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Lee JH, Sergi C, Kast RE, Kanwar BA, Bourbeau J, Oh S, Sohn MG, Lee CJ, Coleman MD. Aggravating mechanisms from COVID-19. Virol J 2024; 21:228. [PMID: 39334442 PMCID: PMC11430051 DOI: 10.1186/s12985-024-02506-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces immune-mediated diseases. The pathophysiology of COVID-19 uses the following three mechanisms: (1) inflammasome activation mechanism; (2) cGAS-STING signaling mechanism; and (3) SAMHD1 tetramerization mechanism, which leads to IFN-I production. Interactions between the host and virus govern induction, resulting in multiorgan impacts. The NLRP3 with cGAS-STING constitutes the primary immune response. The expression of SARS-CoV-2 ORF3a, NSP6, NSP7, and NSP8 blocks innate immune activation and facilitates virus replication by targeting the RIG-I/MDA5, TRIF, and cGAS-STING signaling. SAMHD1 has a target motif for CDK1 to protect virion assembly, threonine 592 to modulate a catalytically active tetramer, and antiviral IFN responses to block retroviral infection. Plastic and allosteric nucleic acid binding of SAMHD1 modulates the antiretroviral activity of SAMHD1. Therefore, inflammasome activation, cGAS-STING signaling, and SAMHD1 tetramerization explain acute kidney injury, hepatic, cardiac, neurological, and gastrointestinal injury of COVID-19. It might be necessary to effectively block the pathological courses of diverse diseases.
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Affiliation(s)
- Jong Hoon Lee
- Science and Research Center, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Geriatrics, Gyeonggi Medical Center Pocheon Hospital, 1648 Pocheon-ro Sin-eup-dong, Pocheon-si, Gyeonggi-do, 11142, Republic of Korea.
| | - Consolato Sergi
- Division of Anatomical Pathology, Children's Hospital of Eastern Ontario (CHEO), University of Ottawa, 401 Smyth Road, Ottawa, ON, K1H 8L1, Canada
| | - Richard E Kast
- IIAIGC Study Center, 11 Arlington Ct, Burlington, 05408 VT, USA
| | - Badar A Kanwar
- Haider Associates, 1999 Forest Ridge Dr, Bedford, TX, 76021, USA
| | - Jean Bourbeau
- Respiratory Epidemiology and Clinical Research Unit, McGill University Health Centre, Montréal, QC, Canada
| | - Sangsuk Oh
- Department of Food Engineering, Food Safety Laboratory, Memory Unit, Ewha Womans University, Seoul, 03670, Korea
| | - Mun-Gi Sohn
- Department of Food Science, KyungHee University College of Life Science, Seoul, 17104, Republic of Korea
| | - Chul Joong Lee
- Department of Anesthesiology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Michael D Coleman
- College of Health and Life Sciences, Aston University, Birmingham, B4 7ET, UK.
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2
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James CD, Youssef A, Prabhakar AT, Otoa R, Roe JD, Witt A, Lewis RL, Bristol ML, Wang X, Zhang K, Li R, Morgan IM. Human papillomavirus 16 replication converts SAMHD1 into a homologous recombination factor and promotes its recruitment to replicating viral DNA. J Virol 2024; 98:e0082624. [PMID: 39194246 PMCID: PMC11406955 DOI: 10.1128/jvi.00826-24] [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: 05/15/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024] Open
Abstract
We have demonstrated that SAMHD1 (sterile alpha motif and histidine-aspartic domain HD-containing protein 1) is a restriction factor for the human papillomavirus 16 (HPV16) life cycle. Here, we demonstrate that in HPV-negative cervical cancer C33a cells and human foreskin keratinocytes immortalized by HPV16 (HFK+HPV16), SAMHD1 is recruited to E1-E2 replicating DNA. Homologous recombination (HR) factors are required for HPV16 replication, and viral replication promotes phosphorylation of SAMHD1, which converts it from a dNTPase to an HR factor independent from E6/E7 expression. A SAMHD1 phospho-mimic (SAMHD1 T592D) reduces E1-E2-mediated DNA replication in C33a cells and has enhanced recruitment to the replicating DNA. In HFK+HPV16 cells, SAMHD1 T592D is recruited to the viral DNA and attenuates cellular growth, but does not attenuate growth in isogenic HFK cells immortalized by E6/E7 alone. SAMHD1 T592D also attenuates the development of viral replication foci following keratinocyte differentiation. The results indicated that enhanced SAMHD1 phosphorylation could be therapeutically beneficial in cells with HPV16 replicating genomes. Protein phosphatase 2A (PP2A) can dephosphorylate SAMHD1, and PP2A function can be inhibited by endothall. We demonstrate that endothall reduces E1-E2 replication and promotes SAMHD1 recruitment to E1-E2 replicating DNA, mimicking the SAMHD1 T592D phenotypes. Finally, we demonstrate that in head and neck cancer cell lines with HPV16 episomal genomes, endothall attenuates their growth and promotes recruitment of SAMHD1 to the viral genome. The results suggest that targeting cellular phosphatases has therapeutic potential for the treatment of HPV infections and cancers. IMPORTANCE Human papillomaviruses (HPVs) are causative agents in around 5% of all human cancers. The development of anti-viral therapeutics depends upon an increased understanding of the viral life cycle. Here, we demonstrate that HPV16 replication converts sterile alpha motif and histidine-aspartic domain HD-containing protein 1 (SAMHD1) into a homologous recombination (HR) factor via phosphorylation. This phosphorylation promotes recruitment of SAMHD1 to viral DNA to assist with replication. A SAMHD1 mutant that mimics phosphorylation is hyper-recruited to viral DNA and attenuates viral replication. Expression of this mutant in HPV16-immortalized cells attenuates the growth of these cells, but not cells immortalized by the viral oncogenes E6/E7 alone. Finally, we demonstrate that the phosphatase inhibitor endothall promotes hyper-recruitment of endogenous SAMHD1 to HPV16 replicating DNA and can attenuate the growth of both HPV16-immortalized human foreskin keratinocytes (HFKs) and HPV16-positive head and neck cancer cell lines. We propose that phosphatase inhibitors represent a novel tool for combating HPV infections and disease.
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Affiliation(s)
- Claire D James
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Aya Youssef
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Apurva T Prabhakar
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Raymonde Otoa
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Jenny D Roe
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Austin Witt
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Rachel L Lewis
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Molly L Bristol
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
- VCU Massey Cancer Center, Richmond, Virginia, USA
| | - Xu Wang
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Kun Zhang
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
| | - Renfeng Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Iain M Morgan
- Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University (VCU), Richmond, Virginia, USA
- VCU Massey Cancer Center, Richmond, Virginia, USA
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3
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Thapa G, Bhattacharya A, Bhattacharya S. Molecular dynamics investigation of DNA fragments bound to the anti-HIV protein SAMHD1 reveals alterations in allosteric communications. J Mol Graph Model 2024; 129:108748. [PMID: 38452417 DOI: 10.1016/j.jmgm.2024.108748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024]
Abstract
The sterile alpha motif and histidine-aspartate domain-containing protein 1 (or SAMHD1), a human dNTP-triphosphohydrolase, contributes to HIV-1 restriction in select terminally differentiated cells of the immune system. While the prevailing hypothesis is that the catalytically active form of the protein is an allosterically triggered tetramer, whose HIV-1 restriction properties are attributed to its dNTP - triphosphohydrolase activity, it is also known to bind to ssRNA and ssDNA oligomers. A complete picture of the structure-function relationship of the enzyme is still elusive and the function corresponding to its nucleic acid binding ability is debated. In this in silico study, we investigate the stability, preference and allosteric effects of DNA oligomers bound to SAMHD1. In particular, we compare the binding of DNA and RNA oligomers of the same sequence and also consider the binding of DNA fragments with phosphorothioate bonds in the backbone. The results are compared with the canonical form with the monomers connected by GTP/dATP crossbridges. The simulations indicate that SAMHD1 dimers preferably bind to DNA and RNA oligomers compared to GTP/dATP. However, allosteric communication channels are altered in the nucleic acid acid bound complexes compared to the canonical form. All results are consistent with the hypothesis that the DNA bound form of the protein correspond to an unproductive off-pathway state where the protein is sequestered and not available for dNTP hydrolysis.
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Affiliation(s)
- Gauri Thapa
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | | | - Swati Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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4
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Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA. Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis. Nat Commun 2024; 15:3775. [PMID: 38710701 PMCID: PMC11074143 DOI: 10.1038/s41467-024-48237-w] [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: 11/03/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes.
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Affiliation(s)
- Oliver J Acton
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ailidh J O Burgess
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biosciences, University of Durham, Durham, DH1 3LE, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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5
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Orris B, Sung MW, Bhat S, Xu Y, Huynh KW, Han S, Johnson DC, Bosbach B, Shields DJ, Stivers JT. Guanine-containing ssDNA and RNA induce dimeric and tetrameric structural forms of SAMHD1. Nucleic Acids Res 2023; 51:12443-12458. [PMID: 37930833 PMCID: PMC10711556 DOI: 10.1093/nar/gkad971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/19/2023] [Accepted: 10/14/2023] [Indexed: 11/08/2023] Open
Abstract
The dNTPase activity of tetrameric SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) plays a critical role in cellular dNTP regulation. SAMHD1 also associates with stalled DNA replication forks, DNA repair foci, ssRNA and telomeres. The above functions require nucleic acid binding by SAMHD1, which may be modulated by its oligomeric state. Here we establish in cryo-EM and biochemical studies that the guanine-specific A1 activator site of each SAMHD1 monomer is used to target the enzyme to guanine nucleotides within single-stranded (ss) DNA and RNA. Remarkably, nucleic acid strands containing a single guanine base induce dimeric SAMHD1, while two or more guanines with ∼20 nucleotide spacing induce a tetrameric form. A cryo-EM structure of ssRNA-bound tetrameric SAMHD1 shows how ssRNA strands bridge two SAMHD1 dimers and stabilize the structure. This ssRNA-bound tetramer is inactive with respect to dNTPase and RNase activity.
