Infection. Cell Metab 2019; 29:611-626.e5. [PMID: 30581119 DOI: 10.1016/j.cmet.2018.11.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 09/04/2018] [Accepted: 11/23/2018] [Indexed: 01/01/2023]
Abstract
HIV persists in long-lived infected cells that are not affected by antiretroviral treatment. These HIV reservoirs are mainly located in CD4+ T cells, but their distribution is variable in the different subsets. Susceptibility to HIV-1 increases with CD4+ T cell differentiation. We evaluated whether the metabolic programming that supports the differentiation and function of CD4+ T cells affected their susceptibility to HIV-1. We found that differences in HIV-1 susceptibility between naive and more differentiated subsets were associated with the metabolic activity of the cells. Indeed, HIV-1 selectively infected CD4+ T cells with high oxidative phosphorylation and glycolysis, independent of their activation phenotype. Moreover, partial inhibition of glycolysis (1) impaired HIV-1 infection in vitro in all CD4+ T cell subsets, (2) decreased the viability of preinfected cells, and (3) precluded HIV-1 amplification in cells from HIV-infected individuals. Our results elucidate the link between cell metabolism and HIV-1 infection and identify a vulnerability in tackling HIV reservoirs.
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Affiliation(s)
- José Carlos Valle-Casuso
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Mathieu Angin
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Stevenn Volant
- Institut Pasteur, Hub Bioinformatique et Biostatistique - C3BI, USR 3756 IP CNRS, Paris, France
| | - Caroline Passaes
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Valérie Monceaux
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Anastassia Mikhailova
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Katia Bourdic
- Assistance Publique Hôpitaux de Paris, Hôpital Bicêtre, Service de Médecine Interne et Immunologie Clinique, 94275 Le Kremlin-Bicêtre, France
| | - Véronique Avettand-Fenoel
- Université Paris Descartes, Sorbonne Paris Cité, 7327 Paris, France; Assistance Publique Hôpitaux de Paris, Laboratoire de Virologie, CHU Necker-Enfants Malades, Paris, France
| | - Faroudy Boufassa
- INSERM U1018, Centre de Recherche en Epidémiologie et Santé des Populations, Université Paris Sud, Le Kremlin-Bicêtre, France
| | - Marc Sitbon
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Olivier Lambotte
- Assistance Publique Hôpitaux de Paris, Hôpital Bicêtre, Service de Médecine Interne et Immunologie Clinique, 94275 Le Kremlin-Bicêtre, France; CEA, Université Paris Sud, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department/IBFJ, Fontenay-aux-Roses, France
| | | | - Michaela Müller-Trutwin
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal H2X 0A9, Canada
| | - Asier Sáez-Cirión
- Institut Pasteur, Unité HIV Inflammation et Persistance, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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22
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Plitnik T, Sharkey ME, Mahboubi B, Kim B, Stevenson M. Incomplete Suppression of HIV-1 by SAMHD1 Permits Efficient Macrophage Infection. Pathog Immun 2018; 3:197-223. [PMID: 30656243 PMCID: PMC6333473 DOI: 10.20411/pai.v3i2.263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Sterile alpha motif and histidine/aspartic acid domain-containing protein (SAMHD1) is a dNTP triphosphorylase that reduces cellular dNTP levels in non-dividing cells, such as macrophages. Since dNTPs are required for reverse transcription, HIV-2 and most SIVs encode a Vpx protein that promotes proteasomal degradation of SAMHD1. It is unclear how HIV-1, which does not appear to harbor a SAMHD1 escape mechanism, is able to infect macrophages in the face of SAMHD1 restriction. Methods: To assess whether HIV-1 had a mechanism to negate SAMHD1 activity, we compared SAMHD1 and dNTP levels in macrophages infected by HIV-1 and SIV. We examined whether macrophages infected by HIV-1 still harbored antiviral levels of SAMHD1 by assessing their susceptibility to superinfection by vpx-deleted SIV. Finally, to assess whether HIV-1 reverse transcriptase (RT) has adapted to a low dNTP environment, we evaluated SAMHD1 sensitivity of chimeric HIV-1 and SIV variants in which the RT regions were functionally exchanged. Results: Here, we demonstrate that HIV-1 efficiently infects macrophages without modulating SAMHD1 activity or cellular dNTP levels, and that macrophages permissive to HIV-1 infection remained refractory to superinfection by vpx-deleted SIV. Furthermore, through the use of chimeric HIV/SIV, we demonstrate that the differential sensitivity of HIV-1 and SIV to SAMHD1 restriction is not dictated by RT. Conclusions: Our study reveals fundamental differences between HIV-1 and SIV in the strategy used to evade restriction by SAMHD1 and suggests a degree of resistance of HIV-1 to the antiviral environment created by SAMHD1. Understanding how these cellular restrictions antagonize viral replication will be important for the design of novel antiviral strategies.
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Affiliation(s)
- Timothy Plitnik
- Department of Microbiology & Immunology; Miller School of Medicine, University of Miami; Miami, Florida
| | - Mark E Sharkey
- Department of Medicine; Miller School of Medicine, University of Miami; Miami, Florida
| | - Bijan Mahboubi
- Department of Pediatrics, Emory University; Atlanta, Georgia.,Center for Drug Discovery, Children's Healthcare of Atlanta; Atlanta, Georgia
| | - Baek Kim
- Department of Pediatrics, Emory University; Atlanta, Georgia.,Center for Drug Discovery, Children's Healthcare of Atlanta; Atlanta, Georgia.,Department of Pharmacy, Kyung-Hee University; Seoul; South Korea
| | - Mario Stevenson
- Department of Microbiology & Immunology; Miller School of Medicine, University of Miami; Miami, Florida.,Department of Medicine; Miller School of Medicine, University of Miami; Miami, Florida
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23
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Bejarano DA, Puertas MC, Börner K, Martinez-Picado J, Müller B, Kräusslich HG. Detailed Characterization of Early HIV-1 Replication Dynamics in Primary Human Macrophages. Viruses 2018; 10:v10110620. [PMID: 30423802 PMCID: PMC6266216 DOI: 10.3390/v10110620] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 02/04/2023] Open
Abstract
Macrophages are natural target cells of human immunodeficiency virus type 1 (HIV-1). Viral replication appears to be delayed in these cells compared to lymphocytes; however, little is known about the kinetics of early post-entry events. Time-of-addition experiments using several HIV-1 inhibitors and the detection of reverse transcriptase (RT) products with droplet digital PCR (ddPCR) revealed that early replication was delayed in primary human monocyte-derived macrophages of several donors and peaked late after infection. Direct imaging of reverse-transcription and pre-integration complexes (RTC/PIC) by click-labeling of newly synthesized DNA further confirmed our findings and showed a concomitant shift to the nuclear stage over time. Altering the entry pathway enhanced infectivity but did not affect kinetics of viral replication. The addition of viral protein X (Vpx) enhanced productive infection and accelerated completion of reverse transcription and nuclear entry. We propose that sterile alpha motif (SAM) and histidine/aspartate (HD) domain-containing protein 1 (SAMHD1) activity lowering deoxyribonucleotide triphosphate (dNTP) pools is the principal factor delaying early HIV-1 replication in macrophages.
