1
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Taylor JP, Blum SI, Graffeo HC, Shang Q, Qiu S, Green TJ, Botta D, Lund FE, Tse HM. The Type 1 Diabetes-Associated Single Nucleotide Polymorphism rs1990760 in IFIH1 Is Associated with Increased Basal Type I IFNs and IFN-stimulated Gene Expression. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:1415-1428. [PMID: 39373578 DOI: 10.4049/jimmunol.2400344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 09/18/2024] [Indexed: 10/08/2024]
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disease that is caused by a combination of genetic and environmental risk factors. In this study, we sought to determine whether a known genetic risk factor, the rs1990760 single nucleotide polymorphism (SNP) (A946T) in IFIH1, resulted in a gain of function in the MDA5 protein and the effects of this mutation on the regulation of type I IFNs during infection with the diabetogenic virus coxsackievirus B3. We found that in cell lines overexpressing the risk variant IFIH1946T there was an elevated level of basal type I IFN signaling and increased basal IFN-stimulated gene expression. An investigation into the mechanism demonstrated that recombinant MDA5 with the A946T mutation had increased ATPase activity in vitro. We also assessed the effect of this SNP in primary human PBMCs from healthy donors to determine whether this SNP influenced their response to infection with coxsackievirus B3. However, we observed no significant changes in type I IFN expression or downstream induction of IFN-stimulated genes in PBMCs from donors carrying the risk allele IFIH1946T. These findings demonstrate the need for a deeper understanding of how mutations in T1D-associated genes contribute to disease onset in specific cellular contexts.
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Affiliation(s)
- Jared P Taylor
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Samuel I Blum
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Hollis C Graffeo
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Qiao Shang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Shihong Qiu
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Todd J Green
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Davide Botta
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
- Heersink School of Medicine, Immunology Institute, University of Alabama at Birmingham, Birmingham, AL
| | - Frances E Lund
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
- Heersink School of Medicine, Immunology Institute, University of Alabama at Birmingham, Birmingham, AL
| | - Hubert M Tse
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS
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2
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Solotchi M, Patel SS. Proofreading mechanisms of the innate immune receptor RIG-I: distinguishing self and viral RNA. Biochem Soc Trans 2024; 52:1131-1148. [PMID: 38884803 PMCID: PMC11346460 DOI: 10.1042/bst20230724] [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: 04/13/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
The RIG-I-like receptors (RLRs), comprising retinoic acid-inducible gene I (RIG-I), melanoma differentiation-associated gene 5 (MDA5), and laboratory of genetics and physiology 2 (LGP2), are pattern recognition receptors belonging to the DExD/H-box RNA helicase family of proteins. RLRs detect viral RNAs in the cytoplasm and respond by initiating a robust antiviral response that up-regulates interferon and cytokine production. RIG-I and MDA5 complement each other by recognizing different RNA features, and LGP2 regulates their activation. RIG-I's multilayered RNA recognition and proofreading mechanisms ensure accurate viral RNA detection while averting harmful responses to host RNAs. RIG-I's C-terminal domain targets 5'-triphosphate double-stranded RNA (dsRNA) blunt ends, while an intrinsic gating mechanism prevents the helicase domains from non-specifically engaging with host RNAs. The ATPase and RNA translocation activity of RIG-I adds another layer of selectivity by minimizing the lifetime of RIG-I on non-specific RNAs, preventing off-target activation. The versatility of RIG-I's ATPase function also amplifies downstream signaling by enhancing the signaling domain (CARDs) exposure on 5'-triphosphate dsRNA and promoting oligomerization. In this review, we offer an in-depth understanding of the mechanisms RIG-I uses to facilitate viral RNA sensing and regulate downstream activation of the immune system.
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Affiliation(s)
- Mihai Solotchi
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, U.S.A
- Graduate School of Biomedical Sciences, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, U.S.A
| | - Smita S. Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, U.S.A
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3
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Huang X, Zhou X, Zhang F, Wang X, Duan X, Liu K. DDX58 variant triggers IFN-β-induced autophagy in trabecular meshwork and influences intraocular pressure. FASEB J 2024; 38:e23651. [PMID: 38752537 DOI: 10.1096/fj.202302265rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 07/16/2024]
Abstract
Singleton-Merten syndrome (SMS) is a rare immunogenetic disorder affecting multiple systems, characterized by dental dysplasia, aortic calcification, glaucoma, skeletal abnormalities, and psoriasis. Glaucoma, a key feature of both classical and atypical SMS, remains poorly understood in terms of its molecular mechanism caused by DDX58 mutation. This study presented a novel DDX58 variant (c.1649A>C [p.Asp550Ala]) in a family with childhood glaucoma. Functional analysis showed that DDX58 variant caused an increase in IFN-stimulated gene expression and high IFN-β-based type-I IFN. As the trabecular meshwork (TM) is responsible for controlling intraocular pressure (IOP), we examine the effect of IFN-β on TM cells. Our study is the first to demonstrate that IFN-β significantly reduced TM cell viability and function by activating autophagy. In addition, anterior chamber injection of IFN-β remarkably increased IOP level in mice, which can be attenuated by treatments with autophagy inhibitor chloroquine. To uncover the specific mechanism underlying IFN-β-induced autophagy in TM cells, we performed microarray analysis in IFN-β-treated and DDX58 p.Asp550Ala TM cells. It showed that RSAD2 is necessary for IFN-β-induced autophagy. Knockdown of RSAD2 by siRNA significantly decreased autophagy flux induced by IFN-β. Our findings suggest that DDX58 mutation leads to the overproduction of IFN-β, which elevates IOP by modulating autophagy through RSAD2 in TM cells.
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Affiliation(s)
- Xinting Huang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xiaoyu Zhou
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Glaucoma Institute, Changsha Aier Eye Hospital, Changsha, Hunan, China
| | - Feng Zhang
- The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xiaobo Wang
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Xuanchu Duan
- Glaucoma Institute, Changsha Aier Eye Hospital, Changsha, Hunan, China
- Aier School of Ophthalmology, Central South University, Changsha, Hunan, China
| | - Ke Liu
- Department of Ophthalmology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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4
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Lee KY, Craig C, Patel SS. Unraveling blunt-end RNA binding and ATPase-driven translocation activities of the RIG-I family helicase LGP2. Nucleic Acids Res 2024; 52:355-369. [PMID: 38015453 PMCID: PMC10783506 DOI: 10.1093/nar/gkad1106] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023] Open
Abstract
The RIG-I family helicases, comprising RIG-I, MDA5 and LGP2, are cytoplasmic RNA sensors that trigger an antiviral immune response by specifically recognizing foreign RNAs. While LGP2 lacks the signaling domain necessary for immune activation, it plays a vital role in regulating the RIG-I/MDA5 signaling pathway. In this study, we investigate the mechanisms underlying this regulation by examining the oligomeric state, RNA binding specificity, and translocation activity of human LGP2 and the impact of ATPase activity. We show that LGP2, like RIG-I, prefers binding blunt-ended double-stranded (ds) RNAs over internal dsRNA regions or RNA overhangs and associates with blunt-ends faster than with overhangs. Unlike RIG-I, a 5'-triphosphate (5'ppp), Cap0, or Cap1 RNA-end does not influence LGP2's RNA binding affinity. LGP2 hydrolyzes ATP in the presence of RNA but at a 5-10 fold slower rate than RIG-I. Nevertheless, LGP2 uses its ATPase activity to translocate and displace biotin-streptavidin interactions. This activity is significantly hindered by a methylated RNA patch, particularly on the 3'-strand, suggesting a 3'-strand tracking mechanism like RIG-I. The preference of LGP2 for blunt-end RNA binding, its insensitivity to Cap0/Cap1 modification, and its translocation/protein displacement ability have substantial implications for how LGP2 regulates the RNA sensing process by MDA5/RIG-I.
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Affiliation(s)
- Kuan-Ying Lee
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Graduate School of Biomedical Sciences at the Robert Wood Johnson Medical School of Rutgers University, 08854, USA
| | - Candice Craig
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Graduate School of Biomedical Sciences at the Robert Wood Johnson Medical School of Rutgers University, 08854, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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5
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Sikorska J, Hou Y, Chiurazzi P, Siu T, Baltus GA, Sheth P, McLaren D, Truong Q, Parish C, Wyss D. Characterization of RNA driven structural changes in full length RIG-I leading to its agonism or antagonism. Nucleic Acids Res 2023; 51:9356-9368. [PMID: 37486777 PMCID: PMC10516622 DOI: 10.1093/nar/gkad606] [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: 11/27/2022] [Revised: 06/30/2023] [Accepted: 07/20/2023] [Indexed: 07/26/2023] Open
Abstract
RIG-I (retinoic acid inducible gene-I) can sense subtle differences between endogenous and viral RNA in the cytoplasm, triggering an anti-viral immune response through induction of type I interferons (IFN) and other inflammatory mediators. Multiple crystal and cryo-EM structures of RIG-I suggested a mechanism in which the C-terminal domain (CTD) is responsible for the recognition of viral RNA with a 5'-triphoshate modification, while the CARD domains serve as a trigger for downstream signaling, leading to the induction of type I IFN. However, to date contradicting conclusions have been reached around the role of ATP in the mechanism of the CARD domains ejection from RIG-I's autoinhibited state. Here we present an application of NMR spectroscopy to investigate changes induced by the binding of 5'-triphosphate and 5'-OH dsRNA, both in the presence and absence of nucleotides, to full length RIG-I with all its methionine residues selectively labeled (Met-[ϵ-13CH3]). With this approach we were able to identify residues on the CTD, helicase domain, and CARDs that served as probes to sense RNA-induced conformational changes in those respective regions. Our results were analyzed in the context of either agonistic or antagonistic RNAs, by and large supporting a mechanism proposed by the Pyle Lab in which CARD release is primarily dependent on the RNA binding event.
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Affiliation(s)
| | - Yan Hou
- Merck & Co., Inc., Rahway, NJ, USA
| | | | - Tony Siu
- Merck & Co., Inc., Rahway, NJ, USA
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6
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Zheng J, Shi W, Yang Z, Chen J, Qi A, Yang Y, Deng Y, Yang D, Song N, Song B, Luo D. RIG-I-like receptors: Molecular mechanism of activation and signaling. Adv Immunol 2023; 158:1-74. [PMID: 37453753 DOI: 10.1016/bs.ai.2023.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
During RNA viral infection, RIG-I-like receptors (RLRs) recognize the intracellular pathogenic RNA species derived from viral replication and activate antiviral innate immune response by stimulating type 1 interferon expression. Three RLR members, namely, RIG-I, MDA5, and LGP2 are homologous and belong to a subgroup of superfamily 2 Helicase/ATPase that is preferably activated by double-stranded RNA. RLRs are significantly different in gene architecture, RNA ligand preference, activation, and molecular functions. As switchable macromolecular sensors, RLRs' activities are tightly regulated by RNA ligands, ATP, posttranslational modifications, and cellular cofactors. We provide a comprehensive review of the structure and function of the RLRs and summarize the molecular understanding of sensing and signaling events during the RLR activation process. The key roles RLR signaling play in both anti-infection and immune disease conditions highlight the therapeutic potential in targeting this important molecular pathway.