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Affiliation(s)
- Benjamin Orris
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
| | | | - Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
| | - Yingrong Xu
- Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Seungil Han
- Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Darren C Johnson
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016, USA
| | - Benedikt Bosbach
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016, USA
| | - David J Shields
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
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6
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James CD, Youssef A, Prabhakar AT, Otoa R, Witt A, Lewis RL, Bristol ML, Wang X, Zhang K, Li R, Morgan IM. Human Papillomavirus 16 replication converts SAMHD1 into a homologous recombination factor and promotes its recruitment to replicating viral DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566899. [PMID: 38014153 PMCID: PMC10680734 DOI: 10.1101/2023.11.13.566899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
We have demonstrated that SAMHD1 (sterile alpha motif and histidine-aspartic domain HD-containing protein 1) is a restriction factor for the HPV16 life cycle. Here we demonstrate that in HPV negative cervical cancer C33a cells and human foreskin keratinocytes immortalized by HPV16 (HFK+HPV16), SAMHD1 is recruited to E1-E2 replicating DNA. Homologous recombination (HR) factors are required for HPV16 replication and viral replication promotes phosphorylation of SAMHD1, which converts it from a dNTPase to an HR factor independent from E6/E7 expression. A SAMHD1 phosphor-mimic (SAMHD1 T592D) reduces E1-E2 mediated DNA replication in C33a cells and has enhanced recruitment to the replicating DNA. In HFK+HPV16 cells SAMHD1 T592D is recruited to the viral DNA and attenuates cellular growth, but does not attenuate growth in isogenic HFK cells immortalized by E6/E7 alone. SAMHD1 T592D also attenuates the development of viral replication foci following keratinocyte differentiation. The results indicated that enhanced SAMHD1 phosphorylation could be therapeutically beneficial in cells with HPV16 replicating genomes. Protein phosphatase 2A (PP2A) can dephosphorylate SAMHD1 and PP2A function can be inhibited by endothall. We demonstrate that endothall reduces E1-E2 replication and promotes SAMHD1 recruitment to E1-E2 replicating DNA, mimicking the SAMHD1 T592D phenotypes. Finally, we demonstrate that in head and neck cancer cell lines with HPV16 episomal genomes endothall attenuates their growth and promotes recruitment of SAMHD1 to the viral genome. The results suggest that targeting cellular phosphatases has therapeutic potential for the treatment of HPV infections and cancers. Importance Human papillomaviruses are causative agents in around 5% of all human cancers. The development of anti-viral therapeutics depends upon an increased understanding of the viral life cycle. Here we demonstrate that HPV16 replication converts SAMHD1 into an HR factor via phosphorylation. This phosphorylation promotes recruitment of SAMHD1 to viral DNA to assist with replication. A SAMHD1 mutant that mimics phosphorylation is hyper-recruited to viral DNA and attenuates viral replication. Expression of this mutant in HPV16 immortalized cells attenuates the growth of these cells, but not cells immortalized by the viral oncogenes E6/E7 alone. Finally, we demonstrate that the phosphatase inhibitor endothall promotes hyper-recruitment of endogenous SAMHD1 to HPV16 replicating DNA and can attenuate the growth of both HPV16 immortalized human foreskin keratinocytes and HPV16 positive head and neck cancer cell lines. We propose that phosphatase inhibitors represent a novel tool for combating HPV infections and disease.
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7
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McCown C, Yu CH, Ivanov DN. Allosteric substrate activation of SAMHD1 shapes deoxynucleotide triphosphate imbalances by interconnecting the depletion and biosynthesis of different dNTPs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567083. [PMID: 38014186 PMCID: PMC10680743 DOI: 10.1101/2023.11.14.567083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
SAMHD1 is a dNTPase that impedes replication of HIV-1 in myeloid cells and resting T lymphocytes. Here we elucidate the substrate activation mechanism of SAMHD1 that depends on dNTP binding at allosteric sites and the concomitant tetramerization of the enzyme. The study reveals that SAMHD1 activation involves an inactive tetrameric intermediate with partial occupancy of the allosteric sites. The equilibrium between the inactive and active tetrameric states, which is coupled to cooperative binding/dissociation of at least two allosteric dNTP ligands, controls the dNTPase activity of the enzyme, which, in addition, depends on the identity of the dNTPs occupying the four allosteric sites of the active tetramer. We show how such allosteric regulation determines deoxynucleotide triphosphate levels established in the dynamic equilibria between dNTP production and SAMHD1-catalyzed depletion. Notably, the mechanism enables a distinctive functionality of SAMHD1, which we call facilitated dNTP depletion, whereby elevated biosynthesis of some dNTPs results in more efficient depletion of others. The regulatory relationship between the biosynthesis and depletion of different dNTPs sheds light on the emerging role of SAMHD1 in the biology of dNTP homeostasis with implications for HIV/AIDS, innate antiviral immunity, T cell disorders, telomere maintenance and therapeutic efficacy of nucleoside analogs.
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8
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Sarmiento-Mañús R, Fontcuberta-Cervera S, González-Bayón R, Hannah MA, Álvarez-Martínez FJ, Barrajón-Catalán E, Micol V, Quesada V, Ponce MR, Micol JL. Analysis of the Arabidopsis venosa4-0 mutant supports the role of VENOSA4 in dNTP metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111819. [PMID: 37562732 DOI: 10.1016/j.plantsci.2023.111819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/07/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
Human Sterile alpha motif and histidine-aspartate domain containing protein 1 (SAMHD1) functions as a dNTPase to maintain dNTP pool balance. In eukaryotes, the limiting step in de novo dNTP biosynthesis is catalyzed by RIBONUCLEOTIDE REDUCTASE (RNR). In Arabidopsis, the RNR1 subunit of RNR is encoded by CRINKLED LEAVES 8 (CLS8), and RNR2 by three paralogous genes, including TSO MEANING 'UGLY' IN CHINESE 2 (TSO2). In plants, DIFFERENTIAL DEVELOPMENT OF VASCULAR ASSOCIATED CELLS 1 (DOV1) catalyzes the first step of the de novo biosynthesis of purines. Here, to explore the role of VENOSA4 (VEN4), the most likely Arabidopsis ortholog of human SAMHD1, we studied the ven4-0 point mutation, whose leaf phenotype was stronger than those of its insertional alleles. Structural predictions suggested that the E249L substitution in the mutated VEN4-0 protein rigidifies its 3D structure. The morphological phenotypes of the ven4, cls8, and dov1 single mutants were similar, and those of the ven4 tso2 and ven4 dov1 double mutants were synergistic. The ven4-0 mutant had reduced levels of four amino acids related to dNTP biosynthesis, including glutamine and glycine, which are precursors in the de novo purine biosynthesis. Our results reveal high functional conservation between VEN4 and SAMHD1 in dNTP metabolism.
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Affiliation(s)
- Raquel Sarmiento-Mañús
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | | | - Rebeca González-Bayón
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Matthew A Hannah
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Francisco Javier Álvarez-Martínez
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Enrique Barrajón-Catalán
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Vicente Micol
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Víctor Quesada
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain.
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain.
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9
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Maehigashi T, Lim C, Wade LR, Bowen NE, Knecht KM, Alvarez NN, Kelly WG, Schinazi RF, Kim DH, Xiong Y, Kim B. Biochemical functions and structure of Caenorhabditis elegans ZK177.8 protein: Aicardi-Goutières syndrome SAMHD1 dNTPase ortholog. J Biol Chem 2023; 299:105148. [PMID: 37567474 PMCID: PMC10485159 DOI: 10.1016/j.jbc.2023.105148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Mutations in sterile alpha motif domain and histidine-aspartate domain-containing protein 1 (SAMHD1) are found in a neurodevelopmental disorder, Aicardi-Goutières syndrome, and cancers, and SAMHD1, which is a deoxynucleoside triphosphate (dNTP) triphosphorylase, was identified as a myeloid-specific HIV-1 restriction factor. Here, we characterized the enzymology and structure of an SAMHD1 ortholog of Caenorhabditis elegans, ZK177.8, which also reportedly induces developmental defects upon gene knockdown. We found ZK177.8 protein is a dNTPase allosterically regulated by dGTP. The active site of ZK177.8 recognizes both 2' OH and triphosphate moieties of dNTPs but not base moiety. The dGTP activator induces the formation of the enzymatically active ZK177.8 tetramers, and ZK177.8 protein lowers cellular dNTP levels in a human monocytic cell line. Finally, ZK177.8 tetramers display very similar X-ray crystal structure with human and mouse SAMHD1s except that its lack of the canonical sterile alpha motif domain. This striking conservation in structure, function, and allosteric regulatory mechanism for the hydrolysis of the DNA building blocks supports their host developmental roles.
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Affiliation(s)
- Tatsuya Maehigashi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Christopher Lim
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Lydia R Wade
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Nicole E Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Kirsten M Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Natalie N Alvarez
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - William G Kelly
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Center for ViroScience and Cure, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Dong-Hyun Kim
- Neurobiota Research Center, College of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Center for ViroScience and Cure, Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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10
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Harada Y, Mizote Y, Suzuki T, Hirayama A, Ikeda S, Nishida M, Hiratsuka T, Ueda A, Imagawa Y, Maeda K, Ohkawa Y, Murai J, Freeze HH, Miyoshi E, Higashiyama S, Udono H, Dohmae N, Tahara H, Taniguchi N. Metabolic clogging of mannose triggers dNTP loss and genomic instability in human cancer cells. eLife 2023; 12:e83870. [PMID: 37461317 DOI: 10.7554/elife.83870] [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: 09/30/2022] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Mannose has anticancer activity that inhibits cell proliferation and enhances the efficacy of chemotherapy. How mannose exerts its anticancer activity, however, remains poorly understood. Here, using genetically engineered human cancer cells that permit the precise control of mannose metabolic flux, we demonstrate that the large influx of mannose exceeding its metabolic capacity induced metabolic remodeling, leading to the generation of slow-cycling cells with limited deoxyribonucleoside triphosphates (dNTPs). This metabolic remodeling impaired dormant origin firing required to rescue stalled forks by cisplatin, thus exacerbating replication stress. Importantly, pharmacological inhibition of de novo dNTP biosynthesis was sufficient to retard cell cycle progression, sensitize cells to cisplatin, and inhibit dormant origin firing, suggesting dNTP loss-induced genomic instability as a central mechanism for the anticancer activity of mannose.
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Affiliation(s)
- Yoichiro Harada
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yu Mizote
- Department of Cancer Drug Discovery and Development, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Mikako Nishida
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toru Hiratsuka
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Ayaka Ueda
- Department of Molecular Biochemistry and Clinical Investigation, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yusuke Imagawa
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Kento Maeda
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan
- Department of Biochemistry and Molecular Genetics, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Eiji Miyoshi
- Department of Molecular Biochemistry and Clinical Investigation, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shigeki Higashiyama
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan
- Department of Biochemistry and Molecular Genetics, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Heiichiro Udono
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Hideaki Tahara
- Department of Cancer Drug Discovery and Development, Research Institute, Osaka International Cancer Institute, Osaka, Japan
- Project Division of Cancer Biomolecular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
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11
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Espada CE, Sari L, Cahill MP, Yang H, Phillips S, Martinez N, Kenney AD, Yount JS, Xiong Y, Lin MM, Wu L. SAMHD1 impairs type I interferon induction through the MAVS, IKKε, and IRF7 signaling axis during viral infection. J Biol Chem 2023; 299:104925. [PMID: 37328105 PMCID: PMC10404699 DOI: 10.1016/j.jbc.2023.104925] [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: 05/02/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/18/2023] Open
Abstract
Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) restricts human immunodeficiency virus type 1 (HIV-1) infection by reducing the intracellular dNTP pool. We have shown that SAMHD1 suppresses nuclear factor kappa-B activation and type I interferon (IFN-I) induction by viral infection and inflammatory stimuli. However, the mechanism by which SAMHD1 inhibits IFN-I remains unclear. Here, we show that SAMHD1 inhibits IFN-I activation induced by the mitochondrial antiviral-signaling protein (MAVS). SAMHD1 interacted with MAVS and suppressed MAVS aggregation in response to Sendai virus infection in human monocytic THP-1 cells. This resulted in increased phosphorylation of TANK binding kinase 1 (TBK1), inhibitor of nuclear factor kappa-B kinase epsilon (IKKε), and IFN regulatory factor 3 (IRF3). SAMHD1 suppressed IFN-I activation induced by IKKε and prevented IRF7 binding to the kinase domain of IKKε. We found that SAMHD1 interaction with the inhibitory domain (ID) of IRF7 (IRF7-ID) was necessary and sufficient for SAMHD1 suppression of IRF7-mediated IFN-I activation in HEK293T cells. Computational docking and molecular dynamics simulations revealed possible binding sites between IRF7-ID and full-length SAMHD1. Individual substitution of F411, E416, or V460 in IRF7-ID significantly reduced IRF7 transactivation activity and SAMHD1 binding. Furthermore, we investigated the role of SAMHD1 inhibition of IRF7-mediated IFN-I induction during HIV-1 infection. We found that THP-1 cells lacking IRF7 expression had reduced HIV-1 infection and viral transcription compared to control cells, indicating a positive role of IRF7 in HIV-1 infection. Our findings suggest that SAMHD1 suppresses IFN-I induction through the MAVS, IKKε, and IRF7 signaling axis.
