Nuclear PYHIN proteins target the host transcription factor Sp1 thereby restricting HIV-1 in human macrophages and CD4+ T cells

Members of the family of pyrin and HIN domain containing (PYHIN) proteins play an emerging role in innate immunity. While absent in melanoma 2 (AIM2) acts a cytosolic sensor of non-self DNA and plays a key role in inflammasome assembly, the γ-interferon-inducible protein 16 (IFI16) restricts retroviral gene expression by sequestering the transcription factor Sp1. Here, we show that the remaining two human PYHIN proteins, i.e. myeloid cell nuclear differentiation antigen (MNDA) and pyrin and HIN domain family member 1 (PYHIN1 or IFIX) share this antiretroviral function of IFI16. On average, knock-down of each of these three nuclear PYHIN proteins increased infectious HIV-1 yield from human macrophages by more than an order of magnitude. Similarly, knock-down of IFI16 strongly increased virus transcription and production in primary CD4+ T cells. The N-terminal pyrin domain (PYD) plus linker region containing a nuclear localization signal (NLS) were generally required and sufficient for Sp1 sequestration and anti-HIV-1 activity of IFI16, MNDA and PYHIN1. Replacement of the linker region of AIM2 by the NLS-containing linker of IFI16 resulted in a predominantly nuclear localization and conferred direct antiviral activity to AIM2 while attenuating its ability to form inflammasomes. The reverse change caused nuclear-to-cytoplasmic relocalization of IFI16 and impaired its antiretroviral activity but did not result in inflammasome assembly. We further show that the Zn-finger domain of Sp1 is critical for the interaction with IFI16 supporting that pyrin domains compete with DNA for Sp1 binding. Finally, we found that human PYHIN proteins also inhibit Hepatitis B virus and simian vacuolating virus 40 as well as the LINE-1 retrotransposon. Altogether, our data show that IFI16, PYHIN1 and MNDA restrict HIV-1 and other viral pathogens by interfering with Sp1-dependent gene expression and support an important role of nuclear PYHIN proteins in innate antiviral immunity.

[1]  Lijie Li,et al.  Nuclear Sensor Interferon‐Inducible Protein 16 Inhibits the Function of Hepatitis B Virus Covalently Closed Circular DNA by Integrating Innate Immune Activation and Epigenetic Suppression , 2020, Hepatology.

[2]  A. Das,et al.  IFI16 Targets the Transcription Factor Sp1 to Suppress HIV-1 Transcription and Latency Reactivation. , 2019, Cell host & microbe.

[3]  J. Boeke,et al.  LINE-1 derepression in senescent cells triggers interferon and inflammaging , 2018, Nature.

[4]  N. Krogan,et al.  CRISPR–Cas9 genome engineering of primary CD4+ T cells for the interrogation of HIV–host factor interactions , 2018, Nature Protocols.

[5]  N. Ferreirós,et al.  The SAMHD1-mediated block of LINE-1 retroelements is regulated by phosphorylation , 2018, Mobile DNA.

[6]  J. Wong,et al.  HIV latency in isolated patient CD4+ T cells may be due to blocks in HIV transcriptional elongation, completion, and splicing , 2018, Science Translational Medicine.

[7]  E. Latz,et al.  The intra‐ and extracellular functions of ASC specks , 2018, Immunological reviews.

[8]  D. Greaves,et al.  The PYRIN domain-only protein POP2 inhibits inflammasome priming and activation , 2017, Nature Communications.

[9]  L. K. Sørensen,et al.  IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP , 2017, Nature Communications.

[10]  I. Cristea,et al.  Human Antiviral Protein IFIX Suppresses Viral Gene Expression during Herpes Simplex Virus 1 (HSV-1) Infection and Is Counteracted by Virus-induced Proteasomal Degradation* , 2017, Molecular & Cellular Proteomics.

[11]  C. Bonifer,et al.  The Role of the Ubiquitously Expressed Transcription Factor Sp1 in Tissue-specific Transcriptional Regulation and in Disease , 2016, The Yale journal of biology and medicine.

[12]  G. Núñez,et al.  Mechanism and Regulation of NLRP3 Inflammasome Activation. , 2016, Trends in biochemical sciences.

[13]  Jared E. Toettcher,et al.  Viral DNA Sensors IFI16 and Cyclic GMP-AMP Synthase Possess Distinct Functions in Regulating Viral Gene Expression, Immune Defenses, and Apoptotic Responses during Herpesvirus Infection , 2016, mBio.

[14]  Noele P. Nelson,et al.  Epidemiology of Hepatitis B Virus Infection and Impact of Vaccination on Disease. , 2016, Clinics in liver disease.

[15]  J. Cui,et al.  TRIM11 Suppresses AIM2 Inflammasome by Degrading AIM2 via p62-Dependent Selective Autophagy. , 2016, Cell reports.

[16]  K. Schroder,et al.  Assessment of Inflammasome Formation by Flow Cytometry , 2016, Current protocols in immunology.