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Affiliation(s)
- Jie Zheng
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Wenjia Shi
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ziqun Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jin Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ao Qi
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yulin Yang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ying Deng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dongyuan Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ning Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bin Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore.
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7
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Blum SI, Taylor JP, Barra JM, Burg AR, Shang Q, Qiu S, Shechter O, Hayes AR, Green TJ, Geurts AM, Chen YG, Tse HM. MDA5-dependent responses contribute to autoimmune diabetes progression and hindrance. JCI Insight 2023; 8:e157929. [PMID: 36512407 PMCID: PMC9977297 DOI: 10.1172/jci.insight.157929] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease resulting in pancreatic β cell destruction. Coxsackievirus B3 (CVB3) infection and melanoma differentiation-associated protein 5-dependent (MDA5-dependent) antiviral responses are linked with T1D development. Mutations within IFIH1, coding for MDA5, are correlated with T1D susceptibility, but how these mutations contribute to T1D remains unclear. Utilizing nonobese diabetic (NOD) mice lacking Ifih1 expression (KO) or containing an in-frame deletion within the ATPase site of the helicase 1 domain of MDA5 (ΔHel1), we tested the hypothesis that partial or complete loss-of-function mutations in MDA5 would delay T1D by impairing proinflammatory pancreatic macrophage and T cell responses. Spontaneous T1D developed in female NOD and KO mice similarly, but was significantly delayed in ΔHel1 mice, which may be partly due to a concomitant increase in myeloid-derived suppressor cells. Interestingly, KO male mice had increased spontaneous T1D compared with NOD mice. Whereas NOD and KO mice developed CVB3-accelerated T1D, ΔHel1 mice were protected partly due to decreased type I IFNs, pancreatic infiltrating TNF+ macrophages, IFN-γ+CD4+ T cells, and perforin+CD8+ T cells. Furthermore, ΔHel1 MDA5 protein had reduced ATP hydrolysis compared with wild-type MDA5. Our results suggest that dampened MDA5 function delays T1D, yet loss of MDA5 promotes T1D.
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Affiliation(s)
- Samuel I. Blum
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jared P. Taylor
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jessie M. Barra
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ashley R. Burg
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Qiao Shang
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shihong Qiu
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Oren Shechter
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Aleah R. Hayes
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Todd J. Green
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Yi-Guang Chen
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Hubert M. Tse
- Department of Microbiology, Comprehensive Diabetes Center, The University of Alabama at Birmingham, Birmingham, Alabama, USA
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8
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Wang W, Pyle AM. The RIG-I receptor adopts two different conformations for distinguishing host from viral RNA ligands. Mol Cell 2022; 82:4131-4144.e6. [DOI: 10.1016/j.molcel.2022.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 08/09/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
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9
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Song J, Li M, Li C, Liu K, Zhu Y, Zhang H. Friend or foe: RIG- I like receptors and diseases. Autoimmun Rev 2022; 21:103161. [PMID: 35926770 PMCID: PMC9343065 DOI: 10.1016/j.autrev.2022.103161] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 07/29/2022] [Indexed: 12/22/2022]
Abstract
Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs), which are pivotal sensors of RNA virus invasions, mediate the transcriptional induction of genes encoding type I interferons (IFNs) and proinflammatory cytokines, successfully establishing host antiviral immune response. A few excellent reviews have elaborated on the structural biology of RLRs and the antiviral mechanisms of RLR activation. In this review, we give a basic understanding of RLR biology and summarize recent findings of how RLR signaling cascade is strictly controlled by host regulatory mechanisms, which include RLR-interacting proteins, post-translational modifications and microRNAs (miRNAs). Furthermore, we pay particular attention to the relationship between RLRs and diseases, especially how RLRs participate in SARS-CoV-2, malaria or bacterial infections, how single-nucleotide polymorphisms (SNPs) or mutations in RLRs and antibodies against RLRs lead to autoinflammatory diseases and autoimmune diseases, and how RLRs are involved in anti-tumor immunity. These findings will provide insights and guidance for antiviral and immunomodulatory therapies targeting RLRs.
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Affiliation(s)
- Jie Song
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha City, Hunan Province, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha City, Hunan Province, China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha City, Hunan Province, China
| | - Muyuan Li
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha City, Hunan Province, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha City, Hunan Province, China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha City, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha City, Hunan Province, China
| | - Caiyan Li
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha City, Hunan Province, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha City, Hunan Province, China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha City, Hunan Province, China
| | - Ke Liu
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha City, Hunan Province, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha City, Hunan Province, China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha City, Hunan Province, China
| | - Yaxi Zhu
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha City, Hunan Province, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha City, Hunan Province, China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha City, Hunan Province, China.
| | - Huali Zhang
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha City, Hunan Province, China; Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha City, Hunan Province, China; Sepsis Translational Medicine Key Lab of Hunan Province, Central South University, Changsha City, Hunan Province, China.
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10
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Schweibenz BD, Devarkar SC, Solotchi M, Craig C, Zheng J, Pascal BD, Gokhale S, Xie P, Griffin PR, Patel SS. The intrinsically disordered CARDs-Helicase linker in RIG-I is a molecular gate for RNA proofreading. EMBO J 2022; 41:e109782. [PMID: 35437807 PMCID: PMC9108607 DOI: 10.15252/embj.2021109782] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 01/22/2023] Open
Abstract
The innate immune receptor RIG-I provides a first line of defense against viral infections. Viral RNAs are recognized by RIG-I's C-terminal domain (CTD), but the RNA must engage the helicase domain to release the signaling CARD (Caspase Activation and Recruitment Domain) domains from their autoinhibitory CARD2:Hel2i interactions. Because the helicase itself lacks RNA specificity, mechanisms to proofread RNAs entering the helicase domain must exist. Although such mechanisms would be crucial in preventing aberrant immune responses by non-specific RNAs, they remain largely uncharacterized to date. This study reveals a previously unknown proofreading mechanism through which RIG-I ensures that the helicase engages RNAs explicitly recognized by the CTD. A crucial part of this mechanism involves the intrinsically disordered CARDs-Helicase Linker (CHL), which connects the CARDs to the helicase subdomain Hel1. CHL uses its negatively charged regions to antagonize incoming RNAs electrostatically. In addition to this RNA gating function, CHL is essential for stabilization of the CARD2:Hel2i interface. Overall, we uncover that the CHL and CARD2:Hel2i interface work together to establish a tunable gating mechanism that allows CTD-chosen RNAs to bind the helicase domain, while at the same time blocking non-specific RNAs. These findings also indicate that CHL could represent a novel target for RIG-I-based therapeutics.
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Affiliation(s)
- Brandon D Schweibenz
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Graduate Program in Biochemistry, Rutgers University, Piscataway, NJ, USA
| | - Swapnil C Devarkar
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Graduate Program in Biochemistry, Rutgers University, Piscataway, NJ, USA
| | - Mihai Solotchi
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Cell and Development Biology, Rutgers University, Piscataway, NJ, USA
| | - Candice Craig
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Graduate Program in Biochemistry, Rutgers University, Piscataway, NJ, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Samantha Gokhale
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA.,Cellular and Molecular Pharmacology, Rutgers University, Piscataway, NJ, USA
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA.,Department of Integrative Structural and Computational Biology, Jupiter, FL, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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11
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Wyss M, Gradauskaite V, Ebert N, Thiel V, Zurbriggen A, Plattet P. Efficient Recovery of Attenuated Canine Distemper Virus from cDNA. Virus Res 2022; 316:198796. [PMID: 35568090 DOI: 10.1016/j.virusres.2022.198796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/21/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
Abstract
To provide insights into the biology of the attenuated canine distemper virus (CDV) Onderstepoort (OP) strain (large plaque forming variant), design next-generation multivalent vaccines, or further investigate its promising potential as an oncolytic vector, we employed contemporary modifications to establish an efficient OP-CDV-based reverse genetics platform. Successful viral rescue was obtained however only upon recovery of a completely conserved charged residue (V13E) residing at the N-terminal region of the large protein (L). Although L-V13 and L-V13E did not display drastic differences in cellular localization and physical interaction with P, efficient polymerase complex (P+L) activity was recorded only with L-V13E. Interestingly, grafting mNeonGreen to the viral N protein via a P2A ribosomal skipping sequence (OPneon) and its derivative V-protein-knockout variant (OPneon-Vko) exhibited delayed replication kinetics in cultured cells. Collectively, we established an efficient OP-CDV-based reverse genetics system that enables the design of various strategies potentially contributing to veterinary medicine and research.
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Affiliation(s)
- Marianne Wyss
- Division of Neurological Sciences, Vetsuisse faculty, University of Bern, Switzerland
| | - Vaiva Gradauskaite
- Division of Neurological Sciences, Vetsuisse faculty, University of Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
| | - Volker Thiel
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Institute of Virology and Immunology, Bern and Mittelhäusern, Switzerland
| | - Andreas Zurbriggen
- Division of Neurological Sciences, Vetsuisse faculty, University of Bern, Switzerland
| | - Philippe Plattet
- Division of Neurological Sciences, Vetsuisse faculty, University of Bern, Switzerland.
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12
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Chen YG, Hur S. Cellular origins of dsRNA, their recognition and consequences. Nat Rev Mol Cell Biol 2022; 23:286-301. [PMID: 34815573 PMCID: PMC8969093 DOI: 10.1038/s41580-021-00430-1] [Citation(s) in RCA: 206] [Impact Index Per Article: 68.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2021] [Indexed: 01/02/2023]
Abstract
Double-stranded RNA (dsRNA) is associated with most viral infections - it either constitutes the viral genome (in the case of dsRNA viruses) or is generated in host cells during viral replication. Hence, nearly all organisms have the capability of recognizing dsRNA and mounting a response, the primary aim of which is to mitigate the potential infection. In vertebrates, a set of innate immune receptors for dsRNA induce a multitude of cell-intrinsic and cell-extrinsic immune responses upon dsRNA recognition. Notably, recent studies showed that vertebrate cells can accumulate self-derived dsRNAs or dsRNA-like species upon dysregulation of several cellular processes, activating the very same immune pathways as in infected cells. On the one hand, such aberrant immune activation in the absence of infection can lead to pathogenesis of immune disorders, such as Aicardi-Goutières syndrome. On the other hand, the same innate immune reaction can be induced in a controlled setting for a therapeutic benefit, as occurs in immunotherapies. In this Review, we describe mechanisms by which immunostimulatory dsRNAs are generated in mammalian cells, either by viruses or by the host cells, and how cells respond to them, with the focus on recent developments regarding the role of cellular dsRNAs in immune modulation.
