1
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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:BST20230724. [PMID: 38884803 DOI: 10.1042/bst20230724] [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: 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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2
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Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL. Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. eLife 2024; 13:RP93979. [PMID: 38747717 PMCID: PMC11095941 DOI: 10.7554/elife.93979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, Caenorhabditis elegans Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1's helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways.
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Affiliation(s)
- Claudia D Consalvo
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
| | | | - Helen M Donelick
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
| | | | - Debra M Eckert
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
| | - Peter S Shen
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
| | - Brenda L Bass
- Department of Biochemistry, University of UtahSalt Lake CityUnited States
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3
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Jarmoskaite I, Li JB. Multifaceted roles of RNA editing enzyme ADAR1 in innate immunity. RNA (NEW YORK, N.Y.) 2024; 30:500-511. [PMID: 38531645 PMCID: PMC11019752 DOI: 10.1261/rna.079953.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/09/2024] [Indexed: 03/28/2024]
Abstract
Innate immunity must be tightly regulated to enable sensitive pathogen detection while averting autoimmunity triggered by pathogen-like host molecules. A hallmark of viral infection, double-stranded RNAs (dsRNAs) are also abundantly encoded in mammalian genomes, necessitating surveillance mechanisms to distinguish "self" from "nonself." ADAR1, an RNA editing enzyme, has emerged as an essential safeguard against dsRNA-induced autoimmunity. By converting adenosines to inosines (A-to-I) in long dsRNAs, ADAR1 covalently marks endogenous dsRNAs, thereby blocking the activation of the cytoplasmic dsRNA sensor MDA5. Moreover, beyond its editing function, ADAR1 binding to dsRNA impedes the activation of innate immune sensors PKR and ZBP1. Recent landmark studies underscore the utility of silencing ADAR1 for cancer immunotherapy, by exploiting the ADAR1-dependence developed by certain tumors to unleash an antitumor immune response. In this perspective, we summarize the genetic and mechanistic evidence for ADAR1's multipronged role in suppressing dsRNA-mediated autoimmunity and explore the evolving roles of ADAR1 as an immuno-oncology target.
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Affiliation(s)
- Inga Jarmoskaite
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- AIRNA Corporation, Cambridge, Massachusetts 02142, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, California 94305, USA
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4
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Yoneyama M, Kato H, Fujita T. Physiological functions of RIG-I-like receptors. Immunity 2024; 57:731-751. [PMID: 38599168 DOI: 10.1016/j.immuni.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/19/2024] [Accepted: 03/04/2024] [Indexed: 04/12/2024]
Abstract
RIG-I-like receptors (RLRs) are crucial for pathogen detection and triggering immune responses and have immense physiological importance. In this review, we first summarize the interferon system and innate immunity, which constitute primary and secondary responses. Next, the molecular structure of RLRs and the mechanism of sensing non-self RNA are described. Usually, self RNA is refractory to the RLR; however, there are underlying host mechanisms that prevent immune reactions. Studies have revealed that the regulatory mechanisms of RLRs involve covalent molecular modifications, association with regulatory factors, and subcellular localization. Viruses have evolved to acquire antagonistic RLR functions to escape the host immune reactions. Finally, the pathologies caused by the malfunction of RLR signaling are described.
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Affiliation(s)
- Mitsutoshi Yoneyama
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan; Division of Pandemic and Post-disaster Infectious Diseases, Research Institute of Disaster Medicine, Chiba University, Chiba, Japan
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Takashi Fujita
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany; Laboratory of Regulatory Information, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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5
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Singh R, Wu Y, Herrero Del Valle A, Leigh KE, Mong S, Cheng MTK, Ferguson BJ, Modis Y. Contrasting functions of ATP hydrolysis by MDA5 and LGP2 in viral RNA sensing. J Biol Chem 2024; 300:105711. [PMID: 38309507 PMCID: PMC10909783 DOI: 10.1016/j.jbc.2024.105711] [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: 08/30/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/05/2024] Open
Abstract
Cytosolic long dsRNA, among the most potent proinflammatory signals, is recognized by melanoma differentiation-associated protein 5 (MDA5). MDA5 binds dsRNA cooperatively forming helical filaments. ATP hydrolysis by MDA5 fulfills a proofreading function by promoting dissociation of shorter endogenous dsRNs from MDA5 while allowing longer viral dsRNAs to remain bound leading to activation of interferon-β responses. Here, we show that adjacent MDA5 subunits in MDA5-dsRNA filaments hydrolyze ATP cooperatively, inducing cooperative filament disassembly. Consecutive rounds of ATP hydrolysis amplify the filament footprint, displacing tightly bound proteins from dsRNA. Our electron microscopy and biochemical assays show that LGP2 binds to dsRNA at internal binding sites through noncooperative ATP hydrolysis. Unlike MDA5, LGP2 has low nucleic acid selectivity and can hydrolyze GTP and CTP as well as ATP. Binding of LGP2 to dsRNA promotes nucleation of MDA5 filament assembly resulting in shorter filaments. Molecular modeling identifies an internally bound MDA5-LGP2-RNA complex, with the LGP2 C-terminal tail forming the key contacts with MDA5. These contacts are specifically required for NTP-dependent internal RNA binding. We conclude that NTPase-dependent binding of LGP2 to internal dsRNA sites complements NTPase-independent binding to dsRNA ends, via distinct binding modes, to increase the number and signaling output of MDA5-dsRNA complexes.
