51
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Genetic interferonopathies: An overview. Best Pract Res Clin Rheumatol 2017; 31:441-459. [DOI: 10.1016/j.berh.2017.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 10/27/2017] [Accepted: 10/27/2017] [Indexed: 11/22/2022]
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52
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White TE, Brandariz-Nuñez A, Martinez-Lopez A, Knowlton C, Lenzi G, Kim B, Ivanov D, Diaz-Griffero F. A SAMHD1 mutation associated with Aicardi-Goutières syndrome uncouples the ability of SAMHD1 to restrict HIV-1 from its ability to downmodulate type I interferon in humans. Hum Mutat 2017; 38:658-668. [PMID: 28229507 DOI: 10.1002/humu.23201] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 02/09/2017] [Accepted: 02/19/2017] [Indexed: 12/23/2022]
Abstract
Mutations in the human SAMHD1 gene are known to correlate with the development of the Aicardi-Goutières syndrome (AGS), which is an inflammatory encephalopathy that exhibits neurological dysfunction characterized by increased production of type I interferon (IFN); this evidence has led to the concept that the SAMHD1 protein negatively regulates the type I IFN response. Additionally, the SAMHD1 protein has been shown to prevent efficient HIV-1 infection of macrophages, dendritic cells, and resting CD4+ T cells. To gain insights on the SAMHD1 molecular determinants that are responsible for the deregulated production of type I IFN, we explored the biochemical, cellular, and antiviral properties of human SAMHD1 mutants known to correlate with the development of AGS. Most of the studied SAMHD1 AGS mutants exhibit defects in the ability to oligomerize, decrease the levels of cellular deoxynucleotide triphosphates in human cells, localize exclusively to the nucleus, and restrict HIV-1 infection. At least half of the tested variants preserved the ability to be degraded by the lentiviral protein Vpx, and all of them interacted with RNA. Our investigations revealed that the SAMHD1 AGS variant p.G209S preserve all tested biochemical, cellular, and antiviral properties, suggesting that this residue is a determinant for the ability of SAMHD1 to negatively regulate the type I IFN response in human patients with AGS. Overall, our work genetically separated the ability of SAMHD1 to negatively regulate the type I IFN response from its ability to restrict HIV-1.
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Affiliation(s)
- Tommy E White
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, New York
| | - Alberto Brandariz-Nuñez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, New York
| | - Alicia Martinez-Lopez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, New York
| | | | - Gina Lenzi
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Baek Kim
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Dmitri Ivanov
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, New York
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53
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Li M, Zhang D, Zhu M, Shen Y, Wei W, Ying S, Korner H, Li J. Roles of SAMHD1 in antiviral defense, autoimmunity and cancer. Rev Med Virol 2017; 27. [PMID: 28444859 DOI: 10.1002/rmv.1931] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 02/26/2017] [Accepted: 03/13/2017] [Indexed: 01/02/2023]
Abstract
The enzyme, sterile α motif and histidine-aspartic acid domain-containing protein 1 (SAMHD1) diminishes infection of human immunodeficiency virus type 1 (HIV-1) by hydrolyzing intracellular deoxynucleotide triphosphates (dNTPs) in myeloid cells and resting CD4+ T cells. This dNTP degradation reduces the dNTP concentration to a level insufficient for viral cDNA synthesis, thereby inhibiting retroviral replication. This antiviral enzymatic activity can be inhibited by viral protein X (Vpx). The HIV-2/SIV Vpx causes degradation of SAMHD1, thus interfering with the SAMHD1-mediated restriction of retroviral replication. Recently, SAMHD1 has been suggested to restrict HIV-1 infection by directly digesting genomic HIV-1 RNA through a still controversial RNase activity. Here, we summarize the current knowledge about structure, antiviral mechanisms, intracellular localization, interferon-regulated expression of SAMHD1. We also describe SAMHD1-deficient animal models and an antiviral drug on the basis of disrupting proteasomal degradation of SAMHD1. In addition, the possible roles of SAMHD1 in regulating innate immune sensing, Aicardi-Goutières syndrome and cancer are discussed in this review.
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Affiliation(s)
- Miaomiao Li
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, PR China
| | - Dong Zhang
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, PR China.,School of Basic Medical Sciences and Biopharmaceutical Research Institute, Anhui Medical University, Hefei, Anhui Province, PR China
| | - Mengying Zhu
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, PR China
| | - Yuxian Shen
- School of Basic Medical Sciences and Biopharmaceutical Research Institute, Anhui Medical University, Hefei, Anhui Province, PR China
| | - Wei Wei
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, Anhui Province, PR China
| | - Songcheng Ying
- Department of Immunology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, PR China.,School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, PR China
| | - Heinrich Korner
- Institute of Clinical Pharmacology, Anhui Medical University, Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, Anhui Province, PR China.,Menzies Institute for Medical Research Tasmania, Hobart, Tasmania, Australia
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Hefei, Anhui Province, PR China
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54
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Herold N, Rudd SG, Sanjiv K, Kutzner J, Bladh J, Paulin CBJ, Helleday T, Henter JI, Schaller T. SAMHD1 protects cancer cells from various nucleoside-based antimetabolites. Cell Cycle 2017; 16:1029-1038. [PMID: 28436707 PMCID: PMC5499833 DOI: 10.1080/15384101.2017.1314407] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Recently, we demonstrated that sterile α motif and HD domain containing protein 1 (SAMHD1) is a major barrier in acute myelogenous leukemia (AML) cells to the cytotoxicity of cytarabine (ara-C), the most important drug in AML treatment. Ara-C is intracellularly converted by the canonical dNTP synthesis pathway to ara-CTP, which serves as a substrate but not an allosteric activator of SAMHD1. Using an AML mouse model, we show here that wild type but not catalytically inactive SAMHD1 reduces ara-C treatment efficacy in vivo. Expanding the clinically relevant substrates of SAMHD1, we demonstrate that THP-1 CRISPR/Cas9 cells lacking a functional SAMHD1 gene showed increased sensitivity to the antimetabolites nelarabine, fludarabine, decitabine, vidarabine, clofarabine, and trifluridine. Within this Extra View, we discuss and build upon both these and our previously reported findings, and propose SAMHD1 is likely active against a variety of nucleoside analog antimetabolites present in anti-cancer chemotherapies. Thus, SAMHD1 may constitute a promising target to improve a wide range of therapies for both hematological and non-haematological malignancies.
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Affiliation(s)
- Nikolas Herold
- a Childhood Cancer Research Unit, Department of Women's and Children's Health , Karolinska Institutet , Stockholm , Sweden.,b Theme of Children's and Women's Health , Astrid Lindgren Children's Hospital, Karolinska University Hospital , Stockholm , Sweden
| | - Sean G Rudd
- c Science for Life Laboratory, Division of Translational Medicine and Chemical Biology , Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Kumar Sanjiv
- c Science for Life Laboratory, Division of Translational Medicine and Chemical Biology , Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Juliane Kutzner
- d Department of Infectious Diseases, Virology , University Hospital Heidelberg , Heidelberg , Germany
| | - Julia Bladh
- a Childhood Cancer Research Unit, Department of Women's and Children's Health , Karolinska Institutet , Stockholm , Sweden
| | - Cynthia B J Paulin
- c Science for Life Laboratory, Division of Translational Medicine and Chemical Biology , Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Thomas Helleday
- c Science for Life Laboratory, Division of Translational Medicine and Chemical Biology , Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Jan-Inge Henter
- a Childhood Cancer Research Unit, Department of Women's and Children's Health , Karolinska Institutet , Stockholm , Sweden.,b Theme of Children's and Women's Health , Astrid Lindgren Children's Hospital, Karolinska University Hospital , Stockholm , Sweden
| | - Torsten Schaller
- d Department of Infectious Diseases, Virology , University Hospital Heidelberg , Heidelberg , Germany
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55
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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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56
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Schott K, Riess M, König R. Role of Innate Genes in HIV Replication. Curr Top Microbiol Immunol 2017; 419:69-111. [PMID: 28685292 DOI: 10.1007/82_2017_29] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cells use an elaborate innate immune surveillance and defense system against virus infections. Here, we discuss recent studies that reveal how HIV-1 is sensed by the innate immune system. Furthermore, we present mechanisms on the counteraction of HIV-1. We will provide an overview how HIV-1 actively utilizes host cellular factors to avoid sensing. Additionally, we will summarize effectors of the innate response that provide an antiviral cellular state. HIV-1 has evolved passive mechanism to avoid restriction and to regulate the innate response. We review in detail two prominent examples of these cellular factors: (i) NLRX1, a negative regulator of the innate response that HIV-1 actively usurps to block cytosolic innate sensing; (ii) SAMHD1, a restriction factor blocking the virus at the reverse transcription step that HIV-1 passively avoids to escape sensing.
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Affiliation(s)
- Kerstin Schott
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225, Langen, Germany
| | - Maximilian Riess
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225, Langen, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, 63225, Langen, Germany. .,Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA. .,German Center for Infection Research (DZIF), 63225, Langen, Germany.
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57
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White TE, Brandariz-Nuñez A, Han K, Sawyer SL, Kim B, Diaz-Griffero F. Modulation of LINE-1 Retrotransposition by a Human SAMHD1 Polymorphism. ACTA ACUST UNITED AC 2016; 6:53-60. [PMID: 27482511 DOI: 10.1016/j.virep.2016.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The HIV-1 restriction factor SAMHD1 has the ability to negatively modulate retrotransposition of the long interspersed element 1(LINE-1). By exploring the ability of human SAMHD1 polymorphisms to inhibit LINE-1, we found that the single nucleotide polymorphism S33A present in the Korean population lose the ability to inhibit LINE-1 retrotransposition. Because SAMHD1 residue S33 is phosphorylated in human cycling and non-cycling cells, we demonstrated that SAMHD1 requires to be either phosphorylated on position 33 or to contain a bulky residue in order to inhibit LINE-1 retrotransposition. Therefore this unique mutation uncouples functions in this important restriction factor.