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Affiliation(s)
- Y Grace Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
| | - Sun Hur
- Harvard Medical School & Boston Children's Hospital, Boston, MA, USA.
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13
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Thoresen D, Wang W, Galls D, Guo R, Xu L, Pyle AM. The molecular mechanism of RIG-I activation and signaling. Immunol Rev 2021; 304:154-168. [PMID: 34514601 PMCID: PMC9293153 DOI: 10.1111/imr.13022] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/10/2021] [Accepted: 08/17/2021] [Indexed: 12/25/2022]
Abstract
RIG‐I is our first line of defense against RNA viruses, serving as a pattern recognition receptor that identifies molecular features common among dsRNA and ssRNA viral pathogens. RIG‐I is maintained in an inactive conformation as it samples the cellular space for pathogenic RNAs. Upon encounter with the triphosphorylated terminus of blunt‐ended viral RNA duplexes, the receptor changes conformation and releases a pair of signaling domains (CARDs) that are selectively modified and interact with an adapter protein (MAVS), thereby triggering a signaling cascade that stimulates transcription of interferons. Here, we describe the structural determinants for specific RIG‐I activation by viral RNA, and we describe the strategies by which RIG‐I remains inactivated in the presence of host RNAs. From the initial RNA triggering event to the final stages of interferon expression, we describe the experimental evidence underpinning our working knowledge of RIG‐I signaling. We draw parallels with behavior of related proteins MDA5 and LGP2, describing evolutionary implications of their collective surveillance of the cell. We conclude by describing the cell biology and immunological investigations that will be needed to accurately describe the role of RIG‐I in innate immunity and to provide the necessary foundation for pharmacological manipulation of this important receptor.
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Affiliation(s)
- Daniel Thoresen
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Wenshuai Wang
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Drew Galls
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Rong Guo
- Chemistry, Yale University, New Haven, CT, USA
| | - Ling Xu
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Anna Marie Pyle
- Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.,Chemistry, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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14
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Yu M, Li R, Wan M, Chen J, Shen X, Li G, Ge M, Zhang R. MDA5 attenuate autophagy in chicken embryo fibroblasts infected with IBDV. Br Poult Sci 2021; 63:154-163. [PMID: 34406094 DOI: 10.1080/00071668.2021.1969643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
1. The role of melanoma differentiation-associated protein 5 (MDA5) in infectious bursal disease virus (IBDV)-induced autophagy was studied in chicken embryos.2. Chicken embryo fibroblasts (CEF) were used as the research model and small interfering RNA (siRNA), western blot, indirect enzyme-linked immunosorbent assay (ELISA), real-time fluorescence quantitative polymerase chain reaction (PCR) and transmission electron microscopy were used to detect autophagy, IBDV replication, CEF damage, and activation of both MDA5 and its signalling pathway.3. The results showed that CEF infected with IBDV activated the intracellular MDA5 signalling pathway and caused autophagy via inactivation of the AKT/mTOR pathway. While autophagy promotes IBDV proliferation, MDA5 weakens IBDV-induced CEF autophagy thus inhibiting IBDV replication and protecting CEF cells.4. The results indicated that chMDA5 can be activated by IBDV and attenuate CEF autophagy caused by IBDV infection, thereby inhibiting IBDV replication. This study provided a foundation for further exploring the relationship between viruses, autophagy and the pathogenic mechanism of the MDA5 pathway involved in IBDV.
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Affiliation(s)
- M Yu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, People's Republic of China
| | - R Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, People's Republic of China
| | - M Wan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, People's Republic of China
| | - J Chen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, People's Republic of China
| | - X Shen
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, People's Republic of China
| | - G Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, People's Republic of China
| | - M Ge
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, People's Republic of China
| | - R Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China.,Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine, Harbin, People's Republic of China
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15
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Quin J, Sedmík J, Vukić D, Khan A, Keegan LP, O'Connell MA. ADAR RNA Modifications, the Epitranscriptome and Innate Immunity. Trends Biochem Sci 2021; 46:758-771. [PMID: 33736931 DOI: 10.1016/j.tibs.2021.02.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/28/2021] [Accepted: 02/18/2021] [Indexed: 12/22/2022]
Abstract
Modified bases act as marks on cellular RNAs so that they can be distinguished from foreign RNAs, reducing innate immune responses to endogenous RNA. In humans, mutations giving reduced levels of one base modification, adenosine-to-inosine deamination, cause a viral infection mimic syndrome, a congenital encephalitis with aberrant interferon induction. These Aicardi-Goutières syndrome 6 mutations affect adenosine deaminase acting on RNA 1 (ADAR1), which generates inosines in endogenous double-stranded (ds)RNA. The inosine base alters dsRNA structure to prevent aberrant activation of antiviral cytosolic helicase RIG-I-like receptors. We review how effects of inosines, ADARs, and other modified bases have been shown to be important in innate immunity and cancer.
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Affiliation(s)
- Jaclyn Quin
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Jiří Sedmík
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Dragana Vukić
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Anzer Khan
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic
| | - Liam P Keegan
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic.
| | - Mary A O'Connell
- Central European Institute of Technology, Masaryk University Brno, Kamenice 753/5, Pavilion A35, Brno CZ-62500, Czech Republic.
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16
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Elesela S, Lukacs NW. Role of Mitochondria in Viral Infections. Life (Basel) 2021; 11:life11030232. [PMID: 33799853 PMCID: PMC7998235 DOI: 10.3390/life11030232] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022] Open
Abstract
Viral diseases account for an increasing proportion of deaths worldwide. Viruses maneuver host cell machinery in an attempt to subvert the intracellular environment favorable for their replication. The mitochondrial network is highly susceptible to physiological and environmental insults, including viral infections. Viruses affect mitochondrial functions and impact mitochondrial metabolism, and innate immune signaling. Resurgence of host-virus interactions in recent literature emphasizes the key role of mitochondria and host metabolism on viral life processes. Mitochondrial dysfunction leads to damage of mitochondria that generate toxic compounds, importantly mitochondrial DNA, inducing systemic toxicity, leading to damage of multiple organs in the body. Mitochondrial dynamics and mitophagy are essential for the maintenance of mitochondrial quality control and homeostasis. Therefore, metabolic antagonists may be essential to gain a better understanding of viral diseases and develop effective antiviral therapeutics. This review briefly discusses how viruses exploit mitochondrial dynamics for virus proliferation and induce associated diseases.
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Affiliation(s)
- Srikanth Elesela
- Department of Pathology, Michigan Medicine, Ann Arbor, MI 48109, USA
- Correspondence:
| | - Nicholas W. Lukacs
- Mary H. Weiser Food Allergy Center, Michigan Medicine, Ann Arbor, MI 48109, USA;
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17
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Khan MI, Nur SM, Adhami V, Mukhtar H. Epigenetic regulation of RNA sensors: Sentinels of immune response. Semin Cancer Biol 2021; 83:413-421. [PMID: 33484869 DOI: 10.1016/j.semcancer.2020.12.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022]
Abstract
Living host system possess mechanisms like innate immune system to combat against inflammation, stress singling, and cancer. These mechanisms are initiated by PAMP and DAMP mediated recognition by PRR. PRR is consist of variety of nucleic acid sensors like-RNA sensors. They play crucial role in identifying exogenous and endogenous RNA molecules, which subsequently mediate pro/inflammatory cytokine, IFN and ISGs response in traumatized or tumorigenic conditions. The sensors can sensitize wide range of nucleic acid particle in term of size and structure, while each category sensors belongs subclasses with differentially expressed in cell and distinguished functioning mechanisms. They are also able to make comparison between self and non-self-nucleic acid molecules through specific mechanisms. Besides exhibiting anti-inflammatory and anti-tumorigenic responses, RNA sensors cover the broad spectrum of response mechanisms. Transcriptionally RNA sensors undergo with tight epigenetic regulations. In this review study, we will be going to discuss about the details of RNA sensors, their functional mechanisms and epi-transactional regulations.
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Affiliation(s)
- Mohammad Imran Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Suza Mohammad Nur
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vaqar Adhami
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, USA
| | - Hasan Mukhtar
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin, Madison, USA.
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18
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Blum SI, Tse HM. Innate Viral Sensor MDA5 and Coxsackievirus Interplay in Type 1 Diabetes Development. Microorganisms 2020; 8:microorganisms8070993. [PMID: 32635205 PMCID: PMC7409145 DOI: 10.3390/microorganisms8070993] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
Type 1 diabetes (T1D) is a polygenic autoimmune disease characterized by immune-mediated destruction of insulin-producing β-cells. The concordance rate for T1D in monozygotic twins is ≈30-50%, indicating that environmental factors also play a role in T1D development. Previous studies have demonstrated that enterovirus infections such as coxsackievirus type B (CVB) are associated with triggering T1D. Prior to autoantibody development in T1D, viral RNA and antibodies against CVB can be detected within the blood, stool, and pancreata. An innate pathogen recognition receptor, melanoma differentiation-associated protein 5 (MDA5), which is encoded by the IFIH1 gene, has been associated with T1D onset. It is unclear how single nucleotide polymorphisms in IFIH1 alter the structure and function of MDA5 that may lead to exacerbated antiviral responses contributing to increased T1D-susceptibility. Binding of viral dsRNA via MDA5 induces synthesis of antiviral proteins such as interferon-alpha and -beta (IFN-α/β). Viral infection and subsequent IFN-α/β synthesis can lead to ER stress within insulin-producing β-cells causing neo-epitope generation, activation of β-cell-specific autoreactive T cells, and β-cell destruction. Therefore, an interplay between genetics, enteroviral infections, and antiviral responses may be critical for T1D development.
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19
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Lin H, Cao X. Nuclear innate sensors for nucleic acids in immunity and inflammation. Immunol Rev 2020; 297:162-173. [PMID: 32564422 DOI: 10.1111/imr.12893] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Innate sensors recognize pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs) to initiate innate immune response by activating downstream signaling. These evolutionarily conserved innate sensors usually locate in the plasma membrane or cytoplasm. However, the nucleus-localized innate sensors are recently found to detect pathogenic nucleic acids for initiating innate response, demonstrating a complicated crosstalk with cytoplasmic sensors and signaling molecules to form an elaborate tiered innate signaling network between nucleus and cytoplasm. Furthermore, these nuclear innate sensors evolve varied mechanisms for discriminating self from non-self nucleic acids to maintain immune homeostasis and avoid autoinflammatory immune response. In this review, we summarize the recent findings on the identification of nuclear innate sensors for nucleic acids, such as hnRNPA2B1, IFI16, SAFA, and their roles in host defense and inflammatory response.