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Affiliation(s)
- David Alejandro Bejarano
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany.
| | - Maria C Puertas
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain.
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany.
- German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany.
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain.
- Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500 Vic, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany.
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany.
- German Center for Infection Research, Partner Site Heidelberg, 69120 Heidelberg, Germany.
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24
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USP18 (UBP43) Abrogates p21-Mediated Inhibition of HIV-1. J Virol 2018; 92:JVI.00592-18. [PMID: 30068654 DOI: 10.1128/jvi.00592-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/25/2018] [Indexed: 12/17/2022] Open
Abstract
The host intrinsic innate immune system drives antiviral defenses and viral restriction, which includes the production of soluble factors, such as type I and III interferon (IFN), and activation of restriction factors, including SAMHD1, a deoxynucleoside triphosphohydrolase. Interferon-stimulated gene 15 (ISG15)-specific ubiquitin-like protease 43 (USP18) abrogates IFN signaling pathways. The cyclin-dependent kinase inhibitor p21 (CIP1/WAF1), which is involved in the differentiation and maturation of monocytes, inhibits human immunodeficiency virus type 1 (HIV-1) in macrophages and dendritic cells. p21 inhibition of HIV-1 replication is thought to occur at the reverse transcription step, likely by suppressing cellular deoxynucleoside triphosphate (dNTP) biosynthesis and increasing the amount of antivirally active form of SAMHD1. SAMHD1 strongly inhibits HIV-1 replication in myeloid and resting CD4+ T cells. Here, we studied how USP18 influences HIV-1 replication in human myeloid THP-1 cells. We found that USP18 has the novel ability to inhibit the antiviral function of p21 in differentiated THP-1 cells. USP18 enhanced reverse transcription of HIV-1 by downregulating p21 expression and upregulating intracellular dNTP levels. p21 downregulation by USP18 was associated with the active form of SAMHD1, phosphorylated at T592. USP18 formed a complex with the E3 ubiquitin ligase recognition factor SKP2 (S-phase kinase associated protein 2) and SAMHD1. CRISPR-Cas9 knockout of USP18 increased p21 protein expression and blocked HIV-1 replication. Overall, we propose USP18 as a regulator of p21 antiviral function in differentiated myeloid THP-1 cells.IMPORTANCE Macrophages and dendritic cells are usually the first point of contact with pathogens, including lentiviruses. Host restriction factors, including SAMHD1, mediate the innate immune response against these viruses. However, HIV-1 has evolved to circumvent the innate immune response and establishes disseminated infection. The cyclin-dependent kinase inhibitor p21, which is involved in differentiation and maturation of monocytes, blocks HIV-1 replication at the reverse transcription step. p21 is thought to suppress key enzymes involved in dNTP biosynthesis and activates SAMHD1 antiviral function. We report here that the human USP18 protein is a novel factor potentially contributing to HIV replication by blocking the antiviral function of p21 in differentiated human myeloid cells. USP18 downregulates p21 protein expression, which correlates with upregulated intracellular dNTP levels and the antiviral inactive form of SAMHD1. Depletion of USP18 stabilizes p21 protein expression, which correlates with dephosphorylated SAMHD1 and a block to HIV-1 replication.
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25
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Goyvaerts C, Breckpot K. The Journey of in vivo Virus Engineered Dendritic Cells From Bench to Bedside: A Bumpy Road. Front Immunol 2018; 9:2052. [PMID: 30254636 PMCID: PMC6141723 DOI: 10.3389/fimmu.2018.02052] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Dendritic cells (DCs) are recognized as highly potent antigen-presenting cells that are able to stimulate cytotoxic T lymphocyte (CTL) responses with antitumor activity. Consequently, DCs have been explored as cellular vaccines in cancer immunotherapy. To that end, DCs are modified with tumor antigens to enable presentation of antigen-derived peptides to CTLs. In this review we discuss the use of viral vectors for in situ modification of DCs, focusing on their clinical applications as anticancer vaccines. Among the viral vectors discussed are those derived from viruses belonging to the families of the Poxviridae, Adenoviridae, Retroviridae, Togaviridae, Paramyxoviridae, and Rhabdoviridae. We will further shed light on how the combination of viral vector-based vaccination with T-cell supporting strategies will bring this strategy to the next level.
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26
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Kueck T, Cassella E, Holler J, Kim B, Bieniasz PD. The aryl hydrocarbon receptor and interferon gamma generate antiviral states via transcriptional repression. eLife 2018; 7:38867. [PMID: 30132758 PMCID: PMC6120754 DOI: 10.7554/elife.38867] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 08/21/2018] [Indexed: 12/13/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor whose activation induces the expression of numerous genes, with many effects on cells. However, AhR activation is not known to affect the replication of viruses. We show that AhR activation in macrophages causes a block to HIV-1 and HSV-1 replication. We find that AhR activation transcriptionally represses cyclin-dependent kinase (CDK)1/2 and their associated cyclins, thereby reducing SAMHD1 phosphorylation, cellular dNTP levels and both HIV-1 and HSV-1 replication. Remarkably, a different antiviral stimulus, interferon gamma (IFN-γ), that induces a largely non-overlapping set of genes, also transcriptionally represses CDK1, CDK2 and their associated cyclins, resulting in similar dNTP depletion and antiviral effects. Concordantly, the SIV Vpx protein provides complete and partial resistance to the antiviral effects of AhR and IFN-γ, respectively. Thus, distinct antiviral signaling pathways converge on CDK/cyclin repression, causing inhibition of viral DNA synthesis and replication.
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Affiliation(s)
- Tonya Kueck
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Elena Cassella
- Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Jessica Holler
- Center for Drug Discovery, The Department of Pediatrics, Emory University, Atlanta, United States
| | - Baek Kim
- Center for Drug Discovery, The Department of Pediatrics, Emory University, Atlanta, United States.,Department of Pharmacy, Kyung Hee University, Seoul, South Korea
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, The Rockefeller University, New York, United States
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27
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Lentiviral infection of proliferating brain macrophages in HIV and simian immunodeficiency virus encephalitis despite sterile alpha motif and histidine-aspartate domain-containing protein 1 expression. AIDS 2018; 32:965-974. [PMID: 29698322 PMCID: PMC5943146 DOI: 10.1097/qad.0000000000001793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Objective: HIV-1 infection of the brain and related cognitive impairment remain prevalent in HIV-1-infected individuals despite combination antiretroviral therapy. Sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1) is a newly identified host restriction factor that blocks the replication of HIV-1 and other retroviruses in myeloid cells. Cell cycle-regulated phosphorylation at residue Thr592 and viral protein X (Vpx)-mediated degradation of SAMHD1 have been shown to bypass SAMHD1 restriction in vitro. Herein, we investigated expression and phosphorylation of SAMHD1 in vivo in relation to macrophage infection and proliferation during the neuropathogenesis of HIV-1 and simian immunodeficiency virus (SIV) encephalitis. Methods: Using brain and other tissues from uninfected and SIV-infected macaques with or without encephalitis, we performed immunohistochemistry, multilabel fluorescence microscopy and western blot to examine the expression, localization and phosphorylation of SAMHD1. Results: The number of SAMHD1+ nuclei increased in encephalitic brains despite the presence of Vpx. Many of these cells were perivascular macrophages, although subsets of SAMHD1+ microglia and endothelial cells were also observed. The SAMHD1+ macrophages were shown to be both infected and proliferating. Moreover, the presence of cycling SAMHD1+ brain macrophages was confirmed in the tissue of HIV-1-infected patients with encephalitis. Finally, western blot analysis of brain-protein extracts from SIV-infected macaques showed that SAMHD1 protein exists in the brain mainly as an inactive Thr592-phosphorylated form. Conclusion: The ability of SAMHD1 to act as a restriction factor for SIV/HIV in the brain is likely bypassed in proliferating brain macrophages through the phosphorylation-mediated inactivation, not Vpx-mediated degradation of SAMHD1.