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Affiliation(s)
- Tommy E White
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, NY 10461
| | - Alberto Brandariz-Nuñez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, NY 10461
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea
| | - Sara L Sawyer
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, 80309, USA
| | - Baek Kim
- Department of Pediatrics, Emory University, Atlanta, GA 30322
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, NY 10461
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58
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St Gelais C, Kim SH, Ding L, Yount JS, Ivanov D, Spearman P, Wu L. A Putative Cyclin-binding Motif in Human SAMHD1 Contributes to Protein Phosphorylation, Localization, and Stability. J Biol Chem 2016; 291:26332-26342. [PMID: 27815502 DOI: 10.1074/jbc.m116.753947] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/26/2016] [Indexed: 01/01/2023] Open
Abstract
SAMHD1 (sterile α motif and HD domain-containing protein 1) is a mammalian protein that regulates intracellular dNTP levels through its hydrolysis of dNTPs. SAMHD1 functions as an important retroviral restriction factor through a mechanism relying on its dNTPase activity. We and others have reported that human SAMHD1 interacts with the cell cycle regulatory proteins cyclin A, CDK1, and CDK2, which mediates phosphorylation of SAMHD1 at threonine 592, a post-translational modification that has been implicated in abrogating SAMHD1 restriction function and ability to form stable tetramers. Utilizing co-immunoprecipitation and co-localization approaches, we show that endogenous SAMHD1 is able to interact with the cyclin A-CDK1-CDK2 complexin monocytic THP-1 cells and primary monocyte-derived macrophages. Sequence analysis of SAMHD1 identifies a putative cyclin-binding motif found in many cyclin-CDK complex substrates. Using a mutagenesis-based approach, we demonstrate that the conserved residues in the putative cyclin-binding motif are important for protein expression, protein half-life, and optimal phosphorylation of SAMHD1 at Thr592 Furthermore, we observed that SAMHD1 mutants of the cyclin-binding motif mislocalized to a nuclear compartment and had reduced ability to interact with cyclin A-CDK complexes and to form the tetramer. These findings help define the mechanisms by which SAMHD1 is phosphorylated and suggest the contribution of cyclin binding to SAMHD1 expression and stability in dividing cells.
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Affiliation(s)
- Corine St Gelais
- From the Center of Retrovirus Research, Department of Veterinary Biosciences and
| | - Sun Hee Kim
- From the Center of Retrovirus Research, Department of Veterinary Biosciences and
| | - Lingmei Ding
- the Department of Pediatrics, Emory University, Atlanta, Georgia 30322
| | - Jacob S Yount
- the Department of Microbial Infection and Immunity, Ohio State University, Columbus, Ohio 43210
| | - Dmitri Ivanov
- the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229
| | - Paul Spearman
- the Department of Pediatrics, Emory University, Atlanta, Georgia 30322.,Children's Healthcare of Atlanta, Atlanta, Georgia 30322, and
| | - Li Wu
- From the Center of Retrovirus Research, Department of Veterinary Biosciences and .,the Department of Microbial Infection and Immunity, Ohio State University, Columbus, Ohio 43210
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59
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Seamon KJ, Bumpus NN, Stivers JT. Single-Stranded Nucleic Acids Bind to the Tetramer Interface of SAMHD1 and Prevent Formation of the Catalytic Homotetramer. Biochemistry 2016; 55:6087-6099. [PMID: 27775344 DOI: 10.1021/acs.biochem.6b00986] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Sterile alpha motif and HD domain protein 1 (SAMHD1) is a unique enzyme that plays important roles in nucleic acid metabolism, viral restriction, and the pathogenesis of autoimmune diseases and cancer. Although much attention has been focused on its dNTP triphosphohydrolase activity in viral restriction and disease, SAMHD1 also binds to single-stranded RNA and DNA. Here we utilize a UV cross-linking method using 5-bromodeoxyuridine-substituted oligonucleotides coupled with high-resolution mass spectrometry to identify the binding site for single-stranded nucleic acids (ssNAs) on SAMHD1. Mapping cross-linked amino acids on the surface of existing crystal structures demonstrated that the ssNA binding site lies largely along the dimer-dimer interface, sterically blocking the formation of the homotetramer required for dNTPase activity. Surprisingly, the disordered C-terminus of SAMHD1 (residues 583-626) was also implicated in ssNA binding. An interaction between this region and ssNA was confirmed in binding studies using the purified SAMHD1 583-626 peptide. Despite a recent report that SAMHD1 possesses polyribonucleotide phosphorylase activity, we did not detect any such activity in the presence of inorganic phosphate, indicating that nucleic acid binding is unrelated to this proposed activity. These data suggest an antagonistic regulatory mechanism in which the mutually exclusive oligomeric state requirements for ssNA binding and dNTP hydrolase activity modulate these two functions of SAMHD1 within the cell.
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Affiliation(s)
- Kyle J Seamon
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine , 725 North Wolfe Street, WBSB 314, Baltimore, Maryland 21205, United States
| | - Namandjé N Bumpus
- Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins University School of Medicine , 725 North Wolfe Street, Biophysics 307, Baltimore, Maryland 21205, United States
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine , 725 North Wolfe Street, WBSB 314, Baltimore, Maryland 21205, United States
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60
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Lam MMW, Mapletoft JP, Miller MS. Abnormal regulation of the antiviral response in neurological/neurodegenerative diseases. Cytokine 2016; 88:251-258. [PMID: 27697702 DOI: 10.1016/j.cyto.2016.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease, Parkinson's disease, multiple sclerosis, and amyotrophic lateral sclerosis are a few examples of debilitating neurological/neurodegenerative diseases for which there are currently no curative treatments. Recent evidence has strongly suggested a role for neuroinflammation in both the onset and progression of these diseases. However, the mechanisms that initiate neuroinflammation are presently unclear. Mounting evidence suggests that environmental factors are likely involved. One proposed mechanism linking both genetic and environmental factors is dysregulation of the antiviral response. Indeed, many mutations that have been linked to neurological conditions occur in genes related to the antiviral response. Although the products of these genes may have potent antiviral activities - they can also have deleterious effects when their expression is not appropriately regulated. For that reason, expression of antiviral genes is a tightly controlled process. Herein, we review the various antiviral genes that have been linked to neurological conditions. We focus specifically on type I interferonopathies, the symptoms of which are often evident at birth, and neurodegenerative diseases, which frequently onset later in life.
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Affiliation(s)
- Mannie Man Wai Lam
- Department of Biochemistry and Biomedical Sciences, Institute of Infectious Diseases Research, McMaster Immunology Research Centre, McMaster University, Ontario, Canada
| | - Jonathan P Mapletoft
- Department of Biochemistry and Biomedical Sciences, Institute of Infectious Diseases Research, McMaster Immunology Research Centre, McMaster University, Ontario, Canada
| | - Matthew S Miller
- Department of Biochemistry and Biomedical Sciences, Institute of Infectious Diseases Research, McMaster Immunology Research Centre, McMaster University, Ontario, Canada.
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61
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Interferon-induced sterile alpha motif and histidine/aspartic acid domain-containing protein 1 expression in astrocytes and microglia is mediated by microRNA-181a. AIDS 2016; 30:2053-64. [PMID: 27219130 DOI: 10.1097/qad.0000000000001166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Sterile alpha motif and histidine/aspartic acid domain-containing protein 1 (SAMHD1), a newly discovered HIV-1 host restriction factor, has been found to be induced by interferons and to be regulated by microRNA-181a (miR-181a). However, the mechanism of interferons-induced SAMHD1 expression is unclear. DESIGN We hypothesized that interferons induce SAMHD1 expression through Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathways, which is mediated by miR-181a. METHODS We examined the effect of IFN-α and IFN-γ on SAMHD1 mRNA and protein expression, as well as the levels of phosphorylated SAMHD1 and miR-181a in astrocytes and microglia. To determine whether interferons-induced SAMHD1 expression was mediated by miR-181a, we overexpressed or inhibited miR-181a in these cells and exposed them to interferons. We also detected the effect of SAMHD1 and miR-181a on HIV-1 infection in astrocytes and microglia. RESULTS Both IFN-α and IFN-γ increased SAMHD1 mRNA and protein expression, and reduced miR-181a levels, particularly in microglia. Phosphorylated SAMHD1was not induced by interferons. Overexpression of miR-181a counteracted induction of SAMHD1 expression by interferons, and inhibition of miR-181a mimicked interferons treatment. Inhibition of JAK-STAT signaling pathways resulted in increased miR-181a levels and decreased SAMHD1 mRNA expression. Knock-down of SAMHD1 or overexpression of miR-181a enhanced HIV-1 infection, whereas inhibition of miR-181a reduced HIV-1 infection. However, inhibition of HIV-1 infection induced by IFN-α was not significantly affected by miR-181a and SAMHD1. CONCLUSION MiR-181a is an important mediator for interferons-induced SAMHD1 expression in astrocytes and microglia, but not for inhibition of HIV-1 infection induced by IFN-α.
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62
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Bhattacharya A, Wang Z, White T, Buffone C, Nguyen LA, Shepard CN, Kim B, Demeler B, Diaz-Griffero F, Ivanov DN. Effects of T592 phosphomimetic mutations on tetramer stability and dNTPase activity of SAMHD1 can not explain the retroviral restriction defect. Sci Rep 2016; 6:31353. [PMID: 27511536 PMCID: PMC4980677 DOI: 10.1038/srep31353] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/18/2016] [Indexed: 12/30/2022] Open
Abstract
SAMHD1, a dNTP triphosphohydrolase, contributes to interferon signaling and restriction of retroviral replication. SAMHD1-mediated retroviral restriction is thought to result from the depletion of cellular dNTP pools, but it remains controversial whether the dNTPase activity of SAMHD1 is sufficient for restriction. The restriction ability of SAMHD1 is regulated in cells by phosphorylation on T592. Phosphomimetic mutations of T592 are not restriction competent, but appear intact in their ability to deplete cellular dNTPs. Here we use analytical ultracentrifugation, fluorescence polarization and NMR-based enzymatic assays to investigate the impact of phosphomimetic mutations on SAMHD1 tetramerization and dNTPase activity in vitro. We find that phosphomimetic mutations affect kinetics of tetramer assembly and disassembly, but their effects on tetramerization equilibrium and dNTPase activity are insignificant. In contrast, the Y146S/Y154S dimerization-defective mutant displays a severe dNTPase defect in vitro, but is indistinguishable from WT in its ability to deplete cellular dNTP pools and to restrict HIV replication. Our data suggest that the effect of T592 phosphorylation on SAMHD1 tetramerization is not likely to explain the retroviral restriction defect, and we hypothesize that enzymatic activity of SAMHD1 is subject to additional cellular regulatory mechanisms that have not yet been recapitulated in vitro.