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Affiliation(s)
- Constanza E Espada
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Levent Sari
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michael P Cahill
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Hua Yang
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Stacia Phillips
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Nicholas Martinez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Adam D Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Milo M Lin
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.
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12
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Orris B, Sung MW, Bhat S, Xu Y, Huynh KW, Han S, Johnson DC, Bosbach B, Shields DJ, Stivers JT. Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.544806. [PMID: 37398126 PMCID: PMC10312740 DOI: 10.1101/2023.06.15.544806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The dNTPase activity of tetrameric SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) plays a critical role in cellular dNTP regulation. SAMHD1 also associates with stalled DNA replication forks, DNA repair foci, ssRNA, and telomeres. The above functions require nucleic acid binding by SAMHD1, which may be modulated by its oligomeric state. Here we establish that the guanine-specific A1 activator site of each SAMHD1 monomer is used to target the enzyme to guanine nucleotides within single-stranded (ss) DNA and RNA. Remarkably, nucleic acid strands containing a single guanine base induce dimeric SAMHD1, while two or more guanines with ~20 nucleotide spacing induce a tetrameric form. A cryo-EM structure of ssRNA-bound tetrameric SAMHD1 shows how ssRNA strands bridge two SAMHD1 dimers and stabilize the structure. This ssRNA-bound tetramer is inactive with respect to dNTPase and RNase activity.
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Affiliation(s)
- Benjamin Orris
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205
| | | | - Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205
| | | | | | | | - Darren C. Johnson
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016
| | - Benedikt Bosbach
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016
| | - David J. Shields
- Centers for Therapeutic Innovation (CTI), Pfizer, New York, NY 10016
| | - James T. Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205
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13
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Yang H, Espada CE, Phillips S, Martinez N, Kenney AD, Yount JS, Xiong Y, Wu L. The host antiviral protein SAMHD1 suppresses NF-κB activation by interacting with the IKK complex during inflammatory responses and viral infection. J Biol Chem 2023; 299:104750. [PMID: 37100289 PMCID: PMC10318468 DOI: 10.1016/j.jbc.2023.104750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
Sterile alpha motif and histidine-aspartate (HD) domain-containing protein 1 (SAMHD1) inhibits HIV-1 replication in nondividing cells by reducing the intracellular dNTP pool. SAMHD1 also suppresses NF-κB activation induced by inflammatory stimuli and viral infections. Specifically, SAMHD1-mediated reduction of NF-κB inhibitory protein (IκBα) phosphorylation is important for the suppression of NF-κB activation. However, while the inhibitors of NF-κB kinase subunit alpha and beta (IKKα and IKKβ) regulate IκBα phosphorylation, the mechanism by which SAMHD1 regulates phosphorylation of IκBα remains unclear. Here, we report that SAMHD1 suppresses phosphorylation of IKKα/β/γ via interaction with IKKα and IKKβ, thus inhibiting subsequent phosphorylation of IκBα in monocytic THP-1 cells and differentiated nondividing THP-1 cells. We show that knockout of SAMHD1 enhanced phosphorylation of IKKα, IKKβ, and IKKγ in THP-1 cells treated with the NF-κB activator lipopolysaccharide or infected with Sendai virus and SAMHD1 reconstitution inhibited phosphorylation of IKKα/β/γ in Sendai virus-infected THP-1 cells. We demonstrate that endogenous SAMHD1 interacted with IKKα and IKKβ in THP-1 cells and recombinant SAMHD1 bound to purified IKKα or IKKβ directly in vitro. Mapping of these protein interactions showed that the HD domain of SAMHD1 interacts with both IKKα and IKKβ and that the kinase domain of IKKα and the ubiquitin-like domain of IKKβ are required for their interactions with SAMHD1, respectively. Moreover, we found that SAMHD1 disrupts the interaction between upstream kinase TAK1 and IKKα or IKKβ. Our findings identify a new regulatory mechanism by which SAMHD1 inhibits phosphorylation of IκBα and NF-κB activation.
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Affiliation(s)
- Hua Yang
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Constanza E Espada
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Stacia Phillips
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA
| | - Nicholas Martinez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Adam D Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Li Wu
- Department of Microbiology and Immunology, Carver College of Medicine, The University of Iowa, Iowa City, Iowa, USA.
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14
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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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15
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Xie Y, Zhang Y, Wang Y, Feng Y. Mechanism and Modulation of SidE Family Proteins in the Pathogenesis of Legionella pneumophila. Pathogens 2023; 12:pathogens12040629. [PMID: 37111515 PMCID: PMC10143409 DOI: 10.3390/pathogens12040629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Legionella pneumophila is the causative agent of Legionnaires' disease, causing fever and lung infection, with a death rate up to 15% in severe cases. In the process of infection, Legionella pneumophila secretes over 330 effectors into host cell via the Dot/Icm type IV secretion system to modulate multiple host cellular physiological processes, thereby changing the environment of the host cell and promoting the growth and propagation of the bacterium. Among these effector proteins, SidE family proteins from Legionella pneumophila catalyze a non-canonical ubiquitination reaction, which combines mono-ADP-ribosylation and phosphodiesterase activities together to attach ubiquitin onto substrates. Meanwhile, the activity of SidE family proteins is also under multiple modulations by other effectors. Herein we summarize the key insights into recent studies in this area, emphasizing the tight link between the modular structure of SidE family proteins and the pathogen virulence as well as the fundamental mechanism and modulation network for further extensive research.
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Affiliation(s)
- Yongchao Xie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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16
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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: 13] [Impact Index Per Article: 6.5] [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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17
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Lee JH, Kanwar B, Khattak A, Balentine J, Nguyen NH, Kast RE, Lee CJ, Bourbeau J, Altschuler EL, Sergi CM, Nguyen TNM, Oh S, Sohn MG, Coleman M. COVID-19 Molecular Pathophysiology: Acetylation of Repurposing Drugs. Int J Mol Sci 2022; 23:13260. [PMID: 36362045 PMCID: PMC9656873 DOI: 10.3390/ijms232113260] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 01/14/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces immune-mediated type 1 interferon (IFN-1) production, the pathophysiology of which involves sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1) tetramerization and the cytosolic DNA sensor cyclic-GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling pathway. As a result, type I interferonopathies are exacerbated. Aspirin inhibits cGAS-mediated signaling through cGAS acetylation. Acetylation contributes to cGAS activity control and activates IFN-1 production and nuclear factor-κB (NF-κB) signaling via STING. Aspirin and dapsone inhibit the activation of both IFN-1 and NF-κB by targeting cGAS. We define these as anticatalytic mechanisms. It is necessary to alleviate the pathologic course and take the lag time of the odds of achieving viral clearance by day 7 to coordinate innate or adaptive immune cell reactions.
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Affiliation(s)
- Jong Hoon Lee
- Science and Research Center, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Korea
| | - Badar Kanwar
- Department of Intensive Care Unit and Neonatal Intensive Care, Hunt Regional Hospital, Greenville, 75401 TX, USA
| | - Asif Khattak
- Department of Intensive Care Unit and Neonatal Intensive Care, Hunt Regional Hospital, Greenville, 75401 TX, USA
| | - Jenny Balentine
- Department of Intensive Care Unit and Neonatal Intensive Care, Hunt Regional Hospital, Greenville, 75401 TX, USA
| | - Ngoc Huy Nguyen
- Department of Health, Phutho Province, Tran Phu Str., Viet Tri City 227, Vietnam
| | | | - Chul Joong Lee
- Department of Anesthesiology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jean Bourbeau
- Respiratory Epidemiology and Clinical Research Unit, McGill University Health Centre, Montréal, QC H4A 3S5, Canada
| | - Eric L. Altschuler
- Department of Physical Medicine and Rehabilitation, Metropolitan Hospital, New York, NY 10029, USA
| | - Consolato M. Sergi
- Division of Anatomical Pathology, Children’s Hospital of Eastern Ontario (CHEO), University of Ottawa, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | | | - Sangsuk Oh
- Department of Food Engineering, Food Safety Laboratory, Memory Unit, Ewha Womans University, Seoul 03600, Korea
| | - Mun-Gi Sohn
- Department of Food Science, KyungHee University College of Life Science, Seoul 17104, Korea
| | - Michael Coleman
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK
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18
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Maharana S, Kretschmer S, Hunger S, Yan X, Kuster D, Traikov S, Zillinger T, Gentzel M, Elangovan S, Dasgupta P, Chappidi N, Lucas N, Maser KI, Maatz H, Rapp A, Marchand V, Chang YT, Motorin Y, Hubner N, Hartmann G, Hyman AA, Alberti S, Lee-Kirsch MA. SAMHD1 controls innate immunity by regulating condensation of immunogenic self RNA. Mol Cell 2022; 82:3712-3728.e10. [PMID: 36150385 DOI: 10.1016/j.molcel.2022.08.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/07/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
Recognition of pathogen-derived foreign nucleic acids is central to innate immune defense. This requires discrimination between structurally highly similar self and nonself nucleic acids to avoid aberrant inflammatory responses as in the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). How vast amounts of self RNA are shielded from immune recognition to prevent autoinflammation is not fully understood. Here, we show that human SAM-domain- and HD-domain-containing protein 1 (SAMHD1), one of the AGS-causing genes, functions as a single-stranded RNA (ssRNA) 3'exonuclease, the lack of which causes cellular RNA accumulation. Increased ssRNA in cells leads to dissolution of RNA-protein condensates, which sequester immunogenic double-stranded RNA (dsRNA). Release of sequestered dsRNA from condensates triggers activation of antiviral type I interferon via retinoic-acid-inducible gene I-like receptors. Our results establish SAMHD1 as a key regulator of cellular RNA homeostasis and demonstrate that buffering of immunogenic self RNA by condensates regulates innate immune responses.