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Mauney CH, Hollis T. SAMHD1: Recurring roles in cell cycle, viral restriction, cancer, and innate immunity. Autoimmunity 2018; 51:96-110. [PMID: 29583030 PMCID: PMC6117824 DOI: 10.1080/08916934.2018.1454912] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/16/2018] [Indexed: 12/24/2022]
Abstract
Sterile alpha motif and histidine-aspartic acid domain-containing protein 1 (SAMHD1) is a deoxynucleotide triphosphate (dNTP) hydrolase that plays an important role in the homeostatic balance of cellular dNTPs. Its emerging role as an effector of innate immunity is affirmed by mutations in the SAMHD1 gene that cause the severe autoimmune disease, Aicardi-Goutieres syndrome (AGS) and that are linked to cancer. Additionally, SAMHD1 functions as a restriction factor for retroviruses, such as HIV. Here, we review the current biochemical and biological properties of the enzyme including its structure, activity, and regulation by post-translational modifications in the context of its cellular function. We outline open questions regarding the biology of SAMHD1 whose answers will be important for understanding its function as a regulator of cell cycle progression, genomic integrity, and in autoimmunity.
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Affiliation(s)
- Christopher H Mauney
- a Department of Biochemistry , Center for Structural Biology, Wake Forest School of Medicine , Winston Salem , NC , USA
| | - Thomas Hollis
- a Department of Biochemistry , Center for Structural Biology, Wake Forest School of Medicine , Winston Salem , NC , USA
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29
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Saragani Y, Hizi A, Rahav G, Zaouch S, Bakhanashvili M. Cytoplasmic p53 contributes to the removal of uracils misincorporated by HIV-1 reverse transcriptase. Biochem Biophys Res Commun 2018; 497:804-810. [PMID: 29470985 DOI: 10.1016/j.bbrc.2018.02.159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 02/18/2018] [Indexed: 01/15/2023]
Abstract
HIV-1 reverse transcriptase (RT) in the cytoplasm of HIV-infected cells efficiently inserts the non-canonical dUTP into the proviral DNA, and extends the dU-terminated DNA. The misincorporation of dUTP leads to mutagenesis, and uracils can down-regulate viral gene expression. However, uracilation might also protect HIV DNA from auto-integration in the cytoplasm. Tumor suppressor p53 protein, exhibiting inherent 3'→5' exonuclease activity, provides a potential host-derived repair mechanism during HIV reverse transcription for the misincorporation of various wrong nucleotides, leading to both base-base mismatches and incorporated non-canonical ribonucleotides. Since the presence of proofreading activity is essential for DNA synthesis accuracy, we elucidated the potential involvement of cytoplasmic p53 in the U-editing activities during insertion of dUTP into DNA by recombinant HIV-1 RT (using isogenic p53-proficient and -deficient HCT116 cells). The biochemical data show that p53 in cytoplasm can participate through the intermolecular pathway in a dU-damage-associated repair mechanism by its ability to remove preformed 3'-terminal dUs, thus preventing further extension of 3' dU-terminated primer during DNA synthesis by HIV-1 RT. The specific depletion of p53 from cytoplasmic lysates of repair-proficient p53-harboring cells reduced this negative effect. Accordingly, the increased abundance of p53 in nutlin-treated cells correlates with enhanced error-correction functions, namely, removal of incorporated uracil. The data substantiate the significance of p53 as a potential proofreader for removal of non-canonical dUTP from HIV DNA, thus preventing the consequences of dUTP misincorporation in cell-type specific infectivity of HIV.
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Affiliation(s)
- Yossi Saragani
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel
| | - Amnon Hizi
- Dep. Cell and Developmental Biology, Sackler School of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel
| | - Galia Rahav
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel
| | - Sara Zaouch
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel
| | - Mary Bakhanashvili
- Infectious Diseases Unit, Sheba Medical Center, Tel-Hashomer 5265601, Israel.
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30
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Dezzutti CS, Park SY, Marks KM, Lawlor SE, Russo JR, Macio I, Chappell CA, Bunge KE. Heterogeneity of HIV-1 Replication in Ectocervical and Vaginal Tissue Ex Vivo. AIDS Res Hum Retroviruses 2018; 34:185-192. [PMID: 28982249 DOI: 10.1089/aid.2017.0107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In clinical trials evaluating HIV-1 prevention products, ex vivo exposure of mucosal tissue to HIV-1 is performed to inform drug levels needed to suppress viral infection. Understanding assay and participant variables that influence HIV-1 replication will help with assay implementation. Demographic and behavioral data were obtained from 61 healthy women aged 21-45. Paired cervical tissue (CT) and vaginal tissue (VT) biopsies were collected and treated with HIV-1BaL or HIV-1JR-CSF, washed, and cultured. On days 3, 7, and/or 11, culture supernatant was collected, and viral replication was monitored by p24 ELISA. Tissue was extracted at study end, and HIV-1 relative RNA copies were determined by polymerase chain reaction. Cumulative p24 and RNA were log-transformed and analyzed using a linear mixed model, t-test, and an intraclass correlation coefficient (ICC). HIV replication was similar between CT and VT for each virus, but HIV-1BaL had 1.5 log10 and 0.9 log10 higher levels of p24 than HIV-1JR-CSF in CT and VT, respectively (p < .001), which correlated with HIV-1 relative RNA copies. Cumulative p24 and RNA copies in both tissues demonstrated low intraperson correlation for both viruses (ICC ≤0.513 HIV-1BaL; ICC ≤0.419 HIV-1JR-CSF). Enrollment into previous clinical studies in which genital biopsies were collected modestly decreased the HIV-1BaL cumulative p24 for CT, but not for VT. To improve the ex vivo challenge assay, viruses should be evaluated for replication in mucosal tissue before study implementation, baseline mucosal tissue is not needed if a placebo/no treatment group is included within the clinical trial, and previous biopsy sites should be avoided.