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Affiliation(s)
- Akash Bhattacharya
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Zhonghua Wang
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Tommy White
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cindy Buffone
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laura A Nguyen
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Caitlin N Shepard
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA.,School of Pharmacy, Kyunghee University, Seoul, South Korea
| | - Borries Demeler
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Dmitri N Ivanov
- Department of Biochemistry, University of Texas Health Science Center, San Antonio, TX 78229, USA
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63
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SAMHD1, the Aicardi-Goutières syndrome gene and retroviral restriction factor, is a phosphorolytic ribonuclease rather than a hydrolytic ribonuclease. Biochem Biophys Res Commun 2016; 477:977-981. [PMID: 27387229 DOI: 10.1016/j.bbrc.2016.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 07/02/2016] [Indexed: 11/21/2022]
Abstract
SAMHD1 plays diverse roles in innate immunity, autoimmune diseases and HIV restriction, but the mechanisms involved are still unclear. SAMHD1 has been reported to have both dNTPase and RNase activities. However, whether SAMHD1 possesses RNase activity remains highly controversial. Here, we found that, unlike conventional hydrolytic exoribonucleases, SAMHD1 requires inorganic phosphate to degrade RNA substrates and produces nucleotide diphosphates rather than nucleoside monophosphates, which indicated that SAMHD1 is a phosphorolytic but not hydrolytic 3'-5' exoribonuclease. Furthermore, SAMHD1 preferentially cleaved single-stranded RNAs comprising A20 or U20, whereas neither C20 nor G20 was susceptible to SAMHD1-mediated degradation. Our findings will facilitate more advanced studies into the role of the SAMHD1 RNase function in the cellular pathogenesis implicated in nucleic acid-triggered inflammatory responses and the anti-retroviral function of SAMHD1.
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Sommer AFR, Rivière L, Qu B, Schott K, Riess M, Ni Y, Shepard C, Schnellbächer E, Finkernagel M, Himmelsbach K, Welzel K, Kettern N, Donnerhak C, Münk C, Flory E, Liese J, Kim B, Urban S, König R. Restrictive influence of SAMHD1 on Hepatitis B Virus life cycle. Sci Rep 2016; 6:26616. [PMID: 27229711 PMCID: PMC4882586 DOI: 10.1038/srep26616] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/06/2016] [Indexed: 12/21/2022] Open
Abstract
Deoxynucleotide triphosphates (dNTPs) are essential for efficient hepatitis B virus (HBV) replication. Here, we investigated the influence of the restriction factor SAMHD1, a dNTP hydrolase (dNTPase) and RNase, on HBV replication. We demonstrated that silencing of SAMHD1 in hepatic cells increased HBV replication, while overexpression had the opposite effect. SAMHD1 significantly affected the levels of extracellular viral DNA as well as intracellular reverse transcription products, without affecting HBV RNAs or cccDNA. SAMHD1 mutations that interfere with the dNTPase activity (D137N) or in the catalytic center of the histidine-aspartate (HD) domain (D311A), and a phospho-mimetic mutation (T592E), abrogated the inhibitory activity. In contrast, a mutation diminishing the potential RNase but not dNTPase activity (Q548A) and a mutation disabling phosphorylation (T592A) did not affect antiviral activity. Moreover, HBV restriction by SAMHD1 was rescued by addition of deoxynucleosides. Although HBV infection did not directly affect protein level or phosphorylation of SAMHD1, the virus upregulated intracellular dATPs. Interestingly, SAMHD1 was dephosphorylated, thus in a potentially antiviral-active state, in primary human hepatocytes. Furthermore, SAMHD1 was upregulated by type I and II interferons in hepatic cells. These results suggest that SAMHD1 is a relevant restriction factor for HBV and restricts reverse transcription through its dNTPase activity.
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Affiliation(s)
| | - Lise Rivière
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, Langen, Germany
| | - Bingqian Qu
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Kerstin Schott
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, Langen, Germany
| | - Maximilian Riess
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, Langen, Germany
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Caitlin Shepard
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, Atlanta, USA
| | | | | | | | - Karin Welzel
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Nadja Kettern
- Division of Virology, Paul-Ehrlich-Institute, Langen, Germany
| | | | - Carsten Münk
- Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Egbert Flory
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Juliane Liese
- General and Visceral Surgery, Goethe-University, Frankfurt, Germany
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, Atlanta, USA
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institute, Langen, Germany.,Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,German Center for Infection Research (DZIF), Langen, Germany
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65
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Li Y, Peng X, Qin X. Recombinant expression, purification, and crystallization of the sterile α-motif/histidine-aspartate domain-containing protein from chicken. Protein Expr Purif 2016; 133:96-101. [PMID: 27131778 DOI: 10.1016/j.pep.2016.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 10/21/2022]
Abstract
The sterile α-motif and HD domain containing protein 1 (SAMHD1) family is a newly identified protein family, involved in innate immunity restriction. This family possesses a broad-spectrum of antiviral activity. The SAMHD1 family in chicken has not been clearly documented. Here, we expressed chicken SAMHD1 (101-614) fused with a SUMO tag in an Escherichia coli (E. coli) system. For the first time, chicken SAMHD1 (101-614) was found to possess dNTPase cleavage activities in vitro. This suggests that chicken SAMHD1 may be a potential antiviral factor against avian viruses. Through a unique purification method, the purity of the protein as estimated by SDS-PAGE was >95% after a double Ni affinity chromatography and gel filtration purification. Using a sitting-drop vapor-diffusion method, protein crystals were obtained. This study provides some essential method and information for further structure and function determinations of chicken SAMHD1.
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Affiliation(s)
- Yanhong Li
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Xin Peng
- School of Life Sciences, Tianjin University, Tianjin 300072, China.
| | - Xiaohong Qin
- School of Life Sciences, Tianjin University, Tianjin 300072, China.
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66
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The crossroads of autoimmunity and immunodeficiency: Lessons from polygenic traits and monogenic defects. J Allergy Clin Immunol 2016; 137:3-17. [DOI: 10.1016/j.jaci.2015.11.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 01/16/2023]
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67
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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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68
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Welbourn S, Strebel K. Low dNTP levels are necessary but may not be sufficient for lentiviral restriction by SAMHD1. Virology 2015; 488:271-7. [PMID: 26655245 DOI: 10.1016/j.virol.2015.11.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 12/14/2022]
Abstract
SAMHD1 is a cellular dNTPase that restricts lentiviral infection presumably by lowering cellular dNTP levels to below a critical threshold required for reverse transcription; however, lowering cellular dNTP levels may not be the sole mechanism of restriction. In particular, an exonuclease activity of SAMHD1 was reported to contribute to virus restriction. We further investigated the requirements for SAMHD1 restriction activity in both differentiated U937 and cycling HeLa cells. Using hydroxyurea treatment to lower baseline dNTP levels in HeLa cells, we were able to document efficient SAMHD1 restriction without significant further reduction in dNTP levels by SAMHD1. These results argue against a requirement for additional myeloid-specific host factors for SAMHD1 function but further support the notion that SAMHD1 possesses an additional dNTP-independent function contributing to lentiviral restriction. However, our own experiments failed to associate this presumed additional SAMHD1 antiviral activity with a reported nuclease activity.
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Affiliation(s)
- Sarah Welbourn
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Building 4, Room 310, 4 Center Drive, MSC 0460, Bethesda, MD 20892-0460, USA
| | - Klaus Strebel
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Building 4, Room 310, 4 Center Drive, MSC 0460, Bethesda, MD 20892-0460, USA.
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69
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Rampazzo C, Tozzi MG, Dumontet C, Jordheim LP. The druggability of intracellular nucleotide-degrading enzymes. Cancer Chemother Pharmacol 2015; 77:883-93. [PMID: 26614508 DOI: 10.1007/s00280-015-2921-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/13/2015] [Indexed: 01/24/2023]
Abstract
Nucleotide metabolism is the target of a large number of anticancer drugs including antimetabolites and specific enzyme inhibitors. We review scientific findings that over the last 10-15 years have allowed the identification of several intracellular nucleotide-degrading enzymes as cancer drug targets, and discuss further potential therapeutic applications for Rcl, SAMHD1, MTH1 and cN-II. We believe that enzymes involved in nucleotide metabolism represent potent alternatives to conventional cancer chemotherapy targets.
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Affiliation(s)
- Chiara Rampazzo
- Department of Biology, University of Padova, 35131, Padua, Italy
| | - Maria Grazia Tozzi
- Department of Biology, Biochemistry Unit, University of Pisa, Pisa, Italy
| | - Charles Dumontet
- Université de Lyon, 69000, Lyon, France.,Université de Lyon 1, 69622, Lyon, France.,Université de Lyon 1, 69000, Lyon, France.,INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France.,CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France.,Centre Léon Bérard, 69008, Lyon, France.,Hospices Civils de Lyon, 69000, Lyon, France
| | - Lars Petter Jordheim
- Université de Lyon, 69000, Lyon, France. .,Université de Lyon 1, 69622, Lyon, France. .,Université de Lyon 1, 69000, Lyon, France. .,INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France. .,CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon, 69000, Lyon, France. .,Centre Léon Bérard, 69008, Lyon, France. .,Equipe Anticorps-Anticancer, INSERM U1052 - CNRS UMR 5286, Faculté Rockefeller, Centre de Recherche en Cancérologie de Lyon, 8 avenue Rockefeller, 69008, Lyon, France.
