1
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Prakash P, Khodke P, Balasubramaniam M, Davids BO, Hollis T, Davis J, Kumbhar B, Dash C. Three prime repair exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural, and conformational properties. J Biol Chem 2024; 300:107438. [PMID: 38838778 PMCID: PMC11259700 DOI: 10.1016/j.jbc.2024.107438] [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: 12/11/2023] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
HIV-1 integration into the human genome is dependent on 3'-processing of the viral DNA. Recently, we reported that the cellular Three Prime Repair Exonuclease 1 (TREX1) enhances HIV-1 integration by degrading the unprocessed viral DNA, while the integration-competent 3'-processed DNA remained resistant. Here, we describe the mechanism by which the 3'-processed HIV-1 DNA resists TREX1-mediated degradation. Our kinetic studies revealed that the rate of cleavage (kcat) of the 3'-processed DNA was significantly lower (approximately 2-2.5-fold) than the unprocessed HIV-1 DNA by TREX1. The kcat values of human TREX1 for the processed U5 and U3 DNA substrates were 3.8 s-1 and 4.5 s-1, respectively. In contrast, the unprocessed U5 and U3 substrates were cleaved at 10.2 s-1 and 9.8 s-1, respectively. The efficiency of degradation (kcat/Km) of the 3'-processed DNA (U5-70.2 and U3-28.05 pM-1s-1) was also significantly lower than the unprocessed DNA (U5-103.1 and U3-65.3 pM-1s-1). Furthermore, the binding affinity (Kd) of TREX1 was markedly lower (∼2-fold) for the 3'-processed DNA than the unprocessed DNA. Molecular docking and dynamics studies revealed distinct conformational binding modes of TREX1 with the 3'-processed and unprocessed HIV-1 DNA. Particularly, the unprocessed DNA was favorably positioned in the active site with polar interactions with the catalytic residues of TREX1. Additionally, a stable complex was formed between TREX1 and the unprocessed DNA compared the 3'-processed DNA. These results pinpoint the mechanism by which TREX1 preferentially degrades the integration-incompetent HIV-1 DNA and reveal the unique structural and conformational properties of the integration-competent 3'-processed HIV-1 DNA.
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Affiliation(s)
- Prem Prakash
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Purva Khodke
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be-) University, Mumbai, Maharashtra, India
| | - Muthukumar Balasubramaniam
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Benem-Orom Davids
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, New York, USA
| | - Thomas Hollis
- Department of Biochemistry and Center for Structural Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Jamaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Bajarang Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be-) University, Mumbai, Maharashtra, India
| | - Chandravanu Dash
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA; Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA; Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA.
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2
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Scott TM, Arnold LM, Powers JA, McCann DA, Christensen DE, Pereira MJ, Zhou W, Torrez RM, Iwasa JH, Kranzusch PJ, Sundquist WI, Johnson JS. Cell-free assays reveal the HIV-1 capsid protects reverse transcripts from cGAS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590513. [PMID: 38712059 PMCID: PMC11071359 DOI: 10.1101/2024.04.22.590513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Retroviruses can be detected by the innate immune sensor cyclic GMP-AMP synthase (cGAS), which recognizes reverse-transcribed DNA and activates an antiviral response. However, the extent to which HIV-1 shields its genome from cGAS recognition remains unclear. To study this process in mechanistic detail, we reconstituted reverse transcription, genome release, and innate immune sensing of HIV-1 in a cell-free system. We found that wild-type HIV-1 capsids protect their genomes from cGAS even after completion of reverse transcription. Viral DNA could be "deprotected" by thermal stress, capsid mutations, or reduced concentrations of inositol hexakisphosphate (IP6) that destabilize the capsid. Strikingly, capsid inhibitors also disrupted viral cores and dramatically potentiated cGAS activity, both in vitro and in cellular infections. Our results provide biochemical evidence that the HIV-1 capsid lattice conceals the genome from cGAS and that chemical or physical disruption of the viral core can expose HIV-1 DNA and activate innate immune signaling.
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Affiliation(s)
- Tiana M. Scott
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Lydia M. Arnold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Jordan A. Powers
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Delaney A. McCann
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Devin E. Christensen
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Miguel J. Pereira
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology; Shenzhen, Guangdong 518055, China
| | - Rachel M. Torrez
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Janet H. Iwasa
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Philip J. Kranzusch
- Department of Microbiology, Harvard Medical School; Boston, MA 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute; Boston, MA 02115, USA
| | - Wesley I. Sundquist
- Department of Biochemistry, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
| | - Jarrod S. Johnson
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine; Salt Lake City, UT 84112, USA
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Eschbach JE, Puray-Chavez M, Mohammed S, Wang Q, Xia M, Huang LC, Shan L, Kutluay SB. HIV-1 capsid stability and reverse transcription are finely balanced to minimize sensing of reverse transcription products via the cGAS-STING pathway. mBio 2024; 15:e0034824. [PMID: 38530034 PMCID: PMC11077976 DOI: 10.1128/mbio.00348-24] [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: 02/05/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
A critical determinant for early post-entry events, the HIV-1 capsid (CA) protein forms the conical core when it rearranges around the dimeric RNA genome and associated viral proteins. Although mutations in CA have been reported to alter innate immune sensing of HIV-1, a direct link between core stability and sensing of HIV-1 nucleic acids has not been established. Herein, we assessed how manipulating the stability of the CA lattice through chemical and genetic approaches affects innate immune recognition of HIV-1. We found that destabilization of the CA lattice resulted in potent sensing of reverse transcription products when destabilization per se does not completely block reverse transcription. Surprisingly, due to the combined effects of enhanced reverse transcription and defects in nuclear entry, two separate CA mutants that form hyperstable cores induced innate immune sensing more potently than destabilizing CA mutations. At low concentrations that allowed the accumulation of reverse transcription products, CA-targeting compounds GS-CA1 and lenacapavir measurably impacted CA lattice stability in cells and modestly enhanced innate immune sensing of HIV. Interestingly, innate immune activation observed with viruses containing unstable cores was abolished by low doses of lenacapavir. Innate immune activation observed with both hyperstable and unstable CA mutants was dependent on the cGAS-STING DNA-sensing pathway and reverse transcription. Overall, our findings demonstrate that CA lattice stability and reverse transcription are finely balanced to support reverse transcription and minimize cGAS-STING-mediated sensing of the resulting viral DNA. IMPORTANCE In HIV-1 particles, the dimeric RNA genome and associated viral proteins and enzymes are encased in a proteinaceous lattice composed of the viral capsid protein. Herein, we assessed how altering the stability of this capsid lattice through orthogonal genetic and chemical approaches impacts the induction of innate immune responses. Specifically, we found that decreasing capsid lattice stability results in more potent sensing of viral reverse transcription products, but not the genomic RNA, in a cGAS-STING-dependent manner. The recently developed capsid inhibitors lenacapavir and GS-CA1 enhanced the innate immune sensing of HIV-1. Unexpectedly, due to increased levels of reverse transcription and cytosolic accumulation of the resulting viral cDNA, capsid mutants with hyperstable cores also resulted in the potent induction of type I interferon-mediated innate immunity. Our findings suggest that HIV-1 capsid lattice stability and reverse transcription are finely balanced to minimize exposure of reverse transcription products in the cytosol of host cells.
