1
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Zhang SM, Paulin CB, Shu H, Yagüe-Capilla M, Michel M, Marttila P, Ortis F, Bwanika HC, Dirks C, Venkatram RP, Wiita E, Jemth AS, Almlöf I, Loseva O, Hormann FM, Koolmeister T, Linde E, Lee S, Llona-Minguez S, Haraldsson M, Axelsson H, Strömberg K, Homan EJ, Scobie M, Lundbäck T, Helleday T, Rudd SG. Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel. iScience 2024; 27:108907. [PMID: 38318365 PMCID: PMC10839966 DOI: 10.1016/j.isci.2024.108907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 09/05/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
SAMHD1 is a dNTP triphosphohydrolase governing nucleotide pool homeostasis and can detoxify chemotherapy metabolites controlling their clinical responses. To understand SAMHD1 biology and investigate the potential of targeting SAMHD1 as neoadjuvant to current chemotherapies, we set out to discover selective small-molecule inhibitors. Here, we report a discovery pipeline encompassing a biochemical screening campaign and a set of complementary biochemical, biophysical, and cell-based readouts for rigorous characterization of the screen output. The identified small molecules, TH6342 and analogs, accompanied by inactive control TH7126, demonstrated specific, low μM potency against both physiological and oncology-drug-derived substrates. By coupling kinetic studies with thermal shift assays, we reveal the inhibitory mechanism of TH6342 and analogs, which engage pre-tetrameric SAMHD1 and deter oligomerization and allosteric activation without occupying nucleotide-binding pockets. Altogether, our study diversifies inhibitory modes against SAMHD1, and the discovery pipeline reported herein represents a thorough framework for future SAMHD1 inhibitor development.
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Affiliation(s)
- Si Min Zhang
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Cynthia B.J. Paulin
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Huazhang Shu
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Miriam Yagüe-Capilla
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Maurice Michel
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Petra Marttila
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Florian Ortis
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Henri Colyn Bwanika
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Christopher Dirks
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Rajagopal Papagudi Venkatram
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Femke M. Hormann
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Erika Linde
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sun Lee
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sabin Llona-Minguez
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Kia Strömberg
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Evert J. Homan
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Sean G. Rudd
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
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2
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Tsai MHC, Caswell SJ, Morris ER, Mann MC, Pennell S, Kelly G, Groom HCT, Taylor IA, Bishop KN. Attenuation of reverse transcriptase facilitates SAMHD1 restriction of HIV-1 in cycling cells. Retrovirology 2023; 20:5. [PMID: 37127613 PMCID: PMC10150492 DOI: 10.1186/s12977-023-00620-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/06/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND SAMHD1 is a deoxynucleotide triphosphohydrolase that restricts replication of HIV-1 in differentiated leucocytes. HIV-1 is not restricted in cycling cells and it has been proposed that this is due to phosphorylation of SAMHD1 at T592 in these cells inactivating the enzymatic activity. To distinguish between theories for how SAMHD1 restricts HIV-1 in differentiated but not cycling cells, we analysed the effects of substitutions at T592 on restriction and dNTP levels in both cycling and differentiated cells as well as tetramer stability and enzymatic activity in vitro. RESULTS We first showed that HIV-1 restriction was not due to SAMHD1 nuclease activity. We then characterised a panel of SAMHD1 T592 mutants and divided them into three classes. We found that a subset of mutants lost their ability to restrict HIV-1 in differentiated cells which generally corresponded with a decrease in triphosphohydrolase activity and/or tetramer stability in vitro. Interestingly, no T592 mutants were able to restrict WT HIV-1 in cycling cells, despite not being regulated by phosphorylation and retaining their ability to hydrolyse dNTPs. Lowering dNTP levels by addition of hydroxyurea did not give rise to restriction. Compellingly however, HIV-1 RT mutants with reduced affinity for dNTPs were significantly restricted by wild-type and T592 mutant SAMHD1 in both cycling U937 cells and Jurkat T-cells. Restriction correlated with reverse transcription levels. CONCLUSIONS Altogether, we found that the amino acid at residue 592 has a strong effect on tetramer formation and, although this is not a simple "on/off" switch, this does correlate with the ability of SAMHD1 to restrict HIV-1 replication in differentiated cells. However, preventing phosphorylation of SAMHD1 and/or lowering dNTP levels by adding hydroxyurea was not enough to restore restriction in cycling cells. Nonetheless, lowering the affinity of HIV-1 RT for dNTPs, showed that restriction is mediated by dNTP levels and we were able to observe for the first time that SAMHD1 is active and capable of inhibiting HIV-1 replication in cycling cells, if the affinity of RT for dNTPs is reduced. This suggests that the very high affinity of HIV-1 RT for dNTPs prevents HIV-1 restriction by SAMHD1 in cycling cells.