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70
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Arnold LH, Groom HCT, Kunzelmann S, Schwefel D, Caswell SJ, Ordonez P, Mann MC, Rueschenbaum S, Goldstone DC, Pennell S, Howell SA, Stoye JP, Webb M, Taylor IA, Bishop KN. Phospho-dependent Regulation of SAMHD1 Oligomerisation Couples Catalysis and Restriction. PLoS Pathog 2015; 11:e1005194. [PMID: 26431200 PMCID: PMC4592219 DOI: 10.1371/journal.ppat.1005194] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/08/2015] [Indexed: 12/02/2022] Open
Abstract
SAMHD1 restricts HIV-1 infection of myeloid-lineage and resting CD4+ T-cells. Most likely this occurs through deoxynucleoside triphosphate triphosphohydrolase activity that reduces cellular dNTP to a level where reverse transcriptase cannot function, although alternative mechanisms have been proposed recently. Here, we present combined structural and virological data demonstrating that in addition to allosteric activation and triphosphohydrolase activity, restriction correlates with the capacity of SAMHD1 to form “long-lived” enzymatically competent tetramers. Tetramer disruption invariably abolishes restriction but has varied effects on in vitro triphosphohydrolase activity. SAMHD1 phosphorylation also ablates restriction and tetramer formation but without affecting triphosphohydrolase steady-state kinetics. However phospho-SAMHD1 is unable to catalyse dNTP turnover under conditions of nucleotide depletion. Based on our findings we propose a model for phosphorylation-dependent regulation of SAMHD1 activity where dephosphorylation switches housekeeping SAMHD1 found in cycling cells to a high-activity stable tetrameric form that depletes and maintains low levels of dNTPs in differentiated cells. SAMHD1 is a restriction factor that blocks infection of certain immune cells by HIV-1. It was discovered to be an enzyme that catalyses the breakdown of dNTPs, suggesting that it inhibits HIV-1 replication by reducing cellular dNTP pools to such low levels that reverse transcriptase cannot function. However, recently, alternative mechanisms have been proposed. SAMHD1 is also regulated by phosphorylation, although the effects of phosphorylation on protein function are unclear. In order to address these issues, we carried out combined structural and virological studies and have demonstrated that in addition to allosteric activation and triphosphohydrolase activity, restriction correlates with the capacity of SAMHD1 to form “long-lived” enzymatically competent tetramers. Disrupting the tetramer in various ways always abolished restriction but had differing effects on enzyme activity in vitro. SAMHD1 phosphorylation also prevented restriction and tetramer formation but without affecting enzyme catalysis under steady-state dNTP conditions. However phosphorylated SAMHD1 was unable to catalyse dNTP turnover at very low nucleotide levels that more accurately represent conditions in the cells in which restriction takes place. Based on our findings we propose a model for phosphorylation-dependent regulation of SAMHD1 activity and substantiate that degradation of dNTPs by SAMHD1 is sufficient to restrict HIV-1.
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Affiliation(s)
- Laurence H. Arnold
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Harriet C. T. Groom
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Simone Kunzelmann
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - David Schwefel
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Sarah J. Caswell
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Paula Ordonez
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Melanie C. Mann
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Sabrina Rueschenbaum
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - David C. Goldstone
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Simon Pennell
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Steven A. Howell
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
| | - Jonathan P. Stoye
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Michelle Webb
- Centre for Genomic Medicine, Institute for Human Development, Faculty of Medicine and Human Sciences, University of Manchester, Manchester, United Kingdom
| | - Ian A. Taylor
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
- * E-mail: (IAT); (KNB)
| | - Kate N. Bishop
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, United Kingdom
- * E-mail: (IAT); (KNB)
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71
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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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72
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Tang C, Ji X, Wu L, Xiong Y. Impaired dNTPase activity of SAMHD1 by phosphomimetic mutation of Thr-592. J Biol Chem 2015; 290:26352-9. [PMID: 26294762 DOI: 10.1074/jbc.m115.677435] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/02/2023] Open
Abstract
SAMHD1 is a cellular protein that plays key roles in HIV-1 restriction and regulation of cellular dNTP levels. Mutations in SAMHD1 are also implicated in the pathogenesis of chronic lymphocytic leukemia and Aicardi-Goutières syndrome. The anti-HIV-1 activity of SAMHD1 is negatively modulated by phosphorylation at residue Thr-592. The mechanism underlying the effect of phosphorylation on anti-HIV-1 activity remains unclear. SAMHD1 forms tetramers that possess deoxyribonucleotide triphosphate triphosphohydrolase (dNTPase) activity, which is allosterically controlled by the combined action of GTP and all four dNTPs. Here we demonstrate that the phosphomimetic mutation T592E reduces the stability of the SAMHD1 tetramer and the dNTPase activity of the enzyme. To better understand the underlying mechanisms, we determined the crystal structures of SAMHD1 variants T592E and T592V. Although the neutral substitution T592V does not perturb the structure, the charged T592E induces large conformational changes, likely triggered by electrostatic repulsion from a distinct negatively charged environment surrounding Thr-592. The phosphomimetic mutation results in a significant decrease in the population of active SAMHD1 tetramers, and hence the dNTPase activity is substantially decreased. These results provide a mechanistic understanding of how SAMHD1 phosphorylation at residue Thr-592 may modulate its cellular and antiviral functions.
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Affiliation(s)
- Chenxiang Tang
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Xiaoyun Ji
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
| | - Li Wu
- the Center for Retrovirus Research, Department of Veterinary Biosciences, Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio 43210
| | - Yong Xiong
- From the Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 and
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73
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Seamon KJ, Sun Z, Shlyakhtenko LS, Lyubchenko YL, Stivers JT. SAMHD1 is a single-stranded nucleic acid binding protein with no active site-associated nuclease activity. Nucleic Acids Res 2015; 43:6486-99. [PMID: 26101257 PMCID: PMC4513882 DOI: 10.1093/nar/gkv633] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 06/05/2015] [Indexed: 12/15/2022] Open
Abstract
The HIV-1 restriction factor SAMHD1 is a tetrameric enzyme activated by guanine nucleotides with dNTP triphosphate hydrolase activity (dNTPase). In addition to this established activity, there have been a series of conflicting reports as to whether the enzyme also possesses single-stranded DNA and/or RNA 3′-5′ exonuclease activity. SAMHD1 was purified using three chromatography steps, over which the DNase activity was largely separated from the dNTPase activity, but the RNase activity persisted. Surprisingly, we found that catalytic and nucleotide activator site mutants of SAMHD1 with no dNTPase activity retained the exonuclease activities. Thus, the exonuclease activity cannot be associated with any known dNTP binding site. Monomeric SAMHD1 was found to bind preferentially to single-stranded RNA, while the tetrameric form required for dNTPase action bound weakly. ssRNA binding, but not ssDNA, induces higher-order oligomeric states that are distinct from the tetrameric form that binds dNTPs. We conclude that the trace exonuclease activities detected in SAMHD1 preparations arise from persistent contaminants that co-purify with SAMHD1 and not from the HD active site. An in vivo model is suggested where SAMHD1 alternates between the mutually exclusive functions of ssRNA binding and dNTP hydrolysis depending on dNTP pool levels and the presence of viral ssRNA.
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Affiliation(s)
- Kyle J Seamon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Zhiqiang Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Luda S Shlyakhtenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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74
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Choi J, Ryoo J, Oh C, Hwang S, Ahn K. SAMHD1 specifically restricts retroviruses through its RNase activity. Retrovirology 2015; 12:46. [PMID: 26032178 PMCID: PMC4450836 DOI: 10.1186/s12977-015-0174-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/15/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human SAMHD1 possesses dual enzymatic functions. It acts as both a dGTP-dependent triphosphohydrolase and as an exoribonuclease. The dNTPase function depletes the cellular dNTP pool, which is required for retroviral reverse transcription in differentiated myeloid cells and resting CD4(+) T cells; thus this activity mainly plays a role in SAMHD1-mediated retroviral restriction. However, a recent study demonstrated that SAMHD1 directly targets HIV-1 genomic RNA via its RNase activity, and that this function (rather than dNTPase activity) is sufficient for HIV-1 restriction. While HIV-1 genomic RNA is a potent target for SAMHD1 during viral infection, the specificity of SAMHD1-mediated RNase activity during infection by other viruses is unclear. RESULTS The results of the present study showed that SAMHD1 specifically degrades retroviral genomic RNA in monocyte-derived macrophage-like cells and in primary monocyte-derived macrophages. Consistent with this, SAMHD1 selectively restricted retroviral replication, but did not affect the replication of other common non-retro RNA genome viruses, suggesting that the RNase-mediated antiviral function of SAMHD1 is limited to retroviruses. In addition, neither inhibiting reverse transcription by treatment with several reverse transcriptase inhibitors nor infection with reverse transcriptase-defective HIV-1 altered RNA levels after viral challenge, indicating that the retrovirus-specific RNase function is not dependent on processes associated with retroviral reverse transcription. CONCLUSIONS The results presented herein suggest that the RNase activity of SAMHD1 is sufficient to control the replication of retroviruses, but not that of non-retro RNA viruses.
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Affiliation(s)
- Jongsu Choi
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul, Republic of Korea. .,Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Jeongmin Ryoo
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul, Republic of Korea. .,Department of the Interdisciplinary Program in Genetic Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Changhoon Oh
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul, Republic of Korea. .,Department of the Interdisciplinary Program in Genetic Engineering, Seoul National University, Seoul, Republic of Korea.
| | - Sungyeon Hwang
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul, Republic of Korea. .,Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Kwangseog Ahn
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul, Republic of Korea. .,Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea.
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75
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Lee-Kirsch MA, Wolf C, Kretschmer S, Roers A. Type I interferonopathies--an expanding disease spectrum of immunodysregulation. Semin Immunopathol 2015; 37:349-57. [PMID: 25998914 DOI: 10.1007/s00281-015-0500-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 05/11/2015] [Indexed: 12/25/2022]
Abstract
Type I interferons (IFNs) play a central role in the immune defense against viral infections. Type I IFN signaling is activated by pattern recognition receptors upon sensing of viral nucleic acids and induces antiviral programs through modulation of innate and adaptive immune responses. Type I interferonopathies comprise a heterogenous group of genetically determined diseases that are characterized by inappropriate activation of type I IFN. While their phenotypic spectrum is broad, ranging from severe neurological impairment to mild cutaneous disease, systemic autoinflammation, and autoimmunity are commonly shared signs of type I interferonopathies. Although the mechanisms underlying various disease phenotypes associated with inappropriate type I IFN activation have yet to be fully elucidated, our current understanding of the molecular pathogenesis of type I interferonopathies has provided a set of candidate molecules that can be interrogated in search of targeted therapies.
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Affiliation(s)
- Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany,
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76
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Jia X, Zhao Q, Xiong Y. HIV suppression by host restriction factors and viral immune evasion. Curr Opin Struct Biol 2015; 31:106-14. [PMID: 25939065 DOI: 10.1016/j.sbi.2015.04.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 04/01/2015] [Accepted: 04/15/2015] [Indexed: 01/30/2023]
Abstract
Antiviral restriction factors are an integral part of the host innate immune system that protects cells from viral pathogens, such as human immunodeficiency virus (HIV). Studies of the interactions between restriction factors and HIV have greatly advanced our understanding of both the viral life cycle and basic cell biology, as well as provided new opportunities for therapeutic intervention of viral infection. Here we review the recent developments towards establishing the structural and biochemical bases of HIV inhibition by, and viral countermeasures of, the restriction factors TRIM5, MxB, APOBEC3, SAMHD1, and BST2/tetherin.