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Affiliation(s)
- Jenna E. Eschbach
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shawn Mohammed
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Qiankun Wang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Ming Xia
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lin-Chen Huang
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Liang Shan
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, Missouri, USA
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4
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Burdick RC, Morse M, Rouzina I, Williams MC, Hu WS, Pathak VK. HIV-1 uncoating requires long double-stranded reverse transcription products. SCIENCE ADVANCES 2024; 10:eadn7033. [PMID: 38657061 PMCID: PMC11042746 DOI: 10.1126/sciadv.adn7033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
HIV-1 cores, which contain the viral genome and replication machinery, must disassemble (uncoat) during viral replication. However, the viral and host factors that trigger uncoating remain unidentified. Recent studies show that infectious cores enter the nucleus and uncoat near the site of integration. Here, we show that efficient uncoating of nuclear cores requires synthesis of a double-stranded DNA (dsDNA) genome >3.5 kb and that the efficiency of uncoating correlates with genome size. Core disruption by capsid inhibitors releases viral DNA, some of which integrates. However, most of the viral DNA is degraded, indicating that the intact core safeguards viral DNA. Atomic force microscopy and core content estimation reveal that synthesis of full-length genomic dsDNA induces substantial internal strain on the core to promote uncoating. We conclude that HIV-1 cores protect viral DNA from degradation by host factors and that synthesis of long double-stranded reverse transcription products is required to trigger efficient HIV-1 uncoating.
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Affiliation(s)
- Ryan C. Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for Retroviral Research and Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
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5
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Prakash P, Khodke P, Balasubramaniam M, Davids BO, Hollis T, Davis J, Pandhare J, Kumbhar B, Dash C. Three Prime Repair Exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural and conformational properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585766. [PMID: 38562877 PMCID: PMC10983988 DOI: 10.1101/2024.03.19.585766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
HIV-1 integration into the human genome is dependent on 3'-processing of the reverse transcribed viral DNA. Recently, we reported that the cellular Three Prime Repair Exonuclease 1 (TREX1) enhances HIV-1 integration by degrading the unprocessed viral DNA, while the integration-competent 3'-processed DNA remained resistant. Here, we describe the mechanism by which the 3'-processed HIV-1 DNA resists TREX1-mediated degradation. Our kinetic studies revealed that the rate of cleavage (kcat) of the 3'-processed DNA was significantly lower than the unprocessed HIV-1 DNA by TREX1. The efficiency of degradation (kcat/KM) of the 3'-processed DNA was also significantly lower than the unprocessed DNA. Furthermore, the binding affinity (Kd) of TREX1 was markedly lower to the 3'-processed DNA compared to the unprocessed DNA. Molecular docking and dynamics studies revealed distinct conformational binding modes of TREX1 with the 3'-processed and unprocessed HIV-1 DNA. Particularly, the unprocessed DNA was favorably positioned in the active site with polar interactions with the catalytic residues of TREX1. Additionally, a stable complex was formed between TREX1 and the unprocessed DNA compared the 3'-processed DNA. These results pinpoint the biochemical mechanism by which TREX1 preferentially degrades the integration-incompetent HIV-1 DNA and reveal the unique structural and conformational properties of the integration-competent 3'-processed HIV-1 DNA.
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Affiliation(s)
- Prem Prakash
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Purva Khodke
- Sunandan Divatia School of Science, NMIMS University, Mumbai, 400056, India
| | - Muthukumar Balasubramaniam
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Benem-Orom Davids
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York City, New York, 10032, USA
| | - Thomas Hollis
- Department of Biochemistry and Center for Structural Biology, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Jamaine Davis
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Bajarang Kumbhar
- Sunandan Divatia School of Science, NMIMS University, Mumbai, 400056, India
| | - Chandravanu Dash
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, 37208, USA
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, 37208, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, 37208, USA
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6
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Tohidi N, Manshadi SAD, Hajiabdolbaghi M. Association of TREX1 polymorphism with disease progression in human immunodeficiency virus type-1 (HIV-1) infected patients. Virus Genes 2023; 59:831-835. [PMID: 37728706 DOI: 10.1007/s11262-023-02032-9] [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: 05/20/2023] [Accepted: 09/07/2023] [Indexed: 09/21/2023]
Abstract
The time interval between HIV-1 infection and AIDS development is not the same in all patients and depends largely on the genetic background of the individual. Polymorphisms in the TREX1 gene, the main enzyme in the clearance of cytosolic DNA, affect type 1 interferon-mediated inflammatory response in HIV-1 infection. We aimed to study the role of a single nucleotide polymorphism (rs3135941) of the TREX1 gene and the rate of disease progression in patients infected with HIV-1. A total of 190 HIV-1 infected patients were recruited. Patients' demographic and laboratory data including CD4 counts, viral load, and antiretroviral therapy (ART) were collected. The genotype of rs3135941 was determined by a PCR-SSP method. The rate of progression to AIDS was calculated with Kaplan-Meier survival analysis using Stata software. The patients were divided into rapid and slow progressors based on time interval of CD4 drop below 350/µl. Kaplan-Meier analysis revealed an accelerated disease progression in patients with TC and CC genotypes (HR = 1.49, 95% CI = 1.01-2.17). The mean values of the first 5-year CD4 counts were significantly different in patients who had CC and TC genotypes compared to the TT group (p = 0.036). The result of this study emphasizes the importance of TREX1 polymorphism in HIV-1 progression. These data warrant further investigation into the role of other polymorphisms of TREX1.
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Affiliation(s)
- Nastaran Tohidi
- Department of Infectious Diseases and Tropical Medicine, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, 1419733141, Iran
| | - Seyed Ali Dehghan Manshadi
- Department of Infectious Diseases and Tropical Medicine, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, 1419733141, Iran
| | - Mahboubeh Hajiabdolbaghi
- Department of Infectious Diseases and Tropical Medicine, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, 1419733141, Iran.
- Iranian Research Center of HIV/AIDS, Iranian Institute for Reduction of High-Risk Behaviors, Tehran University of Medical Sciences, Tehran, Iran.
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7
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Huang KW, Wu CY, Toh SI, Liu TC, Tu CI, Lin YH, Cheng AJ, Kao YT, Chu JW, Hsiao YY. Molecular insight into the specific enzymatic properties of TREX1 revealing the diverse functions in processing RNA and DNA/RNA hybrids. Nucleic Acids Res 2023; 51:11927-11940. [PMID: 37870446 PMCID: PMC10681709 DOI: 10.1093/nar/gkad910] [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: 05/19/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
In various autoimmune diseases, dysfunctional TREX1 (Three prime Repair Exonuclease 1) leads to accumulation of endogenous single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and DNA/RNA hybrids in the cytoplasm and triggers immune activation through the cGAS-STING pathway. Although inhibition of TREX1 could be a useful strategy for cancer immunotherapy, profiling cellular functions in terms of its potential substrates is a key step. Particularly important is the functionality of processing DNA/RNA hybrids and RNA substrates. The exonuclease activity measurements conducted here establish that TREX1 can digest both ssRNA and DNA/RNA hybrids but not dsRNA. The newly solved structures of TREX1-RNA product and TREX1-nucleotide complexes show that 2'-OH does not impose steric hindrance or specific interactions for the recognition of RNA. Through all-atom molecular dynamics simulations, we illustrate that the 2'-OH-mediated intra-chain hydrogen bonding in RNA would affect the binding with TREX1 and thereby reduce the exonuclease activity. This notion of higher conformational rigidity in RNA leading TREX1 to exhibit weaker catalytic cleavage is further validated by the binding affinity measurements with various synthetic DNA-RNA junctions. The results of this work thus provide new insights into the mechanism by which TREX1 processes RNA and DNA/RNA hybrids and contribute to the molecular-level understanding of the complex cellular functions of TREX1 as an exonuclease.