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Affiliation(s)
- Hongyu Lin
- Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuetao Cao
- Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Laboratory of Immunity and Inflammation, College of Life Science, Nankai University, Tianjin, China
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20
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Dumesic PA, Stoddard CI, Catania S, Narlikar GJ, Madhani HD. ATP Hydrolysis by the SNF2 Domain of Dnmt5 Is Coupled to Both Specific Recognition and Modification of Hemimethylated DNA. Mol Cell 2020; 79:127-139.e4. [PMID: 32437639 DOI: 10.1016/j.molcel.2020.04.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/01/2023]
Abstract
C.neoformans Dnmt5 is an unusually specific maintenance-type CpG methyltransferase (DNMT) that mediates long-term epigenome evolution. It harbors a DNMT domain and SNF2 ATPase domain. We find that the SNF2 domain couples substrate specificity to an ATPase step essential for DNA methylation. Coupling occurs independent of nucleosomes. Hemimethylated DNA preferentially stimulates ATPase activity, and mutating Dnmt5's ATP-binding pocket disproportionately reduces ATPase stimulation by hemimethylated versus unmethylated substrates. Engineered DNA substrates that stabilize a reaction intermediate by mimicking a "flipped-out" conformation of the target cytosine bypass the SNF2 domain's requirement for hemimethylation. This result implies that ATP hydrolysis by the SNF2 domain is coupled to the DNMT domain conformational changes induced by preferred substrates. These findings establish a new role for a SNF2 ATPase: controlling an adjoined enzymatic domain's substrate recognition and catalysis. We speculate that this coupling contributes to the exquisite specificity of Dnmt5 via mechanisms related to kinetic proofreading.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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21
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Deng P, Khan A, Jacobson D, Sambrani N, McGurk L, Li X, Jayasree A, Hejatko J, Shohat-Ophir G, O'Connell MA, Li JB, Keegan LP. Adar RNA editing-dependent and -independent effects are required for brain and innate immune functions in Drosophila. Nat Commun 2020; 11:1580. [PMID: 32221286 PMCID: PMC7101428 DOI: 10.1038/s41467-020-15435-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 02/24/2020] [Indexed: 12/31/2022] Open
Abstract
ADAR RNA editing enzymes are high-affinity dsRNA-binding proteins that deaminate adenosines to inosines in pre-mRNA hairpins and also exert editing-independent effects. We generated a Drosophila AdarE374A mutant strain encoding a catalytically inactive Adar with CRISPR/Cas9. We demonstrate that Adar adenosine deamination activity is necessary for normal locomotion and prevents age-dependent neurodegeneration. The catalytically inactive protein, when expressed at a higher than physiological level, can rescue neurodegeneration in Adar mutants, suggesting also editing-independent effects. Furthermore, loss of Adar RNA editing activity leads to innate immune induction, indicating that Drosophila Adar, despite being the homolog of mammalian ADAR2, also has functions similar to mammalian ADAR1. The innate immune induction in fly Adar mutants is suppressed by silencing of Dicer-2, which has a RNA helicase domain similar to MDA5 that senses unedited dsRNAs in mammalian Adar1 mutants. Our work demonstrates that the single Adar enzyme in Drosophila unexpectedly has dual functions.
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Affiliation(s)
- Patricia Deng
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Anzer Khan
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Dionna Jacobson
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Nagraj Sambrani
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Leeanne McGurk
- MRC Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Xianghua Li
- MRC Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Aswathy Jayasree
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Hejatko
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Galit Shohat-Ophir
- The Faculty of Life Sciences and The Multidisciplinary Brain Research Center, Bar Ilan University, Ramat Gan, Israel
| | - Mary A O'Connell
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA.
| | - Liam P Keegan
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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22
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Yong HY, Zheng J, Ho VCY, Nguyen MT, Fink K, Griffin PR, Luo D. Structure-guided design of immunomodulatory RNAs specifically targeting the cytoplasmic viral RNA sensor RIG-I. FEBS Lett 2019; 593:3003-3014. [PMID: 31369683 DOI: 10.1002/1873-3468.13564] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/22/2019] [Accepted: 07/28/2019] [Indexed: 12/22/2022]
Abstract
The cytoplasmic immune sensor RIG-I detects viral RNA and initiates an antiviral immune response upon activation. It has become a potential target for vaccination and immunotherapies. To develop the smallest but potent immunomodulatory RNA (immRNAs) species, we performed structure-guided RNA design and used biochemical, structural, and cell-based methods to select and characterize the immRNAs. We demonstrated that inserting guanosine at position 9 to the 10mer RNA hairpin (3p10LG9) activates RIG-I more robustly than the parental RNA. 3p10LG9 interacts strongly with the RIG-I helicase-CTD RNA sensing module and disrupts the auto-inhibitory interaction between the HEL2i and CARDs domains. We further showed that 3p10LA9 has a stronger cellular activity than 3p10LG9. Collectively, purine insertion at position 9 of the immRNA species triggered more robust activation of RIG-1.
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Affiliation(s)
- Hui Yee Yong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Victor Chin Yong Ho
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore City, Singapore
| | - Mai Trinh Nguyen
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
| | - Katja Fink
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore City, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore City, Singapore
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore City, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
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23
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Dickey TH, Song B, Pyle AM. RNA binding activates RIG-I by releasing an autorepressed signaling domain. SCIENCE ADVANCES 2019; 5:eaax3641. [PMID: 31616790 PMCID: PMC6774723 DOI: 10.1126/sciadv.aax3641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
The retinoic acid-inducible gene I (RIG-I) innate immune receptor is an important immunotherapeutic target, but we lack approaches for monitoring the physical basis for its activation in vitro. This gap in our understanding has led to confusion about mechanisms of RIG-I activation and difficulty discovering agonists and antagonists. We therefore created a novel fluorescence resonance energy transfer-based method for measuring RIG-I activation in vitro using dual site-specific fluorescent labeling of the protein. This approach enables us to measure the conformational change that releases the signaling domain during the first step of RIG-I activation, making it possible to understand the role of stimulatory ligands. We have found that RNA alone is sufficient to eject the signaling domain, ejection is reversible, and adenosine triphosphate plays but a minor role in this process. These findings help explain RIG-I dysfunction in autoimmune disease, and they inform the design of therapeutics targeting RIG-I.
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Affiliation(s)
- T. H. Dickey
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - B. Song
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - A. M. Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
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24
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Yang Q, Bai SY, Li LF, Li S, Zhang Y, Munir M, Qiu HJ. Human Hemoglobin Subunit Beta Functions as a Pleiotropic Regulator of RIG-I/MDA5-Mediated Antiviral Innate Immune Responses. J Virol 2019; 93:e00718-19. [PMID: 31167908 PMCID: PMC6675906 DOI: 10.1128/jvi.00718-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 05/20/2019] [Indexed: 12/28/2022] Open
Abstract
Hemoglobin is an important oxygen-carrying protein and plays crucial roles in establishing host resistance against pathogens and in regulating innate immune responses. The hemoglobin subunit beta (HB) is an essential component of hemoglobin, and we have previously demonstrated that the antiviral role of the porcine HB (pHB) is mediated by promoting type I interferon pathways. Thus, considering the high homology between human HB (hHB) and pHB, we hypothesized that hHB also plays an important role in the antiviral innate immunity. In this study, we characterized hHB as a regulatory factor for the replication of RNA viruses by differentially regulating the RIG-I- and MDA5-mediated antiviral signaling pathways. Furthermore, we showed that hHB directly inhibited MDA5-mediated signaling by reducing the MDA5-double-stranded RNA (dsRNA) interaction. Additionally, hHB required hHB-induced reactive oxygen species (ROS) to promote RIG-I-mediated signaling through enhancement of K63-linked RIG-I ubiquitination. Taken together, our findings suggest that hHB is a pleiotropic regulator of RIG-I/MDA5-mediated antiviral responses and further highlight the importance of the intercellular microenvironment, including the redox state, in regulating antiviral innate immune responses.IMPORTANCE Hemoglobin, the most important oxygen-carrying protein, is involved in the regulation of innate immune responses. We have previously reported that the porcine hemoglobin subunit beta (HB) exerts antiviral activity through regulation of type I interferon production. However, the antiviral activities and the underlying mechanisms of HBs originating from other animals have been poorly understood. Here, we identified human HB (hHB) as a pleiotropic regulator of the replication of RNA viruses through regulation of RIG-I/MDA5-mediated signaling pathways. hHB enhances RIG-I-mediated antiviral responses by promoting RIG-I ubiquitination depending on the hHB-induced reactive oxygen species (ROS), while it blocks MDA5-mediated antiviral signaling by suppressing the MDA5-dsRNA interaction. Our results contribute to an understanding of the crucial roles of hHB in the regulation of the RIG-I/MDA5-mediated signaling pathways. We also provide novel insight into the correlation of the intercellular redox state with the regulation of antiviral innate immunity.
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Affiliation(s)
- Qian Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Si-Yu Bai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Lian-Feng Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Su Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yuexiu Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, United Kingdom
| | - Hua-Ji Qiu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Brisse M, Ly H. Comparative Structure and Function Analysis of the RIG-I-Like Receptors: RIG-I and MDA5. Front Immunol 2019; 10:1586. [PMID: 31379819 PMCID: PMC6652118 DOI: 10.3389/fimmu.2019.01586] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 06/25/2019] [Indexed: 12/12/2022] Open
Abstract
RIG-I (Retinoic acid-inducible gene I) and MDA5 (Melanoma Differentiation-Associated protein 5), collectively known as the RIG-I-like receptors (RLRs), are key protein sensors of the pathogen-associated molecular patterns (PAMPs) in the form of viral double-stranded RNA (dsRNA) motifs to induce expression of type 1 interferons (IFN1) (IFNα and IFNβ) and other pro-inflammatory cytokines during the early stage of viral infection. While RIG-I and MDA5 share many genetic, structural and functional similarities, there is increasing evidence that they can have significantly different strategies to recognize different pathogens, PAMPs, and in different host species. This review article discusses the similarities and differences between RIG-I and MDA5 from multiple perspectives, including their structures, evolution and functional relationships with other cellular proteins, their differential mechanisms of distinguishing between host and viral dsRNAs and interactions with host and viral protein factors, and their immunogenic signaling. A comprehensive comparative analysis can help inform future studies of RIG-I and MDA5 in order to fully understand their functions in order to optimize potential therapeutic approaches targeting them.