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Affiliation(s)
- Ming-Han C Tsai
- Retroviral Replication Laboratory, The Francis Crick Institute, London, UK
- LabGenius, London, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
- AstraZeneca, Granta Park, Cambridge, UK
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
- Department of Biosciences, University of Durham, Durham, UK
| | - Melanie C Mann
- Retroviral Replication Laboratory, The Francis Crick Institute, London, UK
- Sartorius, Ulm, Germany
| | - Simon Pennell
- Structural Biology of DNA-Damage Signalling Laboratory, The Francis Crick Institute, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, London, UK
| | - Harriet C T Groom
- Retroviral Replication Laboratory, The Francis Crick Institute, London, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | - Kate N Bishop
- Retroviral Replication Laboratory, The Francis Crick Institute, London, UK.
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3
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Kapoor-Vazirani P, Rath SK, Liu X, Shu Z, Bowen NE, Chen Y, Haji-Seyed-Javadi R, Daddacha W, Minten EV, Danelia D, Farchi D, Duong DM, Seyfried NT, Deng X, Ortlund EA, Kim B, Yu DS. SAMHD1 deacetylation by SIRT1 promotes DNA end resection by facilitating DNA binding at double-strand breaks. Nat Commun 2022; 13:6707. [PMID: 36344525 PMCID: PMC9640623 DOI: 10.1038/s41467-022-34578-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022] Open
Abstract
Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) has a dNTPase-independent function in promoting DNA end resection to facilitate DNA double-strand break (DSB) repair by homologous recombination (HR); however, it is not known if upstream signaling events govern this activity. Here, we show that SAMHD1 is deacetylated by the SIRT1 sirtuin deacetylase, facilitating its binding with ssDNA at DSBs, to promote DNA end resection and HR. SIRT1 complexes with and deacetylates SAMHD1 at conserved lysine 354 (K354) specifically in response to DSBs. K354 deacetylation by SIRT1 promotes DNA end resection and HR but not SAMHD1 tetramerization or dNTPase activity. Mechanistically, K354 deacetylation by SIRT1 promotes SAMHD1 recruitment to DSBs and binding to ssDNA at DSBs, which in turn facilitates CtIP ssDNA binding, leading to promotion of genome integrity. These findings define a mechanism governing the dNTPase-independent resection function of SAMHD1 by SIRT1 deacetylation in promoting HR and genome stability.
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Affiliation(s)
- Priya Kapoor-Vazirani
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sandip K Rath
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhen Shu
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicole E Bowen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Yitong Chen
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ramona Haji-Seyed-Javadi
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Waaqo Daddacha
- Department of Biochemistry and Molecular Biology, Medical College of Georgia at Augusta University, Augusta, GA, 30912, USA
| | - Elizabeth V Minten
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Diana Danelia
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniela Farchi
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Duc M Duong
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Xingming Deng
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - David S Yu
- Department of Radiation Oncology and Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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4
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SAMHD1 … and Viral Ways around It. Viruses 2021; 13:v13030395. [PMID: 33801276 PMCID: PMC7999308 DOI: 10.3390/v13030395] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
The SAM and HD domain-containing protein 1 (SAMHD1) is a dNTP triphosphohydrolase that plays a crucial role for a variety of different cellular functions. Besides balancing intracellular dNTP concentrations, facilitating DNA damage repair, and dampening excessive immune responses, SAMHD1 has been shown to act as a major restriction factor against various virus species. In addition to its well-described activity against retroviruses such as HIV-1, SAMHD1 has been identified to reduce the infectivity of different DNA viruses such as the herpesviruses CMV and EBV, the poxvirus VACV, or the hepadnavirus HBV. While some viruses are efficiently restricted by SAMHD1, others have developed evasion mechanisms that antagonize the antiviral activity of SAMHD1. Within this review, we summarize the different cellular functions of SAMHD1 and highlight the countermeasures viruses have evolved to neutralize the restriction factor SAMHD1.
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5
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Yu CH, Bhattacharya A, Persaud M, Taylor AB, Wang Z, Bulnes-Ramos A, Xu J, Selyutina A, Martinez-Lopez A, Cano K, Demeler B, Kim B, Hardies SC, Diaz-Griffero F, Ivanov DN. Nucleic acid binding by SAMHD1 contributes to the antiretroviral activity and is enhanced by the GpsN modification. Nat Commun 2021; 12:731. [PMID: 33531504 PMCID: PMC7854603 DOI: 10.1038/s41467-021-21023-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 01/08/2021] [Indexed: 12/26/2022] Open
Abstract
SAMHD1 impedes infection of myeloid cells and resting T lymphocytes by retroviruses, and the enzymatic activity of the protein-dephosphorylation of deoxynucleotide triphosphates (dNTPs)-implicates enzymatic dNTP depletion in innate antiviral immunity. Here we show that the allosteric binding sites of the enzyme are plastic and can accommodate oligonucleotides in place of the allosteric activators, GTP and dNTP. SAMHD1 displays a preference for oligonucleotides containing phosphorothioate bonds in the Rp configuration located 3' to G nucleotides (GpsN), the modification pattern that occurs in a mechanism of antiviral defense in prokaryotes. In the presence of GTP and dNTPs, binding of GpsN-containing oligonucleotides promotes formation of a distinct tetramer with mixed occupancy of the allosteric sites. Mutations that impair formation of the mixed-occupancy complex abolish the antiretroviral activity of SAMHD1, but not its ability to deplete dNTPs. The findings link nucleic acid binding to the antiretroviral activity of SAMHD1, shed light on the immunomodulatory effects of synthetic phosphorothioated oligonucleotides and raise questions about the role of nucleic acid phosphorothioation in human innate immunity.