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Affiliation(s)
- Rahul Singh
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK; Department of Pathology, University of Cambridge, Cambridge, UK
| | - Yuan Wu
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Alba Herrero Del Valle
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kendra E Leigh
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Sai Mong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mark T K Cheng
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Brian J Ferguson
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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6
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Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL. C. elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.21.558868. [PMID: 37790392 PMCID: PMC10542151 DOI: 10.1101/2023.09.21.558868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Invertebrates use the endoribonuclease Dicer to cleave viral dsRNA during antiviral defense, while vertebrates use RIG-I-like Receptors (RLRs), which bind viral dsRNA to trigger an interferon response. While some invertebrate Dicers act alone during antiviral defense, C. elegans Dicer acts in a complex with a dsRNA binding protein called RDE-4, and an RLR ortholog called DRH-1. We used biochemical and structural techniques to provide mechanistic insight into how these proteins function together. We found RDE-4 is important for ATP-independent and ATP-dependent cleavage reactions, while helicase domains of both DCR-1 and DRH-1 contribute to ATP-dependent cleavage. DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition. A cryo-EM structure indicates DRH-1 interacts with DCR-1's helicase domain, suggesting this interaction relieves autoinhibition. Our study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways.
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Affiliation(s)
| | - Adedeji M. Aderounmu
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
- These authors contributed equally
| | - Helen M. Donelick
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
- These authors contributed equally
| | - P. Joe Aruscavage
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
| | - Debra M. Eckert
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
| | - Peter S. Shen
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
| | - Brenda L. Bass
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112
- Lead Contact
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7
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Herbert A. The Intransitive Logic of Directed Cycles and Flipons Enhances the Evolution of Molecular Computers by Augmenting the Kolmogorov Complexity of Genomes. Int J Mol Sci 2023; 24:16482. [PMID: 38003672 PMCID: PMC10671625 DOI: 10.3390/ijms242216482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Cell responses are usually viewed as transitive events with fixed inputs and outputs that are regulated by feedback loops. In contrast, directed cycles (DCs) have all nodes connected, and the flow is in a single direction. Consequently, DCs can regenerate themselves and implement intransitive logic. DCs are able to couple unrelated chemical reactions to each edge. The output depends upon which node is used as input. DCs can also undergo selection to minimize the loss of thermodynamic entropy while maximizing the gain of information entropy. The intransitive logic underlying DCs enhances their programmability and impacts their evolution. The natural selection of DCs favors the persistence, adaptability, and self-awareness of living organisms and does not depend solely on changes to coding sequences. Rather, the process can be RNA-directed. I use flipons, nucleic acid sequences that change conformation under physiological conditions, as a simple example and then describe more complex DCs. Flipons are often encoded by repeats and greatly increase the Kolmogorov complexity of genomes by adopting alternative structures. Other DCs allow cells to regenerate, recalibrate, reset, repair, and rewrite themselves, going far beyond the capabilities of current computational devices. Unlike Turing machines, cells are not designed to halt but rather to regenerate.