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Affiliation(s)
- Kuan-Wei Huang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chia-Yun Wu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Shu-Ing Toh
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Tung-Chang Liu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Chun-I Tu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yin-Hsin Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - An-Ju Cheng
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Ya-Ting Kao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Jhih-Wei Chu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Yu-Yuan Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Drug Development and Value Creation Research Center, Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
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8
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Wang W, Li Y, Zhang Z, Wei W. Human immunodeficiency virus-1 core: The Trojan horse in virus–host interaction. Front Microbiol 2022; 13:1002476. [PMID: 36106078 PMCID: PMC9465167 DOI: 10.3389/fmicb.2022.1002476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/04/2022] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) is the major cause of acquired immunodeficiency syndrome (AIDs) worldwide. In HIV-1 infection, innate immunity is the first defensive line for immune recognition and viral clearance to ensure the normal biological function of the host cell and body health. Under the strong selected pressure generated by the human body over thousands of years, HIV has evolved strategies to counteract and deceive the innate immune system into completing its lifecycle. Recently, several studies have demonstrated that HIV capsid core which is thought to be a protector of the cone structure of genomic RNA, also plays an essential role in escaping innate immunity surveillance. This mini-review summarizes the function of capsid in viral immune evasion, and the comprehensive elucidation of capsid-host cell innate immunity interaction could promote our understanding of HIV-1’s pathogenic mechanism and provide insights for HIV-1 treatment in clinical therapy.
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Affiliation(s)
- Wei Wang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yan Li
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhe Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Wei
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin, China
- *Correspondence: Wei Wei,
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9
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Kazmierski J, Elsner C, Döhner K, Xu S, Ducroux A, Pott F, Jansen J, Thorball CW, Zeymer O, Zhou X, Fedorov R, Fellay J, Löffler MW, Weber ANR, Sodeik B, Goffinet C. A Baseline Cellular Antiviral State Is Maintained by cGAS and Its Most Frequent Naturally Occurring Variant rs610913. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:535-547. [PMID: 35851540 DOI: 10.4049/jimmunol.2100685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/13/2022] [Indexed: 10/17/2023]
Abstract
Upon recognition of aberrantly located DNA, the innate immune sensor cyclic GMP-AMP synthase (cGAS) activates stimulator of IFN genes (STING)/IFN regulatory factor (IRF)3-driven antiviral responses. In this study, we characterized the ability of a specific variant of the human cGAS-encoding gene MB21D1, rs610913, to alter cGAS-mediated DNA sensing and viral infection. rs610913 is a frequent G>T polymorphism resulting in a P261H exchange in the cGAS protein. Data from the International Collaboration for the Genomics of HIV suggested that rs610913 nominally associates with HIV-1 acquisition in vivo. Molecular modeling of cGAS(P261H) hinted toward the possibility for an additional binding site for a potential cellular cofactor in cGAS dimers. However, cGAS(wild-type [WT]) or cGAS(P261H)-reconstituted THP-1 cGAS knockout cells shared steady-state expression of IFN-stimulated genes, as opposed to cells expressing the enzymatically inactive cGAS(G212A/S213A). Accordingly, cGAS(WT) and cGAS(P261H) cells were less susceptible to lentiviral transduction and infection with HIV-1, HSV-1, and Chikungunya virus as compared with cGAS knockout or cGAS(G212A/S213A) cells. Upon DNA challenge, innate immune activation appeared to be mildly reduced upon expression of cGAS(P261H) compared with cGAS(WT). Finally, DNA challenge of PBMCs from donors homozygously expressing rs610913 provoked a trend toward a slightly reduced type I IFN response as compared with PBMCs from GG donors. Taken together, the steady-state activity of cGAS maintains a baseline antiviral state rendering cells more refractory to IFN-stimulated gene-sensitive viral infections. rs610913 failed to grossly differ phenotypically from the WT gene, suggesting that cGAS(P261H) and WT cGAS share a similar ability to sense viral infections in vivo.
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Affiliation(s)
- Julia Kazmierski
- Institute of Virology, Campus Charité Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- Institute of Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Carina Elsner
- Institute of Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Katinka Döhner
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Shuting Xu
- Institute of Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Aurélie Ducroux
- Institute of Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Fabian Pott
- Institute of Virology, Campus Charité Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- Institute of Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Jenny Jansen
- Institute of Virology, Campus Charité Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Christian W Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Ole Zeymer
- Institute for Biophysical Chemistry, Research Division for Structural Biochemistry, Hannover Medical School, Hannover, Germany
- RESIST-Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Xiaoyi Zhou
- Institute for Biophysical Chemistry, Research Division for Structural Biochemistry, Hannover Medical School, Hannover, Germany
- RESIST-Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Roman Fedorov
- Institute for Biophysical Chemistry, Research Division for Structural Biochemistry, Hannover Medical School, Hannover, Germany
- RESIST-Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Markus W Löffler
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen Germany
- Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
- iFIT-Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Alexander N R Weber
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- iFIT-Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
- CMFI-Cluster of Excellence (EXC 2124) "Controlling Microbes to Fight Infection," University of Tübingen, Tübingen, Germany; and
| | - Beate Sodeik
- Institute of Virology, Hannover Medical School, Hannover, Germany
- RESIST-Cluster of Excellence, Hannover Medical School, Hannover, Germany
- German Center for Infection Research, Hannover-Braunschweig Partner Site, Hannover, Germany
| | - Christine Goffinet
- Institute of Virology, Campus Charité Mitte, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- Institute of Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
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10
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Manils J, Marruecos L, Soler C. Exonucleases: Degrading DNA to Deal with Genome Damage, Cell Death, Inflammation and Cancer. Cells 2022; 11:2157. [PMID: 35883600 PMCID: PMC9316158 DOI: 10.3390/cells11142157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023] Open
Abstract
Although DNA degradation might seem an unwanted event, it is essential in many cellular processes that are key to maintaining genomic stability and cell and organism homeostasis. The capacity to cut out nucleotides one at a time from the end of a DNA chain is present in enzymes called exonucleases. Exonuclease activity might come from enzymes with multiple other functions or specialized enzymes only dedicated to this function. Exonucleases are involved in central pathways of cell biology such as DNA replication, repair, and death, as well as tuning the immune response. Of note, malfunctioning of these enzymes is associated with immune disorders and cancer. In this review, we will dissect the impact of DNA degradation on the DNA damage response and its links with inflammation and cancer.
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Affiliation(s)
- Joan Manils
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Spain;
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
| | - Laura Marruecos
- Breast Cancer Laboratory, Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Concepció Soler
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
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11
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Huérfano S, Šroller V, Bruštíková K, Horníková L, Forstová J. The Interplay between Viruses and Host DNA Sensors. Viruses 2022; 14:v14040666. [PMID: 35458396 PMCID: PMC9027975 DOI: 10.3390/v14040666] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 12/12/2022] Open
Abstract
DNA virus infections are often lifelong and can cause serious diseases in their hosts. Their recognition by the sensors of the innate immune system represents the front line of host defence. Understanding the molecular mechanisms of innate immunity responses is an important prerequisite for the design of effective antivirotics. This review focuses on the present state of knowledge surrounding the mechanisms of viral DNA genome sensing and the main induced pathways of innate immunity responses. The studies that have been performed to date indicate that herpesviruses, adenoviruses, and polyomaviruses are sensed by various DNA sensors. In non-immune cells, STING pathways have been shown to be activated by cGAS, IFI16, DDX41, or DNA-PK. The activation of TLR9 has mainly been described in pDCs and in other immune cells. Importantly, studies on herpesviruses have unveiled novel participants (BRCA1, H2B, or DNA-PK) in the IFI16 sensing pathway. Polyomavirus studies have revealed that, in addition to viral DNA, micronuclei are released into the cytosol due to genotoxic stress. Papillomaviruses, HBV, and HIV have been shown to evade DNA sensing by sophisticated intracellular trafficking, unique cell tropism, and viral or cellular protein actions that prevent or block DNA sensing. Further research is required to fully understand the interplay between viruses and DNA sensors.