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Affiliation(s)
- Corey H Yu
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Akash Bhattacharya
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Mirjana Persaud
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander B Taylor
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Zhonghua Wang
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Angel Bulnes-Ramos
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joella Xu
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | - Anastasia Selyutina
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alicia Martinez-Lopez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kristin Cano
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada.,Department of Chemistry and Biochemistry, University of Montana, Missoula, MT, USA
| | - Baek Kim
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | - Stephen C Hardies
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA.
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6
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Thapa G, Bhattacharya A, Bhattacharya S. Dimeric Hold States of Anti-HIV Protein SAMHD1 are Redox Tunable. J Chem Inf Model 2020; 60:6377-6391. [PMID: 33135886 DOI: 10.1021/acs.jcim.0c00629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The sterile α motif and histidine-aspartate domain-containing protein 1 (or SAMHD1) is a human protein that restricts HIV-1 in select terminally differentiated cells of the immune system by acting as a triphosphohydrolase, lowering dNTP pools. The functionally active form of the protein has been reported to be a tetramer where adjacent monomers are linked by GTP-Mg+2-dNTP cross-bridges, although some studies have also suggested the existence of a dimeric form of this protein. In this in silico study, we have investigated the stability of SAMHD1 dimeric "hold states" as well as the role of intrachain disulfide bonds. We have found that dimeric-GTP bound SAMHD1 can exist as a viable meso-stable hold state with extensive motion in the C-terminal domain, which is quenched upon tetramer assembly. The redox switch comprised of residues C341, C350, and C522 was found to be linked to changes in the allosteric site, suggesting a mechanism for initiating tetramer disassembly. The disulfide state of the protein dimer (C341-S-S-C350 vs C341-S-S-C522) also plays a role in driving affinities for the allosteric dATP molecules. In sum, our results suggest a model wherein dimeric SAMHD1 exists as a "hold state" in the cytosol, ready to be activated by dATP concentrations, where the "tunability" of this activation is further regulated by the redox state of the enzyme.
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Affiliation(s)
- Gauri Thapa
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Akash Bhattacharya
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, United States
| | - Swati Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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7
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De Meo S, Dell'Oste V, Molfetta R, Tassinari V, Lotti LV, Vespa S, Pignoloni B, Covino DA, Fantuzzi L, Bona R, Zingoni A, Nardone I, Biolatti M, Coscia A, Paolini R, Benkirane M, Edfors F, Sandalova T, Achour A, Hiscott J, Landolfo S, Santoni A, Cerboni C. SAMHD1 phosphorylation and cytoplasmic relocalization after human cytomegalovirus infection limits its antiviral activity. PLoS Pathog 2020; 16:e1008855. [PMID: 32986788 PMCID: PMC7544099 DOI: 10.1371/journal.ppat.1008855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 10/08/2020] [Accepted: 08/03/2020] [Indexed: 12/16/2022] Open
Abstract
SAMHD1 is a host restriction factor that functions to restrict both retroviruses and DNA viruses, based on its nuclear deoxynucleotide triphosphate (dNTP) hydrolase activity that limits availability of intracellular dNTP pools. In the present study, we demonstrate that SAMHD1 expression was increased following human cytomegalovirus (HCMV) infection, with only a modest effect on infectious virus production. SAMHD1 was rapidly phosphorylated at residue T592 after infection by cellular cyclin-dependent kinases, especially Cdk2, and by the viral kinase pUL97, resulting in a significant fraction of phosho-SAMHD1 being relocalized to the cytoplasm of infected fibroblasts, in association with viral particles and dense bodies. Thus, our findings indicate that HCMV-dependent SAMHD1 cytoplasmic delocalization and inactivation may represent a potential novel mechanism of HCMV evasion from host antiviral restriction activities.