[17]  H. Pospiech,et al.  DNA damage tolerance pathway involving DNA polymerase ι and the tumor suppressor p53 regulates DNA replication fork progression , 2016, Proceedings of the National Academy of Sciences.

[18]  H. Ploegh,et al.  A single domain antibody fragment that recognizes the adaptor ASC defines the role of ASC domains in inflammasome assembly , 2016, The Journal of experimental medicine.

[19]  G. Cheng,et al.  New insights into the structural basis of DNA recognition by HINa and HINb domains of IFI16. , 2016, Journal of molecular cell biology.

[20]  Antoine M. van Oijen,et al.  The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex , 2015, eLife.

[21]  P. Autissier,et al.  Evolutionary and Functional Analysis of Old World Primate TRIM5 Reveals the Ancient Emergence of Primate Lentiviruses and Convergent Evolution Targeting a Conserved Capsid Interface , 2015, PLoS pathogens.

[22]  M. A. Ansari,et al.  Herpesvirus Genome Recognition Induced Acetylation of Nuclear IFI16 Is Essential for Its Cytoplasmic Translocation, Inflammasome and IFN-β Responses , 2015, PLoS pathogens.

[23]  A. Telenti,et al.  Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses , 2015, Retrovirology.

[24]  Karen E. Johnson,et al.  The Nuclear DNA Sensor IFI16 Acts as a Restriction Factor for Human Papillomavirus Replication through Epigenetic Modifications of the Viral Promoters , 2015, Journal of Virology.

[25]  I. Cristea,et al.  The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA , 2015, Molecular systems biology.

[26]  C. Stehlik,et al.  The Domains of Apoptosis and Inflammation an Updated View on the Structure and Function of Pyrin Domains , 2022 .

[27]  S. Paludan,et al.  IFI16: At the interphase between innate DNA sensing and genome regulation. , 2014, Cytokine & growth factor reviews.

[28]  Karen E. Johnson,et al.  IFI16 Restricts HSV-1 Replication by Accumulating on the HSV-1 Genome, Repressing HSV-1 Gene Expression, and Directly or Indirectly Modulating Histone Modifications , 2014, PLoS pathogens.

[29]  Martin S. Taylor,et al.  Long interspersed element-1 protein expression is a hallmark of many human cancers. , 2014, The American journal of pathology.

[30]  D. Stetson,et al.  The enemy within: endogenous retroelements and autoimmune disease , 2014, Nature Immunology.

[31]  Katherine A. Fitzgerald,et al.  Unified Polymerization Mechanism for the Assembly of ASC-Dependent Inflammasomes , 2014, Cell.

[32]  Zhi-Xin Wang,et al.  Purification, characterization and docking studies of the HIN domain of human myeloid nuclear differentiation antigen (MNDA) , 2014, Biotechnology Letters.

[33]  D. Greaves,et al.  The PYRIN domain-only protein POP3 inhibits AIM2-like receptor inflammasomes and regulates responses to DNA virus infections , 2014, Nature Immunology.

[34]  N. Krogan,et al.  IFI16 DNA Sensor Is Required for Death of Lymphoid CD4 T Cells Abortively Infected with HIV , 2014, Science.

[35]  S. Morrone,et al.  Cooperative assembly of IFI16 filaments on dsDNA provides insights into host defense strategy , 2013, Proceedings of the National Academy of Sciences.

[36]  J. Decaprio,et al.  Nuclear interferon-inducible protein 16 promotes silencing of herpesviral and transfected DNA , 2013, Proceedings of the National Academy of Sciences.

[37]  R. Bak,et al.  IFI16 senses DNA forms of the lentiviral replication cycle and controls HIV-1 replication , 2013, Proceedings of the National Academy of Sciences.

[38]  Karen E. Johnson,et al.  Herpes Simplex Virus 1 Infection Induces Activation and Subsequent Inhibition of the IFI16 and NLRP3 Inflammasomes , 2013, Journal of Virology.

[39]  M. A. Ansari,et al.  Kaposi's Sarcoma-Associated Herpesvirus Latency in Endothelial and B Cells Activates Gamma Interferon-Inducible Protein 16-Mediated Inflammasomes , 2013, Journal of Virology.

[40]  N. DeLuca,et al.  Nuclear IFI16 induction of IRF-3 signaling during herpesviral infection and degradation of IFI16 by the viral ICP0 protein , 2012, Proceedings of the National Academy of Sciences.

[41]  Eva Z. Curley,et al.  The mammalian PYHIN gene family: Phylogeny, evolution and expression , 2012, BMC Evolutionary Biology.

[42]  I. Cristea,et al.  Acetylation modulates cellular distribution and DNA sensing ability of interferon-inducible protein IFI16 , 2012, Proceedings of the National Academy of Sciences.

[43]  C. Münk,et al.  An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals , 2012, BMC Evolutionary Biology.