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12
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Zhang MJ, Stear JH, Jacques DA, Böcking T. Insights into HIV uncoating from single-particle imaging techniques. Biophys Rev 2022; 14:23-32. [PMID: 35340594 PMCID: PMC8921429 DOI: 10.1007/s12551-021-00922-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/23/2021] [Indexed: 01/13/2023] Open
Abstract
Human immunodeficiency virus (HIV) is the most extensively researched human pathogen. Despite this massive scientific endeavour, several fundamental viral processes remain enigmatic. One such critical process is uncoating-the event that releases the viral genome from the proteinaceous shell of the capsid during infection. While this process is conceptually simple, the molecular underpinnings, timing, regulation, and cellular location of uncoating remain contentious. This review describes the hurdles that have limited our understanding in this area and presents recently deployed in vitro and in cellulo techniques that have been developed expressly with the aim of directly visualising capsid uncoating at the single-particle level and understanding the mechanics behind this essential aspect of HIV infection.
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Affiliation(s)
- Margaret J. Zhang
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Jeffrey H. Stear
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - David A. Jacques
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052 Australia
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13
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Toll-Like Receptor (TLR) Signaling Enables Cyclic GMP-AMP Synthase (cGAS) Sensing of HIV-1 Infection in Macrophages. mBio 2021; 12:e0281721. [PMID: 34844429 PMCID: PMC8630538 DOI: 10.1128/mbio.02817-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
HIV-1 replicates in cells that express a wide array of innate immune sensors and may do so simultaneously with other pathogens. How a coexisting innate immune stimulus influences the outcome of HIV-1 sensing, however, remains poorly understood. Here, we demonstrate that the activation of a second signaling pathway enables a cyclic GMP-AMP synthase (cGAS)-dependent type I interferon (IFN-I) response to HIV-1 infection. We used RNA sequencing to determine that HIV-1 alone induced few or no signs of an IFN-I response in THP-1 cells. In contrast, when supplemented with suboptimal levels of bacterial lipopolysaccharide (LPS), HIV-1 infection triggered the production of elevated levels of IFN-I and significant upregulation of interferon-stimulated genes. LPS-mediated enhancement of IFN-I production upon HIV-1 infection, which was observed in primary macrophages, was lost by blocking reverse transcription and with a hyperstable capsid, pointing to viral DNA being an essential immunostimulatory molecule. LPS also synergistically enhanced IFN-I production by cyclic GMP-AMP (cGAMP), a second messenger of cGAS. These observations suggest that the DNA sensor cGAS is responsible for a type I IFN response to HIV-1 in concert with LPS receptor Toll-like receptor 4 (TLR4). Small amounts of a TLR2 agonist also cooperate with HIV-1 to induce type I IFN production. These results demonstrate how subtle immunomodulatory activity renders HIV-1 capable of eliciting an IFN-I response through positive cross talk between cGAS and TLR sensing pathways.
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14
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Saito A, Yamashita M. HIV-1 capsid variability: viral exploitation and evasion of capsid-binding molecules. Retrovirology 2021; 18:32. [PMID: 34702294 PMCID: PMC8549334 DOI: 10.1186/s12977-021-00577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV-1 capsid, a conical shell encasing viral nucleoprotein complexes, is involved in multiple post-entry processes during viral replication. Many host factors can directly bind to the HIV-1 capsid protein (CA) and either promote or prevent HIV-1 infection. The viral capsid is currently being explored as a novel target for therapeutic interventions. In the past few decades, significant progress has been made in our understanding of the capsid–host interactions and mechanisms of action of capsid-targeting antivirals. At the same time, a large number of different viral capsids, which derive from many HIV-1 mutants, naturally occurring variants, or diverse lentiviruses, have been characterized for their interactions with capsid-binding molecules in great detail utilizing various experimental techniques. This review provides an overview of how sequence variation in CA influences phenotypic properties of HIV-1. We will focus on sequence differences that alter capsid–host interactions and give a brief account of drug resistant mutations in CA and their mutational effects on viral phenotypes. Increased knowledge of the sequence-function relationship of CA helps us deepen our understanding of the adaptive potential of the viral capsid.
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Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Masahiro Yamashita
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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15
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Ryabchenko B, Soldatova I, Šroller V, Forstová J, Huérfano S. Immune sensing of mouse polyomavirus DNA by p204 and cGAS DNA sensors. FEBS J 2021; 288:5964-5985. [PMID: 33969628 PMCID: PMC8596513 DOI: 10.1111/febs.15962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/20/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022]
Abstract
The mechanism by which DNA viruses interact with different DNA sensors and their connection with the activation of interferon (IFN) type I pathway are poorly understood. We investigated the roles of protein 204 (p204) and cyclic guanosine-adenosine synthetase (cGAS) sensors during infection with mouse polyomavirus (MPyV). The phosphorylation of IFN regulatory factor 3 (IRF3) and the stimulator of IFN genes (STING) proteins and the upregulation of IFN beta (IFN-β) and MX Dynamin Like GTPase 1 (MX-1) genes were detected at the time of replication of MPyV genomes in the nucleus. STING knockout abolished the IFN response. Infection with a mutant virus that exhibits defective nuclear entry via nucleopores and that accumulates in the cytoplasm confirmed that replication of viral genomes in the nucleus is required for IFN induction. The importance of both DNA sensors, p204 and cGAS, in MPyV-induced IFN response was demonstrated by downregulation of the IFN pathway observed in p204-knockdown and cGAS-knockout cells. Confocal microscopy revealed the colocalization of p204 with MPyV genomes in the nucleus. cGAS was found in the cytoplasm, colocalizing with viral DNA leaked from the nucleus and with DNA within micronucleus-like bodies, but also with the MPyV genomes in the nucleus. However, 2'3'-Cyclic guanosine monophosphate-adenosine monophosphate synthesized by cGAS was detected exclusively in the cytoplasm. Biochemical assays revealed no evidence of functional interaction between cGAS and p204 in the nucleus. Our results provide evidence for the complex interactions of MPyV and DNA sensors including the sensing of viral genomes in the nucleus by p204 and of leaked viral DNA and micronucleus-like bodies in the cytoplasm by cGAS.
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Affiliation(s)
- Boris Ryabchenko
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
| | - Irina Soldatova
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
| | - Vojtech Šroller
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
| | - Jitka Forstová
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
| | - Sandra Huérfano
- Department of Genetics and MicrobiologyFaculty of ScienceCharles UniversityBiocevCzech Republic
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16
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Davids BO, Balasubramaniam M, Sapp N, Prakash P, Ingram S, Li M, Craigie R, Hollis T, Pandhare J, Dash C. Human Three Prime Repair Exonuclease 1 Promotes HIV-1 Integration by Preferentially Degrading Unprocessed Viral DNA. J Virol 2021; 95:e0055521. [PMID: 34105995 PMCID: PMC8354242 DOI: 10.1128/jvi.00555-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/25/2021] [Indexed: 11/20/2022] Open
Abstract
Three prime repair exonuclease 1 (TREX1) is the most abundant 3'→5' exonuclease in mammalian cells. It has been suggested that TREX1 degrades HIV-1 DNA to enable the virus to evade the innate immune system. However, the exact role of TREX1 during early steps of HIV-1 infection is not clearly understood. In this study, we report that HIV-1 infection is associated with upregulation, perinuclear accumulation, and nuclear localization of TREX1. However, TREX1 overexpression did not affect reverse transcription or nuclear entry of the virus. Surprisingly, HIV-1 DNA integration was increased in TREX1-overexpressing cells, suggesting a role of the exonuclease in the post-nuclear entry step of infection. Accordingly, preintegration complexes (PICs) extracted from TREX1-overexpressing cells retained higher levels of DNA integration activity. TREX1 depletion resulted in reduced levels of proviral integration, and PICs formed in TREX1-depleted cells retained lower DNA integration activity. Addition of purified TREX1 to PICs also enhanced DNA integration activity, suggesting that TREX1 promotes HIV-1 integration by stimulating PIC activity. To understand the mechanism, we measured TREX1 exonuclease activity on substrates containing viral DNA ends. These studies revealed that TREX1 preferentially degrades the unprocessed viral DNA, but the integration-competent 3'-processed viral DNA remains resistant to degradation. Finally, we observed that TREX1 addition stimulates the activity of HIV-1 intasomes assembled with the unprocessed viral DNA but not that of intasomes containing the 3'-processed viral DNA. These biochemical analyses provide a mechanism by which TREX1 directly promotes HIV-1 integration. Collectively, our study demonstrates that HIV-1 infection upregulates TREX1 to facilitate viral DNA integration. IMPORTANCE Productive HIV-1 infection is dependent on a number of cellular factors. Therefore, a clear understanding of how the virus exploits the cellular machinery will identify new targets for inhibiting HIV-1 infection. The three prime repair exonuclease 1 (TREX1) is the most active cellular exonuclease in mammalian cells. It has been reported that TREX1 prevents accumulation of HIV-1 DNA and enables the virus to evade the host innate immune response. Here, we show that HIV-1 infection results in the upregulation, perinuclear accumulation, and nuclear localization of TREX1. We also provide evidence that TREX1 promotes HIV-1 integration by preferentially degrading viral DNAs that are incompatible with chromosomal insertion. These observations identify a novel role of TREX1 in a post-nuclear entry step of HIV-1 infection.