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Affiliation(s)
- Shovamayee Maharana
- Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany; Department of Microbiology and Cell Biology, Indian Institute of Science, 560012 Bengaluru, India.
| | - Stefanie Kretschmer
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Susan Hunger
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Xiao Yan
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - David Kuster
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Sofia Traikov
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Thomas Zillinger
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Marc Gentzel
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany
| | - Shobha Elangovan
- Department of Microbiology and Cell Biology, Indian Institute of Science, 560012 Bengaluru, India
| | - Padmanava Dasgupta
- Department of Microbiology and Cell Biology, Indian Institute of Science, 560012 Bengaluru, India
| | - Nagaraja Chappidi
- Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Nadja Lucas
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Katharina Isabell Maser
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Henrike Maatz
- Max Delbrück Center for Molecular Medicine, 13235 Berlin, Germany
| | - Alexander Rapp
- Department of Biology, Universität Darmstadt, 64287 Darmstadt, Germany
| | - Virginie Marchand
- Université de Lorraine, IMoPA UMR7365 CNRS-UL and UMS2008 IBSLor CNRS-Inserm-UL, 54505 Nancy, France
| | - Young-Tae Chang
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Yuri Motorin
- Université de Lorraine, IMoPA UMR7365 CNRS-UL and UMS2008 IBSLor CNRS-Inserm-UL, 54505 Nancy, France
| | - Norbert Hubner
- Max Delbrück Center for Molecular Medicine, 13235 Berlin, Germany; Charité Universitätsmedizin Berlin, 10117 Berlin, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Berlin, 13235 Berlin, Germany
| | - Gunther Hartmann
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Simon Alberti
- Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; University Centre for Rare Diseases, Technische Universität Dresden, 01307 Dresden, Germany.
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19
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Bowen NE, Oo A, Kim B. Mechanistic Interplay between HIV-1 Reverse Transcriptase Enzyme Kinetics and Host SAMHD1 Protein: Viral Myeloid-Cell Tropism and Genomic Mutagenesis. Viruses 2022; 14:v14081622. [PMID: 35893688 PMCID: PMC9331428 DOI: 10.3390/v14081622] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) has been the primary interest among studies on antiviral discovery, viral replication kinetics, drug resistance, and viral evolution. Following infection and entry into target cells, the HIV-1 core disassembles, and the viral RT concomitantly converts the viral RNA into double-stranded proviral DNA, which is integrated into the host genome. The successful completion of the viral life cycle highly depends on the enzymatic DNA polymerase activity of RT. Furthermore, HIV-1 RT has long been known as an error-prone DNA polymerase due to its lack of proofreading exonuclease properties. Indeed, the low fidelity of HIV-1 RT has been considered as one of the key factors in the uniquely high rate of mutagenesis of HIV-1, which leads to efficient viral escape from immune and therapeutic antiviral selective pressures. Interestingly, a series of studies on the replication kinetics of HIV-1 in non-dividing myeloid cells and myeloid specific host restriction factor, SAM domain, and HD domain-containing protein, SAMHD1, suggest that the myeloid cell tropism and high rate of mutagenesis of HIV-1 are mechanistically connected. Here, we review not only HIV-1 RT as a key antiviral target, but also potential evolutionary and mechanistic crosstalk among the unique enzymatic features of HIV-1 RT, the replication kinetics of HIV-1, cell tropism, viral genetic mutation, and host SAMHD1 protein.
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Affiliation(s)
- Nicole E. Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA 30329, USA; (N.E.B.); (A.O.)
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
- Correspondence:
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20
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Orris B, Huynh KW, Ammirati M, Han S, Bolaños B, Carmody J, Petroski MD, Bosbach B, Shields DJ, Stivers JT. Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation and ssDNA binding kinetics. Nucleic Acids Res 2022; 50:7545-7559. [PMID: 35801923 PMCID: PMC9303311 DOI: 10.1093/nar/gkac573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/24/2022] [Accepted: 07/06/2022] [Indexed: 01/07/2023] Open
Abstract
SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) is driven into its activated tetramer form by binding of GTP activator and dNTP activators/substrates. In addition, the inactive monomeric and dimeric forms of the enzyme bind to single-stranded (ss) nucleic acids. During DNA replication SAMHD1 can be phosphorylated by CDK1 and CDK2 at its C-terminal threonine 592 (pSAMHD1), localizing the enzyme to stalled replication forks (RFs) to promote their restart. Although phosphorylation has only a small effect on the dNTPase activity and ssDNA binding affinity of SAMHD1, perturbation of the native T592 by phosphorylation decreased the thermal stability of tetrameric SAMHD1 and accelerated tetramer dissociation in the absence and presence of ssDNA (∼15-fold). In addition, we found that ssDNA binds competitively with GTP to the A1 site. A full-length SAMHD1 cryo-EM structure revealed substantial dynamics in the C-terminal domain (which contains T592), which could be modulated by phosphorylation. We propose that T592 phosphorylation increases tetramer dynamics and allows invasion of ssDNA into the A1 site and the previously characterized DNA binding surface at the dimer-dimer interface. These features are consistent with rapid and regiospecific inactivation of pSAMHD1 dNTPase at RFs or other sites of free ssDNA in cells.
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Affiliation(s)
- Benjamin Orris
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
| | | | | | - Seungil Han
- Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Ben Bolaños
- Oncology Research and Development, Pfizer, San Diego, CA 92121, USA
| | - Jason Carmody
- Oncology Research and Development, Pfizer, San Diego, CA 92121, USA
| | | | - Benedikt Bosbach
- Centers for Therapeutic Innovation (CTI), Pfizer, NY, NY 10016, USA
| | - David J Shields
- Centers for Therapeutic Innovation (CTI), Pfizer, NY, NY 10016, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine 725 North Wolfe Street Baltimore, MD 21205, USA
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21
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Klemm BP, Sikkema AP, Hsu AL, Horng JC, Hall TMT, Borgnia MJ, Schaaper RM. High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP. J Biol Chem 2022; 298:102073. [PMID: 35643313 PMCID: PMC9257424 DOI: 10.1016/j.jbc.2022.102073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 10/27/2022] Open
Abstract
Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to innate immunity against viruses. Among the homologs that are best studied are human sterile alpha motif and HD domain-containing protein 1 (SAMHD1), a tetrameric dNTPase, and the hexameric Escherichia coli dGTPase; however, it is unclear whether these are representative of all dNTPases given their wide distribution throughout life. Here, we investigated a hexameric homolog from the marine bacterium Leeuwenhoekiella blandensis, revealing that it is a dGTPase that is subject to allosteric activation by dATP, specifically. Allosteric regulation mediated solely by dATP represents a novel regulatory feature among dNTPases that may facilitate maintenance of cellular dNTP pools in L. blandensis. We present high-resolution X-ray crystallographic structures (1.80-2.26 Å) in catalytically important conformations as well as cryo-EM structures (2.1-2.7 Å) of the enzyme bound to dGTP and dATP ligands. The structures, the highest resolution cryo-EM structures of any SAMHD1-like dNTPase to date, reveal an intact metal-binding site with the dGTP substrate coordinated to three metal ions. These structural and biochemical data yield insights into the catalytic mechanism and support a conserved catalytic mechanism for the tetrameric and hexameric dNTPase homologs. We conclude that the allosteric activation by dATP appears to rely on structural connectivity between the allosteric and active sites, as opposed to the changes in oligomeric state upon ligand binding used by SAMHD1.
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Affiliation(s)
- Bradley P Klemm
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Andrew P Sikkema
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - James C Horng
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Roel M Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA.
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22
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Targeting SAMHD1: to overcome multiple anti-cancer drugs resistance in hematological malignancies. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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23
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Rothenburger T, Thomas D, Schreiber Y, Wratil PR, Pflantz T, Knecht K, Digianantonio K, Temple J, Schneider C, Baldauf HM, McLaughlin KM, Rothweiler F, Bilen B, Farmand S, Bojkova D, Costa R, Ferreirós N, Geisslinger G, Oellerich T, Xiong Y, Keppler OT, Wass MN, Michaelis M, Cinatl J. Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells. J Exp Clin Cancer Res 2021; 40:317. [PMID: 34641952 PMCID: PMC8507139 DOI: 10.1186/s13046-021-02093-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SAMHD1 mediates resistance to anti-cancer nucleoside analogues, including cytarabine, decitabine, and nelarabine that are commonly used for the treatment of leukaemia, through cleavage of their triphosphorylated forms. Hence, SAMHD1 inhibitors are promising candidates for the sensitisation of leukaemia cells to nucleoside analogue-based therapy. Here, we investigated the effects of the cytosine analogue CNDAC, which has been proposed to be a SAMHD1 inhibitor, in the context of SAMHD1. METHODS CNDAC was tested in 13 acute myeloid leukaemia (AML) cell lines, in 26 acute lymphoblastic leukaemia (ALL) cell lines, ten AML sublines adapted to various antileukaemic drugs, 24 single cell-derived clonal AML sublines, and primary leukaemic blasts from 24 AML patients. Moreover, 24 CNDAC-resistant sublines of the AML cell lines HL-60 and PL-21 were established. The SAMHD1 gene was disrupted using CRISPR/Cas9 and SAMHD1 depleted using RNAi, and the viral Vpx protein. Forced DCK expression was achieved by lentiviral transduction. SAMHD1 promoter methylation was determined by PCR after treatment of genomic DNA with the methylation-sensitive HpaII endonuclease. Nucleoside (analogue) triphosphate levels were determined by LC-MS/MS. CNDAC interaction with SAMHD1 was analysed by an enzymatic assay and by crystallisation. RESULTS Although the cytosine analogue CNDAC was anticipated to inhibit SAMHD1, SAMHD1 mediated intrinsic CNDAC resistance in leukaemia cells. Accordingly, SAMHD1 depletion increased CNDAC triphosphate (CNDAC-TP) levels and CNDAC toxicity. Enzymatic assays and crystallisation studies confirmed CNDAC-TP to be a SAMHD1 substrate. In 24 CNDAC-adapted acute myeloid leukaemia (AML) sublines, resistance was driven by DCK (catalyses initial nucleoside phosphorylation) loss. CNDAC-adapted sublines displayed cross-resistance only to other DCK substrates (e.g. cytarabine, decitabine). Cell lines adapted to drugs not affected by DCK or SAMHD1 remained CNDAC sensitive. In cytarabine-adapted AML cells, increased SAMHD1 and reduced DCK levels contributed to cytarabine and CNDAC resistance. CONCLUSION Intrinsic and acquired resistance to CNDAC and related nucleoside analogues are driven by different mechanisms. The lack of cross-resistance between SAMHD1/ DCK substrates and non-substrates provides scope for next-line therapies after treatment failure.