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Affiliation(s)
- Charlene S. Dezzutti
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
| | - Seo Young Park
- Department of Medicine Bio Statisics, and Clinical and Translational Science, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | - Julie R. Russo
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
| | - Ingrid Macio
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Catherine A. Chappell
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
| | - Katherine E. Bunge
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania
- Magee-Womens Research Institute, Pittsburgh, Pennsylvania
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31
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Soper A, Kimura I, Nagaoka S, Konno Y, Yamamoto K, Koyanagi Y, Sato K. Type I Interferon Responses by HIV-1 Infection: Association with Disease Progression and Control. Front Immunol 2018; 8:1823. [PMID: 29379496 PMCID: PMC5775519 DOI: 10.3389/fimmu.2017.01823] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/04/2017] [Indexed: 01/08/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is the causative agent of acquired immunodeficiency syndrome and its infection leads to the onset of several disorders such as the depletion of peripheral CD4+ T cells and immune activation. HIV-1 is recognized by innate immune sensors that then trigger the production of type I interferons (IFN-Is). IFN-Is are well-known cytokines eliciting broad anti-viral effects by inducing the expression of anti-viral genes called interferon-stimulated genes (ISGs). Extensive in vitro studies using cell culture systems have elucidated that certain ISGs such as APOBEC3G, tetherin, SAM domain and HD domain-containing protein 1, MX dynamin-like GTPase 2, guanylate-binding protein 5, and schlafen 11 exert robust anti-HIV-1 activity, suggesting that IFN-I responses triggered by HIV-1 infection are detrimental for viral replication and spread. However, recent studies using animal models have demonstrated that at both the acute and chronic phase of infection, the role of IFN-Is produced by HIV or SIV infection in viral replication, spread, and pathogenesis, may not be that straightforward. In this review, we describe the pluses and minuses of HIV-1 infection stimulated IFN-I responses on viral replication and pathogenesis, and further discuss the possibility for therapeutic approaches.
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Affiliation(s)
- Andrew Soper
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Izumi Kimura
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Shumpei Nagaoka
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yoriyuki Konno
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Keisuke Yamamoto
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kei Sato
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, Japan
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32
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Malik O, Khamis H, Rudnizky S, Marx A, Kaplan A. Pausing kinetics dominates strand-displacement polymerization by reverse transcriptase. Nucleic Acids Res 2017; 45:10190-10205. [PMID: 28973474 PMCID: PMC5737391 DOI: 10.1093/nar/gkx720] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/08/2017] [Indexed: 12/20/2022] Open
Abstract
Reverse transcriptase (RT) catalyzes the conversion of the viral RNA into an integration-competent double-stranded DNA, with a variety of enzymatic activities that include the ability to displace a non-template strand concomitantly with polymerization. Here, using high-resolution optical tweezers to follow the activity of the murine leukemia Virus RT, we show that strand-displacement polymerization is frequently interrupted. Abundant pauses are modulated by the strength of the DNA duplex ∼8 bp ahead, indicating the existence of uncharacterized RT/DNA interactions, and correspond to backtracking of the enzyme, whose recovery is also modulated by the duplex strength. Dissociation and reinitiation events, which induce long periods of inactivity and are likely the rate-limiting step in the synthesis of the genome in vivo, are modulated by the template structure and the viral nucleocapsid protein. Our results emphasize the potential regulatory role of conserved structural motifs, and may provide useful information for the development of potent and specific inhibitors.
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Affiliation(s)
- Omri Malik
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Hadeel Khamis
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Faculty of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Sergei Rudnizky
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ailie Marx
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.,Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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33
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p21 Restricts HIV-1 in Monocyte-Derived Dendritic Cells through the Reduction of Deoxynucleoside Triphosphate Biosynthesis and Regulation of SAMHD1 Antiviral Activity. J Virol 2017; 91:JVI.01324-17. [PMID: 28931685 DOI: 10.1128/jvi.01324-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/15/2017] [Indexed: 02/07/2023] Open
Abstract
HIV-1 infection of noncycling cells, such as dendritic cells (DCs), is impaired due to limited availability of deoxynucleoside triphosphates (dNTPs), which are needed for HIV-1 reverse transcription. The levels of dNTPs are tightly regulated during the cell cycle and depend on the balance between dNTP biosynthesis and degradation. SAMHD1 potently blocks HIV-1 replication in DCs, although the underlying mechanism is still unclear. SAMHD1 has been reported to be able to degrade dNTPs and viral nucleic acids, which may both hamper HIV-1 reverse transcription. The relative contribution of these activities may differ in cycling and noncycling cells. Here, we show that inhibition of HIV-1 replication in monocyte-derived DCs (MDDCs) is associated with an increased expression of p21cip1/waf, a cell cycle regulator that is involved in the differentiation and maturation of DCs. Induction of p21 in MDDCs decreases the pool of dNTPs and increases the antiviral active isoform of SAMHD1. Although both processes are complementary in inhibiting HIV-1 replication, the antiviral activity of SAMHD1 in our primary cell model appears to be, at least partially, independent of its dNTPase activity. The reduction in the pool of dNTPs in MDDCs appears rather mostly due to a p21-mediated suppression of several enzymes involved in dNTP synthesis (i.e., RNR2, TYMS, and TK-1). These results are important to better understand the interplay between HIV-1 and DCs and may inform the design of new therapeutic approaches to decrease viral dissemination and improve immune responses against HIV-1.IMPORTANCE DCs play a key role in the induction of immune responses against HIV. However, HIV has evolved ways to exploit these cells, facilitating immune evasion and virus dissemination. We have found that the expression of p21, a cyclin-dependent kinase inhibitor involved in cell cycle regulation and monocyte differentiation and maturation, potentially can contribute to the inhibition of HIV-1 replication in monocyte-derived DCs through multiple mechanisms. p21 decreased the size of the intracellular dNTP pool. In parallel, p21 prevented SAMHD1 phosphorylation and promoted SAMHD1 dNTPase-independent antiviral activity. Thus, induction of p21 resulted in conditions that allowed the effective inhibition of HIV-1 replication through complementary mechanisms. Overall, p21 appears to be a key regulator of HIV infection in myeloid cells.
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34
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Antonucci JM, St Gelais C, Wu L. The Dynamic Interplay between HIV-1, SAMHD1, and the Innate Antiviral Response. Front Immunol 2017; 8:1541. [PMID: 29176984 PMCID: PMC5686096 DOI: 10.3389/fimmu.2017.01541] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 10/30/2017] [Indexed: 01/03/2023] Open
Abstract
The innate immune response constitutes the first cellular line of defense against initial HIV-1 infection. Immune cells sense invading virus and trigger signaling cascades that induce antiviral defenses to control or eliminate infection. Professional antigen-presenting cells located in mucosal tissues, including dendritic cells and macrophages, are critical for recognizing HIV-1 at the site of initial exposure. These cells are less permissive to HIV-1 infection compared to activated CD4+ T-cells, which is mainly due to host restriction factors that serve an immediate role in controlling the establishment or spread of viral infection. However, HIV-1 can exploit innate immune cells and their cellular factors to avoid detection and clearance by the host immune system. Sterile alpha motif and HD-domain containing protein 1 (SAMHD1) is the mammalian deoxynucleoside triphosphate triphosphohydrolase responsible for regulating intracellular dNTP pools and restricting the replication of HIV-1 in non-dividing myeloid cells and quiescent CD4+ T-cells. Here, we review and analyze the latest literature on the antiviral function of SAMHD1, including the mechanism of HIV-1 restriction and the ability of SAMHD1 to regulate the innate immune response to viral infection. We also provide an overview of the dynamic interplay between HIV-1, SAMHD1, and the cell-intrinsic antiviral response to elucidate how SAMHD1 modulates HIV-1 infection in non-dividing immune cells. A more complete understanding of SAMHD1’s role in the innate immune response to HIV-1 infection may help develop stratagems to enhance its antiviral effects and to more efficiently block HIV-1 replication and avoid the pathogenic result of viral infection.