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Affiliation(s)
- Alan Herbert
- InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA
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8
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Li T, Cai Y, Li C, Huang J, Chen J, Zhang Z, Cao R, Zhou B, Feng X. MDA5 with Complete CARD2 Region Inhibits the Early Replication of H9N2 AIV and Enhances the Immune Response during Vaccination. Vaccines (Basel) 2023; 11:1542. [PMID: 37896944 PMCID: PMC10611263 DOI: 10.3390/vaccines11101542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Chicken melanoma differentiation-associated gene 5 (MDA5) is a member of the RLRs family that recognizes the viral RNAs invading cells and activates downstream interferon regulatory pathways, thereby inhibiting viral replication. The caspase activation and recruitment domain (CARD) is the most important region in MDA5 protein. However, the antiviral and immune enhancement of MDA5 with the CARD region remains unclear. In this study, two truncated MDA5 genes with different CARD regions, namely MDA5-1 with CARD1 plus partial CARD2 domain and MDA5-2 with CARD1 plus complete CARD2 domain, were cloned via reverse transcription PCR and ligated into plasmid Flag-N vector to be Flag-MDA5-1 and Flag-MDA5-2 plasmids. DF-1 cells were transfected with two plasmids for 24 h and then inoculated with H9N2 virus (0.1 MOI) for 6 h to detect the levels of IFN-β, PKR, MAVS, and viral HA, NA, and NS proteins expression. The results showed that MDA5-1 and MDA5-2 increased the expression of IFN-β and PKR, activated the downstream molecule MAVS production, and inhibited the expression of HA, NA, and NS proteins. The knockdown of MDA5 genes confirmed that MDA5-2 had a stronger antiviral effect than that of MDA5-1. Furthermore, the recombinant proteins MDA5-1 and MDA5-2 were combined with H9N2 inactivated vaccine to immunize SPF chickens subcutaneously injected in the neck three times. The immune response of the immunized chicken was investigated. It was observed that the antibody titers and expressions of immune-related molecules from the chicken immunized with MDA5-1 and MDA5-2 group were increased, in which the inducing function of MDA5-2 groups was the highest among all immunization groups. These results suggested that the truncated MDA5 recombinant proteins with complete CARD2 region could play vital roles in antiviral and immune enhancement. This study provides important material for the further study of the immunoregulatory function and clinical applications of MDA5 protein.
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Affiliation(s)
- Tongtong Li
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (T.L.); (Y.C.); (C.L.); (J.H.); (J.C.); (Z.Z.); (R.C.); (B.Z.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiqin Cai
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (T.L.); (Y.C.); (C.L.); (J.H.); (J.C.); (Z.Z.); (R.C.); (B.Z.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Chenfei Li
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (T.L.); (Y.C.); (C.L.); (J.H.); (J.C.); (Z.Z.); (R.C.); (B.Z.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingwen Huang
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (T.L.); (Y.C.); (C.L.); (J.H.); (J.C.); (Z.Z.); (R.C.); (B.Z.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiajing Chen
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (T.L.); (Y.C.); (C.L.); (J.H.); (J.C.); (Z.Z.); (R.C.); (B.Z.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ze Zhang
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (T.L.); (Y.C.); (C.L.); (J.H.); (J.C.); (Z.Z.); (R.C.); (B.Z.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruibing Cao
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (T.L.); (Y.C.); (C.L.); (J.H.); (J.C.); (Z.Z.); (R.C.); (B.Z.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Zhou
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (T.L.); (Y.C.); (C.L.); (J.H.); (J.C.); (Z.Z.); (R.C.); (B.Z.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiuli Feng
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (T.L.); (Y.C.); (C.L.); (J.H.); (J.C.); (Z.Z.); (R.C.); (B.Z.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
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9
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Herbert A. Flipons and small RNAs accentuate the asymmetries of pervasive transcription by the reset and sequence-specific microcoding of promoter conformation. J Biol Chem 2023; 299:105140. [PMID: 37544644 PMCID: PMC10474125 DOI: 10.1016/j.jbc.2023.105140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023] Open
Abstract
The role of alternate DNA conformations such as Z-DNA in the regulation of transcription is currently underappreciated. These structures are encoded by sequences called flipons, many of which are enriched in promoter and enhancer regions. Through a change in their conformation, flipons provide a tunable mechanism to mechanically reset promoters for the next round of transcription. They act as actuators that capture and release energy to ensure that the turnover of the proteins at promoters is optimized to cell state. Likewise, the single-stranded DNA formed as flipons cycle facilitates the docking of RNAs that are able to microcode promoter conformations and canalize the pervasive transcription commonly observed in metazoan genomes. The strand-specific nature of the interaction between RNA and DNA likely accounts for the known asymmetry of epigenetic marks present on the histone tetramers that pair to form nucleosomes. The role of these supercoil-dependent processes in promoter choice and transcriptional interference is reviewed. The evolutionary implications are examined: the resilience and canalization of flipon-dependent gene regulation is contrasted with the rapid adaptation enabled by the spread of flipon repeats throughout the genome. Overall, the current findings underscore the important role of flipons in modulating the readout of genetic information and how little we know about their biology.