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Affiliation(s)
- Benem-Orom Davids
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Muthukumar Balasubramaniam
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Nicklas Sapp
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Prem Prakash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Shalonda Ingram
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
| | - Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Thomas Hollis
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jui Pandhare
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, Tennessee, USA
- School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee, USA
| | - Chandravanu Dash
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, Tennessee, USA
- Department of Biochemistry, Cancer Biology, Pharmacology and Neuroscience, Meharry Medical College, Nashville, Tennessee, USA
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17
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Brezgin S, Kostyusheva A, Bayurova E, Volchkova E, Gegechkori V, Gordeychuk I, Glebe D, Kostyushev D, Chulanov V. Immunity and Viral Infections: Modulating Antiviral Response via CRISPR-Cas Systems. Viruses 2021; 13:1373. [PMID: 34372578 PMCID: PMC8310348 DOI: 10.3390/v13071373] [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: 05/26/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/13/2022] Open
Abstract
Viral infections cause a variety of acute and chronic human diseases, sometimes resulting in small local outbreaks, or in some cases spreading across the globe and leading to global pandemics. Understanding and exploiting virus-host interactions is instrumental for identifying host factors involved in viral replication, developing effective antiviral agents, and mitigating the severity of virus-borne infectious diseases. The diversity of CRISPR systems and CRISPR-based tools enables the specific modulation of innate immune responses and has contributed impressively to the fields of virology and immunology in a very short time. In this review, we describe the most recent advances in the use of CRISPR systems for basic and translational studies of virus-host interactions.
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Affiliation(s)
- Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (S.B.); (A.K.); (V.C.)
- Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (S.B.); (A.K.); (V.C.)
| | - Ekaterina Bayurova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia; (E.B.); (I.G.)
| | - Elena Volchkova
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
| | - Vladimir Gegechkori
- Department of Pharmaceutical and Toxicological Chemistry, Sechenov University, 119991 Moscow, Russia;
| | - Ilya Gordeychuk
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia; (E.B.); (I.G.)
- Department of Organization and Technology of Immunobiological Drugs, Sechenov University, 119991 Moscow, Russia
| | - Dieter Glebe
- National Reference Center for Hepatitis B Viruses and Hepatitis D Viruses, Institute of Medical Virology, Justus Liebig University of Giessen, 35392 Giessen, Germany;
| | - Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (S.B.); (A.K.); (V.C.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, 127994 Moscow, Russia; (S.B.); (A.K.); (V.C.)
- Scientific Center for Genetics and Life Sciences, Division of Biotechnology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Infectious Diseases, Sechenov University, 119991 Moscow, Russia;
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18
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Hu J, Tang L, Cheng J, Zhou T, Li Y, Chang J, Zhao Q, Guo JT. Hepatitis B virus nucleocapsid uncoating: biological consequences and regulation by cellular nucleases. Emerg Microbes Infect 2021; 10:852-864. [PMID: 33870849 PMCID: PMC8812769 DOI: 10.1080/22221751.2021.1919034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Upon infection of hepatocyte, Hepatitis B virus (HBV) genomic DNA in nucleocapsid is transported into the nucleus and converted into a covalently closed circular (ccc) DNA to serve as the template for transcription of viral RNAs. Viral DNA in the cytoplasmic progeny nucleocapsid is another resource to fuel cccDNA amplification. Apparently, nucleocapsid disassembly, or viral genomic DNA uncoating, is an essential step for cccDNA synthesis from both de novo infection and intracellular amplification pathways, and has a potential to activate DNA sensors and induce an innate immune response in infected hepatocytes. However, where and how the nucleocapsid disassembly occurs is not well understood. The work reported herein showed that the enhanced disassembly of progeny mature nucleocapsids in the cytoplasm supported cccDNA intracellular amplification, but failed to activate the cGAS-STING-mediated innate immune response in hepatocytes. Interestingly, while expression of a cytoplasmic exonuclease TREX1 in human hepatoma cells supporting HBV replication significantly reduced the amounts of cccDNA as well as its precursor, deproteinized relaxed circular (rc) DNA, expression of TREX1 in sodium taurocholate cotransporting polypeptide-expressing human hepatoma cells did not inhibit cccDNA synthesis from de novo HBV infection. The results from this cytoplasmic nuclease protection assay imply that the disassembly of progeny mature nucleocapsids and removal of viral DNA polymerase covalently linked to the 5′ end of minus strand of rcDNA take place in the cytoplasm. On the contrary, the disassembly of virion-derived nucleocapsids during de novo infection may occur at a different subcellular compartment and possibly via distinct mechanisms.
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Affiliation(s)
- Jin Hu
- Department of Experimental Medicine, Baruch S. Blumberg Institute, Doylestown, PA, USA.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Liudi Tang
- Department of Experimental Medicine, Baruch S. Blumberg Institute, Doylestown, PA, USA.,Microbiology and Immunology Graduate Program, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Junjun Cheng
- Department of Experimental Medicine, Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Tianlun Zhou
- Department of Experimental Medicine, Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Yuhuan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jinhong Chang
- Department of Experimental Medicine, Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Qiong Zhao
- Department of Experimental Medicine, Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Ju-Tao Guo
- Department of Experimental Medicine, Baruch S. Blumberg Institute, Doylestown, PA, USA
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19
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Ramdas P, Sahu AK, Mishra T, Bhardwaj V, Chande A. From Entry to Egress: Strategic Exploitation of the Cellular Processes by HIV-1. Front Microbiol 2020; 11:559792. [PMID: 33343516 PMCID: PMC7746852 DOI: 10.3389/fmicb.2020.559792] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/05/2020] [Indexed: 01/23/2023] Open
Abstract
HIV-1 employs a rich arsenal of viral factors throughout its life cycle and co-opts intracellular trafficking pathways. This exquisitely coordinated process requires precise manipulation of the host microenvironment, most often within defined subcellular compartments. The virus capitalizes on the host by modulating cell-surface proteins and cleverly exploiting nuclear import pathways for post entry events, among other key processes. Successful virus–cell interactions are indeed crucial in determining the extent of infection. By evolving defenses against host restriction factors, while simultaneously exploiting host dependency factors, the life cycle of HIV-1 presents a fascinating montage of an ongoing host–virus arms race. Herein, we provide an overview of how HIV-1 exploits native functions of the host cell and discuss recent findings that fundamentally change our understanding of the post-entry replication events.