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Affiliation(s)
- Jenna M Antonucci
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, United States
| | - Corine St Gelais
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, United States
| | - Li Wu
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, United States
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Potent Inhibition of HIV-1 Replication in Resting CD4 T Cells by Resveratrol and Pterostilbene. Antimicrob Agents Chemother 2017; 61:AAC.00408-17. [PMID: 28652233 DOI: 10.1128/aac.00408-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/20/2017] [Indexed: 12/12/2022] Open
Abstract
HIV-1 infection of resting CD4 T cells plays a crucial and numerically dominant role during virus transmission at mucosal sites and during subsequent acute replication and T cell depletion. Resveratrol and pterostilbene are plant stilbenoids associated with several health-promoting benefits. Resveratrol has been shown to inhibit the replication of several viruses, including herpes simplex viruses 1 and 2, papillomaviruses, severe acute respiratory syndrome virus, and influenza virus. Alone, resveratrol does not inhibit HIV-1 infection of activated T cells, but it does synergize with nucleoside reverse transcriptase inhibitors in these cells to inhibit reverse transcription. Here, we demonstrate that resveratrol and pterostilbene completely block HIV-1 infection at a low micromolar dose in resting CD4 T cells, primarily at the reverse transcription step. The anti-HIV effect was fully reversed by exogenous deoxynucleosides and Vpx, an HIV-1 and simian immunodeficiency virus protein that increases deoxynucleoside triphosphate (dNTP) levels. These findings are consistent with the reported ability of resveratrol to inhibit ribonucleotide reductase and to lower dNTP levels in cells. This study supports the potential use of resveratrol, pterostilbene, or related compounds as adjuvants in anti-HIV preexposure prophylaxis (PrEP) formulations.
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Ordonez P, Kunzelmann S, Groom HCT, Yap MW, Weising S, Meier C, Bishop KN, Taylor IA, Stoye JP. SAMHD1 enhances nucleoside-analogue efficacy against HIV-1 in myeloid cells. Sci Rep 2017; 7:42824. [PMID: 28220857 PMCID: PMC5318888 DOI: 10.1038/srep42824] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/16/2017] [Indexed: 11/17/2022] Open
Abstract
SAMHD1 is an intracellular enzyme that specifically degrades deoxynucleoside triphosphates into component nucleoside and inorganic triphosphate. In myeloid-derived dendritic cells and macrophages as well as resting T-cells, SAMHD1 blocks HIV-1 infection through this dNTP triphosphohydrolase activity by reducing the cellular dNTP pool to a level that cannot support productive reverse transcription. We now show that, in addition to this direct effect on virus replication, manipulating cellular SAMHD1 activity can significantly enhance or decrease the anti-HIV-1 efficacy of nucleotide analogue reverse transcription inhibitors presumably as a result of modulating dNTP pools that compete for recruitment by viral polymerases. Further, a variety of other nucleotide-based analogues, not normally considered antiretrovirals, such as the anti-herpes drugs Aciclovir and Ganciclovir and the anti-cancer drug Clofarabine are now revealed as potent anti-HIV-1 agents, under conditions of low dNTPs. This in turn suggests novel uses for nucleotide analogues to inhibit HIV-1 in differentiated cells low in dNTPs.
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Affiliation(s)
- Paula Ordonez
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Harriet C. T. Groom
- Infection and Replication of Retroviruses Laboratory, The Francis Crick Institute, London, UK
| | - Melvyn W. Yap
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London, UK
| | - Simon Weising
- Organic Chemistry, Department of Chemistry, Faculty of Sciences, University of Hamburg, Germany
| | - Chris Meier
- Organic Chemistry, Department of Chemistry, Faculty of Sciences, University of Hamburg, Germany
| | - Kate N. Bishop
- Infection and Replication of Retroviruses Laboratory, The Francis Crick Institute, London, UK
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, London, UK
- Faculty of Medicine, Imperial College London, London, UK
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Removal of ribonucleotides by p53 protein incorporated during DNA synthesis by HIV-1 reverse transcriptase. AIDS 2017; 31:343-353. [PMID: 28081035 DOI: 10.1097/qad.0000000000001339] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVE(S) HIV-1 reverse transcriptase frequently incorporates ribonucleotides into the proviral DNA in macrophages, but not in lymphocytes. The enzyme exerts an efficient ribonucleotide-terminated primer extension capacity. Furthermore, ribonucleotide-editing repair is attenuated in macrophages. Tumor suppressor p53 protein, displaying an intrinsic 3'→5' exonuclease activity, was found to be involved in efficient proofreading of base-base mismatches produced during DNA synthesis. As the presence of proofreading activity is cardinal for the DNA synthesis accuracy, it was of interest to assess whether p53 can serve as a trans-acting proofreader for HIV-1 reverse transcriptase during ribonucleotide incorporation. DESIGN We investigated the potential involvement of cytoplasmic p53 in error correction during insertion of ribonucleotides into DNA by recombinant HIV-1 reverse transcriptase in a p53-proficient and deficient background. METHODS Primer extension reactions were carried out to elucidate the incorporation and removal of ribonucleotides. RESULTS The biochemical studies suggest that p53 is involved in a ribonucleotide damage-associated repair mechanism through its capacity to remove preformed 3'-terminal ribonucleotides, to decrease ribonucleotide incorporation and to prevent the 3'-ribo-terminated primer extension during ongoing DNA synthesis by HIV-1 reverse transcriptase. A positive correlation exists between the presence of endogenous p53 and decrease in stable incorporation of ribonucleotides into DNA with p53-harboring lysates of HCT116 cells. p53, by preferential removal of purine over pyrimidine ribonucleotides, may affect the ribonucleotide mutation spectra produced by HIV-1 reverse transcriptase. CONCLUSION The data implies that p53 can excise incorrect sugar in addition to base mispairs, thereby expanding the role of p53 in the repair of nucleic acids replication errors.
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Jang S, Zhou X, Ahn J. Substrate Specificity of SAMHD1 Triphosphohydrolase Activity Is Controlled by Deoxyribonucleoside Triphosphates and Phosphorylation at Thr592. Biochemistry 2016; 55:5635-5646. [PMID: 27588835 DOI: 10.1021/acs.biochem.6b00627] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The sterile alpha motif (SAM) and histidine-aspartate (HD) domain containing protein 1 (SAMHD1) constitute a triphosphohydrolase that converts deoxyribonucleoside triphosphates (dNTPs) into deoxyribonucleosides and triphosphates. SAMHD1 exists in multiple states. The monomer and apo- or GTP-bound dimer are catalytically inactive. Binding of dNTP at allosteric site 2 (AS2), adjacent to GTP-binding allosteric site 1 (AS1), induces formation of the tetramer, the catalytically active form. We have developed an enzyme kinetic assay, tailored to control specific dNTP binding at each site, allowing us to determine the kinetic binding parameters of individual dNTPs at both the AS2 and catalytic sites for all possible combinations of dNTP binding at both sites. Here, we show that the apparent Km values of dNTPs at AS2 vary in the order of dCTP < dGTP < dATP < dTTP. Interestingly, dCTP binding at AS2 significantly reduces the dCTP hydrolysis rate, which is restored to a rate comparable to that of other dNTPs upon dGTP, dATP, or dTTP binding at AS2. Strikingly, a phosphomimetic mutant, Thr592Asp SAMHD1 as well as phospho-Thr592, show a significantly altered substrate specificity, with the rate of dCTP hydrolysis being selectively reduced regardless of which dNTP binds at AS2. Furthermore, cyclin A2 binding at the C-terminus of SAMHD1 induces the disassembly of the SAMHD1 tetramer, suggesting an additional layer of SAMHD1 activity modulation by cyclin A2/CDK2 kinase. Together, our results reveal multiple allosteric mechanisms for controlling the rate of dNTP destruction by SAMHD1.