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Affiliation(s)
- Alan Herbert
- Discovery Division, InsideOutBio, Charlestown, Massachusetts, USA.
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10
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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: 3] [Impact Index Per Article: 3.0] [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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11
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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; 8:157929. [PMID: 36512407 PMCID: PMC9977297 DOI: 10.1172/jci.insight.157929] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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12
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Endogenous Retroviruses as Modulators of Innate Immunity. Pathogens 2023; 12:pathogens12020162. [PMID: 36839434 PMCID: PMC9963469 DOI: 10.3390/pathogens12020162] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Endogenous retroviruses (ERVs), or LTR retrotransposons, are a class of transposable elements that are highly represented in mammalian genomes. Human ERVs (HERVs) make up roughly 8.3% of the genome and over the course of evolution, HERV elements underwent positive selection and accrued mutations that rendered them non-infectious; thereby, the genome could co-opt them into constructive roles with important biological functions. In the past two decades, with the help of advances in sequencing technology, ERVs are increasingly considered to be important components of the innate immune response. While typically silenced, expression of HERVs can be induced in response to traumatic, toxic, or infection-related stress, leading to a buildup of viral transcripts and under certain circumstances, proteins, including functionally active reverse transcriptase and viral envelopes. The biological activity of HERVs in the context of the innate immune response can be based on the functional effect of four major viral components: (1) HERV LTRs, (2) HERV-derived RNAs, (3) HERV-derived RNA:DNA duplexes and cDNA, and (4) HERV-derived proteins and ribonucleoprotein complexes. In this review, we will discuss the implications of HERVs in all four contexts in relation to innate immunity and their association with various pathological disease states.
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13
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Andreou A, Papakyriakou A, Zervou MI, Goulielmos GN, Eliopoulos EE. Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics? J Mol Evol 2023; 91:204-213. [PMID: 36651965 PMCID: PMC10082101 DOI: 10.1007/s00239-022-10090-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023]
Abstract
Interferon induced with helicase C domain-containing protein 1 (IFIH1) gene encodes a cytoplasmic RNA helicase otherwise known as melanoma differentiation-associated 5 (MDA5), a RIG-1-like RNA helicase that recognizes viral RNA and is involved in innate immunity through recognition of viral RNA. Upon binding to double-stranded (ds) RNA, MDA5 forms a filamentous assembly along the length of dsRNA and utilizes molecular signatures to discriminate self, versus non-self on the basis of dsRNA length and methylation. Its missense variant rs35667974 is protective for type 1 diabetes, psoriasis, and psoriatic arthritis, but is also found to be associated with an increased risk for ankylosing spondylitis, Crohn's disease, and ulcerative colitis. To gain insight into the complex role of this variant we performed a structural analysis of MDA5 in complex with dsRNA using molecular dynamics simulations. Our data suggest that while the Ile923Val mutation of the rs35667974 variant does not affect binding to native dsRNA significantly, it displays a destabilizing effect in the presence of 2'-O uridine methylation. Thus, the presence of 2'-O-methylation at the dsRNA introduces a sensing signature that leads to selective reduction of the overall MDA catalytic activity. This study represents an evaluation of the role of the shared rs35667974 variant of autoimmune locus IFIH1, reported to lead to selectively reduced catalytic activity of the modified MDA5 phenotype and, as a consequence, reduced negative feedback on cytokine and chemokine signaling and selectively protection against autoimmunity.
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Affiliation(s)
- Athena Andreou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855, Athens, Greece
| | - Athanasios Papakyriakou
- Institute of Biosciences and Applications, National Centre for Scientific Research "Demokritos", 15341, Athens, Greece
| | - Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003, Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003, Heraklion, Greece.,Department of Internal Medicine, University Hospital of Heraklion, 71500, Heraklion, Greece
| | - Elias E Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855, Athens, Greece.