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Affiliation(s)
- Pavitra Ramdas
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Amit Kumar Sahu
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Tarun Mishra
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Vipin Bhardwaj
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Ajit Chande
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
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Elsner C, Ponnurangam A, Kazmierski J, Zillinger T, Jansen J, Todt D, Döhner K, Xu S, Ducroux A, Kriedemann N, Malassa A, Larsen PK, Hartmann G, Barchet W, Steinmann E, Kalinke U, Sodeik B, Goffinet C. Absence of cGAS-mediated type I IFN responses in HIV-1-infected T cells. Proc Natl Acad Sci U S A 2020; 117:19475-19486. [PMID: 32709741 PMCID: PMC7431009 DOI: 10.1073/pnas.2002481117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The DNA sensor cGAS catalyzes the production of the cyclic dinucleotide cGAMP, resulting in type I interferon responses. We addressed the functionality of cGAS-mediated DNA sensing in human and murine T cells. Activated primary CD4+ T cells expressed cGAS and responded to plasmid DNA by upregulation of ISGs and release of bioactive interferon. In mouse T cells, cGAS KO ablated sensing of plasmid DNA, and TREX1 KO enabled cells to sense short immunostimulatory DNA. Expression of IFIT1 and MX2 was downregulated and upregulated in cGAS KO and TREX1 KO T cell lines, respectively, compared to parental cells. Despite their intact cGAS sensing pathway, human CD4+ T cells failed to mount a reverse transcriptase (RT) inhibitor-sensitive immune response following HIV-1 infection. In contrast, infection of human T cells with HSV-1 that is functionally deficient for the cGAS antagonist pUL41 (HSV-1ΔUL41N) resulted in a cGAS-dependent type I interferon response. In accordance with our results in primary CD4+ T cells, plasmid challenge or HSV-1ΔUL41N inoculation of T cell lines provoked an entirely cGAS-dependent type I interferon response, including IRF3 phosphorylation and expression of ISGs. In contrast, no RT-dependent interferon response was detected following transduction of T cell lines with VSV-G-pseudotyped lentiviral or gammaretroviral particles. Together, T cells are capable to raise a cGAS-dependent cell-intrinsic response to both plasmid DNA challenge or inoculation with HSV-1ΔUL41N. However, HIV-1 infection does not appear to trigger cGAS-mediated sensing of viral DNA in T cells, possibly by revealing viral DNA of insufficient quantity, length, and/or accessibility to cGAS.
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Affiliation(s)
- Carina Elsner
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, 45147 Essen, Germany
| | - Aparna Ponnurangam
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany
| | - Julia Kazmierski
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Berlin Institute of Health, 10178 Berlin, Germany
| | - Thomas Zillinger
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53127 Bonn, Germany
| | - Jenny Jansen
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Berlin Institute of Health, 10178 Berlin, Germany
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany
- European Virus Bioinformatics Center, 07743 Jena, Germany
| | - Katinka Döhner
- Institute of Virology, Hanover Medical School, 30625 Hanover, Germany
| | - Shuting Xu
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany
| | - Aurélie Ducroux
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany
| | - Nils Kriedemann
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany
| | - Angelina Malassa
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany
| | - Pia-Katharina Larsen
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53127 Bonn, Germany
| | - Winfried Barchet
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, 53127 Bonn, Germany
- German Center for Infection Research, 50935 Cologne-Bonn, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany
| | - Beate Sodeik
- Institute of Virology, Hanover Medical School, 30625 Hanover, Germany
- Cluster of Excellence Resolving Infection Susceptibility (Excellence Cluster 2155), Hanover Medical School, 30625 Hanover, Germany
| | - Christine Goffinet
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hanover, Germany;
- Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Berlin Institute of Health, 10178 Berlin, Germany
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21
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Insights into Sensing of Murine Retroviruses. Viruses 2020; 12:v12080836. [PMID: 32751803 PMCID: PMC7472155 DOI: 10.3390/v12080836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/28/2020] [Accepted: 07/28/2020] [Indexed: 02/07/2023] Open
Abstract
Retroviruses are major causes of disease in animals and human. Better understanding of the initial host immune response to these viruses could provide insight into how to limit infection. Mouse retroviruses that are endemic in their hosts provide an important genetic tool to dissect the different arms of the innate immune system that recognize retroviruses as foreign. Here, we review what is known about the major branches of the innate immune system that respond to mouse retrovirus infection, Toll-like receptors and nucleic acid sensors, and discuss the importance of these responses in activating adaptive immunity and controlling infection.
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Simpson SR, Hemphill WO, Hudson T, Perrino FW. TREX1 - Apex predator of cytosolic DNA metabolism. DNA Repair (Amst) 2020; 94:102894. [PMID: 32615442 DOI: 10.1016/j.dnarep.2020.102894] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022]
Abstract
The cytosolic Three prime Repair EXonuclease 1 (TREX1) is a powerful DNA-degrading enzyme required for clearing cytosolic DNA to prevent aberrant inflammation and autoimmunity. In the absence of TREX1 activity, cytosolic DNA pattern recognition receptors of the innate immune system are constitutively activated by undegraded TREX1 substrates. This triggers a chronic inflammatory response in humans expressing mutant TREX1 alleles, eliciting a spectrum of rare autoimmune diseases dependent on the nature of the mutation. The precise origins of cytosolic DNA targeted by TREX1 continue to emerge, but DNA emerging from the nucleus or taken up by the cell could represent potential sources. In this Review, we explore the biochemical and immunological data supporting the role of TREX1 in suppressing cytosolic DNA sensing, and discuss the possibility that TREX1 may contribute to maintenance of genome integrity.
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Affiliation(s)
- Sean R Simpson
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Wayne O Hemphill
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Teesha Hudson
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States
| | - Fred W Perrino
- Department of Biochemistry, Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, United States.
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23
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Wan D, Jiang W, Hao J. Research Advances in How the cGAS-STING Pathway Controls the Cellular Inflammatory Response. Front Immunol 2020; 11:615. [PMID: 32411126 PMCID: PMC7198750 DOI: 10.3389/fimmu.2020.00615] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022] Open
Abstract
Double-stranded DNA (dsDNA) sensor cyclic-GMP-AMP synthase (cGAS) along with the downstream stimulator of interferon genes (STING) acting as essential immune-surveillance mediators have become hot topics of research. The intrinsic function of the cGAS-STING pathway facilitates type-I interferon (IFN) inflammatory signaling responses and other cellular processes such as autophagy, cell survival, senescence. cGAS-STING pathway interplays with other innate immune pathways, by which it participates in regulating infection, inflammatory disease, and cancer. The therapeutic approaches targeting this pathway show promise for future translation into clinical applications. Here, we present a review of the important previous works and recent advances regarding the cGAS-STING pathway, and provide a comprehensive understanding of the modulatory pattern of the cGAS-STING pathway under multifarious pathologic states.