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Affiliation(s)
- Simone De Meo
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Valentina Dell'Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Rosa Molfetta
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Valentina Tassinari
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | - Simone Vespa
- Laboratory of General Pathology, Center of Aging Science and Translational Medicine (CeSI-MeT) and Department of Medical, Oral and Biotechnological Sciences G. d'Annunzio University, Chieti, Italy
| | - Benedetta Pignoloni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | | | - Laura Fantuzzi
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Roberta Bona
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Zingoni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Ilaria Nardone
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Alessandra Coscia
- Neonatal Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Rossella Paolini
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Monsef Benkirane
- Institut de Génétique Humaine, Laboratoire de Virologie Moléculaire, CNRS-Université de Montpellier, Montpellier, France
| | - Fredrik Edfors
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - John Hiscott
- Istituto Pasteur Italia-Cenci Bolognetti Foundation, Rome, Italy
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Angela Santoni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
- IRCCS, Neuromed, Pozzilli, Isernia, Italy
| | - Cristina Cerboni
- Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
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8
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Wang Z, Bhattacharya A, White T, Buffone C, McCabe A, Nguyen LA, Shepard CN, Pardo S, Kim B, Weintraub ST, Demeler B, Diaz-Griffero F, Ivanov DN. Functionality of Redox-Active Cysteines Is Required for Restriction of Retroviral Replication by SAMHD1. Cell Rep 2020; 24:815-823. [PMID: 30044979 PMCID: PMC6067006 DOI: 10.1016/j.celrep.2018.06.090] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 05/01/2018] [Accepted: 06/21/2018] [Indexed: 01/04/2023] Open
Abstract
SAMHD1 is a dNTP triphosphohydrolase (dNTPase) that impairs retroviral replication in a subset of noncycling immune cells. Here we show that SAMHD1 is a redox-sensitive enzyme and identify three redox-active cysteines within the protein: C341, C350, and C522. The three cysteines reside near one another and the allosteric nucleotide binding site. Mutations C341S and C522S abolish the ability of SAMHD1 to restrict HIV replication, whereas the C350S mutant remains restriction competent. The C522S mutation makes the protein resistant to inhibition by hydrogen peroxide but has no effect on the tetramerization-dependent dNTPase activity of SAMHD1 in vitro or on the ability of SAMHD1 to deplete cellular dNTPs. Our results reveal that enzymatic activation of SAMHD1 via nucleotide-dependent tetramerization is not sufficient for the establishment of the antiviral state and that retroviral restriction depends on the ability of the protein to undergo redox transformations.
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Affiliation(s)
- Zhonghua Wang
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Akash Bhattacharya
- Department of Biochemistry & Structural Biology, 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
| | - Aine McCabe
- 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
| | - Sammy Pardo
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, 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
| | - Susan T Weintraub
- Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Borries Demeler
- Department of Biochemistry & Structural Biology, 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 & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA.
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9
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The missing link: allostery and catalysis in the anti-viral protein SAMHD1. Biochem Soc Trans 2019; 47:1013-1027. [PMID: 31296733 PMCID: PMC7045340 DOI: 10.1042/bst20180348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 12/11/2022]
Abstract
Vertebrate protein SAMHD1 (sterile-α-motif and HD domain containing protein 1) regulates the cellular dNTP (2′-deoxynucleoside-5′-triphosphate) pool by catalysing the hydrolysis of dNTP into 2′-deoxynucleoside and triphosphate products. As an important regulator of cell proliferation and a key player in dNTP homeostasis, mutations to SAMHD1 are implicated in hypermutated cancers, and germline mutations are associated with Chronic Lymphocytic Leukaemia and the inflammatory disorder Aicardi–Goutières Syndrome. By limiting the supply of dNTPs for viral DNA synthesis, SAMHD1 also restricts the replication of several retroviruses, such as HIV-1, and some DNA viruses in dendritic and myeloid lineage cells and resting T-cells. SAMHD1 activity is regulated throughout the cell cycle, both at the level of protein expression and post-translationally, through phosphorylation. In addition, allosteric regulation further fine-tunes the catalytic activity of SAMHD1, with a nucleotide-activated homotetramer as the catalytically active form of the protein. In cells, GTP and dATP are the likely physiological activators of two adjacent allosteric sites, AL1 (GTP) and AL2 (dATP), that bridge monomer–monomer interfaces to stabilise the protein homotetramer. This review summarises the extensive X-ray crystallographic, biophysical and molecular dynamics experiments that have elucidated important features of allosteric regulation in SAMHD1. We present a comprehensive mechanism detailing the structural and protein dynamics components of the allosteric coupling between nucleotide-induced tetramerization and the catalysis of dNTP hydrolysis by SAMHD1.
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10
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Patra KK, Bhattacharya A, Bhattacharya S. Molecular dynamics investigation of a redox switch in the anti-HIV protein SAMHD1. Proteins 2019; 87:748-759. [PMID: 31017331 DOI: 10.1002/prot.25701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/11/2019] [Accepted: 04/22/2019] [Indexed: 12/17/2022]
Abstract
HIV-1 is restricted in macrophages and certain quiescent myeloid cells due to a "Scorched Earth" dNTP starvation strategy attributed to the sterile alpha motif and HD domain protein-SAMHD1. Active SAMHD1 tetramers are assembled by GTP-Mg+2-dNTP cross bridges and cleave the triphosphate groups of dNTPs at a K m of ~10 μM, which is consistent with dNTP concentrations in cycling cells, but far higher than the equivalent concentration in quiescent cells. Given the substantial disparity between the dNTP concentrations required to activate SAMHD1 tetramers (~10 μM) and the dNTP concentrations in noncycling cells (~10 nM), the possibility of alternate enzymatically active forms of SAMHD1, including monomers remains open. In particular, the possibility of redox regulation of such monomers is also an open question. There have been experimental studies on the regulation of SAMHD1 by Glutathione driven redox reactions recently. Therefore, in this work, we have performed all-atom molecular dynamics simulations to study the dynamics of monomeric SAMHD1 constructs in the context of the three redox-susceptible Cysteine residues and compared them to monomers assembled within a tetramer. Our results indicate that assembly into a tetramer causes ordering of the catalytic core and increased solvent accessibility of the Catalytic Site. We have also found that glutathionylation of surface exposed C522 causes long range allosteric disruptions extending into the protein core. Finally, we see evidence suggesting a transient interaction between C522 and C341. Such a disulfide linkage has been hypothesized by experimental models, but has never been observed in crystal structures before.