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Affiliation(s)
- Sunbok Jang
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Xiaohong Zhou
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
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Matheson NJ, Greenwood EJ, Lehner PJ. Manipulation of immunometabolism by HIV-accessories to the crime? Curr Opin Virol 2016; 19:65-70. [PMID: 27448768 DOI: 10.1016/j.coviro.2016.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 06/17/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
Abstract
Evolutionary pressure has produced an 'arms race' between cellular restriction factors (limiting viral replication) and viral proteins (overcoming host restriction). The host factors SAMHD1 and SLFN1 patrol metabolic bottlenecks required for HIV replication. Conversely, the HIV accessory proteins Vpx, Vpu and Nef manipulate cellular metabolism to enable viral replication. Recent work identifying Vpu-mediated downregulation of the alanine transporter SNAT1 and Nef-mediated downregulation of the serine carriers SERINC3/5 has uncovered the importance of HIV manipulation of the amino acid supply. Interference with CD4(+) T-cell amino acid metabolism suggests a novel paradigm of viral immunomodulation, and signposts fundamental aspects of lymphocyte biology.
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Affiliation(s)
- Nicholas J Matheson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.
| | - Edward Jd Greenwood
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Paul J Lehner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK.
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Kharytonchyk S, King SR, Ndongmo CB, Stilger KL, An W, Telesnitsky A. Resolution of Specific Nucleotide Mismatches by Wild-Type and AZT-Resistant Reverse Transcriptases during HIV-1 Replication. J Mol Biol 2016; 428:2275-2288. [PMID: 27075671 DOI: 10.1016/j.jmb.2016.04.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/16/2016] [Accepted: 04/04/2016] [Indexed: 12/14/2022]
Abstract
A key contributor to HIV-1 genetic variation is reverse transcriptase errors. Some mutations result because reverse transcriptase (RT) lacks 3' to 5' proofreading exonuclease and can extend mismatches. However, RT also excises terminal nucleotides to a limited extent, and this activity contributes to AZT resistance. Because HIV-1 mismatch resolution has been studied in vitro but only indirectly during replication, we developed a novel system to study mismatched base pair resolution during HIV-1 replication in cultured cells using vectors that force template switching at defined locations. These vectors generated mismatched reverse transcription intermediates, with proviral products diagnostic of mismatch resolution mechanisms. Outcomes for wild-type (WT) RT and an AZT-resistant (AZT(R)) RT containing a thymidine analog mutation set-D67N, K70R, D215F, and K219Q-were compared. AZT(R) RT did not excise terminal nucleotides more frequently than WT, and for the majority of tested mismatches, both WT and AZT(R) RTs extended mismatches in more than 90% of proviruses. However, striking enzyme-specific differences were observed for one mispair, with WT RT preferentially resolving dC-rC pairs either by excising the mismatched base or switching templates prematurely, while AZT(R) RT primarily misaligned the primer strand, causing deletions via dislocation mutagenesis. Overall, the results confirmed HIV-1 RT's high capacity for mismatch extension during virus replication and revealed dramatic differences in aberrant intermediate resolution repertoires between WT and AZT(R) RTs on one mismatched replication intermediate. Correlating mismatch extension frequencies observed here with reported viral mutation rates suggests a complex interplay of nucleotide discrimination and mismatch extension drives HIV-1 mutagenesis.
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Affiliation(s)
- Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Steven R King
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Clement B Ndongmo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Krista L Stilger
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Wenfeng An
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA.
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Daly MB, Roth ME, Bonnac L, Maldonado JO, Xie J, Clouser CL, Patterson SE, Kim B, Mansky LM. Dual anti-HIV mechanism of clofarabine. Retrovirology 2016; 13:20. [PMID: 27009333 PMCID: PMC4806454 DOI: 10.1186/s12977-016-0254-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HIV-1 replication kinetics inherently depends on the availability of cellular dNTPs for viral DNA synthesis. In activated CD4(+) T cells and other rapidly dividing cells, the concentrations of dNTPs are high and HIV-1 reverse transcription occurs in an efficient manner. In contrast, nondividing cells such as macrophages have lower dNTP pools, which restricts efficient reverse transcription. Clofarabine is an FDA approved ribonucleotide reductase inhibitor, which has shown potent antiretroviral activity in transformed cell lines. Here, we explore the potency, toxicity and mechanism of action of clofarabine in the human primary HIV-1 target cells: activated CD4(+) T cells and macrophages. RESULTS Clofarabine is a potent HIV-1 inhibitor in both activated CD4(+) T cells and macrophages. Due to its minimal toxicity in macrophages, clofarabine displays a selectivity index over 300 in this nondividing cell type. The anti-HIV-1 activity of clofarabine correlated with a significant decrease in both cellular dNTP levels and viral DNA synthesis. Additionally, we observed that clofarabine triphosphate was directly incorporated into DNA by HIV-1 reverse transcriptase and blocked processive DNA synthesis, particularly at the low dNTP levels found in macrophages. CONCLUSIONS Taken together, these data provide strong mechanistic evidence that clofarabine is a dual action inhibitor of HIV-1 replication that both limits dNTP substrates for viral DNA synthesis and directly inhibits the DNA polymerase activity of HIV-1 reverse transcriptase.
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Affiliation(s)
- Michele B Daly
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Megan E Roth
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA.,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Laurent Bonnac
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - José O Maldonado
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA.,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jiashu Xie
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Christine L Clouser
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Steven E Patterson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA. .,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA. .,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA. .,Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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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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Hollenbaugh JA, Montero C, Schinazi RF, Munger J, Kim B. Metabolic profiling during HIV-1 and HIV-2 infection of primary human monocyte-derived macrophages. Virology 2016; 491:106-14. [PMID: 26895248 DOI: 10.1016/j.virol.2016.01.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/26/2016] [Accepted: 01/29/2016] [Indexed: 12/14/2022]
Abstract
We evaluated cellular metabolism profiles of HIV-1 and HIV-2 infected primary human monocyte-derived macrophages (MDMs). First, HIV-2 GL-AN displays faster production kinetics and greater amounts of virus as compared to HIV-1s: YU-2, 89.6 and JR-CSF. Second, quantitative LC-MS/MS metabolomics analysis demonstrates very similar metabolic profiles in glycolysis and TCA cycle metabolic intermediates between HIV-1 and HIV-2 infected macrophages, with a few notable exceptions. The most striking metabolic change in MDMs infected with HIV-2 relative to HIV-1-infected MDMs was the increased levels of quinolinate, a metabolite in the tryptophan catabolism pathway that has been linked to HIV/AIDS pathogenesis. Third, both HIV-1 and HIV-2 infected MDMs showed elevated levels of ribose-5-phosphate, a key metabolic component in nucleotide biosynthesis. Finally, HIV-2 infected MDMs display increased dNTP concentrations as predicted by Vpx-mediated SAMHD1 degradation. Collectively, these data show differential metabolic changes during HIV-1 and HIV-2 infection of macrophages.