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Affiliation(s)
- Xiaofei Jia
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Qi Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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Abstract
Mutations in SAMHD1 cause Aicardi-Goutières syndrome (AGS), a Mendelian inflammatory disease which displays remarkable clinical and biochemical overlap with congenital viral infection. SAMHD1 (SAM domain and HD domain-containing protein 1) has also been defined as an HIV-1 restriction-factor that, through a novel triphosphohydrolase activity, inhibits early stage HIV-1 replication in myeloid-derived dendritic cells (MDDCs), macrophages and resting CD4+ T-cells. The potent activity of SAMHD1 is likely to be the subject of a variety of regulatory mechanisms. Knowledge of proteins that interact with SAMHD1 may not only enhance our understanding of the pathogenesis of AGS, but may also provide further details on the link between the regulation of cellular dNTPs and HIV-1 restriction. In the present study, we used a yeast two-hybrid screen and pull-down analysis followed by MS to identify the eukaryotic elongation factor 1A1 (eEF1A1) as a potential interaction partner of SAMHD1. This interaction was confirmed by unbiased co-immunoprecipitation and demonstrated in situ by a proximity ligation assay (PLA). We show that this interaction is enhanced in mutant SAMHD1 cell lines and suggest that eEF1A1 may mediate SAMHD1 turnover by targeting it to the proteosome for degradation through association with Cullin4A and Rbx1.
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78
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Jin C, Peng X, Liu F, Cheng L, Lu X, Yao H, Wu H, Wu N. MicroRNA-181 expression regulates specific post-transcriptional level of SAMHD1 expression in vitro. Biochem Biophys Res Commun 2014; 452:760-7. [PMID: 25201733 DOI: 10.1016/j.bbrc.2014.08.151] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 08/28/2014] [Indexed: 12/12/2022]
Abstract
SAM domain and HD domain 1 (SAMHD1) is a newly discovered human immunodeficiency virus (HIV)-1 host restriction factor with high expression in HIV-1-non-permissive cells and low expression in HIV-1-permissive cells. The regulatory mechanism of SAMHD1 expression is still unclear. We examined the relationship between the expression levels of SAMHD1 mRNA and protein and microRNA-181 (miR-181) level in different cell lines. MiR-181 level was negatively correlated with SAMHD1 expression level. By examining the impact of miR-181 on SAMHD1 3' untranslated region (UTR) reporter luciferase activity and on SAMHD1 mRNA and argonaute RISC catalytic component 2 (AGO2) binding, we found that miR-181 acted directly on the SAMHD1 3' UTR and regulated SAMHD1 mRNA levels after transcription. MiR-181 over-expression significantly reduced the level of SAMHD1 expression in THP-1 cells; miR-181 inhibition up-regulated SAMHD1 expression in THP-1 and Jurkat cells. Our results suggest that miR-181 regulates the level of post-transcriptional SAMHD1 expression negatively by directly binding to the 3' UTR in SAMHD1.
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Affiliation(s)
- Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Xiaorong Peng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Fumin Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Linfang Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Xiangyun Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Haibo Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Nanping Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China.
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Hollenbaugh JA, Tao S, Lenzi GM, Ryu S, Kim DH, Diaz-Griffero F, Schinazi RF, Kim B. dNTP pool modulation dynamics by SAMHD1 protein in monocyte-derived macrophages. Retrovirology 2014; 11:63. [PMID: 25158827 PMCID: PMC4161909 DOI: 10.1186/s12977-014-0063-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/18/2014] [Indexed: 02/03/2023] Open
Abstract
Background SAMHD1 degrades deoxyribonucleotides (dNTPs), suppressing viral DNA synthesis in macrophages. Recently, viral protein X (Vpx) of HIV-2/SIVsm was shown to target SAMHD1 for proteosomal degradation and led to elevation of dNTP levels, which in turn accelerated proviral DNA synthesis of lentiviruses in macrophages. Results We investigated both time-dependent and quantitative interplays between SAMHD1 level and dNTP concentrations during multiple exposures of Vpx in macrophages. The following were observed. First, SAMHD1 level was rapidly reduced by Vpx + VLP to undetectable levels by Western blot analysis. Recovery of SAMHD1 was very slow with less than 3% of the normal macrophage level detected at day 6 post Vpx treatment and only ~30% recovered at day 14. Second, dGTP, dCTP and dTTP levels peaked at day 1 post Vpx treatment, whereas dATP peaked at day 2. However, all dNTPs rapidly decreased starting at day 3, while SAMHD1 level was below the level of detection. Third, when Vpx pretreated macrophages were re-exposed to a second Vpx treatment at day 7, we observed dNTP elevation that had faster kinetics than the first Vpx + VLP treatment. Moreover, we performed a short kinetic analysis of the second Vpx treatment to find that dATP and dGTP levels peaked at 8 hours post secondary VLP treatment. dGTP peak was consistently higher than the primary, whereas peak dATP concentration was basically equivalent to the first Vpx + VLP treatment. Lastly, HIV-1 replication kinetics were faster in macrophages treated after the secondary Vpx treatments when compared to the initial single Vpx treatment. Conclusion This study reveals that a very low level of SAMHD1 sufficiently modulates the normally low dNTP levels in macrophages and proposes potential diverse mechanisms of Vpx-mediated dNTP regulation in macrophages. Electronic supplementary material The online version of this article (doi:10.1186/s12977-014-0063-2) contains supplementary material, which is available to authorized users.
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Ryoo J, Choi J, Oh C, Kim S, Seo M, Kim S, Seo D, Kim J, White TE, Brandariz-Nunez A, Diaz-Griffero F, Yun CH, Hollenbaugh JA, Kim B, Baek D, Ahn K. The ribonuclease activity of SAMHD1 is required for HIV-1 restriction. Nat Med 2014; 20:936-41. [PMID: 25038827 PMCID: PMC4318684 DOI: 10.1038/nm.3626] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/03/2014] [Indexed: 01/21/2023]
Abstract
The HIV-1 restriction factor SAM domain- and HD domain-containing protein 1 (SAMHD1) is proposed to inhibit HIV-1 replication by depleting the intracellular dNTP pool. However, phosphorylation of SAMHD1 regulates its ability to restrict HIV-1 without decreasing cellular dNTP levels, which is not consistent with a role for SAMHD1 dNTPase activity in HIV-1 restriction. Here, we show that SAMHD1 possesses RNase activity and that the RNase but not the dNTPase function is essential for HIV-1 restriction. By enzymatically characterizing Aicardi-Goutières syndrome (AGS)-associated SAMHD1 mutations and mutations in the allosteric dGTP-binding site of SAMHD1 for defects in RNase or dNTPase activity, we identify SAMHD1 point mutants that cause loss of one or both functions. The RNase-positive and dNTPase-negative SAMHD1D137N mutant is able to restrict HIV-1 infection, whereas the RNase-negative and dNTPase-positive SAMHD1Q548A mutant is defective for HIV-1 restriction. SAMHD1 associates with HIV-1 RNA and degrades it during the early phases of cell infection. SAMHD1 silencing in macrophages and CD4(+) T cells from healthy donors increases HIV-1 RNA stability, rendering the cells permissive for HIV-1 infection. Furthermore, phosphorylation of SAMHD1 at T592 negatively regulates its RNase activity in cells and impedes HIV-1 restriction. Our results reveal that the RNase activity of SAMHD1 is responsible for preventing HIV-1 infection by directly degrading the HIV-1 RNA.
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Affiliation(s)
- Jeongmin Ryoo
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul 151-747, Republic of Korea
- Department of the Interdisciplinary Program in Genetic Engineering, Seoul National University, Seoul 151-747, Republic of Korea
| | - Jongsu Choi
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul 151-747, Republic of Korea
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Changhoon Oh
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul 151-747, Republic of Korea
- Department of the Interdisciplinary Program in Genetic Engineering, Seoul National University, Seoul 151-747, Republic of Korea
| | - Sungchul Kim
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul 151-747, Republic of Korea
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Minji Seo
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul 151-747, Republic of Korea
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Seokyoung Kim
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul 151-747, Republic of Korea
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Daekwan Seo
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
| | - Jongkyu Kim
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
- Center for RNA Research, Institute for Basic Science, Seoul 151-747, Republic of Korea
| | - Tommy E. White
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Alberto Brandariz-Nunez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Cheol-Heui Yun
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Joseph A. Hollenbaugh
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia, USA
| | - Daehyun Baek
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
- Bioinformatics Institute, Seoul National University, Seoul 151-747, Republic of Korea
- Center for RNA Research, Institute for Basic Science, Seoul 151-747, Republic of Korea
| | - Kwangseog Ahn
- Creative Research Initiative Center for Antigen Presentation, Seoul National University, Seoul 151-747, Republic of Korea
- Department of Biological Sciences, Seoul National University, Seoul 151-747, Republic of Korea
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81
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White TE, Brandariz-Nuñez A, Valle-Casuso JC, Knowlton C, Kim B, Sawyer SL, Diaz-Griffero F. Effects of human SAMHD1 polymorphisms on HIV-1 susceptibility. Virology 2014; 460-461:34-44. [PMID: 25010268 DOI: 10.1016/j.virol.2014.04.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 01/11/2014] [Accepted: 04/17/2014] [Indexed: 11/29/2022]
Abstract
SAMHD1 is a human restriction factor that prevents efficient infection of macrophages, dendritic cells and resting CD4+ T cells by HIV-1. Here we explored the antiviral activity and biochemical properties of human SAMHD1 polymorphisms. Our studies focused on human SAMHD1 polymorphisms that were previously identified as evolving under positive selection for rapid amino acid replacement during primate speciation. The different human SAMHD1 polymorphisms were tested for their ability to block HIV-1, HIV-2 and equine infectious anemia virus (EIAV). All studied SAMHD1 variants block HIV-1, HIV-2 and EIAV infection when compared to wild type. We found that these variants did not lose their ability to oligomerize or to bind RNA. Furthermore, all tested variants were susceptible to degradation by Vpx, and localized to the nuclear compartment. We tested the ability of human SAMHD1 polymorphisms to decrease the dNTP cellular levels. In agreement, none of the different SAMHD1 variants lost their ability to reduce cellular levels of dNTPs. Finally, we found that none of the tested human SAMHD1 polymorphisms affected the ability of the protein to block LINE-1 retrotransposition.