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Affiliation(s)
- Dongshan Wan
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China.,Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Wei Jiang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Junwei Hao
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
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24
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Miller CM, Barrett BS, Chen J, Morrison JH, Radomile C, Santiago ML, Poeschla EM. Systemic Expression of a Viral RdRP Protects against Retrovirus Infection and Disease. J Virol 2020; 94:e00071-20. [PMID: 32051266 PMCID: PMC7163129 DOI: 10.1128/jvi.00071-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/07/2020] [Indexed: 12/11/2022] Open
Abstract
The innate immune system is normally programmed for immediate but transient upregulation in response to invading pathogens, and interferon (IFN)-stimulated gene (ISG) activation is a central feature. In contrast, chronic innate immune system activation is typically associated with autoimmunity and a broad array of autoinflammatory diseases that include the interferonopathies. Here, we studied retroviral susceptibility in a transgenic mouse model with lifelong innate immune system hyperactivation. The mice transgenically express low levels of a picornaviral RNA-dependent RNA polymerase (RdRP), which synthesizes double-stranded RNAs that are sensed by melanoma differentiation-associated protein 5 (MDA5) to trigger constitutive upregulation of many ISGs. However, in striking counterpoint to the paradigm established by numerous human and murine examples of ISG hyperactivation, including constitutive MDA5 activation, they lack autoinflammatory sequelae. RdRP-transgenic mice (RdRP mice) resist infection and disease caused by several pathogenic RNA and DNA viruses. However, retroviruses are sensed through other mechanisms, persist in the host, and have distinctive replication and immunity-evading properties. We infected RdRP mice and wild-type (WT) mice with various doses of a pathogenic retrovirus (Friend virus) and assessed immune parameters and disease at 1, 4, and 8 weeks. Compared to WT mice, RdRP mice had significantly reduced splenomegaly, viral loads, and infection of multiple target cell types in the spleen and the bone marrow. During chronic infection, RdRP mice had 2.35 ± 0.66 log10 lower circulating viral RNA than WT. Protection required ongoing type I IFN signaling. The results show that the reconfigured RdRP mouse innate immune system substantially reduced retroviral replication, set point, and pathogenesis.IMPORTANCE Immune control of retroviruses is notoriously difficult, a fundamental problem that has been most clinically consequential with the HIV-1 pandemic. As humans expand further into previously uninhabited areas, the likelihood of new zoonotic retroviral exposures increases. The role of the innate immune system, including ISGs, in controlling retroviral infections is currently an area of intensive study. This work provides evidence that a primed innate immune system is an effective defense against retroviral pathogenesis, resulting in reduced viral replication and burden of disease outcomes. RdRP mice also had considerably lower Friend retrovirus (FV) viremia. The results could have implications for harnessing ISG responses to reduce transmission or control pathogenesis of human retroviral pathogens.
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Affiliation(s)
- Caitlin M Miller
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado, USA
| | - Bradley S Barrett
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado, USA
| | - Jianfang Chen
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado, USA
| | - James H Morrison
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado, USA
| | - Caleb Radomile
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado, USA
| | - Mario L Santiago
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Center, Aurora, Colorado, USA
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25
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Bankers L, Miller C, Liu G, Thongkittidilok C, Morrison J, Poeschla EM. Development of IFN-Stimulated Gene Expression from Embryogenesis through Adulthood, with and without Constitutive MDA5 Pathway Activation. THE JOURNAL OF IMMUNOLOGY 2020; 204:2791-2807. [PMID: 32277054 DOI: 10.4049/jimmunol.1901421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/26/2020] [Indexed: 11/19/2022]
Abstract
Pathogen-associated molecular patterns (e.g., dsRNA) activate expression of IFN-stimulated genes (ISGs), which protect hosts from infection. Although transient ISG upregulation is essential for effective innate immunity, constitutive activation typically causes harmful autoimmunity in mice and humans, often including severe developmental abnormalities. We have shown that transgenic mice expressing a picornavirus RNA-dependent RNA polymerase (RdRP) outside the viral context (RdRP mice) exhibit constitutive, MDA5-dependent, and quantitatively dramatic upregulation of many ISGs, which confers broad viral infection resistance. Remarkably, RdRP mice never develop autoinflammation, interferonopathy, or other discernible abnormalities. In this study, we used RNA sequencing and other methods to analyze ISG expression across five time points from fetal development to adulthood in wild-type and RdRP mice. In RdRP mice, the proportion of upregulated ISGs increased during development, with the most dramatic induction occurring 2 wk postnatally. The amplified ISG profile is then maintained lifelong. Molecular pathways and biological functions associated with innate immune and IFN signaling are only activated postnatally, suggesting constrained fetal responsiveness to innate immune stimuli. Biological functions supporting replication of viruses are only inhibited postnatally. We further determined that the RdRP is expressed at low levels and that blocking Ifnar1 reverses the amplified ISG transcriptome in adults. In conclusion, the upregulated ISG profile of RdRP mice is mostly triggered early postnatally, is maintained through adulthood, and requires ongoing type I IFN signaling to maintain it. The model provides opportunities to study the systems biology of innate immunity and to determine how sustained ISG upregulation can be compatible with robust health.
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Affiliation(s)
- Laura Bankers
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado Denver School of Medicine, Aurora, CO 80045
| | - Caitlin Miller
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado Denver School of Medicine, Aurora, CO 80045
| | - Guoqi Liu
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado Denver School of Medicine, Aurora, CO 80045
| | - Chommanart Thongkittidilok
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado Denver School of Medicine, Aurora, CO 80045
| | - James Morrison
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado Denver School of Medicine, Aurora, CO 80045
| | - Eric M Poeschla
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado Denver School of Medicine, Aurora, CO 80045
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26
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Yin X, Langer S, Zhang Z, Herbert KM, Yoh S, König R, Chanda SK. Sensor Sensibility-HIV-1 and the Innate Immune Response. Cells 2020; 9:E254. [PMID: 31968566 PMCID: PMC7016969 DOI: 10.3390/cells9010254] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 02/07/2023] Open
Abstract
Innate immunity represents the human immune system's first line of defense against a pathogenic intruder and is initiated by the recognition of conserved molecular structures known as pathogen-associated molecular patterns (PAMPs) by specialized cellular sensors, called pattern recognition receptors (PRRs). Human immunodeficiency virus type 1 (HIV-1) is a unique human RNA virus that causes acquired immunodeficiency syndrome (AIDS) in infected individuals. During the replication cycle, HIV-1 undergoes reverse transcription of its RNA genome and integrates the resulting DNA into the human genome. Subsequently, transcription of the integrated provirus results in production of new virions and spreading infection of the virus. Throughout the viral replication cycle, numerous nucleic acid derived PAMPs can be recognized by a diverse set of innate immune sensors in infected cells. However, HIV-1 has evolved efficient strategies to evade or counteract this immune surveillance and the downstream responses. Understanding the molecular underpinnings of the concerted actions of the innate immune system, as well as the corresponding viral evasion mechanisms during infection, is critical to understanding HIV-1 transmission and pathogenesis, and may provide important guidance for the design of appropriate adjuvant and vaccine strategies. Here, we summarize current knowledge of the molecular basis for sensing HIV-1 in human cells, including CD4+ T cells, dendritic cells, and macrophages. Furthermore, we discuss the underlying mechanisms by which innate sensing is regulated, and describe the strategies developed by HIV-1 to evade sensing and immune responses.