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Affiliation(s)
- Joseph A Hollenbaugh
- Center for Drug Discovery, Department of Pediatrics, Health Sciences Research Building, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Catherine Montero
- Center for Drug Discovery, Department of Pediatrics, Health Sciences Research Building, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Raymond F Schinazi
- Center for Drug Discovery, Department of Pediatrics, Health Sciences Research Building, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14627, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Health Sciences Research Building, Emory University, 1760 Haygood Drive, Atlanta, GA 30322, USA; Department of Pharmacy, Kyung-Hee University, Seoul, South Korea; Children's Healthcare of Atlanta, Emory University, Atlanta, GA 30322, USA.
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Dumond JB, Francis O, Cottrell M, Trezza C, Prince HM, Mollan K, Sykes C, Torrice C, White N, Malone S, Wang R, Van Dam C, Patterson KB, Hudgens MG, Sharpless NE, Forrest A. Tenofovir/emtricitabine metabolites and endogenous nucleotide exposures are associated with p16(INK4a) expression in subjects on combination therapy. Antivir Ther 2016; 21:441-5. [PMID: 26731175 PMCID: PMC5266614 DOI: 10.3851/imp3017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND HIV may amplify immunological, physiological and functional changes of ageing. We determined associations of frailty phenotype, a T-cell senescence marker (p16(INK4a) expression), age and demographics with exposures of the intracellular metabolites (IM) and endogenous nucleotides (EN) of tenofovir/emtricitabine (TFV/FTC), efavirenz (EFV), atazanavir (ATV) and ritonavir (RTV). METHODS Plasma and peripheral blood mononuclear cell samples for drug, IM and EN concentrations were collected at four time points in HIV+ adults receiving TFV/FTC with EFV or ATV/RTV. Subjects underwent frailty phenotyping and p16(INK4a) expression analysis. Non-compartmental analysis generated an area under the curve (AUC) for each analyte. Spearman rank correlation and Kruskal-Wallis tests were used to assess associations between AUC, demographics and ageing markers, adjusting for multiple comparisons with the Holm procedure. RESULTS Subjects (n=79) ranged in age from 22-73 years (median 48 years); 48 were African-American, 24 were female, 54 received EFV. Three subjects (range 51-60 years) demonstrated frailty, with 17 subjects (range 26-60 years) demonstrating pre-frailty. Negative associations were observed between p16(INK4a) expression and each of FTC-triphosphate (r=-0.45), deoxyadenosine triphosphate (dATP; r=-0.47) and deoxycytidine triphosphate (dCTP; r=-0.57) AUCs (P-values <0.02). TFV and FTC AUCs were larger among subjects with lower renal function or higher chronological age (P-values ≤0.05). No associations were observed for EFV, ATV or RTV AUCs. CONCLUSIONS Associations of IM/EN exposure and p16(INK4a) expression observed here suggest that senescence may alter drug phosphorylation, metabolism or transport. This finding warrants further mechanistic study to ensure optimal treatment in the ageing HIV+ population. Clinicaltrials.gov NCT01180075.
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Affiliation(s)
- Julie B Dumond
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Wittmann S, Behrendt R, Eissmann K, Volkmann B, Thomas D, Ebert T, Cribier A, Benkirane M, Hornung V, Bouzas NF, Gramberg T. Phosphorylation of murine SAMHD1 regulates its antiretroviral activity. Retrovirology 2015; 12:103. [PMID: 26667483 PMCID: PMC4678485 DOI: 10.1186/s12977-015-0229-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 11/26/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human SAMHD1 is a triphosphohydrolase that restricts the replication of retroviruses, retroelements and DNA viruses in noncycling cells. While modes of action have been extensively described for human SAMHD1, only little is known about the regulation of SAMHD1 in the mouse. Here, we characterize the antiviral activity of murine SAMHD1 with the help of knockout mice to shed light on the regulation and the mechanism of the SAMHD1 restriction and to validate the SAMHD1 knockout mouse model for the use in future infectivity studies. RESULTS We found that endogenous mouse SAMHD1 restricts not only HIV-1 but also MLV reporter virus infection at the level of reverse transcription in primary myeloid cells. Similar to the human protein, the antiviral activity of murine SAMHD1 is regulated through phosphorylation at threonine 603 and is limited to nondividing cells. Comparing the susceptibility to infection with intracellular dNTP levels and SAMHD1 phosphorylation in different cell types shows that both functions are important determinants of the antiviral activity of murine SAMHD1. In contrast, we found the proposed RNase activity of SAMHD1 to be less important and could not detect any effect of mouse or human SAMHD1 on the level of incoming viral RNA. CONCLUSION Our findings show that SAMHD1 in the mouse blocks retroviral infection at the level of reverse transcription and is regulated through cell cycle-dependent phosphorylation. We show that the antiviral restriction mediated by murine SAMHD1 is mechanistically similar to what is known for the human protein, making the SAMHD1 knockout mouse model a valuable tool to characterize the influence of SAMHD1 on the replication of different viruses in vivo.
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Affiliation(s)
- Sabine Wittmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany.
| | - Rayk Behrendt
- Institute for Immunology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Fetscherstrasse 74, 01307, Dresden, Germany.
| | - Kristin Eissmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany.
| | - Bianca Volkmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany.
| | - Dominique Thomas
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe-University, Frankfurt Theodor Stern Kai 7, 60590, Frankfurt am Main, Germany.
| | - Thomas Ebert
- Institute of Molecular Medicine, University Hospital, University of Bonn, Bonn, Germany.
| | - Alexandra Cribier
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, 34000, France.
| | - Monsef Benkirane
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, 34000, France.
| | - Veit Hornung
- Institute of Molecular Medicine, University Hospital, University of Bonn, Bonn, Germany.
| | - Nerea Ferreirós Bouzas
- Pharmazentrum Frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe-University, Frankfurt Theodor Stern Kai 7, 60590, Frankfurt am Main, Germany.
| | - Thomas Gramberg
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, Schlossgarten 4, 91054, Erlangen, Germany.