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Affiliation(s)
- Kajwal Kumar Patra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Akash Bhattacharya
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Swati Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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11
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Buffone C, Kutzner J, Opp S, Martinez-Lopez A, Selyutina A, Coggings SA, Studdard LR, Ding L, Kim B, Spearman P, Schaller T, Diaz-Griffero F. The ability of SAMHD1 to block HIV-1 but not SIV requires expression of MxB. Virology 2019; 531:260-268. [PMID: 30959264 DOI: 10.1016/j.virol.2019.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/20/2022]
Abstract
SAMHD1 is a human restriction factor known to prevent infection of macrophages, resting CD4+ T cells, and dendritic cells by HIV-1. To test the contribution of MxB to the ability of SAMHD1 to block HIV-1 infection, we created human THP-1 cell lines that were knocked out for expression of MxB, SAMHD1, or both. Interestingly, MxB depletion renders SAMHD1 ineffective against HIV-1 but not SIVmac. We observed similar results in human primary macrophages that were knockdown for the expression of MxB. To understand how MxB assists SAMHD1 restriction of HIV-1, we examined direct interaction between SAMHD1 and MxB in pull-down experiments. In addition, we investigated several properties of SAMHD1 in the absence of MxB expression, including subcellular localization, phosphorylation of the SAMHD1 residue T592, and dNTPs levels. These experiments showed that SAMHD1 restriction of HIV-1 requires expression of MxB.
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Affiliation(s)
- Cindy Buffone
- Albert Einstein College of Medicine, Microbiology and Immunology, Bronx, NY, 10461, USA
| | - Juliane Kutzner
- University Hospital Heidelberg, Department of Infectious Diseases, Heidelberg, 69120, Germany
| | - Silvana Opp
- Albert Einstein College of Medicine, Microbiology and Immunology, Bronx, NY, 10461, USA
| | - Alicia Martinez-Lopez
- Albert Einstein College of Medicine, Microbiology and Immunology, Bronx, NY, 10461, USA
| | - Anastasia Selyutina
- Albert Einstein College of Medicine, Microbiology and Immunology, Bronx, NY, 10461, USA
| | | | | | - Lingmei Ding
- Cincinnati Children's Hospital, Infectious Diseases, Cincinnati, OH, 45229, USA
| | - Baek Kim
- Emory University, Pediatrics, Atlanta, 30322, Georgia
| | - Paul Spearman
- Cincinnati Children's Hospital, Infectious Diseases, Cincinnati, OH, 45229, USA
| | - Torsten Schaller
- University Hospital Heidelberg, Department of Infectious Diseases, Heidelberg, 69120, Germany
| | - Felipe Diaz-Griffero
- Albert Einstein College of Medicine, Microbiology and Immunology, Bronx, NY, 10461, USA.
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12
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Plitnik T, Sharkey ME, Mahboubi B, Kim B, Stevenson M. Incomplete Suppression of HIV-1 by SAMHD1 Permits Efficient Macrophage Infection. Pathog Immun 2018; 3:197-223. [PMID: 30656243 PMCID: PMC6333473 DOI: 10.20411/pai.v3i2.263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Sterile alpha motif and histidine/aspartic acid domain-containing protein (SAMHD1) is a dNTP triphosphorylase that reduces cellular dNTP levels in non-dividing cells, such as macrophages. Since dNTPs are required for reverse transcription, HIV-2 and most SIVs encode a Vpx protein that promotes proteasomal degradation of SAMHD1. It is unclear how HIV-1, which does not appear to harbor a SAMHD1 escape mechanism, is able to infect macrophages in the face of SAMHD1 restriction. Methods: To assess whether HIV-1 had a mechanism to negate SAMHD1 activity, we compared SAMHD1 and dNTP levels in macrophages infected by HIV-1 and SIV. We examined whether macrophages infected by HIV-1 still harbored antiviral levels of SAMHD1 by assessing their susceptibility to superinfection by vpx-deleted SIV. Finally, to assess whether HIV-1 reverse transcriptase (RT) has adapted to a low dNTP environment, we evaluated SAMHD1 sensitivity of chimeric HIV-1 and SIV variants in which the RT regions were functionally exchanged. Results: Here, we demonstrate that HIV-1 efficiently infects macrophages without modulating SAMHD1 activity or cellular dNTP levels, and that macrophages permissive to HIV-1 infection remained refractory to superinfection by vpx-deleted SIV. Furthermore, through the use of chimeric HIV/SIV, we demonstrate that the differential sensitivity of HIV-1 and SIV to SAMHD1 restriction is not dictated by RT. Conclusions: Our study reveals fundamental differences between HIV-1 and SIV in the strategy used to evade restriction by SAMHD1 and suggests a degree of resistance of HIV-1 to the antiviral environment created by SAMHD1. Understanding how these cellular restrictions antagonize viral replication will be important for the design of novel antiviral strategies.