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Affiliation(s)
- Tamara Rothenburger
- Institute for Medical Virology, Goethe-University, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe-University, Frankfurt am Main, Germany
| | - Dominique Thomas
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, Germany
| | - Yannick Schreiber
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, Germany
| | - Paul R Wratil
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Tamara Pflantz
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Kirsten Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Katie Digianantonio
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Constanze Schneider
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Hanna-Mari Baldauf
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | | | - Florian Rothweiler
- Institute for Medical Virology, Goethe-University, Frankfurt am Main, Germany
| | - Berna Bilen
- Faculty of Biological Sciences, Goethe-University, Frankfurt am Main, Germany
| | - Samira Farmand
- Faculty of Biological Sciences, Goethe-University, Frankfurt am Main, Germany
| | - Denisa Bojkova
- Institute for Medical Virology, Goethe-University, Frankfurt am Main, Germany
| | - Rui Costa
- Institute for Medical Virology, Goethe-University, Frankfurt am Main, Germany
| | - Nerea Ferreirós
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, Germany
| | - Gerd Geisslinger
- Pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project group Translational Medicine and Pharmacology (TMP), Frankfurt am Main, Germany
| | - Thomas Oellerich
- Department of Hematology/Oncology, Goethe-University, Frankfurt am Main, Germany
- Molecular Diagnostics Unit, Frankfurt Cancer Institute, Frankfurt am Main, Germany
- German Cancer Consortium/German Cancer Research Center, Heidelberg, Germany
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Oliver T Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Mark N Wass
- School of Biosciences, University of Kent, Canterbury, UK
| | | | - Jindrich Cinatl
- Institute for Medical Virology, Goethe-University, Frankfurt am Main, Germany.
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24
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Ren H, Yin X, Su C, Guo M, Wang XF, Na L, Lin Y, Wang X. Equine lentivirus counteracts SAMHD1 restriction by Rev-mediated degradation of SAMHD1 via the BECN1-dependent lysosomal pathway. Autophagy 2021; 17:2800-2817. [PMID: 33172327 PMCID: PMC8525956 DOI: 10.1080/15548627.2020.1846301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 10/16/2020] [Accepted: 10/30/2020] [Indexed: 02/09/2023] Open
Abstract
The innate immune restriction factor SAMHD1 can inhibit diverse viruses in myeloid cells. Mechanistically, SAMHD1 inhibits lentiviral replication including HIV-1 by depleting the nucleotide pool to interfere with their reverse transcription. Equine infectious anemia virus (EIAV) is an ancient lentivirus that preferentially attacks macrophages. However, the mechanism by which EIAV successfully establishes infection in macrophages with functional SAMHD1 remains unclear. Here, we demonstrate that while equine SAMDH1 can limit EIAV replication in equine macrophages at the reverse transcription stage, the antiviral effect is counteracted by the well-known transcriptional regulator Rev, which downregulates equine SAMHD1 through the lysosomal pathway. Remarkably, Rev hijacks BECN1 (beclin 1) and PIK3C3 to mediate SAMHD1 degradation in a canonical macroautophagy/autophagy-independent pathway. Our study illustrates that equine lentiviral Rev possesses important functions in evading cellular innate immunity in addition to its RNA regulatory function, and may provide new insights into the co-evolutionary arms race between SAMHD1 and lentiviruses.Abbreviations:3-MA: 3-methyladenine; AA: amino acid; ACTB: actin beta; AD: activation domain; ATG: autophagy related; Baf A1: bafilomycin A1; BD: binding domain; BECN1: beclin 1; BH3: BCL2-homology-3 domain; BiFC: bimolecular fluorescence complementation; CCD: coiled-coil domain; class III PtdIns3K: class III phosphatidylinositol 3-kinase; CQ: chloroquine; Co-IP: co-immunoprecipitation; dNTPase: dGTP-stimulated deoxynucleoside triphosphate triphosphohydrolase; ECD: evolutionarily conserved domain; EIAV: equine infectious anemia virus; eMDMs: equine monocyte-derived macrophages; GFP: green fluorescent protein; HD: histidine-aspartic; HIV-1: human immunodeficiency virus-1; hpi: hours post infection; hpt: hours post transfection; KO: knockout; LAMP2: lysosomal associated membrane protein 2; LMB: leptomycin B; PMA: phorbol 12-myristate 13-acetate; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; ND: unknown non-essential domain; NES: nuclear export signal; NLS: localization signal; NS: statistically non-significant; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; RBD: RNA binding domain; RT: reverse transcriptase; siRNAs: small interfering RNAs; SAMHD1: SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1; SIV: simian immunodeficiency virus; VN: C-terminal residues of Venus 174 to 238; VC: N-terminal residues 2 to 173 of Venus.
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Affiliation(s)
- Huiling Ren
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xin Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Chao Su
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Miaomiao Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xue-Feng Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lei Na
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuezhi Lin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
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25
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Bowen NE, Temple J, Shepard C, Oo A, Arizaga F, Kapoor-Vazirani P, Persaud M, Yu CH, Kim DH, Schinazi RF, Ivanov DN, Diaz-Griffero F, Yu DS, Xiong Y, Kim B. Structural and functional characterization explains loss of dNTPase activity of the cancer-specific R366C/H mutant SAMHD1 proteins. J Biol Chem 2021; 297:101170. [PMID: 34492268 PMCID: PMC8497992 DOI: 10.1016/j.jbc.2021.101170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023] Open
Abstract
Elevated intracellular levels of dNTPs have been shown to be a biochemical marker of cancer cells. Recently, a series of mutations in the multifunctional dNTP triphosphohydrolase (dNTPase), sterile alpha motif and histidine-aspartate domain-containing protein 1 (SAMHD1), have been reported in various cancers. Here, we investigated the structure and functions of SAMHD1 R366C/H mutants, found in colon cancer and leukemia. Unlike many other cancer-specific mutations, the SAMHD1 R366 mutations do not alter cellular protein levels of the enzyme. However, R366C/H mutant proteins exhibit a loss of dNTPase activity, and their X-ray structures demonstrate the absence of dGTP substrate in their active site, likely because of a loss of interaction with the γ-phosphate of the substrate. The R366C/H mutants failed to reduce intracellular dNTP levels and restrict HIV-1 replication, functions of SAMHD1 that are dependent on the ability of the enzyme to hydrolyze dNTPs. However, these mutants retain dNTPase-independent functions, including mediating dsDNA break repair, interacting with CtIP and cyclin A2, and suppressing innate immune responses. Finally, SAMHD1 degradation in human primary-activated/dividing CD4+ T cells further elevates cellular dNTP levels. This study suggests that the loss of SAMHD1 dNTPase activity induced by R366 mutations can mechanistically contribute to the elevated dNTP levels commonly found in cancer cells.
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Affiliation(s)
- Nicole E Bowen
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Caitlin Shepard
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Adrian Oo
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Fidel Arizaga
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Priya Kapoor-Vazirani
- Department of Radiation Oncology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Mirjana Persaud
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Corey H Yu
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Dong-Hyun Kim
- School of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Raymond F Schinazi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Dmitri N Ivanov
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - David S Yu
- Department of Radiation Oncology, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, School of Medicine, Yale University, New Haven, Connecticut, USA.
| | - Baek Kim
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA; Children's Healthcare of Atlanta, Atlanta, Georgia, USA.
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26
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Batalis S, Rogers LC, Hemphill WO, Mauney CH, Ornelles DA, Hollis T. SAMHD1 Phosphorylation at T592 Regulates Cellular Localization and S-phase Progression. Front Mol Biosci 2021; 8:724870. [PMID: 34513928 PMCID: PMC8426622 DOI: 10.3389/fmolb.2021.724870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/16/2021] [Indexed: 12/02/2022] Open
Abstract
SAMHD1 activity is regulated by a network of mechanisms including phosphorylation, oxidation, oligomerization, and others. Significant questions remain about the effects of phosphorylation on SAMHD1 function and activity. We investigated the effects of a SAMHD1 T592E phosphorylation mimic on its cellular localization, catalytic activity, and cell cycle progression. We found that the SAMHD1 T592E is a catalytically active enzyme that is inhibited by protein oxidation. SAMHD1 T592E is retained in the nucleus at higher levels than the wild-type protein during growth factor-mediated signaling. This nuclear localization protects SAMHD1 from oxidation by cytoplasmic reactive oxygen species. The SAMHD1 T592E phosphomimetic further inhibits the cell cycle S/G2 transition. This has significant implications for SAMHD1 function in regulating innate immunity, antiviral response and DNA replication.
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Affiliation(s)
- Stephanie Batalis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - LeAnn C Rogers
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Wayne O Hemphill
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Christopher H Mauney
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - David A Ornelles
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Thomas Hollis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, United States
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27
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Schott K, Majer C, Bulashevska A, Childs L, Schmidt MHH, Rajalingam K, Munder M, König R. SAMHD1 in cancer: curse or cure? J Mol Med (Berl) 2021; 100:351-372. [PMID: 34480199 PMCID: PMC8843919 DOI: 10.1007/s00109-021-02131-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/15/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Human sterile α motif and HD domain-containing protein 1 (SAMHD1), originally described as the major cellular deoxyribonucleoside triphosphate triphosphohydrolase (dNTPase) balancing the intracellular deoxynucleotide (dNTP) pool, has come recently into focus of cancer research. As outlined in this review, SAMHD1 has been reported to be mutated in a variety of cancer types and the expression of SAMHD1 is dysregulated in many cancers. Therefore, SAMHD1 is regarded as a tumor suppressor in certain tumors. Moreover, it has been proposed that SAMHD1 might fulfill the requirements of a driver gene in tumor development or might promote a so-called mutator phenotype. Besides its role as a dNTPase, several novel cellular functions of SAMHD1 have come to light only recently, including a role as negative regulator of innate immune responses and as facilitator of DNA end resection during DNA replication and repair. Therefore, SAMHD1 can be placed at the crossroads of various cellular processes. The present review summarizes the negative role of SAMHD1 in chemotherapy sensitivity, highlights reported SAMHD1 mutations found in various cancer types, and aims to discuss functional consequences as well as underlying mechanisms of SAMHD1 dysregulation potentially involved in cancer development.
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Affiliation(s)
- Kerstin Schott
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Catharina Majer
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Alla Bulashevska
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Liam Childs
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Mirko H H Schmidt
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, Dresden, Germany
| | - Krishnaraj Rajalingam
- Cell Biology Unit, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- University Cancer Center Mainz, University Medical Center Mainz, Mainz, Germany
| | - Markus Munder
- Third Department of Medicine, University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany.
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28
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Banchenko S, Krupp F, Gotthold C, Bürger J, Graziadei A, O’Reilly FJ, Sinn L, Ruda O, Rappsilber J, Spahn CMT, Mielke T, Taylor IA, Schwefel D. Structural insights into Cullin4-RING ubiquitin ligase remodelling by Vpr from simian immunodeficiency viruses. PLoS Pathog 2021; 17:e1009775. [PMID: 34339457 PMCID: PMC8360603 DOI: 10.1371/journal.ppat.1009775] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/12/2021] [Accepted: 07/02/2021] [Indexed: 12/21/2022] Open
Abstract
Viruses have evolved means to manipulate the host's ubiquitin-proteasome system, in order to down-regulate antiviral host factors. The Vpx/Vpr family of lentiviral accessory proteins usurp the substrate receptor DCAF1 of host Cullin4-RING ligases (CRL4), a family of modular ubiquitin ligases involved in DNA replication, DNA repair and cell cycle regulation. CRL4DCAF1 specificity modulation by Vpx and Vpr from certain simian immunodeficiency viruses (SIV) leads to recruitment, poly-ubiquitylation and subsequent proteasomal degradation of the host restriction factor SAMHD1, resulting in enhanced virus replication in differentiated cells. To unravel the mechanism of SIV Vpr-induced SAMHD1 ubiquitylation, we conducted integrative biochemical and structural analyses of the Vpr protein from SIVs infecting Cercopithecus cephus (SIVmus). X-ray crystallography reveals commonalities between SIVmus Vpr and other members of the Vpx/Vpr family with regard to DCAF1 interaction, while cryo-electron microscopy and cross-linking mass spectrometry highlight a divergent molecular mechanism of SAMHD1 recruitment. In addition, these studies demonstrate how SIVmus Vpr exploits the dynamic architecture of the multi-subunit CRL4DCAF1 assembly to optimise SAMHD1 ubiquitylation. Together, the present work provides detailed molecular insight into variability and species-specificity of the evolutionary arms race between host SAMHD1 restriction and lentiviral counteraction through Vpx/Vpr proteins.