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Affiliation(s)
- Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
| | - Simon Langer
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
- Boehringer Ingelheim Pharma GmbH & Co. KG, 55216 Ingelheim am Rhein, Germany
| | - Zeli Zhang
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
- Division of Vaccine Discovery, La Jolla Institute for Immunology, 9420 Athena Cir, La Jolla, CA 92037, USA
| | - Kristina M. Herbert
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
| | - Sunnie Yoh
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
| | - Renate König
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Sumit K. Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
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A Novel Phenotype Links HIV-1 Capsid Stability to cGAS-Mediated DNA Sensing. J Virol 2019; 93:JVI.00706-19. [PMID: 31167922 DOI: 10.1128/jvi.00706-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/19/2019] [Indexed: 01/27/2023] Open
Abstract
The HIV-1 capsid executes essential functions that are regulated by capsid stability and host factors. In contrast to increasing knowledge on functional roles of capsid-interacting host proteins during postentry steps, less is known about capsid stability and its impact on intracellular events. Here, using the antiviral compound PF-3450074 (PF74) as a probe for capsid function, we uncovered a novel phenotype of capsid stability that has a profound effect on innate sensing of viral DNA by the DNA sensor cGAS. A single mutation, R143A, in the capsid protein conferred resistance to high concentrations of PF74, without affecting capsid binding to PF74. A cell-free assay showed that the R143A mutant partially counteracted the capsid-destabilizing activity of PF74, pointing to capsid stabilization as a resistance mechanism for the R143A mutant. In monocytic THP-1 cells, the R143A virus, but not the wild-type virus, suppressed cGAS-dependent innate immune activation. These results suggest that capsid stabilization improves the shielding of viral DNA from innate sensing. We found that a naturally occurring transmitted founder (T/F) variant shares the same properties as the R143A mutant with respect to PF74 resistance and DNA sensing. Imaging assays revealed delayed uncoating kinetics of this T/F variant and the R143A mutant. All these phenotypes of this T/F variant were controlled by a genetic polymorphism located at the trimeric interface between capsid hexamers, thus linking these capsid-dependent properties. Overall, this work functionally connects capsid stability to innate sensing of viral DNA and reveals naturally occurring phenotypic variation in HIV-1 capsid stability.IMPORTANCE The HIV-1 capsid, which is made from individual viral capsid proteins (CA), is a target for a number of antiviral compounds, including the small-molecule inhibitor PF74. In the present study, we utilized PF74 to identify a transmitted/founder (T/F) strain that shows increased capsid stability. Interestingly, PF74-resistant variants prevented cGAS-dependent innate immune activation under a condition where the other T/F strains induced type I interferon. These observations thus reveal a new CA-specific phenotype that couples capsid stability to viral DNA recognition by cytosolic DNA sensors.
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Heil M, Brockmeyer NH. Self-DNA Sensing Fuels HIV-1-Associated Inflammation. Trends Mol Med 2019; 25:941-954. [PMID: 31300343 DOI: 10.1016/j.molmed.2019.06.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/01/2019] [Accepted: 06/17/2019] [Indexed: 02/07/2023]
Abstract
Inflammation, over-reacting innate immunity, and CD4+ T cell depletion are hallmarks of HIV-1 infection. Self-DNA is usually not considered in the context of HIV-1-associated inflammation, although self-DNA contributes to inflammation in diverse pathologies, including autoimmune diseases, cancer, multiorgan failure after trauma, and even virus infections. Cells undergoing HIV-1-associated pyroptotic bystander cell death release self-DNA and other damage-associated molecular patterns (DAMPs), including chaperones and histones. In complexes with such DAMPs or extracellular vesicles, self-DNA gains immunogenic potential and becomes accessible to intracellular DNA sensors. Therefore, we hypothesize that self-DNA can contribute to HIV-1-associated inflammation. Self-DNA might not only drive HIV-1-associated 'inflamm-ageing' but also provide new opportunities for 'shock and kill' strategies aimed at eliminating latent HIV-1.
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Affiliation(s)
- Martin Heil
- Department of Genetic Engineering, CINVESTAV-Irapuato, Irapuato, Guanajuato, Mexico.
| | - Norbert H Brockmeyer
- WIR 'Walk In Ruhr' - Center for Sexual Health and Medicine, German Competence Net HIV/AIDS, University of Bochum, Bochum, Germany
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29
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Boswell MT, Rowland-Jones SL. Delayed disease progression in HIV-2: the importance of TRIM5α and the retroviral capsid. Clin Exp Immunol 2019; 196:305-317. [PMID: 30773620 DOI: 10.1111/cei.13280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 12/21/2022] Open
Abstract
HIV-2 is thought to have entered the human population in the 1930s through cross-species transmission of SIV from sooty mangabeys in West Africa. Unlike HIV-1, HIV-2 has not led to a global pandemic, and recent data suggest that HIV-2 prevalence is declining in some West African states where it was formerly endemic. Although many early isolates of HIV-2 were derived from patients presenting with AIDS-defining illnesses, it was noted that a much larger proportion of HIV-2-infected subjects behaved as long-term non-progressors (LTNP) than their HIV-1-infected counterparts. Many HIV-2-infected adults are asymptomatic, maintaining an undetectable viral load for over a decade. However, despite lower viral loads, HIV-2 progresses to clinical AIDS without therapeutic intervention in most patients. In addition, successful treatment with anti-retroviral therapy (ART) is more challenging than for HIV-1. HIV-2 is significantly more sensitive to restriction by host restriction factor tripartite motif TRIM5α than HIV-1, and this difference in sensitivity is linked to differences in capsid structure. In this review we discuss the determinants of HIV-2 disease progression and focus on the important interactions between TRIM5α and HIV-2 capsid in long-term viral control.
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Affiliation(s)
- M T Boswell
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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30
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Sugawara S, Thomas DL, Balagopal A. HIV-1 Infection and Type 1 Interferon: Navigating Through Uncertain Waters. AIDS Res Hum Retroviruses 2019; 35:25-32. [PMID: 29999412 DOI: 10.1089/aid.2018.0161] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
HIV-1 remains a chronic viral infection of global health importance. Although HIV-1 replication can be controlled by antiretroviral therapy (ART), there is no cure due to persistence of a long-lived latent reservoir. In addition, people living with HIV-1 who are taking ART still bear signatures of persistent immune activation that include continued type 1 interferon (IFN) signaling. Paradoxically, type 1 IFN exerts a limited role on the control of chronic HIV-1. Indeed, recent reports from humanized mice suggest that type 1 IFN may partly maintain the latent reservoir. In this review, we discuss the molecular interactions between HIV-1 and the type 1 IFN signaling pathway, and examine the efficacy of type 1 IFNs in vivo. We also explore whether limited type 1 IFN manipulation may have a therapeutic role.
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Affiliation(s)
- Sho Sugawara
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David L. Thomas
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ashwin Balagopal
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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31
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DDX41 Recognizes RNA/DNA Retroviral Reverse Transcripts and Is Critical for In Vivo Control of Murine Leukemia Virus Infection. mBio 2018; 9:mBio.00923-18. [PMID: 29871919 PMCID: PMC5989071 DOI: 10.1128/mbio.00923-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Host recognition of viral nucleic acids generated during infection leads to the activation of innate immune responses essential for early control of virus. Retrovirus reverse transcription creates numerous potential ligands for cytosolic host sensors that recognize foreign nucleic acids, including single-stranded RNA (ssRNA), RNA/DNA hybrids, and double-stranded DNA (dsDNA). We and others recently showed that the sensors cyclic GMP-AMP synthase (cGAS), DEAD-box helicase 41 (DDX41), and members of the Aim2-like receptor (ALR) family participate in the recognition of retroviral reverse transcripts. However, why multiple sensors might be required and their relative importance in in vivo control of retroviral infection are not known. Here, we show that DDX41 primarily senses the DNA/RNA hybrid generated at the first step of reverse transcription, while cGAS recognizes dsDNA generated at the next step. We also show that both DDX41 and cGAS are needed for the antiretroviral innate immune response to murine leukemia virus (MLV) and HIV in primary mouse macrophages and dendritic cells (DCs). Using mice with cell type-specific knockout of the Ddx41 gene, we show that DDX41 sensing in DCs but not macrophages was critical for controlling in vivo MLV infection. This suggests that DCs are essential in vivo targets for infection, as well as for initiating the antiviral response. Our work demonstrates that the innate immune response to retrovirus infection depends on multiple host nucleic acid sensors that recognize different reverse transcription intermediates. Viruses are detected by many different host sensors of nucleic acid, which in turn trigger innate immune responses, such as type I interferon (IFN) production, required to control infection. We show here that at least two sensors are needed to initiate a highly effective innate immune response to retroviruses—DDX41, which preferentially senses the RNA/DNA hybrid generated at the first step of retrovirus replication, and cGAS, which recognizes double-stranded DNA generated at the second step. Importantly, we demonstrate using mice lacking DDX41 or cGAS that both sensors are needed for the full antiviral response needed to control in vivo MLV infection. These findings underscore the need for multiple host factors to counteract retroviral infection.
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