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Badia R, Angulo G, Riveira-Muñoz E, Pujantell M, Puig T, Ramirez C, Torres-Torronteras J, Martí R, Pauls E, Clotet B, Ballana E, Esté JA. Inhibition of herpes simplex virus type 1 by the CDK6 inhibitor PD-0332991 (palbociclib) through the control of SAMHD1. J Antimicrob Chemother 2015; 71:387-94. [PMID: 26542306 DOI: 10.1093/jac/dkv363] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/02/2015] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) has been shown to restrict retroviruses and DNA viruses by decreasing the pool of intracellular deoxynucleotides. In turn, SAMHD1 is controlled by cyclin-dependent kinases (CDK) that regulate the cell cycle and cell proliferation. Here, we explore the effect of CDK6 inhibitors on the replication of herpes simplex virus type 1 (HSV-1) in primary monocyte-derived macrophages (MDM). METHODS MDM were treated with palbociclib, a selective CDK4/6 inhibitor, and then infected with a GFP-expressing HSV-1. Intracellular deoxynucleotide triphosphate (dNTP) content was determined using a polymerase-based method. RESULTS CDK6 inhibitor palbociclib blocked SAMHD1 phosphorylation, intracellular dNTP levels and HSV-1 replication in MDM at subtoxic concentrations. Treatment of MDM with palbociclib reduced CDK2 activation, measured as the phosphorylation of the T-loop at Thr160. The antiviral activity of palbociclib was lost when SAMHD1 was degraded by viral protein X. Similarly, palbociclib did not block HSV-1 replication in SAMHD1-negative Vero cells at subtoxic concentrations, providing further evidence for a role of SAMHD1 in mediating the antiviral effect. CONCLUSIONS SAMHD1-mediated HSV-1 restriction is controlled by CDK and points to a preferential role for CDK6 and CDK2 as mediators of SAMHD1 activation. Similarly, the restricting activity of SAMHD1 against DNA viruses suggests that control of dNTP availability is the major determinant of its antiviral activity. This is the first study describing the anti-HSV-1 activity of palbociclib.
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Affiliation(s)
- Roger Badia
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Guillem Angulo
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Eva Riveira-Muñoz
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Maria Pujantell
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Teresa Puig
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Cristina Ramirez
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Javier Torres-Torronteras
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, and Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ramón Martí
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, and Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Eduardo Pauls
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Bonaventura Clotet
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Ester Ballana
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - José A Esté
- AIDS Research Institute - IrsiCaixa, and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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Abstract
In a mature, infectious HIV-1 virion, the viral genome is housed within a conical capsid core made from the viral capsid (CA) protein. The CA protein and the structure into which it assembles facilitate virtually every step of infection through a series of interactions with multiple host cell factors. This Review describes our understanding of the interactions between the viral capsid core and several cellular factors that enable efficient HIV-1 genome replication, timely core disassembly, nuclear import and the integration of the viral genome into the genome of the target cell. We then discuss how elucidating these interactions can reveal new targets for therapeutic interactions against HIV-1.
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48
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Ballana E, Esté JA. SAMHD1: at the crossroads of cell proliferation, immune responses, and virus restriction. Trends Microbiol 2015; 23:680-692. [PMID: 26439297 DOI: 10.1016/j.tim.2015.08.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 07/28/2015] [Accepted: 08/07/2015] [Indexed: 12/31/2022]
Abstract
SAMHD1 is a triphosphohydrolase enzyme that controls the intracellular level of deoxyribonucleoside triphosphates (dNTPs) and plays a role in innate immune sensing and autoimmune disease. SAMHD1 has also been identified as an intrinsic virus restriction factor, inactivated through degradation by HIV-2 Vpx or through a post-transcriptional regulatory mechanism. Phosphorylation of SAMHD1 by cyclin-dependent kinases has been strongly associated with inactivation of the virus restriction mechanism, providing an association between virus replication and cell proliferation. Tight regulation of cell proliferation suggests that viruses, particularly HIV-1 replication, latency, and reactivation, may be similarly controlled by multiple checkpoint mechanisms that, in turn, regulate dNTP levels. In this review, we discuss how SAMHD1 is a viral restriction factor, the mechanism associated with viral restriction, the pathway leading to its inactivation in proliferating cells, and how strategies aimed at controlling virus restriction could lead to a functional cure for HIV.
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Affiliation(s)
- Ester Ballana
- AIDS Research Institute-IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - José A Esté
- AIDS Research Institute-IrsiCaixa and Health Research Institute Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain.
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49
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Goodwin CM, Xu S, Munger J. Stealing the Keys to the Kitchen: Viral Manipulation of the Host Cell Metabolic Network. Trends Microbiol 2015; 23:789-798. [PMID: 26439298 PMCID: PMC4679435 DOI: 10.1016/j.tim.2015.08.007] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/07/2015] [Accepted: 08/17/2015] [Indexed: 12/23/2022]
Abstract
Host cells possess the metabolic assets required for viral infection. Recent studies indicate that control of the host's metabolic resources is a core host–pathogen interaction. Viruses have evolved mechanisms to usurp the host's metabolic resources, funneling them towards the production of virion components as well as the organization of specialized compartments for replication, maturation, and dissemination. Consequently, hosts have developed a variety of metabolic countermeasures to sense and resist these viral changes. The complex interplay between virus and host over metabolic control has only just begun to be deconvoluted. However, it is clear that virally induced metabolic reprogramming can substantially impact infectious outcomes, highlighting the promise of targeting these processes for antiviral therapeutic development. Numerous viruses modulate host-cell metabolic processes to ensure successful infection. The host-cell metabolic network contributes the energy, precursors, and specialized components necessary to produce infectious virions. Viruses deploy host-cell metabolic activities to organize viral maturation compartments. Metabolic control is a host–pathogen interaction that can sway the outcome of viral infection.
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Affiliation(s)
- Christopher M Goodwin
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Shihao Xu
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.
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Li D, Schlaepfer E, Audigé A, Rochat MA, Ivic S, Knowlton CN, Kim B, Keppler OT, Speck RF. Vpx mediated degradation of SAMHD1 has only a very limited effect on lentiviral transduction rate in ex vivo cultured HSPCs. Stem Cell Res 2015. [PMID: 26207584 PMCID: PMC4766840 DOI: 10.1016/j.scr.2015.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Understanding how to achieve efficient transduction of hematopoietic stem and progenitor cells (HSPCs), while preserving their long-term ability to self-reproduce, is key for applying lentiviral-based gene engineering methods. SAMHD1 is an HIV-1 restriction factor in myeloid and resting CD4+ T cells that interferes with reverse transcription by decreasing the nucleotide pools or by its RNase activity. Here we show that SAMHD1 is expressed at high levels in HSPCs cultured in a medium enriched with cytokines. Thus, we hypothesized that degrading SAMHD1 in HSPCs would result in more efficient lentiviral transduction rates. We used viral like particles (VLPs) containing Vpx, shRNA against SAMHD1, or provided an excess of dNTPs or dNs to study this question. Regardless of the method applied, we saw no increase in the lentiviral transduction rate. The result was different when we used viruses (HR-GFP-Vpx+) which carry Vpx and encode GFP. These viruses allow assessment of the effects of Vpx specifically in the transduced cells. Using HR-GFP-Vpx+ viruses, we observed a modest but significant increase in the transduction efficiency. These data suggest that SAMHD1 has some limited efficacy in blocking reverse transcription but the major barrier for efficient lentiviral transduction occurs before reverse transcription.
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Affiliation(s)
- Duo Li
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091, Switzerland.
| | - Erika Schlaepfer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091, Switzerland
| | - Annette Audigé
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091, Switzerland
| | - Mary-Aude Rochat
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091, Switzerland
| | - Sandra Ivic
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091, Switzerland
| | - Caitlin N Knowlton
- Center for Drug Discovery, Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Oliver T Keppler
- Institute of Medical Virology, National Reference Center for Retroviruses, University of Frankfurt, Frankfurt am Main 60054, Germany
| | - Roberto F Speck
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, 8091, Switzerland.
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