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Affiliation(s)
- Sofia Banchenko
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Ferdinand Krupp
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Christine Gotthold
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Jörg Bürger
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Andrea Graziadei
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Francis J. O’Reilly
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Ludwig Sinn
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Olga Ruda
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Christian M. T. Spahn
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
| | - David Schwefel
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
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29
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Morris ER, Kunzelmann S, Caswell SJ, Purkiss AG, Kelly G, Taylor IA. Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of R p- and S p-dNTPαS Diastereomers. Biochemistry 2021; 60:1682-1698. [PMID: 33988981 PMCID: PMC8173608 DOI: 10.1021/acs.biochem.0c00944] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SAMHD1 is a fundamental regulator of cellular dNTPs that catalyzes their hydrolysis into 2'-deoxynucleoside and triphosphate, restricting the replication of viruses, including HIV-1, in CD4+ myeloid lineage and resting T-cells. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome (AGS) and certain cancers. More recently, SAMHD1 has been linked to anticancer drug resistance and the suppression of the interferon response to cytosolic nucleic acids after DNA damage. Here, we probe dNTP hydrolysis and inhibition of SAMHD1 using the Rp and Sp diastereomers of dNTPαS nucleotides. Our biochemical and enzymological data show that the α-phosphorothioate substitution in Sp-dNTPαS but not Rp-dNTPαS diastereomers prevents Mg2+ ion coordination at both the allosteric and catalytic sites, rendering SAMHD1 unable to form stable, catalytically active homotetramers or hydrolyze substrate dNTPs at the catalytic site. Furthermore, we find that Sp-dNTPαS diastereomers competitively inhibit dNTP hydrolysis, while Rp-dNTPαS nucleotides stabilize tetramerization and are hydrolyzed with similar kinetic parameters to cognate dNTPs. For the first time, we present a cocrystal structure of SAMHD1 with a substrate, Rp-dGTPαS, in which an Fe-Mg-bridging water species is poised for nucleophilic attack on the Pα. We conclude that it is the incompatibility of Mg2+, a hard Lewis acid, and the α-phosphorothioate thiol, a soft Lewis base, that prevents the Sp-dNTPαS nucleotides coordinating in a catalytically productive conformation. On the basis of these data, we present a model for SAMHD1 stereospecific hydrolysis of Rp-dNTPαS nucleotides and for a mode of competitive inhibition by Sp-dNTPαS nucleotides that competes with formation of the enzyme-substrate complex.
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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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30
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Dual roles of SAMHD1 in tumor development and chemoresistance to anticancer drugs. Oncol Lett 2021; 21:451. [PMID: 33907561 PMCID: PMC8063254 DOI: 10.3892/ol.2021.12712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/10/2021] [Indexed: 11/05/2022] Open
Abstract
Human sterile alpha motif and HD-domain-containing protein 1 (SAMHD1) has been identified as a GTP or dGTP-dependent deoxynucleotide triphosphohydrolase (dNTPase) and acts as an antiviral factor against certain retroviruses and DNA viruses. Genetic mutation in SAMHD1 causes the inflammatory Aicardi-Goutières Syndrome and abnormal intracellular deoxyribonucleoside triphosphates (dNTPs) pool. At present, the role of SAMHD1 in numerous types of cancer, such as chronic lymphocytic leukemia, lung cancer and colorectal cancer, is highly studied. Furthermore, it has been found that methylation, acetylation and phosphorylation are involved in the regulation of SAMHD1 expression, and that genetic mutations can cause changes in its activities, including dNTPase activity, long interspersed element type 1 (LINE-1) suppression and DNA damage repair, which could lead to uncontrolled cell cycle progression and cancer development. In addition, SAMHD1 has been reported to have a negative regulatory role in the chemosensitivity to anticancer drugs through its dNTPase activity. The present review aimed to summarize the regulation of SAMHD1 expression in cancer and its function in tumor growth and chemotherapy sensitivity, and discussed controversial points and future directions.
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31
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Wang C, Meng L, Wang J, Zhang K, Duan S, Ren P, Wei Y, Fu X, Yu B, Wu J, Yu X. Role of Intracellular Distribution of Feline and Bovine SAMHD1 Proteins in Lentiviral Restriction. Virol Sin 2021; 36:981-996. [PMID: 33751400 DOI: 10.1007/s12250-021-00351-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/28/2020] [Indexed: 11/28/2022] Open
Abstract
Human SAMHD1 (hSAM) restricts lentiviruses at the reverse transcription step through its dNTP triphosphohydrolase (dNTPase) activity. Besides humans, several mammalian species such as cats and cows that carry their own lentiviruses also express SAMHD1. However, the intracellular distribution of feline and bovine SAMHD1 (fSAM and bSAM) and its significance in their lentiviral restriction function is not known. Here, we demonstrated that fSAM and bSAM were both predominantly localized to the nucleus and nuclear localization signal (11KRPR14)-deleted fSAM and bSAM relocalized to the cytoplasm. Both cytoplasmic fSAM and bSAM retained the antiviral function against different lentiviruses and cytoplasmic fSAM could restrict Vpx-encoding SIV and HIV-2 more efficiently than its wild-type (WT) protein as cytoplasmic hSAM. Further investigation revealed that cytoplasmic fSAM was resistant to Vpx-induced degradation like cytoplasmic hSAM, while cytoplasmic bSAM was not, but they all demonstrated the same in vitro dNTPase activity and all could interact with Vpx as their WT proteins, indicating that cytoplasmic hSAM and fSAM can suppress more SIV and HIV-2 by being less sensitive to Vpx-mediated degradation. Our results suggested that fSAM- and bSAM-mediated lentiviral restriction does not require their nuclear localization and that fSAM shares more common features with hSAM. These findings may provide insights for the establishment of alternative animal models to study SAMHD1 in vivo.
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Affiliation(s)
- Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China.,The First Hospital and Institute of Immunology, Jilin University, Changchun, 130012, China
| | - Lina Meng
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Jialin Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Kaikai Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Sizhu Duan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Pengyu Ren
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Yingzhe Wei
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Xinyu Fu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China.,Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Jiaxin Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China. .,Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China.
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China. .,Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China.
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32
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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: 13] [Impact Index Per Article: 4.3] [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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33
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Abstract
Exogenous retroviruses are RNA viruses that require reverse transcription for their replication. Among these viruses, human immunodeficiency virus (HIV) is infectious to humans and causes the development of acquired immune deficiency syndrome (AIDS). There are also endogenous retroelements that require reverse transcription for their retrotransposition, among which the type 1 long interspersed element (LINE-1) is the only type of retroelement that can replicate autonomously. It was once believed that retroviruses like HIV and retroelements like LINE-1 share similarities in processes such as reverse transcription and integration. Accordingly, many HIV suppressors are also potent LINE-1 inhibitors. However, in many cases, one suppressor uses two or more distinct mechanisms to repress HIV and LINE-1. In this review, we discuss some of these suppressors, focusing on their alternative mechanisms opposing the replication of HIV and LINE-1. Based on the differences in HIV and LINE-1 activity, the subcellular localization of these suppressors, and the impact of LINE-1 retrotransposition on human cells, we propose possible reasons for the inhibition of HIV and LINE-1 through different pathways by these suppressors, with the hope of accelerating future studies in associated research fields.
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Affiliation(s)
- Juan Du
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China.,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, China
| | - Ke Zhao
- Institute of Virology and AIDS Research, First Hospital of Jilin University, Changchun, China.,Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, First Hospital of Jilin University, Changchun, China
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34
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Yagüe-Capilla M, Castillo-Acosta VM, Bosch-Navarrete C, Ruiz-Pérez LM, González-Pacanowska D. A Mitochondrial Orthologue of the dNTP Triphosphohydrolase SAMHD1 Is Essential and Controls Pyrimidine Homeostasis in Trypanosoma brucei. ACS Infect Dis 2021; 7:318-332. [PMID: 33417760 DOI: 10.1021/acsinfecdis.0c00551] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The maintenance of deoxyribonucleotide triphosphate (dNTP) homeostasis through synthesis and degradation is critical for accurate genomic and mitochondrial DNA replication fidelity. Trypanosoma brucei makes use of both the salvage and de novo pathways for the provision of pyrimidine dNTPs. In this respect, the sterile α motif and histidine-aspartate domain-containing protein 1 (SAMHD1) appears to be the most relevant dNTPase controlling dNTP/deoxynucleoside homeostasis in mammalian cells. Here, we have characterized the role of a unique trypanosomal SAMHD1 orthologue denominated TbHD52. Our results show that TbHD52 is a mitochondrial enzyme essential in bloodstream forms of T. brucei. Knockout cells are pyrimidine auxotrophs that exhibit strong defects in genomic integrity, cell cycle progression, and nuclear DNA and kinetoplast segregation in the absence of extracellular thymidine. The lack of TbHD52 can be counteracted by the overexpression of human dCMP deaminase, an enzyme that is directly involved in dUMP formation yet absent in trypanosomes. Furthermore, the cellular dNTP quantification and metabolomic analysis of TbHD52 null mutants revealed perturbations in the nucleotide metabolism with a substantial accumulation of dCTP and cytosine-derived metabolites while dTTP formation was significantly reduced. We propose that this HD-domain-containing protein unique to kinetoplastids plays an essential role in pyrimidine dNTP homeostasis and contributes to the provision of deoxycytidine required for cellular dTTP biosynthesis.
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Affiliation(s)
- Miriam Yagüe-Capilla
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
| | - Víctor M. Castillo-Acosta
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
| | - Cristina Bosch-Navarrete
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
| | - Luis Miguel Ruiz-Pérez
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina “López-Neyra”, Consejo Superior de Investigaciones Científicas, Parque Tecnológico de Ciencias de la Salud, Armilla (Granada) 18016, Spain
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35
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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: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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36
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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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37
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Langton M, Sun S, Ueda C, Markey M, Chen J, Paddy I, Jiang P, Chin N, Milne A, Pandelia ME. The HD-Domain Metalloprotein Superfamily: An Apparent Common Protein Scaffold with Diverse Chemistries. Catalysts 2020; 10:1191. [PMID: 34094591 PMCID: PMC8177086 DOI: 10.3390/catal10101191] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The histidine-aspartate (HD)-domain protein superfamily contains metalloproteins that share common structural features but catalyze vastly different reactions ranging from oxygenation to hydrolysis. This chemical diversion is afforded by (i) their ability to coordinate most biologically relevant transition metals in mono-, di-, and trinuclear configurations, (ii) sequence insertions or the addition of supernumerary ligands to their active sites, (iii) auxiliary substrate specificity residues vicinal to the catalytic site, (iv) additional protein domains that allosterically regulate their activities or have catalytic and sensory roles, and (v) their ability to work with protein partners. More than 500 structures of HD-domain proteins are available to date that lay out unique structural features which may be indicative of function. In this respect, we describe the three known classes of HD-domain proteins (hydrolases, oxygenases, and lyases) and identify their apparent traits with the aim to portray differences in the molecular details responsible for their functional divergence and reconcile existing notions that will help assign functions to yet-to-be characterized proteins. The present review collects data that exemplify how nature tinkers with the HD-domain scaffold to afford different chemistries and provides insight into the factors that can selectively modulate catalysis.