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Affiliation(s)
- Morgan Brisse
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Twin Cities, St. Paul, MN, United States
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, MN, United States
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The long noncoding RNA Lnczc3h7a promotes a TRIM25-mediated RIG-I antiviral innate immune response. Nat Immunol 2019; 20:812-823. [PMID: 31036902 DOI: 10.1038/s41590-019-0379-0] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/18/2019] [Indexed: 12/22/2022]
Abstract
The helicase RIG-I initiates an antiviral immune response after recognition of pathogenic RNA. TRIM25, an E3 ubiquitin ligase, mediates K63-linked ubiquitination of RIG-I, which is crucial for RIG-I downstream signaling and the antiviral innate immune response. The components and mode of the RIG-I-initiated innate signaling remain to be fully understood. Here we identify a novel long noncoding RNA (Lnczc3h7a) that binds to TRIM25 and promotes RIG-I-mediated antiviral innate immune responses. Depletion of Lnczc3h7a impairs RIG-I signaling and the antiviral innate response to RNA viruses in vitro and in vivo. Mechanistically, Lnczc3h7a binds to both TRIM25 and activated RIG-I, serving as a molecular scaffold for stabilization of the RIG-I-TRIM25 complex at the early stage of viral infection. Lnczc3h7a facilitates TRIM25-mediated K63-linked ubiquitination of RIG-I and thus promotes downstream signaling transduction. Our findings reveal that host RNAs can enhance the response of innate immune sensors to foreign RNAs, ensuring effective antiviral defense.
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27
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Jabłońska A, Neumayer C, Bolliger M, Gollackner B, Klinger M, Paradowska E, Nanobachvili J, Huk I. Analysis of host Toll-like receptor 3 and RIG-I-like receptor gene expression in patients with abdominal aortic aneurysm. J Vasc Surg 2018; 68:39S-46S. [PMID: 29567028 DOI: 10.1016/j.jvs.2017.10.087] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 10/25/2017] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Abdominal aortic aneurysm (AAA) is a vascular disease relatively common in the elderly population. Although some events that contribute to the development and progression of AAA are known, there are limited data examining the association of Toll-like receptor 3 (TLR3) and RIG-I-like receptor expression with the pathogenesis of AAAs. In this study, we investigated the gene and protein expression of TLR3 and RIG-I-like receptors (RIG-I and MDA5) in aortic wall and blood of AAA patients and examined the relationship between their expression and immune response. METHODS Total RNA was extracted from aortic wall tissues and blood samples collected from 20 patients with AAA and blood samples of 17 healthy volunteers without aortic aneurysm. To evaluate the DDX58 (RIG-I), IFIH1 (MDA5), and TLR3 gene expression level, quantitative real-time polymerase chain reaction was used. Extracellular cytokine and pattern recognition receptor levels were quantified by enzyme-linked immunosorbent assays. RESULTS TLR3, RIG-I, and MDA5 were constitutively expressed in both aortic tissues and blood samples from AAA patients and healthy volunteers. In patients with AAA, higher TLR3 expression in aortic tissues than in blood was found (P = .004). The DDX58 messenger RNA expression was higher in blood of patients with AAA compared with healthy subjects (P = .021). A significantly higher level of plasma interleukin 4 was noticed in patients with AAA than in healthy individuals (P = .008). CONCLUSIONS This study suggests that RIG-I and TLR3 seem to be important factors in the pathogenesis of AAA.
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MESH Headings
- Aged
- Aorta, Abdominal/chemistry
- Aorta, Abdominal/immunology
- Aorta, Abdominal/virology
- Aortic Aneurysm, Abdominal/blood
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/immunology
- Aortic Aneurysm, Abdominal/virology
- Case-Control Studies
- DEAD Box Protein 58/blood
- DEAD Box Protein 58/genetics
- Female
- Human papillomavirus 11/isolation & purification
- Humans
- Interferon-Induced Helicase, IFIH1/blood
- Interferon-Induced Helicase, IFIH1/genetics
- Interleukin-4/blood
- Male
- Middle Aged
- Receptors, Immunologic
- Toll-Like Receptor 3/blood
- Toll-Like Receptor 3/genetics
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Affiliation(s)
- Agnieszka Jabłońska
- Department of Surgery, Medical University of Vienna, Vienna, Austria; Laboratory of Molecular Virology and Biological Chemistry, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland.
| | | | - Michael Bolliger
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Bernd Gollackner
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Markus Klinger
- Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Edyta Paradowska
- Laboratory of Molecular Virology and Biological Chemistry, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | | | - Ihor Huk
- Department of Surgery, Medical University of Vienna, Vienna, Austria
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28
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Devarkar SC, Schweibenz B, Wang C, Marcotrigiano J, Patel SS. RIG-I Uses an ATPase-Powered Translocation-Throttling Mechanism for Kinetic Proofreading of RNAs and Oligomerization. Mol Cell 2018; 72:355-368.e4. [PMID: 30270105 PMCID: PMC6434538 DOI: 10.1016/j.molcel.2018.08.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/15/2018] [Accepted: 08/14/2018] [Indexed: 12/25/2022]
Abstract
RIG-I has a remarkable ability to specifically select viral 5'ppp dsRNAs for activation from a pool of cytosolic self-RNAs. The ATPase activity of RIG-I plays a role in RNA discrimination and activation, but the underlying mechanism was unclear. Using transient-state kinetics, we elucidated the ATPase-driven "kinetic proofreading" mechanism of RIG-I activation and RNA discrimination, akin to DNA polymerases, ribosomes, and T cell receptors. Even in the autoinhibited state of RIG-I, the C-terminal domain kinetically discriminates against self-RNAs by fast off rates. ATP binding facilitates dsRNA engagement but, interestingly, makes RIG-I promiscuous, explaining the constitutive signaling by Singleton-Merten syndrome-linked mutants that bind ATP without hydrolysis. ATP hydrolysis dissociates self-RNAs faster than 5'ppp dsRNA but, more importantly, drives RIG-I oligomerization through translocation, which we show to be regulated by helicase motif IVa. RIG-I translocates directionally from the dsRNA end into the stem region, and the 5'ppp end "throttles" translocation to provide a mechanism for threading and building a signaling-active oligomeric complex.
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Affiliation(s)
- Swapnil C Devarkar
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Brandon Schweibenz
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Chen Wang
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Joseph Marcotrigiano
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA.
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29
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Lässig C, Lammens K, Gorenflos López JL, Michalski S, Fettscher O, Hopfner KP. Unified mechanisms for self-RNA recognition by RIG-I Singleton-Merten syndrome variants. eLife 2018; 7:e38958. [PMID: 30047865 PMCID: PMC6086658 DOI: 10.7554/elife.38958] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
The innate immune sensor retinoic acid-inducible gene I (RIG-I) detects cytosolic viral RNA and requires a conformational change caused by both ATP and RNA binding to induce an active signaling state and to trigger an immune response. Previously, we showed that ATP hydrolysis removes RIG-I from lower-affinity self-RNAs (Lässig et al., 2015), revealing how ATP turnover helps RIG-I distinguish viral from self-RNA and explaining why a mutation in a motif that slows down ATP hydrolysis causes the autoimmune disease Singleton-Merten syndrome (SMS). Here we show that a different, mechanistically unexplained SMS variant, C268F, which is localized in the ATP-binding P-loop, can signal independently of ATP but is still dependent on RNA. The structure of RIG-I C268F in complex with double-stranded RNA reveals that C268F helps induce a structural conformation in RIG-I that is similar to that induced by ATP. Our results uncover an unexpected mechanism to explain how a mutation in a P-loop ATPase can induce a gain-of-function ATP state in the absence of ATP.
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Affiliation(s)
- Charlotte Lässig
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Katja Lammens
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Jacob Lucián Gorenflos López
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Sebastian Michalski
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Olga Fettscher
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Karl-Peter Hopfner
- Department of BiochemistryLudwig-Maximilians-Universität MünchenMunichGermany
- Gene Center, Ludwig-Maximilians-Universität MünchenMunichGermany
- Center for Integrated Protein Science MunichMunichGermany
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30
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Zhang Z, Filzmayer C, Ni Y, Sültmann H, Mutz P, Hiet MS, Vondran FWR, Bartenschlager R, Urban S. Hepatitis D virus replication is sensed by MDA5 and induces IFN-β/λ responses in hepatocytes. J Hepatol 2018. [PMID: 29524530 DOI: 10.1016/j.jhep.2018.02.021] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Hepatitis B virus (HBV) and D virus (HDV) co-infections cause the most severe form of viral hepatitis. HDV induces an innate immune response, but it is unknown how the host cell senses HDV and if this defense affects HDV replication. We aim to characterize interferon (IFN) activation by HDV, identify the responsible sensor and evaluate the effect of IFN on HDV replication. METHODS HDV and HBV susceptible hepatoma cell lines and primary human hepatocytes (PHH) were used for infection studies. Viral markers and cellular gene expression were analyzed at different time points after infection. Pattern recognition receptors (PRRs) required for HDV-mediated IFN activation and the impact on HDV replication were studied using stable knock-down or overexpression of the PRRs. RESULTS Microarray analysis revealed that HDV but not HBV infection activated a broad range of interferon stimulated genes (ISGs) in HepG2NTCP cells. HDV strongly activated IFN-β and IFN-λ in cell lines and PHH. HDV induced IFN levels remained unaltered upon RIG-I (DDX58) or TLR3 knock-down, but were almost completely abolished upon MDA5 (IFIH1) depletion. Conversely, overexpression of MDA5 but not RIG-I and TLR3 in HuH7.5NTCP cells partially restored ISG induction. During long-term infection, IFN levels gradually diminished in both HepG2NTCP and HepaRGNTCP cell lines. MDA5 depletion had little effect on HDV replication despite dampening HDV-induced IFN response. Moreover, treatment with type I or type III IFNs did not abolish HDV replication. CONCLUSION Active replication of HDV induces an IFN-β/λ response, which is predominantly mediated by MDA5. This IFN response and exogenous IFN treatment have only a moderate effect on HDV replication in vitro indicating the adaption of HDV replication to an IFN-activated state. LAY SUMMARY In contrast to hepatitis B virus, infection with hepatitis D virus induces a strong IFN-β/λ response in innate immune competent cell lines. MDA5 is the key sensor for the recognition of hepatitis D virus replicative intermediates. An IFN-activated state did not prevent hepatitis D virus replication in vitro, indicating that hepatitis D virus is resistant to self-induced innate immune responses and therapeutic IFN treatment.
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Affiliation(s)
- Zhenfeng Zhang
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christina Filzmayer
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Holger Sültmann
- Cancer Genome Research Group, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg, Germany; Translational Lung Research Center (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Pascal Mutz
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marie-Sophie Hiet
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Florian W R Vondran
- Regenerative Medicine and Experimental Surgery (ReMediES), Department of General, Visceral and Transplant Surgery, Hannover Medical School, Hannover, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany; German Center for Infection Research (DZIF) - Heidelberg Partner Site, Heidelberg, Germany; Division of Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany; German Center for Infection Research (DZIF) - Heidelberg Partner Site, Heidelberg, Germany.