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Affiliation(s)
- Tommy E White
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, 1301 Morris Park - Price Center 501, New York, NY 10461, USA
| | - Alberto Brandariz-Nuñez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, 1301 Morris Park - Price Center 501, New York, NY 10461, USA
| | - Jose Carlos Valle-Casuso
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, 1301 Morris Park - Price Center 501, New York, NY 10461, USA
| | - Caitlin Knowlton
- Department of Microbiology & Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Baek Kim
- Department of Microbiology & Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Sara L Sawyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, 1301 Morris Park - Price Center 501, New York, NY 10461, USA.
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82
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Mouse knockout models for HIV-1 restriction factors. Cell Mol Life Sci 2014; 71:3749-66. [PMID: 24854580 PMCID: PMC4160573 DOI: 10.1007/s00018-014-1646-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/24/2014] [Accepted: 05/05/2014] [Indexed: 12/21/2022]
Abstract
Infection of cells with human immunodeficiency virus 1 (HIV-1) is controlled by restriction factors, host proteins that counteract a variety of steps in the life cycle of this lentivirus. These include SAMHD1, APOBEC3G and tetherin, which block reverse transcription, hypermutate viral DNA and prevent progeny virus release, respectively. These and other HIV-1 restriction factors are conserved and have clear orthologues in the mouse. This review summarises studies in knockout mice lacking HIV-1 restriction factors. In vivo experiments in such animals have not only validated in vitro data obtained from cultured cells, but have also revealed new findings about the biology of these proteins. Indeed, genetic ablation of HIV-1 restriction factors in the mouse has provided evidence that restriction factors control retroviruses and other viruses in vivo and has led to new insights into the mechanisms by which these proteins counteract infection. For example, in vivo experiments in knockout mice demonstrate that virus control exerted by restriction factors can shape adaptive immune responses. Moreover, the availability of animals lacking restriction factors opens the possibility to study the function of these proteins in other contexts such as autoimmunity and cancer. Further in vivo studies of more recently identified HIV-1 restriction factors in gene targeted mice are, therefore, justified.
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83
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Schaller T, Bauby H, Hué S, Malim MH, Goujon C. New insights into an X-traordinary viral protein. Front Microbiol 2014; 5:126. [PMID: 24782834 PMCID: PMC3986551 DOI: 10.3389/fmicb.2014.00126] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 03/11/2014] [Indexed: 11/13/2022] Open
Abstract
Vpx is a protein encoded by members of the HIV-2/SIVsmm and SIVrcm/SIVmnd-2 lineages of primate lentiviruses, and is packaged into viral particles. Vpx plays a critical role during the early steps of the viral life cycle and has been shown to counteract SAMHD1, a restriction factor in myeloid and resting T cells. However, it is becoming evident that Vpx is a multifunctional protein in that SAMHD1 antagonism is likely not its sole role. This review summarizes the current knowledge on this X-traordinary protein.
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Affiliation(s)
- Torsten Schaller
- Department of Infectious Diseases, King's College London London, UK
| | - Hélène Bauby
- Department of Infectious Diseases, King's College London London, UK
| | - Stéphane Hué
- Department of Infection, Division of Infection and Immunity, Centre for Medical Molecular Virology, University College London London, UK
| | - Michael H Malim
- Department of Infectious Diseases, King's College London London, UK
| | - Caroline Goujon
- Department of Infectious Diseases, King's College London London, UK
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Schaller T, Pollpeter D, Apolonia L, Goujon C, Malim MH. Nuclear import of SAMHD1 is mediated by a classical karyopherin α/β1 dependent pathway and confers sensitivity to VpxMAC induced ubiquitination and proteasomal degradation. Retrovirology 2014; 11:29. [PMID: 24712655 PMCID: PMC4098787 DOI: 10.1186/1742-4690-11-29] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 03/27/2014] [Indexed: 12/21/2022] Open
Abstract
Background The deoxynucleotide-triphosphate (dNTP) hydrolase sterile alpha motif domain and HD domain 1 (SAMHD1) is a nuclear protein that inhibits HIV-1 infection in myeloid cells as well as quiescent CD4 T-cells, by decreasing the intracellular dNTP concentration below a level that is required for efficient reverse transcription. The Vpx proteins of the SIVSMM/HIV-2 lineage of lentiviruses bind SAMHD1 and recruit an ubiquitin ligase, leading to polyubiquitination and proteasomal degradation. Results Here, we have investigated the importance of nuclear localization for SAMHD1′s antiviral function as well as its sensitivity to the Vpx protein of SIVMAC. Using GST pull down assays, as well as RNA silencing approaches, we show that SAMHD1 preferentially uses karyopherin α2 (KPNA2) and a classical N-terminal nuclear localization signal (14KRPR17) to enter the nucleus. Reduction of karyopherin β1 (KPNB1) or KPNA2 by RNAi also led to cytoplasmic re-distribution of SAMHD1. Using primary human monocyte-derived macrophages (MDM), a cell type in which SAMHD1 is naturally expressed to high levels, we demonstrate that nuclear localization is not required for its antiviral activity. Cytoplasmic SAMHD1 still binds to VpxMAC, is efficiently polyubiquitinated, but is not degraded. We also find that VpxMAC-induced SAMHD1 degradation was partially reversed by ubiquitin carrying the K48R or K11R substitution mutations, suggesting involvement of K48 and K11 linkages in SAMHD1 polyubiquitination. Using ubiquitin K-R mutants also revealed differences in the ubiquitin linkages between wild type and cytoplasmic forms of SAMHD1, suggesting a potential association with the resistance of cytoplasmic SAMHD1 to VpxMAC induced degradation. Conclusions Our work extends published observations on SAMHD1 nuclear localization to a natural cell type for HIV-1 infection, identifies KPNA2/KPNB1 as cellular proteins important for SAMHD1 nuclear import, and indicates that components of the nuclear proteasomal degradation machinery are required for SAMHD1 degradation.
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Affiliation(s)
- Torsten Schaller
- Department of Infectious Diseases, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London Bridge, London SE1 9RT, UK.
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85
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Identification of cellular proteins interacting with the retroviral restriction factor SAMHD1. J Virol 2014; 88:5834-44. [PMID: 24623419 DOI: 10.1128/jvi.00155-14] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Human and mouse SAMHD1 proteins block human immunodeficiency virus type 1 (HIV-1) infection in noncycling human monocytic cells by reducing the intracellular deoxynucleoside triphosphate (dNTP) concentrations. Phosphorylation of human SAMHD1 at threonine 592 (T592) by cyclin-dependent kinase 1 (CDK1) and cyclin A2 impairs its HIV-1 restriction activity, but not the dNTP hydrolase activity, suggesting that dNTP depletion is not the sole mechanism of SAMHD1-mediated HIV-1 restriction. Using coimmunoprecipitation and mass spectrometry, we identified and validated two additional host proteins interacting with human SAMHD1, namely, cyclin-dependent kinase 2 (CDK2) and S-phase kinase-associated protein 2 (SKP2). We observed that mouse SAMHD1 specifically interacted with cyclin A2, cyclin B1, CDK1, and CDK2. Given the role of these SAMHD1-interacting proteins in cell cycle progression, we investigated the regulation of these host proteins by monocyte differentiation and activation of CD4+ T cells and examined their effect on the phosphorylation of human SAMHD1 at T592. Our results indicate that primary monocyte differentiation and CD4+ T-cell activation regulate the expression of these SAMHD1-interacting proteins. Furthermore, our results suggest that, in addition to CDK1 and cyclin A2, CDK2 phosphorylates T592 of human SAMHD1 and thereby regulates its HIV-1 restriction function. IMPORTANCE SAMHD1 is the first dNTP triphosphohydrolase found in mammalian cells. Human and mouse SAMHD1 proteins block HIV-1 infection in noncycling cells. Previous studies suggested that phosphorylation of human SAMHD1 at threonine 592 by CDK1 and cyclin A2 negatively regulates its HIV-1 restriction activity. However, it is unclear whether human SAMHD1 interacts with other host proteins in the cyclin A2 and CDK1 complex and whether mouse SAMHD1 shares similar cellular interacting partners. Here, we identify five cell cycle-related host proteins that interact with human and mouse SAMHD1, including three previously unknown cellular proteins (CDK2, cyclin B1, and SKP2). Our results demonstrate that several SAMHD1-interacting cellular proteins regulate phosphorylation of SAMHD1 and play an important role in HIV-1 restriction function. Our findings help define the role of these cellular interacting partners of SAMHD1 that regulate its HIV-1 restriction function.
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The retroviral restriction ability of SAMHD1, but not its deoxynucleotide triphosphohydrolase activity, is regulated by phosphorylation. Cell Host Microbe 2014; 13:441-51. [PMID: 23601106 DOI: 10.1016/j.chom.2013.03.005] [Citation(s) in RCA: 244] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/11/2013] [Accepted: 03/19/2013] [Indexed: 01/08/2023]
Abstract
SAMHD1 is a cellular enzyme that depletes intracellular deoxynucleoside triphosphates (dNTPs) and inhibits the ability of retroviruses, notably HIV-1, to infect myeloid cells. Although SAMHD1 is expressed in both cycling and noncycling cells, the antiviral activity of SAMHD1 is limited to noncycling cells. We determined that SAMHD1 is phosphorylated on residue T592 in cycling cells but that this phosphorylation is lost when cells are in a noncycling state. Reverse genetic experiments revealed that SAMHD1 phosphorylated on residue T592 is unable to block retroviral infection, but this modification does not affect the ability of SAMHD1 to decrease cellular dNTP levels. SAMHD1 contains a target motif for cyclin-dependent kinase 1 (cdk1) ((592)TPQK(595)), and cdk1 activity is required for SAMHD1 phosphorylation. Collectively, these findings indicate that phosphorylation modulates the ability of SAMHD1 to block retroviral infection without affecting its ability to decrease cellular dNTP levels.