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Affiliation(s)
- Michelle Langton
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Sining Sun
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Chie Ueda
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Max Markey
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Jiahua Chen
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Isaac Paddy
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Paul Jiang
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Natalie Chin
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Amy Milne
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02453, USA
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38
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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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Morris ER, Caswell SJ, Kunzelmann S, Arnold LH, Purkiss AG, Kelly G, Taylor IA. Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis. Nat Commun 2020; 11:3165. [PMID: 32576829 PMCID: PMC7311409 DOI: 10.1038/s41467-020-16983-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/03/2020] [Indexed: 12/29/2022] Open
Abstract
SAMHD1 regulates cellular 2'-deoxynucleoside-5'-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2'-deoxynucleosides and triphosphate. In CD4+ myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi-Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the Pα-O5' bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.
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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,AstraZeneca, 50F49, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Laurence H Arnold
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Pelago Bioscience, Banvaktsvägen 20, 171 48, Solna, Sweden
| | - Andrew G Purkiss
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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40
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SAMHD1 Functions and Human Diseases. Viruses 2020; 12:v12040382. [PMID: 32244340 PMCID: PMC7232136 DOI: 10.3390/v12040382] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/12/2022] Open
Abstract
Deoxynucleoside triphosphate (dNTP) molecules are essential for the replication and maintenance of genomic information in both cells and a variety of viral pathogens. While the process of dNTP biosynthesis by cellular enzymes, such as ribonucleotide reductase (RNR) and thymidine kinase (TK), has been extensively investigated, a negative regulatory mechanism of dNTP pools was recently found to involve sterile alpha motif (SAM) domain and histidine-aspartate (HD) domain-containing protein 1, SAMHD1. When active, dNTP triphosphohydrolase activity of SAMHD1 degrades dNTPs into their 2'-deoxynucleoside (dN) and triphosphate subparts, steadily depleting intercellular dNTP pools. The differential expression levels and activation states of SAMHD1 in various cell types contributes to unique dNTP pools that either aid (i.e., dividing T cells) or restrict (i.e., nondividing macrophages) viral replication that consumes cellular dNTPs. Genetic mutations in SAMHD1 induce a rare inflammatory encephalopathy called Aicardi-Goutières syndrome (AGS), which phenotypically resembles viral infection. Recent publications have identified diverse roles for SAMHD1 in double-stranded break repair, genome stability, and the replication stress response through interferon signaling. Finally, a series of SAMHD1 mutations were also reported in various cancer cell types while why SAMHD1 is mutated in these cancer cells remains to investigated. Here, we reviewed a series of studies that have begun illuminating the highly diverse roles of SAMHD1 in virology, immunology, and cancer biology.
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41
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Wang C, Zhang K, Meng L, Zhang X, Song Y, Zhang Y, Gai Y, Zhang Y, Yu B, Wu J, Wang S, Yu X. The C-terminal domain of feline and bovine SAMHD1 proteins has a crucial role in lentiviral restriction. J Biol Chem 2020; 295:4252-4264. [PMID: 32075911 PMCID: PMC7105322 DOI: 10.1074/jbc.ra120.012767] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/14/2020] [Indexed: 01/29/2023] Open
Abstract
SAM and HD domain-containing protein 1 (SAMHD1) is a host factor that restricts reverse transcription of lentiviruses such as HIV in myeloid cells and resting T cells through its dNTP triphosphohydrolase (dNTPase) activity. Lentiviruses counteract this restriction by expressing the accessory protein Vpx or Vpr, which targets SAMHD1 for proteasomal degradation. SAMHD1 is conserved among mammals, and the feline and bovine SAMHD1 proteins (fSAM and bSAM) restrict lentiviruses by reducing cellular dNTP concentrations. However, the functional regions of fSAM and bSAM that are required for their biological functions are not well-characterized. Here, to establish alternative models to investigate SAMHD1 in vivo, we studied the restriction profile of fSAM and bSAM against different primate lentiviruses. We found that both fSAM and bSAM strongly restrict primate lentiviruses and that Vpx induces the proteasomal degradation of both fSAM and bSAM. Further investigation identified one and five amino acid sites in the C-terminal domain (CTD) of fSAM and bSAM, respectively, that are required for Vpx-mediated degradation. We also found that the CTD of bSAM is directly involved in mediating bSAM's antiviral activity by regulating dNTPase activity, whereas the CTD of fSAM is not. Our results suggest that the CTDs of fSAM and bSAM have important roles in their antiviral functions. These findings advance our understanding of the mechanism of fSAM- and bSAM-mediated viral restriction and might inform strategies for improving HIV animal models.
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Affiliation(s)
- Chu Wang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; The First Hospital and Institute of Immunology, Jilin University, Changchun 130012, China
| | - Kaikai Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Lina Meng
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xin Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yanan Song
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Ying Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yanxin Gai
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yuepeng Zhang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Bin Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jiaxin Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Song Wang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering, the Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
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42
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Rudd SG, Tsesmetzis N, Sanjiv K, Paulin CBJ, Sandhow L, Kutzner J, Hed Myrberg I, Bunten SS, Axelsson H, Zhang SM, Rasti A, Mäkelä P, Coggins SA, Tao S, Suman S, Branca RM, Mermelekas G, Wiita E, Lee S, Walfridsson J, Schinazi RF, Kim B, Lehtiö J, Rassidakis GZ, Pokrovskaja Tamm K, Warpman‐Berglund U, Heyman M, Grandér D, Lehmann S, Lundbäck T, Qian H, Henter J, Schaller T, Helleday T, Herold N. Ribonucleotide reductase inhibitors suppress SAMHD1 ara-CTPase activity enhancing cytarabine efficacy. EMBO Mol Med 2020; 12:e10419. [PMID: 31950591 PMCID: PMC7059017 DOI: 10.15252/emmm.201910419] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 01/23/2023] Open
Abstract
The deoxycytidine analogue cytarabine (ara-C) remains the backbone treatment of acute myeloid leukaemia (AML) as well as other haematological and lymphoid malignancies, but must be combined with other chemotherapeutics to achieve cure. Yet, the underlying mechanism dictating synergistic efficacy of combination chemotherapy remains largely unknown. The dNTPase SAMHD1, which regulates dNTP homoeostasis antagonistically to ribonucleotide reductase (RNR), limits ara-C efficacy by hydrolysing the active triphosphate metabolite ara-CTP. Here, we report that clinically used inhibitors of RNR, such as gemcitabine and hydroxyurea, overcome the SAMHD1-mediated barrier to ara-C efficacy in primary blasts and mouse models of AML, displaying SAMHD1-dependent synergy with ara-C. We present evidence that this is mediated by dNTP pool imbalances leading to allosteric reduction of SAMHD1 ara-CTPase activity. Thus, SAMHD1 constitutes a novel biomarker for combination therapies of ara-C and RNR inhibitors with immediate consequences for clinical practice to improve treatment of AML.
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43
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Zhang Z, Zheng L, Yu Y, Wu J, Yang F, Xu Y, Guo Q, Wu X, Cao S, Cao L, Song X. Involvement of SAMHD1 in dNTP homeostasis and the maintenance of genomic integrity and oncotherapy (Review). Int J Oncol 2020; 56:879-888. [PMID: 32319570 DOI: 10.3892/ijo.2020.4988] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/07/2020] [Indexed: 11/06/2022] Open
Abstract
Sterile alpha motif and histidine/aspartic acid domain‑containing protein 1 (SAMHD1), the only deoxynucleotide triphosphate (dNTP) hydrolase in eukaryotes, plays a crucial role in regulating the dynamic balance and ratio of cellular dNTP pools. Furthermore, SAMHD1 has been reported to be involved in the pathological process of several diseases. Homozygous SAMHD1 mutations have been identified in immune system disorders, such as autoimmune disease Aicardi‑Goutières syndrome (AGS), whose primary pathogenesis is associated with the abnormal accumulation and disproportion of dNTPs. SAMHD1 is also considered to be an intrinsic virus‑restriction factor by suppressing the viral infection process, including reverse transcription, replication, packaging and transmission. In addition, SAMHD1 has been shown to promote genome integrity during homologous recombination following DNA damage, thus being considered a promising candidate for oncotherapy applications. The present review summarizes the molecular mechanisms of SAMHD1 regarding the regulation of dNTP homeostasis and DNA damage response. Additionally, its potential effects on tumorigenesis and oncotherapy are reported.
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Affiliation(s)
- Zhou Zhang
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Lixia Zheng
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yang Yu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Jinying Wu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Fan Yang
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yingxi Xu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Qiqiang Guo
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Xuan Wu
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Sunrun Cao
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Liu Cao
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Xiaoyu Song
- College of Basic Medical Science, Institute of Translational Medicine, China Medical University, Shenyang, Liaoning 110122, P.R. China
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44
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Qin Z, Bonifati S, St Gelais C, Li TW, Kim SH, Antonucci JM, Mahboubi B, Yount JS, Xiong Y, Kim B, Wu L. The dNTPase activity of SAMHD1 is important for its suppression of innate immune responses in differentiated monocytic cells. J Biol Chem 2020; 295:1575-1586. [PMID: 31914403 PMCID: PMC7008377 DOI: 10.1074/jbc.ra119.010360] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/22/2019] [Indexed: 12/18/2022] Open
Abstract
Sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a deoxynucleoside triphosphohydrolase (dNTPase) with a nuclear localization signal (NLS). SAMHD1 suppresses innate immune responses to viral infection and inflammatory stimuli by inhibiting the NF-κB and type I interferon (IFN-I) pathways. However, whether the dNTPase activity and nuclear localization of SAMHD1 are required for its suppression of innate immunity remains unknown. Here, we report that the dNTPase activity, but not nuclear localization of SAMHD1, is important for its suppression of innate immune responses in differentiated monocytic cells. We generated monocytic U937 cell lines stably expressing WT SAMHD1 or mutated variants defective in dNTPase activity (HD/RN) or nuclear localization (mNLS). WT SAMHD1 in differentiated U937 cells significantly inhibited lipopolysaccharide-induced expression of tumor necrosis factor α (TNF-α) and interleukin-6 (IL-6) mRNAs, as well as IFN-α, IFN-β, and TNF-α mRNA levels induced by Sendai virus infection. In contrast, the HD/RN mutant did not exhibit this inhibition in either U937 or THP-1 cells, indicating that the dNTPase activity of SAMHD1 is important for suppressing NF-κB activation. Of note, in lipopolysaccharide-treated or Sendai virus-infected U937 or THP-1 cells, the mNLS variant reduced TNF-α or IFN-β mRNA expression to a similar extent as did WT SAMHD1, suggesting that SAMHD1-mediated inhibition of innate immune responses is independent of SAMHD1's nuclear localization. Moreover, WT and mutant SAMHD1 similarly interacted with key proteins in NF-κB and IFN-I pathways in cells. This study further defines the role and mechanisms of SAMHD1 in suppressing innate immunity.