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31
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Arenaviral Nucleoproteins Suppress PACT-Induced Augmentation of RIG-I Function To Inhibit Type I Interferon Production. J Virol 2018; 92:JVI.00482-18. [PMID: 29669840 DOI: 10.1128/jvi.00482-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/13/2018] [Indexed: 12/28/2022] Open
Abstract
RIG-I is a major cytoplasmic sensor of viral pathogen-associated molecular pattern (PAMP) RNA and induces type I interferon (IFN) production upon viral infection. A double-stranded RNA (dsRNA)-binding protein, PACT, plays an important role in potentiating RIG-I function. We have shown previously that arenaviral nucleoproteins (NPs) suppress type I IFN production via their RNase activity to degrade PAMP RNA. We report here that NPs of arenaviruses block the PACT-induced enhancement of RIG-I function to mediate type I IFN production and that this inhibition is dependent on the RNase function of NPs, which is different from that of a known mechanism of other viral proteins to abolish the interaction between PACT and RIG-I. To understand the biological roles of PACT and RIG-I in authentic arenavirus infection, we analyze growth kinetics of recombinant Pichinde virus (PICV), a prototypical arenavirus, in RIG-I knockout (KO) and PACT KO mouse embryonic fibroblast (MEF) cells. Wild-type (WT) PICV grew at higher titers in both KO MEF lines than in normal MEFs, suggesting the important roles of these cellular proteins in restricting virus replication. PICV carrying the NP RNase catalytically inactive mutation could not grow in normal MEFs but could replicate to some extent in both KO MEF lines. The level of virus growth was inversely correlated with the amount of type I IFNs produced. These results suggest that PACT plays an important role in potentiating RIG-I function to produce type I IFNs in order to restrict arenavirus replication and that viral NP RNase activity is essential for optimal viral replication by suppressing PACT-induced RIG-I activation.IMPORTANCE We report here a new role of the nucleoproteins of arenaviruses that can block type I IFN production via their specific inhibition of the cellular protein sensors of virus infection (RIG-I and PACT). Our results suggest that PACT plays an important role in potentiating RIG-I function to produce type I IFNs in order to restrict arenavirus replication. This new knowledge can be exploited for the development of novel antiviral treatments and/or vaccines against some arenaviruses that can cause severe and lethal hemorrhagic fever diseases in humans.
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32
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Jiang M, Zhang S, Yang Z, Lin H, Zhu J, Liu L, Wang W, Liu S, Liu W, Ma Y, Zhang L, Cao X. Self-Recognition of an Inducible Host lncRNA by RIG-I Feedback Restricts Innate Immune Response. Cell 2018; 173:906-919.e13. [DOI: 10.1016/j.cell.2018.03.064] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 02/17/2018] [Accepted: 03/26/2018] [Indexed: 12/25/2022]
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33
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Lee W, Lee SH, Kim M, Moon JS, Kim GW, Jung HG, Kim IH, Oh JE, Jung HE, Lee HK, Ku KB, Ahn DG, Kim SJ, Kim KS, Oh JW. Vibrio vulnificus quorum-sensing molecule cyclo(Phe-Pro) inhibits RIG-I-mediated antiviral innate immunity. Nat Commun 2018; 9:1606. [PMID: 29686409 PMCID: PMC5913291 DOI: 10.1038/s41467-018-04075-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 04/03/2018] [Indexed: 02/06/2023] Open
Abstract
The recognition of pathogen-derived ligands by pattern recognition receptors activates the innate immune response, but the potential interaction of quorum-sensing (QS) signaling molecules with host anti-viral defenses remains largely unknown. Here we show that the Vibrio vulnificus QS molecule cyclo(Phe-Pro) (cFP) inhibits interferon (IFN)-β production by interfering with retinoic-acid-inducible gene-I (RIG-I) activation. Binding of cFP to the RIG-I 2CARD domain induces a conformational change in RIG-I, preventing the TRIM25-mediated ubiquitination to abrogate IFN production. cFP enhances susceptibility to hepatitis C virus (HCV), as well as Sendai and influenza viruses, each known to be sensed by RIG-I but did not affect the melanoma-differentiation-associated gene 5 (MDA5)-recognition of norovirus. Our results reveal an inter-kingdom network between bacteria, viruses and host that dysregulates host innate responses via a microbial quorum-sensing molecule modulating the response to viral infection.
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Affiliation(s)
- Wooseong Lee
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Seung-Hoon Lee
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Minwoo Kim
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Jae-Su Moon
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Geon-Woo Kim
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - Hae-Gwang Jung
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea
| | - In Hwang Kim
- Department of Life Science, Sogang University, Seoul, 04107, Korea
| | - Ji Eun Oh
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Hi Eun Jung
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Heung Kyu Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Keun Bon Ku
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Dae-Gyun Ahn
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Korea
| | - Kun-Soo Kim
- Department of Life Science, Sogang University, Seoul, 04107, Korea
| | - Jong-Won Oh
- Department of Biotechnology, Yonsei University, Seoul, 03722, Korea.
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34
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Shah N, Beckham SA, Wilce JA, Wilce M. Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis. Nucleic Acids Res 2018; 46:3169-3186. [PMID: 29346611 PMCID: PMC5887321 DOI: 10.1093/nar/gkx1307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/24/2022] Open
Abstract
RIG-I (retinoic acid inducible gene-I) is a cytosolic innate immune protein that senses viral dsRNA with a 5'-triphosphate overhang. Upon interaction with dsRNA a de-repression of the RIG-I CARD domains takes place that ultimately leads to the production of type I interferons and pro-inflammatory cytokines. Here we investigate the RIG-I conformational rearrangement upon interaction with an activating 5'-triphosphate-10-base pair dsRNA hairpin loop (10bp) compared with a less active 5'-triphosphate-8-base pair dsRNA hairpin loop (8bp). We use size-exclusion chromatography-coupled small-angle X-ray scattering (SAXS) and limited tryptic digest experiments to show that that upon binding to 10 bp, but not 8 bp, RIG-I becomes extended and shows greater flexibility, reflecting the release of its CARDs. We also examined the effect of different ATP analogues on the conformational changes of RIG-I/dsRNA complexes. Of the analogues tested, the addition of ATP transition state analogue ADP-AlFx further assisted in the complete activation of RIG-I in complex with 10bp and also to some extent RIG-I bound to 8bp. Together these data provide solution-based evidence for the molecular mechanism of innate immune signaling by RIG-I as stimulated by short hairpin RNA and ATP.
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Affiliation(s)
- Neelam Shah
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Simone A Beckham
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Jacqueline A Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Matthew C J Wilce
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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35
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Tan P, He L, Cui J, Qian C, Cao X, Lin M, Zhu Q, Li Y, Xing C, Yu X, Wang HY, Wang RF. Assembly of the WHIP-TRIM14-PPP6C Mitochondrial Complex Promotes RIG-I-Mediated Antiviral Signaling. Mol Cell 2017; 68:293-307.e5. [PMID: 29053956 DOI: 10.1016/j.molcel.2017.09.035] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 08/09/2017] [Accepted: 09/25/2017] [Indexed: 01/30/2023]
Abstract
Mitochondrial antiviral signaling platform protein (MAVS) acts as a central hub for RIG-I receptor proximal signal propagation. However, key components in the assembly of the MAVS mitochondrial platform that promote RIG-I mitochondrial localization and optimal activation are still largely undefined. Employing pooled RNAi and yeast two-hybrid screenings, we report that the mitochondrial adaptor protein tripartite motif (TRIM)14 provides a docking platform for the assembly of the mitochondrial signaling complex required for maximal activation of RIG-I-mediated signaling, consisting of WHIP and protein phosphatase PPP6C. Following viral infection, the ubiquitin-binding domain in WHIP bridges RIG-I with MAVS by binding to polyUb chains of RIG-I at lysine 164. The ATPase domain in WHIP contributes to stabilization of the RIG-I-dsRNA interaction. Moreover, phosphatase PPP6C is responsible for RIG-I dephosphorylation. Together, our findings define the WHIP-TRIM14-PPP6C mitochondrial signalosome required for RIG-I-mediated innate antiviral immunity.
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Affiliation(s)
- Peng Tan
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Lian He
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, College of Life Sciences, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Chen Qian
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Xin Cao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Meng Lin
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Qingyuan Zhu
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yinyin Li
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Changsheng Xing
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Xiao Yu
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Helen Y Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Rong-Fu Wang
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.
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Miyamoto M, Komuro A. PACT is required for MDA5-mediated immunoresponses triggered by Cardiovirus infection via interaction with LGP2. Biochem Biophys Res Commun 2017; 494:227-233. [PMID: 29032202 DOI: 10.1016/j.bbrc.2017.10.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/10/2017] [Indexed: 12/21/2022]
Abstract
Laboratory of genetics and physiology 2 (LGP2) and melanoma differentiation-associated gene 5 (MDA5) cooperatively detect viral RNA in the cytoplasm of Cardiovirus-infected cells and activate innate immune responses. Here, we evaluated whether the double-stranded RNA-binding protein PACT plays a role in this anti-viral response to further elucidate the mechanism. Immunoprecipitation experiments demonstrated that PACT interacts with LGP2 and that this interaction is enhanced by encephalomyocarditis virus (EMCV) infection. In vitro interaction analyses using purified recombinant proteins confirmed that the single-stranded Theiler's murine encephalitis virus genome enhanced the interaction between LGP2 and PACT. Small interfering RNA knockdown experiments further indicated that PACT is required for Cardiovirus-triggered interferon responses. To support this functional interaction with LGP2, overexpressed PACT was shown to enhance EMCV-triggered interferon promoter activity only when LGP2 and MDA5 were co-expressed but not when MDA5 is expressed alone. Together, our findings indicate a possible role of PACT in regulating the Cardiovirus-triggered immune responses mediated by MDA5 and LGP2, which opens the door to novel therapeutic strategies in interferon-related autoimmune diseases and cancer.
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Affiliation(s)
- Masahiko Miyamoto
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan
| | - Akihiko Komuro
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata 956-8603, Japan.
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Lu C, MacDougall M. RIG-I-Like Receptor Signaling in Singleton-Merten Syndrome. Front Genet 2017; 8:118. [PMID: 28955379 PMCID: PMC5600918 DOI: 10.3389/fgene.2017.00118] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022] Open
Abstract
Singleton-Merten syndrome (SMS) is an autosomal dominant, multi-system innate immune disorder characterized by early and severe aortic and valvular calcification, dental and skeletal abnormalities, psoriasis, glaucoma, and other varying clinical findings. Recently we identified a specific gain-of-function mutation in IFIH1, interferon induced with helicase C domain 1, segregated with this disease. SMS disease without hallmark dental anomalies, termed atypical SMS, has recently been reported caused by variants in DDX58, DEXD/H-box helicase 58. IFIH1 and DDX58 encode retinoic acid-inducible gene I (RIG-I)-like receptors family members melanoma differentiation-associated gene 5 and RIG-I, respectively. These cytosolic pattern recognition receptors function in viral RNA detection initiating an innate immune response through independent pathways that promote type I and type III interferon expression and proinflammatory cytokines. In this review, we focus on SMS as an innate immune disorder summarizing clinical features, molecular aspects of the pathogenetic pathway and discussing underlying mechanisms of the disease.