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Affiliation(s)
- Timothy Plitnik
- Department of Microbiology & Immunology; Miller School of Medicine, University of Miami; Miami, Florida
| | - Mark E Sharkey
- Department of Medicine; Miller School of Medicine, University of Miami; Miami, Florida
| | - Bijan Mahboubi
- Department of Pediatrics, Emory University; Atlanta, Georgia.,Center for Drug Discovery, Children's Healthcare of Atlanta; Atlanta, Georgia
| | - Baek Kim
- Department of Pediatrics, Emory University; Atlanta, Georgia.,Center for Drug Discovery, Children's Healthcare of Atlanta; Atlanta, Georgia.,Department of Pharmacy, Kyung-Hee University; Seoul; South Korea
| | - Mario Stevenson
- Department of Microbiology & Immunology; Miller School of Medicine, University of Miami; Miami, Florida.,Department of Medicine; Miller School of Medicine, University of Miami; Miami, Florida
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13
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Martinez-Lopez A, Martin-Fernandez M, Buta S, Kim B, Bogunovic D, Diaz-Griffero F. SAMHD1 deficient human monocytes autonomously trigger type I interferon. Mol Immunol 2018; 101:450-460. [PMID: 30099227 DOI: 10.1016/j.molimm.2018.08.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/24/2018] [Accepted: 08/02/2018] [Indexed: 01/04/2023]
Abstract
Germline mutations in the human SAMHD1 gene cause the development of Aicardi-Goutières Syndrome (AGS), with a dominant feature being increased systemic type I interferon(IFN) production. Here we tested the state of type I IFN induction and response to, in SAMHD1 knockout (KO) human monocytic cells. SAMHD1 KO cells exhibited spontaneous transcription and translation of IFN-β and subsequent interferon-stimulated genes (ISGs) as compared to parental wild-type cells. This elevation of IFN-β and ISGs was abrogated via inhibition of the TBK1-IRF3 pathway in the SAMHD1 KO cells. In agreement, we found that SAMHD1 KO cells present high levels of phosphorylated TBK1 when compared to control cells. Moreover, addition of blocking antibody against type I IFN also reversed elevation of ISGs. These experiments suggested that SAMHD1 KO cells are persistently auto-stimulating the TBK1-IRF3 pathway, leading to an enhanced production of type I IFN and subsequent self-induction of ISGs.
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Affiliation(s)
- Alicia Martinez-Lopez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Marta Martin-Fernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Sofija Buta
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Baek Kim
- Department of Pediatrics, Emory University, Atlanta, GA 30322, United States
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, United States.
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14
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SAMHD1 Promotes DNA End Resection to Facilitate DNA Repair by Homologous Recombination. Cell Rep 2018; 20:1921-1935. [PMID: 28834754 DOI: 10.1016/j.celrep.2017.08.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/05/2017] [Accepted: 07/28/2017] [Indexed: 12/28/2022] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) is initiated by CtIP/MRN-mediated DNA end resection to maintain genome integrity. SAMHD1 is a dNTP triphosphohydrolase, which restricts HIV-1 infection, and mutations are associated with Aicardi-Goutières syndrome and cancer. We show that SAMHD1 has a dNTPase-independent function in promoting DNA end resection to facilitate DSB repair by HR. SAMHD1 deficiency or Vpx-mediated degradation causes hypersensitivity to DSB-inducing agents, and SAMHD1 is recruited to DSBs. SAMHD1 complexes with CtIP via a conserved C-terminal domain and recruits CtIP to DSBs to facilitate end resection and HR. Significantly, a cancer-associated mutant with impaired CtIP interaction, but not dNTPase-inactive SAMHD1, fails to rescue the end resection impairment of SAMHD1 depletion. Our findings define a dNTPase-independent function for SAMHD1 in HR-mediated DSB repair by facilitating CtIP accrual to promote DNA end resection, providing insight into how SAMHD1 promotes genome integrity.
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15
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Mauney CH, Hollis T. SAMHD1: Recurring roles in cell cycle, viral restriction, cancer, and innate immunity. Autoimmunity 2018; 51:96-110. [PMID: 29583030 PMCID: PMC6117824 DOI: 10.1080/08916934.2018.1454912] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/16/2018] [Indexed: 12/24/2022]
Abstract
Sterile alpha motif and histidine-aspartic acid domain-containing protein 1 (SAMHD1) is a deoxynucleotide triphosphate (dNTP) hydrolase that plays an important role in the homeostatic balance of cellular dNTPs. Its emerging role as an effector of innate immunity is affirmed by mutations in the SAMHD1 gene that cause the severe autoimmune disease, Aicardi-Goutieres syndrome (AGS) and that are linked to cancer. Additionally, SAMHD1 functions as a restriction factor for retroviruses, such as HIV. Here, we review the current biochemical and biological properties of the enzyme including its structure, activity, and regulation by post-translational modifications in the context of its cellular function. We outline open questions regarding the biology of SAMHD1 whose answers will be important for understanding its function as a regulator of cell cycle progression, genomic integrity, and in autoimmunity.