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Affiliation(s)
- Zhihua Qin
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210; Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Serena Bonifati
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Corine St Gelais
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Tai-Wei Li
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Sun-Hee Kim
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Jenna M Antonucci
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210
| | - Bijan Mahboubi
- Center for Drug Discovery, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Li Wu
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio 43210; Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242; Department of Microbial Infection and Immunity, Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210.
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45
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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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46
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HIV-2/SIV Vpx targets a novel functional domain of STING to selectively inhibit cGAS-STING-mediated NF-κB signalling. Nat Microbiol 2019; 4:2552-2564. [PMID: 31659299 DOI: 10.1038/s41564-019-0585-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 09/10/2019] [Indexed: 12/28/2022]
Abstract
Innate immunity is the first line of host defence against pathogens. Suppression of innate immune responses is essential for the survival of all viruses. However, the interplay between innate immunity and HIV/SIV is only poorly characterized. We have discovered Vpx as a novel inhibitor of innate immune activation that associates with STING signalosomes and interferes with the nuclear translocation of NF-κB and the induction of innate immune genes. This new function of Vpx could be separated from its role in mediating degradation of the antiviral factor SAMHD1, and is conserved among diverse HIV-2/SIV Vpx. Vpx selectively suppressed cGAS-STING-mediated nuclear factor-κB signalling. Furthermore, Vpx and Vpr had complementary activities against cGAS-STING activity. Since SIVMAC lacking both Vpx and Vpr was less pathogenic than SIV deficient for Vpr or Vpx alone, suppression of innate immunity by HIV/SIV is probably a key pathogenic determinant, making it a promising target for intervention.
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47
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Morris ER, Taylor IA. 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: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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Affiliation(s)
- Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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48
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SAMHD1 Regulates Human Papillomavirus 16-Induced Cell Proliferation and Viral Replication during Differentiation of Keratinocytes. mSphere 2019; 4:4/4/e00448-19. [PMID: 31391281 PMCID: PMC6686230 DOI: 10.1128/msphere.00448-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Human papillomaviruses induce a host of anogenital cancers, as well as oropharyngeal cancer (HPV+OPC); human papillomavirus 16 (HPV16) is causative in around 90% of HPV+OPC cases. Using telomerase reverse transcriptase (TERT) immortalized foreskin keratinocytes (N/Tert-1), we have identified significant host gene reprogramming by HPV16 (N/Tert-1+HPV16) and demonstrated that N/Tert-1+HPV16 support late stages of the viral life cycle. Expression of the cellular dNTPase and homologous recombination factor sterile alpha motif and histidine-aspartic domain HD-containing protein 1 (SAMHD1) is transcriptionally regulated by HPV16 in N/Tert-1. CRISPR/Cas9 removal of SAMHD1 from N/Tert-1 and N/Tert-1+HPV16 demonstrates that SAMHD1 controls cell proliferation of N/Tert-1 only in the presence of HPV16; the deletion of SAMHD1 promotes hyperproliferation of N/Tert-1+HPV16 cells in organotypic raft cultures but has no effect on N/Tert-1. Viral replication is also elevated in the absence of SAMHD1. This new system has allowed us to identify a specific interaction between SAMHD1 and HPV16 that regulates host cell proliferation and viral replication; such studies are problematic in nonimmortalized primary keratinocytes due to their limited life span. To confirm the relevance of our results, we repeated the analysis with human tonsil keratinocytes (HTK) immortalized by HPV16 (HTK+HPV16) and observed the same hyperproliferative phenotype following CRISPR/Cas9 editing of SAMHD1. Identical results were obtained with three independent CRISPR/Cas9 guide RNAs. The isogenic pairing of N/Tert-1 with N/Tert-1+HPV16, combined with HTK+HPV16, presents a unique system to identify host genes whose products functionally interact with HPV16 to regulate host cellular growth in keratinocytes.IMPORTANCE HPVs are causative agents in human cancers and are responsible for around of 5% of all cancers. A better understanding of the viral life cycle in keratinocytes will facilitate the development of novel therapeutics to combat HPV-positive cancers. Here, we present a unique keratinocyte model to identify host proteins that specifically interact with HPV16. Using this system, we report that a cellular gene, SAMHD1, is regulated by HPV16 at the RNA and protein levels in keratinocytes. Elimination of SAMHD1 from these cells using CRISPR/Cas9 editing promotes enhanced cellular proliferation by HPV16 in keratinocytes and elevated viral replication but not in keratinocytes that do not have HPV16. Our study demonstrates a specific intricate interplay between HPV16 and SAMHD1 during the viral life cycle and establishes a unique model system to assist exploring host factors critical for HPV pathogenesis.
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49
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Oellerich T, Schneider C, Thomas D, Knecht KM, Buzovetsky O, Kaderali L, Schliemann C, Bohnenberger H, Angenendt L, Hartmann W, Wardelmann E, Rothenburger T, Mohr S, Scheich S, Comoglio F, Wilke A, Ströbel P, Serve H, Michaelis M, Ferreirós N, Geisslinger G, Xiong Y, Keppler OT, Cinatl J. Selective inactivation of hypomethylating agents by SAMHD1 provides a rationale for therapeutic stratification in AML. Nat Commun 2019; 10:3475. [PMID: 31375673 PMCID: PMC6677770 DOI: 10.1038/s41467-019-11413-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 07/08/2019] [Indexed: 02/08/2023] Open
Abstract
Hypomethylating agents decitabine and azacytidine are regarded as interchangeable in the treatment of acute myeloid leukemia (AML). However, their mechanisms of action remain incompletely understood, and predictive biomarkers for HMA efficacy are lacking. Here, we show that the bioactive metabolite decitabine triphosphate, but not azacytidine triphosphate, functions as activator and substrate of the triphosphohydrolase SAMHD1 and is subject to SAMHD1-mediated inactivation. Retrospective immunohistochemical analysis of bone marrow specimens from AML patients at diagnosis revealed that SAMHD1 expression in leukemic cells inversely correlates with clinical response to decitabine, but not to azacytidine. SAMHD1 ablation increases the antileukemic activity of decitabine in AML cell lines, primary leukemic blasts, and xenograft models. AML cells acquire resistance to decitabine partly by SAMHD1 up-regulation. Together, our data suggest that SAMHD1 is a biomarker for the stratified use of hypomethylating agents in AML patients and a potential target for the treatment of decitabine-resistant leukemia. In acute myeloid leukemia, hypomethylating agents decitabine and azacytidine are used interchangeably. Here, the authors show that the major metabolite of decitabine, but not azacytidine, is subject to SAMHD1 inactivation, highlighting SAMHD1 as a potential biomarker and therapeutic target
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Affiliation(s)
- Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany.,German Cancer Consortium/German Cancer Research Center, Heidelberg, 69120, Germany.,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, 60596, Germany
| | - Constanze Schneider
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany.,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, 60596, Germany.,Institute of Medical Virology, University of Frankfurt, Frankfurt, 60590, Germany
| | - Dominique Thomas
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Kirsten M Knecht
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Olga Buzovetsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, 17475, Germany
| | | | | | - Linus Angenendt
- Department of Medicine A, University Hospital Münster, Münster, 48149, Germany
| | - Wolfgang Hartmann
- Gerhard Domagk Institute for Pathology, University Hospital Münster, Münster, 48149, Germany
| | - Eva Wardelmann
- Gerhard Domagk Institute for Pathology, University Hospital Münster, Münster, 48149, Germany
| | - Tamara Rothenburger
- Institute of Medical Virology, University of Frankfurt, Frankfurt, 60590, Germany
| | - Sebastian Mohr
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Sebastian Scheich
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Federico Comoglio
- Department of Haematology, Cambridge Institute of Medical Research, Cambridge University, Cambridge, CB2 0XY, UK
| | - Anne Wilke
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center, Göttingen, 37075, Germany
| | - Hubert Serve
- Department of Medicine II, Hematology/Oncology, Goethe University of Frankfurt, Frankfurt, 60590, Germany.,German Cancer Consortium/German Cancer Research Center, Heidelberg, 69120, Germany.,Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, 60596, Germany
| | - Martin Michaelis
- Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Nerea Ferreirós
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, 60590, Germany
| | - Gerd Geisslinger
- pharmazentrum frankfurt/ZAFES, Institute of Clinical Pharmacology, Goethe University of Frankfurt, Frankfurt, 60590, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Project group Translational Medicine and Pharmacology (TMP), Frankfurt, 60596, Germany
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Oliver T Keppler
- Institute of Medical Virology, University of Frankfurt, Frankfurt, 60590, Germany. .,Max von Pettenkofer Institute, Virology, Faculty of Medicine, LMU München, Munich, 80336, Germany.
| | - Jindrich Cinatl
- Institute of Medical Virology, University of Frankfurt, Frankfurt, 60590, Germany.
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50
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Kong J, Wang MM, He SY, Peng X, Qin XH. Structural characterization and directed modification of Sus scrofa SAMHD1 reveal the mechanism underlying deoxynucleotide regulation. FEBS J 2019; 286:3844-3857. [PMID: 31152619 DOI: 10.1111/febs.14943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/12/2019] [Accepted: 05/30/2019] [Indexed: 12/12/2022]
Abstract
Sterile α-motif/histidine-aspartate domain-containing protein 1 (SAMHD1) is an intrinsic antiviral restriction factor known to play a vital role in preventing multiple viral infections and in the control of the cellular deoxynucleoside triphosphate (dNTP) pool. Human and mouse SAMHD1 have both been extensively studied; however, our knowledge on porcine SAMHD1 is limited. Here, we report our findings from comprehensive structural and functional studies on porcine SAMHD1. We determined the crystal structure of porcine SAMHD1 and showed that it forms a symmetric tetramer. Moreover, we modified the deoxynucleotide triphosphohydrolase (dNTPase) activity of SAMHD1 by site-directed mutagenesis based on the crystal structure, and obtained an artificial dimeric enzyme possessing high dNTPase activity. Taken together, our results define the mechanism underlying dNTP regulation and provide a deeper understanding of the regulation of porcine SAMHD1 functions. Directed modification of key residues based on the protein structure enhances the activity of the enzyme, which will be beneficial in the search for new antiviral strategies and for future translational applications.
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Affiliation(s)
- Jia Kong
- School of Chemical Engineering and Technology, Tianjin University, China.,School of Life Sciences, Tianjin University, China
| | - Mei-Mei Wang
- School of Life Sciences, Tianjin University, China
| | - Shuang-Yi He
- School of Life Sciences, Tianjin University, China
| | - Xin Peng
- School of Life Sciences, Tianjin University, China
| | - Xiao-Hong Qin
- School of Life Sciences, Tianjin University, China.,State Key Laboratory of Medicinal Chemical Biology, NanKai University, Tianjin, China
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