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Affiliation(s)
- Changming Lu
- Institute of Oral Health Research, School of Dentistry, University of Alabama at Birmingham, BirminghamAL, United States
| | - Mary MacDougall
- Faculty of Dentistry, University of British Columbia, VancouverBC, Canada
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38
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Uchikawa E, Lethier M, Malet H, Brunel J, Gerlier D, Cusack S. Structural Analysis of dsRNA Binding to Anti-viral Pattern Recognition Receptors LGP2 and MDA5. Mol Cell 2017; 62:586-602. [PMID: 27203181 PMCID: PMC4885022 DOI: 10.1016/j.molcel.2016.04.021] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/21/2016] [Accepted: 04/19/2016] [Indexed: 12/14/2022]
Abstract
RIG-I and MDA5 sense virus-derived short 5′ppp blunt-ended or long dsRNA, respectively, causing interferon production. Non-signaling LGP2 appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. Co-crystal structures of chicken (ch) LGP2 with dsRNA display a fully or semi-closed conformation depending on the presence or absence of nucleotide. LGP2 caps blunt, 3′ or 5′ overhang dsRNA ends with 1 bp longer overall footprint than RIG-I. Structures of 1:1 and 2:1 complexes of chMDA5 with short dsRNA reveal head-to-head packing rather than the polar head-to-tail orientation described for long filaments. chLGP2 and chMDA5 make filaments with a similar axial repeat, although less co-operatively for chLGP2. Overall, LGP2 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. Functionally, RNA binding is required for LGP2-mediated enhancement of MDA5 activation. We propose that LGP2 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. chLPG2-dsRNA structures reveal RIG-I like end binding, but overhangs are possible chMDA5-dsRNA complex structures show head-to-head packing on short dsRNAs LGP2 also has MDA5-like behavior, coating dsRNA but with less cooperativity Both human and chicken LGP2 enhance MDA5 signaling in an RNA-dependent manner
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MESH Headings
- Adenosine Diphosphate/metabolism
- Adenosine Triphosphatases/chemistry
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Adenosine Triphosphate/metabolism
- Animals
- Avian Proteins/chemistry
- Avian Proteins/genetics
- Avian Proteins/metabolism
- Binding Sites
- Cell Line
- Chickens
- DEAD Box Protein 58/chemistry
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/metabolism
- Humans
- Hydrolysis
- Interferon-Induced Helicase, IFIH1/chemistry
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/metabolism
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Interaction Domains and Motifs
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptors, Pattern Recognition/chemistry
- Receptors, Pattern Recognition/genetics
- Receptors, Pattern Recognition/metabolism
- Structure-Activity Relationship
- Transfection
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Affiliation(s)
- Emiko Uchikawa
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; University Grenoble Alpes, Centre National de la Recherche Scientifique, EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Mathilde Lethier
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; University Grenoble Alpes, Centre National de la Recherche Scientifique, EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Hélène Malet
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; University Grenoble Alpes, Centre National de la Recherche Scientifique, EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Joanna Brunel
- CIRI, International Center for Infectiology Research, Université de Lyon, 69007 Lyon, France; Inserm, U1111, 69007 Lyon, France; CNRS, UMR5308, 69007 Lyon, France; Ecole Normale Supérieure de Lyon, 69007 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69007 Lyon, France
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, Université de Lyon, 69007 Lyon, France; Inserm, U1111, 69007 Lyon, France; CNRS, UMR5308, 69007 Lyon, France; Ecole Normale Supérieure de Lyon, 69007 Lyon, France; Université Lyon 1, Centre International de Recherche en Infectiologie, 69007 Lyon, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; University Grenoble Alpes, Centre National de la Recherche Scientifique, EMBL Unit of Virus Host-Cell Interactions, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
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Lui PY, Wong LYR, Ho TH, Au SWN, Chan CP, Kok KH, Jin DY. PACT Facilitates RNA-Induced Activation of MDA5 by Promoting MDA5 Oligomerization. THE JOURNAL OF IMMUNOLOGY 2017; 199:1846-1855. [PMID: 28760879 DOI: 10.4049/jimmunol.1601493] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 06/27/2017] [Indexed: 12/24/2022]
Abstract
MDA5 is a RIG-I-like cytoplasmic sensor of dsRNA and certain RNA viruses, such as encephalomyocarditis virus, for the initiation of the IFN signaling cascade in the innate antiviral response. The affinity of MDA5 toward dsRNA is low, and its activity becomes optimal in the presence of unknown cellular coactivators. In this article, we report an essential coactivator function of dsRNA-binding protein PACT in mediating the MDA5-dependent type I IFN response. Virus-induced and polyinosinic-polycytidylic acid-induced activation of MDA5 were severely impaired in PACT-knockout cells and attenuated in PACT-knockdown cells, but they were potentiated when PACT was overexpressed. PACT augmented IRF3-dependent type I IFN production subsequent to dsRNA-induced activation of MDA5. In contrast, PACT had no influence on MDA5-mediated activation of NF-κB. PACT required dsRNA interaction for its action on MDA5 and promoted dsRNA-induced oligomerization of MDA5. PACT had little stimulatory effect on MDA5 mutants deficient for oligomerization and filament assembly. PACT colocalized with MDA5 in the cytoplasm and potentiated MDA5 recruitment to the dsRNA ligand. Taken together, these findings suggest that PACT functions as an essential cellular coactivator of RIG-I, as well as MDA5, and it facilitates RNA-induced formation of MDA5 oligomers.
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Affiliation(s)
- Pak-Yin Lui
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong.,Shenzhen Institute of Research and Innovation, The University of Hong Kong, Nanshan, Shenzhen, China 518057
| | - Lok-Yin Roy Wong
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong.,Shenzhen Institute of Research and Innovation, The University of Hong Kong, Nanshan, Shenzhen, China 518057
| | - Ting-Hin Ho
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong.,Shenzhen Institute of Research and Innovation, The University of Hong Kong, Nanshan, Shenzhen, China 518057
| | - Shannon Wing Ngor Au
- School of Life Sciences, Chinese University of Hong Kong, Shatin, Hong Kong; and
| | - Chi-Ping Chan
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong.,Shenzhen Institute of Research and Innovation, The University of Hong Kong, Nanshan, Shenzhen, China 518057
| | - Kin-Hang Kok
- Shenzhen Institute of Research and Innovation, The University of Hong Kong, Nanshan, Shenzhen, China 518057; .,Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong; .,Shenzhen Institute of Research and Innovation, The University of Hong Kong, Nanshan, Shenzhen, China 518057
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40
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Raghuraman P, Jesu Jaya Sudan R, Lesitha Jeeva Kumari J, Sudandiradoss C. Systematic prioritization of functional hotspot in RIG-1 domains using pattern based conventional molecular dynamic simulation. Life Sci 2017; 184:58-70. [PMID: 28705469 DOI: 10.1016/j.lfs.2017.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/29/2017] [Accepted: 07/09/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Retinoic acid inducible gene 1 (RIG-1), multi-domain protein has a role-play in detecting viral nucleic acids and stimulates the antiviral response. Dysfunction of this protein due to mutations makes the route vulnerable to viral diseases. AIM Identification of functional hotspots that maintains conformational stability in RIG-1 domains. METHODS In this study, we employed a systematic in silico strategy on RIG-1 protein to understand the mechanism of structural changes upon mutation. We computationally investigated the protein sequence signature for all the three domains of RIG-1 protein that encloses the mutation within the motif. Further, we carried out a structural comparison between RIG-1 domains with their respective distant orthologs which revealed the minimal number of interactions required to maintain its structural fold. This intra-protein network paved the way to infer hotspot residues crucial for the maintenance of the structural architecture and folding pattern. KEY FINDINGS Our analysis revealed about 40 hotspot residues that determine the folding pattern of the RIG-1 domains. Also, conventional molecular dynamic simulation coupled with essential dynamics provides conformational transitions of hot spot residues among native and mutant structures. Structural variations owing to hotspot residues in mutants again confirm the significance of these residues in structural characterization of RIG-1 domains. We believe our results will help the researchers to better comprehend towards regulatory regions and target-binding sites for therapeutic design within the pattern recognition receptor proteins. SIGNIFICANCE Our protocol employed in this work describes a novel approach in identifying signature residues that would provide structural insights in protein folding.
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Affiliation(s)
- P Raghuraman
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore 632014, India
| | - R Jesu Jaya Sudan
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore 632014, India
| | - J Lesitha Jeeva Kumari
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore 632014, India
| | - C Sudandiradoss
- Department of Biotechnology, School of Biosciences and Technology, VIT University, Vellore 632014, India.
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41
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Abstract
RIG-I-like receptors (RLRs) are cytosolic innate immune sensors that detect pathogenic RNA and induce a systemic antiviral response. During the last decade, many studies focused on their molecular characterization and the identification of RNA agonists. Therefore, it became more and more clear that RLR activation needs to be carefully regulated, because constitutive signaling or detection of endogenous RNA through loss of specificity is detrimental. Here, we review the current understanding of RLR activation and selectivity. We specifically focus upon recent findings on the function of the helicase domain in discriminating between different RNAs, and whose malfunctioning causes serious autoimmune diseases.
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Affiliation(s)
- Charlotte Lässig
- From the Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, 81377 Munich and
| | - Karl-Peter Hopfner
- From the Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität, 81377 Munich and
- the Center for Integrated Protein Sciences, 81377 Munich, Germany
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42
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Fitzgerald ME, Rawling DC, Potapova O, Ren X, Kohlway A, Pyle AM. Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding. Nucleic Acids Res 2017; 45:1442-1454. [PMID: 28180316 PMCID: PMC5388420 DOI: 10.1093/nar/gkw816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/31/2016] [Accepted: 09/03/2016] [Indexed: 12/25/2022] Open
Abstract
RIG-I is an innate immune receptor that detects and responds to infection by deadly RNA viruses such as influenza, and Hepatitis C. In the cytoplasm, RIG-I is faced with a difficult challenge: it must sensitively detect viral RNA while ignoring the abundance of host RNA. It has been suggested that RIG-I has a ‘proof-reading’ mechanism for rejecting host RNA targets, and that disruptions of this selectivity filter give rise to autoimmune diseases. Here, we directly monitor RNA proof-reading by RIG-I and we show that it is controlled by a set of conserved amino acids that couple RNA and ATP binding to the protein (Motif III). Mutations of this motif directly modulate proof-reading by eliminating or enhancing selectivity for viral RNA, with major implications for autoimmune disease and cancer. More broadly, the results provide a physical explanation for the ATP-gated behavior of SF2 RNA helicases and receptor proteins.