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Affiliation(s)
- Christopher H Mauney
- a Department of Biochemistry , Center for Structural Biology, Wake Forest School of Medicine , Winston Salem , NC , USA
| | - Thomas Hollis
- a Department of Biochemistry , Center for Structural Biology, Wake Forest School of Medicine , Winston Salem , NC , USA
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16
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A Cyclin-Binding Motif in Human SAMHD1 Is Required for Its HIV-1 Restriction, dNTPase Activity, Tetramer Formation, and Efficient Phosphorylation. J Virol 2018; 92:JVI.01787-17. [PMID: 29321329 DOI: 10.1128/jvi.01787-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022] Open
Abstract
Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) regulates intracellular deoxynucleoside triphosphate (dNTP) levels and functions as a retroviral restriction factor through its dNTP triphosphohydrolase (dNTPase) activity. Human SAMHD1 interacts with cell cycle regulatory proteins cyclin A2, cyclin-dependent kinase 1 (CDK1), and CDK2. This interaction mediates phosphorylation of SAMHD1 at threonine 592 (T592), which negatively regulates HIV-1 restriction. We previously reported that the interaction is mediated, at least in part, through a cyclin-binding motif (RXL, amino acids [aa] 451 to 453). To understand the role of the RXL motif in regulating SAMHD1 activity, we performed structural and functional analyses of RXL mutants and the effect on HIV-1 restriction. We found that the RXL mutation (R451A and L453A, termed RL/AA) disrupted SAMHD1 tetramer formation and abolished its dNTPase activity in vitro and in cells. Compared to wild-type (WT) SAMHD1, the RL/AA mutant failed to restrict HIV-1 infection and had reduced binding to cyclin A2. WT SAMHD1 and RL/AA mutant proteins were degraded by Vpx from HIV-2 but were not spontaneously ubiquitinated in the absence of Vpx. Analysis of proteasomal and autophagy degradation revealed that WT and RL/AA SAMHD1 protein levels were enhanced only when both pathways of degradation were simultaneously inhibited. Our results demonstrate that the RXL motif of human SAMHD1 is required for its HIV-1 restriction, tetramer formation, dNTPase activity, and efficient phosphorylation at T592. These findings identify a new functional domain of SAMHD1 important for its structural integrity, enzyme activity, phosphorylation, and HIV-1 restriction.IMPORTANCE SAMHD1 is the first mammalian dNTPase identified as a restriction factor that inhibits HIV-1 replication by decreasing the intracellular dNTP pool in nondividing cells, although the critical mechanisms regulating SAMHD1 function remain unclear. We previously reported that mutations of a cyclin-binding RXL motif in human SAMHD1 significantly affect protein expression levels, half-life, nuclear localization, and phosphorylation, suggesting an important role of this motif in modulating SAMHD1 functions in cells. To further understand the significance and mechanisms of the RXL motif in regulating SAMHD1 activity, we performed structural and functional analyses of the RXL motif mutation and its effect on HIV-1 restriction. Our results indicate that the RXL motif is critical for tetramer formation, dNTPase activity, and HIV-1 restriction. These findings help us understand SAMHD1 interactions with other host proteins and the mechanisms regulating SAMHD1 structure and functions in cells.