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87
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Behrendt R, Roers A. Mouse models for Aicardi-Goutières syndrome provide clues to the molecular pathogenesis of systemic autoimmunity. Clin Exp Immunol 2014; 175:9-16. [PMID: 23713592 DOI: 10.1111/cei.12147] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2013] [Indexed: 12/31/2022] Open
Abstract
Aicardi-Goutières syndrome (AGS) is a hereditary autoimmune disease which overlaps clinically and pathogenetically with systemic lupus erythematosus (SLE), and can be regarded as a monogenic variant of SLE. Both conditions are characterized by chronic activation of anti-viral type I interferon (IFN) responses. AGS can be caused by mutations in one of several genes encoding intracellular enzymes all involved in nucleic acid metabolism. Mouse models of AGS-associated defects yielded distinct phenotypes and reproduced important features of the disease. Analysis of these mutant mouse lines stimulated a new concept of autoimmunity caused by intracellular accumulations of nucleic acids, which trigger a chronic cell-intrinsic antiviral type I IFN response and thereby autoimmunity. This model is of major relevance for our understanding of SLE pathogenesis. Findings in gene-targeted mice deficient for AGS associated enzymes are summarized in this review.
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Affiliation(s)
- R Behrendt
- Institute for Immunology, Medical Faculty Carl Gustav Carus, University of Technology Dresden, Dresden, Germany
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88
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Lee-Kirsch MA, Wolf C, Günther C. Aicardi-Goutières syndrome: a model disease for systemic autoimmunity. Clin Exp Immunol 2014; 175:17-24. [PMID: 23786362 DOI: 10.1111/cei.12160] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2013] [Indexed: 02/06/2023] Open
Abstract
Systemic autoimmunity is a complex disease process that results from a loss of immunological tolerance characterized by the inability of the immune system to discriminate self from non-self. In patients with the prototypic autoimmune disease systemic lupus erythematosus (SLE), formation of autoantibodies targeting ubiquitous nuclear antigens and subsequent deposition of immune complexes in the vascular bed induces inflammatory tissue injury that can affect virtually any organ system. Given the extraordinary genetic and phenotypic heterogeneity of SLE, one approach to the genetic dissection of complex SLE is to study monogenic diseases, for which a single gene defect is responsible. Considerable success has been achieved from the analysis of the rare monogenic disorder Aicardi-Goutières syndrome (AGS), an inflammatory encephalopathy that clinically resembles in-utero-acquired viral infection and that also shares features with SLE. Progress in understanding the cellular and molecular functions of the AGS causing genes has revealed novel pathways of the metabolism of intracellular nucleic acids, the major targets of the autoimmune attack in patients with SLE. Induction of autoimmunity initiated by immune recognition of endogenous nucleic acids originating from processes such as DNA replication/repair or endogenous retro-elements represents novel paradigms of SLE pathogenesis. These findings illustrate how investigating rare monogenic diseases can also fuel discoveries that advance our understanding of complex disease. This will not only aid the development of improved tools for SLE diagnosis and disease classification, but also the development of novel targeted therapeutic approaches.
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Affiliation(s)
- M A Lee-Kirsch
- Department of Pediatrics, University Hospital, Technical University Dresden, Dresden, Germany
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89
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Boasso A. Type I Interferon at the Interface of Antiviral Immunity and Immune Regulation: The Curious Case of HIV-1. SCIENTIFICA 2013; 2013:580968. [PMID: 24455433 PMCID: PMC3885208 DOI: 10.1155/2013/580968] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
Type I interferon (IFN-I) play a critical role in the innate immune response against viral infections. They actively participate in antiviral immunity by inducing molecular mechanisms of viral restriction and by limiting the spread of the infection, but they also orchestrate the initial phases of the adaptive immune response and influence the quality of T cell immunity. During infection with the human immunodeficiency virus type 1 (HIV-1), the production of and response to IFN-I may be severely altered by the lymphotropic nature of the virus. In this review I consider the different aspects of virus sensing, IFN-I production, signalling, and effects on target cells, with a particular focus on the alterations observed following HIV-1 infection.
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Affiliation(s)
- Adriano Boasso
- Immunology Section, Chelsea and Westminster Hospital, 369 Fulham Road, London SW10 9NH, UK
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90
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Rustagi A, Gale M. Innate antiviral immune signaling, viral evasion and modulation by HIV-1. J Mol Biol 2013; 426:1161-77. [PMID: 24326250 DOI: 10.1016/j.jmb.2013.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 02/08/2023]
Abstract
The intracellular innate antiviral response in human cells is an essential component of immunity against virus infection. As obligate intracellular parasites, all viruses must evade the actions of the host cell's innate immune response in order to replicate and persist. Innate immunity is induced when pathogen recognition receptors of the host cell sense viral products including nucleic acid as "non-self". This process induces downstream signaling through adaptor proteins to activate latent transcription factors that drive the expression of genes encoding antiviral and immune modulatory effector proteins that restrict virus replication and regulate adaptive immunity. The interferon regulatory factors (IRFs) are transcription factors that play major roles in innate immunity. In particular, IRF3 is activated in response to infection by a range of viruses including RNA viruses, DNA viruses and retroviruses. Among these viruses, human immunodeficiency virus type 1 (HIV-1) remains a major global health problem mediating chronic infection in millions of people wherein recent studies show that viral persistence is linked with the ability of the virus to dysregulate and evade the innate immune response. In this review, we discuss viral pathogen sensing, innate immune signaling pathways and effectors that respond to viral infection, the role of IRF3 in these processes and how it is regulated by pathogenic viruses. We present a contemporary overview of the interplay between HIV-1 and innate immunity, with a focus on understanding how innate immune control impacts infection outcome and disease.
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Affiliation(s)
- Arjun Rustagi
- Departments of Immunology and Global Health, University of Washington, Seattle, WA 98195-8059, USA
| | - Michael Gale
- Departments of Immunology and Global Health, University of Washington, Seattle, WA 98195-8059, USA.
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91
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Sze A, Olagnier D, Lin R, van Grevenynghe J, Hiscott J. SAMHD1 Host Restriction Factor: A Link with Innate Immune Sensing of Retrovirus Infection. J Mol Biol 2013; 425:4981-94. [DOI: 10.1016/j.jmb.2013.10.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 10/15/2013] [Accepted: 10/16/2013] [Indexed: 02/02/2023]
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92
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Strebel K. HIV accessory proteins versus host restriction factors. Curr Opin Virol 2013; 3:692-9. [PMID: 24246762 PMCID: PMC3855913 DOI: 10.1016/j.coviro.2013.08.004] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 02/05/2023]
Abstract
Primate immunodeficiency viruses, including HIV-1, are characterized by the presence of accessory genes such as vif, vpr, vpx, vpu, and nef. Current knowledge indicates that none of the primate lentiviral accessory proteins has enzymatic activity. Instead, these proteins interact with cellular ligands to either act as adapter molecules to redirect the normal function of host factors for virus-specific purposes or to inhibit a normal host function by mediating degradation or causing intracellular mislocalization/sequestration of the factors involved. This review aims at providing an update of our current understanding of how Vif, Vpu, and Vpx control the cellular restriction factors APOBEC3G, BST-2, and SAMHD1, respectively.
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Affiliation(s)
- Klaus Strebel
- Laboratory of Molecular Microbiology, Viral Biochemistry Section, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892-0460, United States.
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93
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Contribution of oligomerization to the anti-HIV-1 properties of SAMHD1. Retrovirology 2013; 10:131. [PMID: 24219908 PMCID: PMC3882887 DOI: 10.1186/1742-4690-10-131] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 10/10/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND SAMHD1 is a restriction factor that potently blocks infection by HIV-1 and other retroviruses. We have previously demonstrated that SAMHD1 oligomerizes in mammalian cells by immunoprecipitation. Here we investigated the contribution of SAMHD1 oligomerization to retroviral restriction. RESULTS Structural analysis of SAMHD1 and homologous HD domain proteins revealed that key hydrophobic residues Y146, Y154, L428 and Y432 stabilize the extensive dimer interface observed in the SAMHD1 crystal structure. Full-length SAMHD1 variants Y146S/Y154S and L428S/Y432S lost their ability to oligomerize tested by immunoprecipitation in mammalian cells. In agreement with these observations, the Y146S/Y154S variant of a bacterial construct expressing the HD domain of human SAMHD1 (residues 109-626) disrupted the dGTP-dependent tetramerization of SAMHD1 in vitro. Tetramerization-defective variants of the full-length SAMHD1 immunoprecipitated from mammalian cells and of the bacterially-expressed HD domain construct lost their dNTPase activity. The nuclease activity of the HD domain construct was not perturbed by the Y146S/Y154S mutations. Remarkably, oligomerization-deficient SAMHD1 variants potently restricted HIV-1 infection. CONCLUSIONS These results suggested that SAMHD1 oligomerization is not required for the ability of the protein to block HIV-1 infection.
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94
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Mechanism of allosteric activation of SAMHD1 by dGTP. Nat Struct Mol Biol 2013; 20:1304-9. [PMID: 24141705 PMCID: PMC3833828 DOI: 10.1038/nsmb.2692] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/10/2013] [Indexed: 01/21/2023]
Abstract
SAMHD1, a dNTP triphosphohydrolase (dNTPase), has a key role in human innate immunity. It inhibits infection of blood cells by retroviruses, including HIV, and prevents the development of the autoinflammatory Aicardi-Goutières syndrome (AGS). The inactive apo-SAMHD1 interconverts between monomers and dimers, and in the presence of dGTP the protein assembles into catalytically active tetramers. Here, we present the crystal structure of the human tetrameric SAMHD1-dGTP complex. The structure reveals an elegant allosteric mechanism of activation through dGTP-induced tetramerization of two inactive dimers. Binding of dGTP to four allosteric sites promotes tetramerization and induces a conformational change in the substrate-binding pocket to yield the catalytically active enzyme. Structure-based biochemical and cell-based biological assays confirmed the proposed mechanism. The SAMHD1 tetramer structure provides the basis for a mechanistic understanding of its function in HIV restriction and the pathogenesis of AGS.