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MESH Headings
- Adenosine Triphosphatases/chemistry
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Adenosine Triphosphate/metabolism
- Amino Acid Substitution
- Autoimmunity
- Binding Sites/genetics
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- DEAD Box Protein 58/metabolism
- HEK293 Cells
- Humans
- Immunity, Innate
- Models, Molecular
- Mutagenesis, Site-Directed
- Neoplasms/genetics
- Neoplasms/metabolism
- Protein Interaction Domains and Motifs
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA Viruses/genetics
- RNA Viruses/immunology
- RNA Viruses/pathogenicity
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Immunologic
- Receptors, Pattern Recognition/chemistry
- Receptors, Pattern Recognition/genetics
- Receptors, Pattern Recognition/metabolism
- Signal Transduction
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Affiliation(s)
- Megan E. Fitzgerald
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - David C. Rawling
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Olga Potapova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Xiaoming Ren
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Andrew Kohlway
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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43
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Domsgen E, Lind K, Kong L, Hühn MH, Rasool O, van Kuppeveld F, Korsgren O, Lahesmaa R, Flodström-Tullberg M. An IFIH1 gene polymorphism associated with risk for autoimmunity regulates canonical antiviral defence pathways in Coxsackievirus infected human pancreatic islets. Sci Rep 2016; 6:39378. [PMID: 28000722 PMCID: PMC5175199 DOI: 10.1038/srep39378] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 11/23/2016] [Indexed: 02/08/2023] Open
Abstract
The IFIH1 gene encodes the pattern recognition receptor MDA5. A common polymorphism in IFIH1 (rs1990760, A946T) confers increased risk for autoimmune disease, including type 1-diabetes (T1D). Coxsackievirus infections are linked to T1D and cause beta-cell damage in vitro. Here we demonstrate that the rs1990760 polymorphism regulates the interferon (IFN) signature expressed by human pancreatic islets following Coxsackievirus infection. A strong IFN signature was associated with high expression of IFNλ1 and IFNλ2, linking rs1990760 to the expression of type III IFNs. In the high-responding genotype, IRF-1 expression correlated with that of type III IFN, suggesting a positive-feedback on type III IFN transcription. In summary, our study uncovers an influence of rs1990760 on the canonical effector function of MDA5 in response to an acute infection of primary human parenchymal cells with a clinically relevant virus linked to human T1D. It also highlights a previously unrecognized connection between the rs1990760 polymorphism and the expression level of type III IFNs.
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Affiliation(s)
- Erna Domsgen
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Karolinska University Hospital, Stockholm, 141 86, Sweden
| | - Katharina Lind
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Karolinska University Hospital, Stockholm, 141 86, Sweden
| | - Lingjia Kong
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, 205 20, Finland
| | - Michael H Hühn
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Karolinska University Hospital, Stockholm, 141 86, Sweden
| | - Omid Rasool
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, 205 20, Finland
| | - Frank van Kuppeveld
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584, The Netherlands
| | - Olle Korsgren
- Department of Immunology, Genetics, and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, 751 05, Sweden
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, 205 20, Finland
| | - Malin Flodström-Tullberg
- The Center for Infectious Medicine, Department of Medicine HS, Karolinska Institutet, Karolinska University Hospital, Stockholm, 141 86, Sweden.,Institute of Biosciences and Medical Technologies, University of Tampere, Tampere, 33520, Finland
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RNAs Containing Modified Nucleotides Fail To Trigger RIG-I Conformational Changes for Innate Immune Signaling. mBio 2016; 7:mBio.00833-16. [PMID: 27651356 PMCID: PMC5030355 DOI: 10.1128/mbio.00833-16] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Invading pathogen nucleic acids are recognized and bound by cytoplasmic (retinoic acid-inducible gene I [RIG-I]-like) and membrane-bound (Toll-like) pattern recognition receptors to activate innate immune signaling. Modified nucleotides, when present in RNA molecules, diminish the magnitude of these signaling responses. However, mechanisms explaining the blunted signaling have not been elucidated. In this study, we used several independent biological assays, including inhibition of virus replication, RIG-I:RNA binding assays, and limited trypsin digestion of RIG-I:RNA complexes, to begin to understand how RNAs containing modified nucleotides avoid or suppress innate immune signaling. The experiments were based on a model innate immune activating RNA molecule, the polyU/UC RNA domain of hepatitis C virus, which was transcribed in vitro with canonical nucleotides or with one of eight modified nucleotides. The approach revealed signature assay responses associated with individual modified nucleotides or classes of modified nucleotides. For example, while both N-6-methyladenosine (m6A) and pseudouridine nucleotides correlate with diminished signaling, RNA containing m6A modifications bound RIG-I poorly, while RNA containing pseudouridine bound RIG-I with high affinity but failed to trigger the canonical RIG-I conformational changes associated with robust signaling. These data advance understanding of RNA-mediated innate immune signaling, with additional relevance for applying nucleotide modifications to RNA therapeutics. The innate immune system provides the first response to virus infections and must distinguish between host and pathogen nucleic acids to mount a protective immune response without activating autoimmune responses. While the presence of nucleotide modifications in RNA is known to correlate with diminished innate immune signaling, the underlying mechanisms have not been explored. The data reported here are important for defining mechanistic details to explain signaling suppression by RNAs containing modified nucleotides. The results suggest that RNAs containing modified nucleotides interrupt signaling at early steps of the RIG-I-like innate immune activation pathway and also that nucleotide modifications with similar chemical structures can be organized into classes that suppress or evade innate immune signaling steps. These data contribute to defining the molecular basis for innate immune signaling suppression by RNAs containing modified nucleotides. The results have important implications for designing therapeutic RNAs that evade innate immune detection.
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45
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Jia P, Jia K, Chen L, Le Y, Jin Y, Zhang J, Zhu L, Zhang L, Yi M. Identification and characterization of the melanoma differentiation - associated gene 5 in sea perch, Lateolabrax japonicus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 61:161-8. [PMID: 27039216 DOI: 10.1016/j.dci.2016.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 03/28/2016] [Accepted: 03/28/2016] [Indexed: 05/07/2023]
Abstract
The RIG-I-like receptors family is a group of cytosolic RNA helicase proteins that can recognize viral RNA via binding to pathogen associated molecular pattern motifs within RNA ligands. A novel vertebrate RLR counterpart named LjMDA5 was firstly identified from the marine fish sea perch Lateolabrax japonicus in this study. The full-length cDNA of LjMDA5 is 3750 bp and encodes a polypeptide of 988 amino acids, containing two N-terminal tandem caspase activation and recruitment domains, a DExH (Asp-Glu-X-His) box domain, an HELICc domain, and a C-terminal domain RIG-I. Phylogenetic analysis showed that LjMDA5 shared the closest genetic relationship with the MDA5 of Larimichthys crocea. Quantitative RT-PCR analysis showed that LjMDA5 was ubiquitously expressed and up-regulated significantly in all selected tissues in vivo post NNV infection. Time course analysis showed that LjMDA5 transcripts significantly increased in spleen and kidney. We found LjMDA5 could be regulated in the sea perch LJB and LJF cell lines after lipopolysaccharide, polyinosinic-polycytidylic acid treatment and NNV challenge. RNA interference experiment indicated that silencing of LjMDA5 significantly increased RGNNV replication and virus production in NNV infected LJF cells. Our results revealed that MDA5 was essential for host defense against NNV, which provided new insights into the function of RLR signaling pathway during NNV infection in fish.
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Affiliation(s)
- Peng Jia
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Zhuhai Key Laboratory of Marine Bioresources and Environment, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Kuntong Jia
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Zhuhai Key Laboratory of Marine Bioresources and Environment, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Limin Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Zhuhai Key Laboratory of Marine Bioresources and Environment, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Yao Le
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Zhuhai Key Laboratory of Marine Bioresources and Environment, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Yilin Jin
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Zhuhai Key Laboratory of Marine Bioresources and Environment, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jing Zhang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Zhuhai Key Laboratory of Marine Bioresources and Environment, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Limei Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Li Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
| | - Meisheng Yi
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Zhuhai Key Laboratory of Marine Bioresources and Environment, School of Marine Sciences, Sun Yat-sen University, Guangzhou, China.
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Leung DW, Amarasinghe GK. When your cap matters: structural insights into self vs non-self recognition of 5' RNA by immunomodulatory host proteins. Curr Opin Struct Biol 2016; 36:133-41. [PMID: 26916433 PMCID: PMC5218996 DOI: 10.1016/j.sbi.2016.02.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 12/13/2022]
Abstract
Cytosolic recognition of viral RNA is important for host innate immune responses. Differential recognition of self vs non-self RNA is a considerable challenge as the inability to differentiate may trigger aberrant immune responses. Recent work identified the composition of the RNA 5', including the 5' cap and its methylation state, as an important determinant of recognition by the host. Recent studies have advanced our understanding of the modified 5' RNA recognition and viral antagonism of RNA receptors. Here, we will discuss RIG-I and IFIT proteins as examples of host proteins that detect dsRNA and ssRNA, respectively.
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Affiliation(s)
- Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, United States.
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, United States.
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Lässig C, Matheisl S, Sparrer KMJ, de Oliveira Mann CC, Moldt M, Patel JR, Goldeck M, Hartmann G, García-Sastre A, Hornung V, Conzelmann KK, Beckmann R, Hopfner KP. ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA. eLife 2015; 4:e10859. [PMID: 26609812 PMCID: PMC4733034 DOI: 10.7554/elife.10859] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/25/2015] [Indexed: 12/24/2022] Open
Abstract
The cytosolic antiviral innate immune sensor RIG-I distinguishes 5' tri- or diphosphate containing viral double-stranded (ds) RNA from self-RNA by an incompletely understood mechanism that involves ATP hydrolysis by RIG-I's RNA translocase domain. Recently discovered mutations in ATPase motifs can lead to the multi-system disorder Singleton-Merten Syndrome (SMS) and increased interferon levels, suggesting misregulated signaling by RIG-I. Here we report that SMS mutations phenocopy a mutation that allows ATP binding but prevents hydrolysis. ATPase deficient RIG-I constitutively signals through endogenous RNA and co-purifies with self-RNA even from virus infected cells. Biochemical studies and cryo-electron microscopy identify a 60S ribosomal expansion segment as a dominant self-RNA that is stably bound by ATPase deficient RIG-I. ATP hydrolysis displaces wild-type RIG-I from this self-RNA but not from 5' triphosphate dsRNA. Our results indicate that ATP-hydrolysis prevents recognition of self-RNA and suggest that SMS mutations lead to unintentional signaling through prolonged RNA binding.
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Affiliation(s)
- Charlotte Lässig
- Gene Center, Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany
| | - Sarah Matheisl
- Gene Center, Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany
| | - Konstantin MJ Sparrer
- Max von Pettenkofer-Institute, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Manuela Moldt
- Gene Center, Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany
| | - Jenish R Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Marion Goldeck
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Gunther Hartmann
- Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, United States
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Veit Hornung
- Institute of Molecular Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Karl-Klaus Conzelmann
- Max von Pettenkofer-Institute, Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany
- Center for Integrated Protein Science Munich, Munich, Germany
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