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17
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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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18
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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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19
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Patra KK, Bhattacharya A, Bhattacharya S. Uncovering allostery and regulation in SAMHD1 through molecular dynamics simulations. Proteins 2017; 85:1266-1275. [PMID: 28321930 DOI: 10.1002/prot.25287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 03/03/2017] [Accepted: 03/14/2017] [Indexed: 11/09/2022]
Abstract
The human sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a retroviral restriction factor in myeloid cells and non-cycling CD4+ T cells, a feature imputed to its phosphohydrolase activity-the enzyme depletes the cellular dNTP levels inhibiting reverse transcription. The functionally active form of SAMHD1 is an allosterically triggered tetramer which utilizes GTP-Mg+2 -dNTP cross bridges to link and stabilize adjacent monomers. However, very little is known about how it assembles into a tetramer and how long the tetramer stays intact. In this computational study, we provide a molecular dynamics based analysis of the structural stability and allosteric site dynamics in SAMHD1. We have investigated the allosteric links which assemble and hold the tetramer together. We have also extended this analysis to a regulatory mutant of SAMHD1. Experimental studies have indicated that phosphorylation of T592 downregulates HIV-1 restriction. A similar result is also achieved by a phosphomimetic mutation T592E. While a mechanistic understanding of the process is still elusive, the loss of structural integrity of the enzyme is conjectured to be the cause of the impaired dNTPase activity of the T592E mutant. MD simulations show that the T592E mutation causes slightly elevated local motions which remain confined to the short helix (residues 591-595), which contains the phosphorylation site and do not cause long-range destabilization of the SAMHD1 tetramer within the timeframe of the simulations. Thus, the regulatory mechanism of SAMHD1 is a more subtle mechanism than has been previously suspected. Proteins 2017; 85:1266-1275. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kajwal Kumar Patra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India, 400076
| | - Akash Bhattacharya
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas, 78229-3900
| | - Swati Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India, 400076
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20
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Hollenbaugh JA, Shelton J, Tao S, Amiralaei S, Liu P, Lu X, Goetze RW, Zhou L, Nettles JH, Schinazi RF, Kim B. Substrates and Inhibitors of SAMHD1. PLoS One 2017; 12:e0169052. [PMID: 28046007 PMCID: PMC5207538 DOI: 10.1371/journal.pone.0169052] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/09/2016] [Indexed: 11/19/2022] Open
Abstract
SAMHD1 hydrolyzes 2'-deoxynucleoside-5'-triphosphates (dNTPs) into 2'-deoxynucleosides and inorganic triphosphate products. In this paper, we evaluated the impact of 2' sugar moiety substitution for different nucleotides on being substrates for SAMHD1 and mechanisms of actions for the results. We found that dNTPs ((2'R)-2'-H) are only permissive in the catalytic site of SAMHD1 due to L150 exclusion of (2'R)-2'-F and (2'R)-2'-OH nucleotides. However, arabinose ((2'S)-2'-OH) nucleoside-5'-triphosphates analogs are permissive to bind in the catalytic site and be hydrolyzed by SAMHD1. Moreover, when the (2'S)-2' sugar moiety is increased to a (2'S)-2'-methyl as with the SMDU-TP analog, we detect inhibition of SAMHD1’s dNTPase activity. Our computational modeling suggests that (2'S)-2'-methyl sugar moiety clashing with the Y374 of SAMHD1. We speculate that SMDU-TP mechanism of action requires that the analog first docks in the catalytic pocket of SAMHD1 but prevents the A351-V378 helix conformational change from being completed, which is needed before hydrolysis can occur. Collectively we have identified stereoselective 2' substitutions that reveal nucleotide substrate specificity for SAMHD1, and a novel inhibitory mechanism for the dNTPase activity of SAMHD1. Importantly, our data is beneficial for understanding if FDA-approved antiviral and anticancer nucleosides are hydrolyzed by SAMHD1 in vivo.
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Affiliation(s)
- Joseph A. Hollenbaugh
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Jadd Shelton
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Sijia Tao
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Sheida Amiralaei
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Peng Liu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Xiao Lu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Russell W. Goetze
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Longhu Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - James H. Nettles
- Department of Biomedical Informatics and Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Baek Kim
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia United States of America
- College of Pharmacy, Kyung-Hee University, Seoul, South Korea
- * E-mail:
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21
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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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22
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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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23
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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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24
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Wang Z, Bhattacharya A, Villacorta J, Diaz-Griffero F, Ivanov DN. Allosteric Activation of SAMHD1 Protein by Deoxynucleotide Triphosphate (dNTP)-dependent Tetramerization Requires dNTP Concentrations That Are Similar to dNTP Concentrations Observed in Cycling T Cells. J Biol Chem 2016; 291:21407-21413. [PMID: 27566548 DOI: 10.1074/jbc.c116.751446] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/25/2016] [Indexed: 12/16/2022] Open
Abstract
SAMHD1 is a dNTP hydrolase, whose activity is required for maintaining low dNTP concentrations in non-cycling T cells, dendritic cells, and macrophages. SAMHD1-dependent dNTP depletion is thought to impair retroviral replication in these cells, but the relationship between the dNTPase activity and retroviral restriction is not fully understood. In this study, we investigate allosteric activation of SAMHD1 by deoxynucleotide-dependent tetramerization and measure how the lifetime of the enzymatically active tetramer is affected by different dNTP ligands bound in the allosteric site. The EC50dNTP values for SAMHD1 activation by dNTPs are in the 2-20 μm range, and the half-life of the assembled tetramer after deoxynucleotide depletion varies from minutes to hours depending on what dNTP is bound in the A2 allosteric site. Comparison of the wild-type SAMHD1 and the T592D mutant reveals that the phosphomimetic mutation affects the rates of tetramer dissociation, but has no effect on the equilibrium of allosteric activation by deoxynucleotides. Collectively, our data suggest that deoxynucleotide-dependent tetramerization contributes to regulation of deoxynucleotide levels in cycling cells, whereas in non-cycling cells restrictive to retroviral replication, SAMHD1 activation is likely to be achieved through a distinct mechanism.
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Affiliation(s)
- Zhonghua Wang
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229 and
| | - Akash Bhattacharya
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229 and
| | - Jessica Villacorta
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229 and
| | - Felipe Diaz-Griffero
- the Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Dmitri N Ivanov
- From the Department of Biochemistry, University of Texas Health Science Center, San Antonio, Texas 78229 and
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25
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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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26
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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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27
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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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28
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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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29
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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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