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95
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SAMHD1 restricts herpes simplex virus 1 in macrophages by limiting DNA replication. J Virol 2013; 87:12949-56. [PMID: 24067963 DOI: 10.1128/jvi.02291-13] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Macrophages play important roles in host immune defense against virus infection. During infection by herpes simplex virus 1 (HSV-1), macrophages acquire enhanced antiviral potential. Restriction of HSV-1 replication and progeny production is important to prevent viral spread, but the cellular mechanisms that inhibit the DNA virus in macrophages are unknown. SAMHD1 was recently identified as a retrovirus restriction factor highly expressed in macrophages. The SAMHD1 protein is expressed in both undifferentiated monocytes and differentiated macrophages, but retroviral restriction is limited to differentiated cells by modulation of SAMHD1 phosphorylation. It is proposed to block reverse transcription of retroviral RNA into DNA by depleting cellular deoxynucleotide triphosphates (dNTPs). Viruses with DNA genomes do not employ reverse transcription during infection, but replication of their viral genomes is also dependent on intracellular dNTP concentrations. Here, we demonstrate that SAMHD1 restricts replication of the HSV-1 DNA genome in differentiated macrophage cell lines. Depleting SAMHD1 in THP-1 cells enhanced HSV-1 replication, while ectopic overexpression of SAMHD1 in U937 cells repressed HSV-1 replication. SAMHD1 did not impact viral gene expression from incoming HSV-1 viral genomes. HSV-1 restriction involved the dNTP triphosphohydrolase activity of SAMHD1 and was partially overcome by addition of exogenous deoxynucleosides. Unlike retroviruses, restriction of HSV-1 was not affected by SAMHD1 phosphorylation status. Our results suggest that SAMHD1 functions broadly to inhibit replication of DNA viruses in nondividing macrophages.
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96
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Zhao K, Du J, Han X, Goodier JL, Li P, Zhou X, Wei W, Evans SL, Li L, Zhang W, Cheung LE, Wang G, Kazazian HH, Yu XF. Modulation of LINE-1 and Alu/SVA retrotransposition by Aicardi-Goutières syndrome-related SAMHD1. Cell Rep 2013; 4:1108-15. [PMID: 24035396 PMCID: PMC3988314 DOI: 10.1016/j.celrep.2013.08.019] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 06/25/2013] [Accepted: 08/15/2013] [Indexed: 01/01/2023] Open
Abstract
Long interspersed elements 1 (LINE-1) occupy at least 17% of the human genome and are its only active autonomous retrotransposons. However, the host factors that regulate LINE-1 retrotransposition are not fully understood. Here, we demonstrate that the Aicardi-Goutières syndrome gene product SAMHD1, recently revealed to be an inhibitor of HIV/simian immunodeficiency virus (SIV) infectivity and neutralized by the viral Vpx protein, is also a potent regulator of LINE-1 and LINE-1-mediated Alu/SVA retrotransposition. We also found that mutant SAMHD1s of Aicardi-Goutières syndrome patients are defective in LINE-1 inhibition. Several domains of SAMHD1 are critical for LINE-1 regulation. SAMHD1 inhibits LINE-1 retrotransposition in dividing cells. An enzymatic active site mutant SAMHD1 maintained substantial anti-LINE-1 activity. SAMHD1 inhibits ORF2p-mediated LINE-1 reverse transcription in isolated LINE-1 ribonucleoproteins by reducing ORF2p level. Thus, SAMHD1 may be a cellular regulator of LINE-1 activity that is conserved in mammals.
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Affiliation(s)
- Ke Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, 519 E. Minzhu Avenue, Changchun, Jilin Province 130061, China
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97
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Rehwinkel J, Maelfait J, Bridgeman A, Rigby R, Hayward B, Liberatore RA, Bieniasz PD, Towers GJ, Moita LF, Crow YJ, Bonthron DT, Reis e Sousa C. SAMHD1-dependent retroviral control and escape in mice. EMBO J 2013; 32:2454-62. [PMID: 23872947 PMCID: PMC3770946 DOI: 10.1038/emboj.2013.163] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/01/2013] [Indexed: 12/12/2022] Open
Abstract
SAMHD1 is a host restriction factor for human immunodeficiency virus 1 (HIV-1) in cultured human cells. SAMHD1 mutations cause autoimmune Aicardi-Goutières syndrome and are found in cancers including chronic lymphocytic leukaemia. SAMHD1 is a triphosphohydrolase that depletes the cellular pool of deoxynucleoside triphosphates, thereby preventing reverse transcription of retroviral genomes. However, in vivo evidence for SAMHD1's antiviral activity has been lacking. We generated Samhd1 null mice that do not develop autoimmune disease despite displaying a type I interferon signature in spleen, macrophages and fibroblasts. Samhd1(-/-) cells have elevated deoxynucleoside triphosphate (dNTP) levels but, surprisingly, SAMHD1 deficiency did not lead to increased infection with VSV-G-pseudotyped HIV-1 vectors. The lack of restriction is likely attributable to the fact that dNTP concentrations in SAMHD1-sufficient mouse cells are higher than the KM of HIV-1 reverse transcriptase (RT). Consistent with this notion, an HIV-1 vector mutant bearing an RT with lower affinity for dNTPs was sensitive to SAMHD1-dependent restriction in cultured cells and in mice. This shows that SAMHD1 can restrict lentiviruses in vivo and that nucleotide starvation is an evolutionarily conserved antiviral mechanism.
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Affiliation(s)
- Jan Rehwinkel
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, UK
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jonathan Maelfait
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Anne Bridgeman
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rachel Rigby
- Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Bruce Hayward
- Leeds Institute of Molecular Medicine, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Rachel A Liberatore
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - Luis F Moita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Yanick J Crow
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - David T Bonthron
- Leeds Institute of Molecular Medicine, University of Leeds, St James’s University Hospital, Leeds, UK
| | - Caetano Reis e Sousa
- Immunobiology Laboratory, Cancer Research UK, London Research Institute, London, UK
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98
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Restriction of virus infection but not catalytic dNTPase activity is regulated by phosphorylation of SAMHD1. J Virol 2013; 87:11516-24. [PMID: 23966382 DOI: 10.1128/jvi.01642-13] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
SAMHD1 is a host protein responsible, at least in part, for the inefficient infection of dendritic, myeloid, and resting T cells by HIV-1. Interestingly, HIV-2 and SIVsm viruses are able to counteract SAMHD1 by targeting it for proteasomal degradation using their Vpx proteins. It has been proposed that SAMHD1 is a dGTP-dependent deoxynucleoside triphosphohydrolase (dNTPase) that restricts HIV-1 by reducing cellular dNTP levels to below that required for reverse transcription. However, nothing is known about SAMHD1 posttranslational modifications and their potential role in regulating SAMHD1 function. We used (32)P labeling and immunoblotting with phospho-specific antibodies to identify SAMHD1 as a phosphoprotein. Several amino acids in SAMHD1 were identified to be sites of phosphorylation using direct mass spectrometry. Mutation of these residues to alanine to prevent phosphorylation or to glutamic acid to mimic phosphorylation had no effect on the nuclear localization of SAMHD1 or its sensitivity to Vpx-mediated degradation. Furthermore, neither alanine nor glutamic acid substitutions had a significant effect on SAMHD1 dNTPase activity in an in vitro assay. Interestingly, however, we found that a T592E mutation, mimicking constitutive phosphorylation at a main phosphorylation site, severely affected the ability of SAMHD1 to restrict HIV-1 in a U937 cell-based restriction assay. In contrast, a T592A mutant was still capable of restricting HIV-1. These results indicate that SAMHD1 phosphorylation may be a negative regulator of SAMHD1 restriction activity. This conclusion is supported by our finding that SAMHD1 is hyperphosphorylated in monocytoid THP-1 cells under nonrestrictive conditions.
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Abstract
Replication of HIV-1 and other retroviruses is dependent on numerous host proteins in the cells. Some of the host proteins, however, function as restriction factors to block retroviral infection of target cells. The host protein SAMHD1 has been identified as the first mammalian deoxynucleoside triphosphate triphosphohydrolase (dNTPase), which blocks the infection of HIV-1 and other retroviruses in non-cycling immune cells. SAMHD1 protein is highly expressed in human myeloid-lineage cells and CD4+ T-lymphocytes, but its retroviral restriction function is only observed in noncycling cells. Recent studies have revealed biochemical mechanisms of SAMHD1-mediated retroviral restriction. In this review, the latest progress on SAMHD1 research is summarized and the mechanisms by which SAMHD1 mediates retroviral restriction are analyzed. Although the physiological function of SAMHD1 is largely unknown, this review provides perspectives about the role of endogenous SAMHD1 protein in maintaining normal cellular function, such as nucleic acid metabolism and the proliferation of cells.
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100
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DeLucia M, Mehrens J, Wu Y, Ahn J. HIV-2 and SIVmac accessory virulence factor Vpx down-regulates SAMHD1 enzyme catalysis prior to proteasome-dependent degradation. J Biol Chem 2013; 288:19116-26. [PMID: 23677995 DOI: 10.1074/jbc.m113.469007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
SAMHD1, a dGTP-regulated deoxyribonucleoside triphosphate (dNTP) triphosphohydrolase, down-regulates dNTP pools in terminally differentiated and quiescent cells, thereby inhibiting HIV-1 infection at the reverse transcription step. HIV-2 and simian immunodeficiency virus (SIV) counteract this restriction via a virion-associated virulence accessory factor, Vpx (Vpr in some SIVs), which loads SAMHD1 onto CRL4-DCAF1 E3 ubiquitin ligase for polyubiquitination, programming it for proteasome-dependent degradation. However, the detailed molecular mechanisms of SAMHD1 recruitment to the E3 ligase have not been defined. Further, whether divergent, orthologous Vpx proteins, encoded by distinct HIV/SIV strains, bind SAMHD1 in a similar manner, at a molecular level, is not known. We applied surface plasmon resonance analysis to assess the requirements for and kinetics of binding between various primate SAMHD1 proteins and Vpx proteins from SIV or HIV-2 strains. Our data indicate that Vpx proteins, bound to DCAF1, interface with the C terminus of primate SAMHD1 proteins with nanomolar affinity, manifested by rapid association and slow dissociation. Further, we provide evidence that Vpx binding to SAMHD1 inhibits its catalytic activity and induces disassembly of a dGTP-dependent oligomer. Our studies reveal a previously unrecognized biochemical mechanism of Vpx-mediated SAMHD1 inhibition: direct down-modulation of its catalytic activity, mediated by the same binding event that leads to SAMHD1 recruitment to the E3 ubiquitin ligase for proteasome-dependent degradation.
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Affiliation(s)
- Maria DeLucia
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260, USA
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