[44]  A. Bowie,et al.  Structures of the HIN domain:DNA complexes reveal ligand binding and activation mechanisms of the AIM2 inflammasome and IFI16 receptor. , 2012, Immunity.

[45]  A. Luganini,et al.  The Intracellular DNA Sensor IFI16 Gene Acts as Restriction Factor for Human Cytomegalovirus Replication , 2012, PLoS pathogens.

[46]  M. Batzer,et al.  Repetitive Elements May Comprise Over Two-Thirds of the Human Genome , 2011, PLoS genetics.

[47]  K. Fitzgerald,et al.  The PYHIN protein family as mediators of host defenses , 2011, Immunological reviews.

[48]  Yoshihiro Hayakawa,et al.  STING is a direct innate immune sensor of cyclic-di-GMP , 2011, Nature.

[49]  B. Chandran,et al.  IFI16 acts as a nuclear pathogen sensor to induce the inflammasome in response to Kaposi Sarcoma-associated herpesvirus infection. , 2011, Cell host & microbe.

[50]  R. Vance,et al.  Differential requirement for Caspase-1 autoproteolysis in pathogen-induced cell death and cytokine processing. , 2010, Cell host & microbe.

[51]  A. Bowie,et al.  IFI16 is an innate immune sensor for intracellular DNA , 2010, Nature Immunology.

[52]  Lin Li,et al.  The role of Sp1 and Sp3 in normal and cancer cell biology. , 2010, Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft.

[53]  G. Núñez,et al.  The inflammasome: a caspase-1-activation platform that regulates immune responses and disease pathogenesis , 2009, Nature Immunology.

[54]  P. Boudinot,et al.  A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish , 2009, BMC Biology.

[55]  Daniel R. Caffrey,et al.  AIM2 recognizes cytosolic dsDNA and forms a caspase-1 activating inflammasome with ASC , 2009, Nature.

[56]  M. Hung,et al.  Interferon‐inducible protein IFIXα inhibits cell invasion by upregulating the metastasis suppressor maspin , 2008, Molecular carcinogenesis.

[57]  Mario Schelhaas,et al.  Simian Virus 40 Depends on ER Protein Folding and Quality Control Factors for Entry into Host Cells , 2007, Cell.

[58]  Hua Lu,et al.  Interferon-Inducible Protein IFIXα1 Functions as a Negative Regulator of HDM2 , 2006, Molecular and Cellular Biology.

[59]  A. Fedorov,et al.  Identification of the proteins specifically binding to the rat LINE1 promoter. , 2006, Biochemical and biophysical research communications.

[60]  K. Hunt,et al.  Antitumor activity of IFIX, a novel interferon-inducible HIN-200 gene, in breast cancer , 2004, Oncogene.

[61]  V. Dixit,et al.  The PYRIN domain: A member of the death domain‐fold superfamily , 2001, Protein science : a publication of the Protein Society.

[62]  J. Bertin,et al.  The PYRIN domain: a novel motif found in apoptosis and inflammation proteins , 2000, Cell Death and Differentiation.

[63]  R. Briggs,et al.  Human hematopoietic cell specific nuclear protein MNDA interacts with the multifunctional transcription factor YY1 and stimulates YY1 DNA binding , 1998, Journal of cellular biochemistry.

[64]  B. Chesebro,et al.  Effects of CCR5 and CD4 Cell Surface Concentrations on Infections by Macrophagetropic Isolates of Human Immunodeficiency Virus Type 1 , 1998, Journal of Virology.

[65]  R. Briggs,et al.  Regulation and specificity of MNDA expression in monocytes, macrophages, and leukemia/B lymophoma cell lines , 1994, Journal of cellular biochemistry.

[66]  G. Lutfalla,et al.  Domains of interaction between alpha interferon and its receptor components. , 1994, Journal of molecular biology.

[67]  G. Stein,et al.  cis-diamminedichloroplatinum(II) cross-linking of the human myeloid cell nuclear differentiation antigen to DNA in HL-60 cells following 1,25-dihydroxy vitamin D3-induced monocyte differentiation. , 1990, Cancer research.

[68]  J. Miller,et al.  Analysis of mutation in human cells by using an Epstein-Barr virus shuttle system , 1987, Molecular and cellular biology.

[69]  Ivan Damjanov,et al.  Controlled synthesis of HBsAg in a differentiated human liver carcinoma-derived cell line , 1979, Nature.

[70]  F. Jensen,et al.  INFECTION OF HUMAN AND SIMIAN TISSUE CULTURES WITH ROUS SARCOMA VIRUS. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

[71]  Lijie Li,et al.  Nuclear Sensor Interferon‐Inducible Protein 16 Inhibits the Function of Hepatitis B Virus Covalently Closed Circular DNA by Integrating Innate Immune Activation and Epigenetic Suppression , 2019, Hepatology.

[72]  D. Choubey,et al.  Interferon-inducible p200-family protein IFI16, an innate immune sensor for cytosolic and nuclear double-stranded DNA: regulation of subcellular localization. , 2012, Molecular immunology.