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14
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Li X, Liu S, Rai KR, Zhou W, Wang S, Chi X, Guo G, Chen JL, Liu S. Initial activation of STAT2 induced by IAV infection is critical for innate antiviral immunity. Front Immunol 2022; 13:960544. [PMID: 36148221 PMCID: PMC9486978 DOI: 10.3389/fimmu.2022.960544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
STAT2 is an important transcription factor activated by interferons (IFNs) upon viral infection and plays a key role in antiviral responses. Interestingly, here we found that phosphorylation of STAT2 could be induced by several viruses at early infection stage, including influenza A virus (IAV), and such initial activation of STAT2 was independent of type I IFNs and JAK kinases. Furthermore, it was observed that the early activation of STAT2 during viral infection was mainly regulated by the RIG-I/MAVS-dependent pathway. Disruption of STAT2 phosphorylation at Tyr690 restrained antiviral response, as silencing STAT2 or blocking STAT2 Y690 phosphorylation suppressed the expression of several interferon-stimulated genes (ISGs), thereby facilitating viral replication. In vitro experiments using overexpression system or kinase inhibitors showed that several kinases including MAPK12 and Syk were involved in regulation of the early phosphorylation of STAT2 triggered by IAV infection. Moreover, when MAPK12 kinase was inhibited, expression of several ISGs was clearly decreased in cells infected with IAV at the early infection stage. Accordingly, inhibition of MAPK12 accelerated the replication of influenza virus in host. These results provide a better understanding of how initial activation of STAT2 and the early antiviral responses are induced by the viral infection.
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Affiliation(s)
- Xinxin Li
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siya Liu
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kul Raj Rai
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenzhuo Zhou
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Song Wang
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaojuan Chi
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guijie Guo
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ji-Long Chen
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Ji-Long Chen, ; Shasha Liu,
| | - Shasha Liu
- Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Ji-Long Chen, ; Shasha Liu,
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15
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Zervou MI, Andreou AC, Eliopoulos EE, Goulielmos GN. Functional significance of the rare rs35667974 IFIH1 gene polymorphism, associated with multiple autoimmune diseases, using a structural biological approach. Autoimmunity 2022; 55:455-461. [PMID: 35918839 DOI: 10.1080/08916934.2022.2103799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Autoimmune diseases, which affect approximately 5% of human population, are a range of diseases in which the immune response to self-antigens results in damage or dysfunction of tissues. Recent genome wide association studies (GWAS) have successfully identified novel autoimmune disease-associated loci, with many of them shared by multiple disease-associated pathways but much of the genetics and pathophysiological mechanisms remain still obscure. Considering that most of the potential causal variants are still unknown, many studies showed that the missense variant rs35667974 at interferon-induced with helicase C domain 1 (IFIH1) gene is protective for type 1 diabetes (T1D), psoriasis (PS) and psoriatic arthritis (PsA). Recently, this variant was found to be also associated with ankylosing spondylitis (AS), Crohn's disease (CD) and ulcerative colitis (UC). The IFIH1 gene encodes a cytoplasmic RNA helicase otherwise known as melanoma differentiation-associated 5 (MDA5) that recognizes viral RNA and is involved in innate immunity through recognition of viral RNA. In the present study we sought to investigate the association of the rare rs35667974 variant of IFIH1 gene, which resides in exon 14 and changes a conserved isoleucine at position #923 to valine, in the development of various autoimmune diseases and give a reason for the selectivity affecting different autoimmune diseases. Evolutionary studies and three-dimensional (3 D) homology modelling were employed on the MDA5 protein product, through its association with dsRNA, recognition factor controlling cytokine and chemokine signalling, to investigate the protective role of the MDA5 variant for certain autoimmune diseases.
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Affiliation(s)
- Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Athena C Andreou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Elias E Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, Heraklion, Greece.,Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Greece
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16
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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: 2] [Impact Index Per Article: 1.0] [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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17
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Tong J, Zhang W, Chen Y, Yuan Q, Qin NN, Qu G. The Emerging Role of RNA Modifications in the Regulation of Antiviral Innate Immunity. Front Microbiol 2022; 13:845625. [PMID: 35185855 PMCID: PMC8851159 DOI: 10.3389/fmicb.2022.845625] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
Posttranscriptional modifications have been implicated in regulation of nearly all biological aspects of cellular RNAs, from stability, translation, splicing, nuclear export to localization. Chemical modifications also have been revealed for virus derived RNAs several decades before, along with the potential of their regulatory roles in virus infection. Due to the dynamic changes of RNA modifications during virus infection, illustrating the mechanisms of RNA epigenetic regulations remains a challenge. Nevertheless, many studies have indicated that these RNA epigenetic marks may directly regulate virus infection through antiviral innate immune responses. The present review summarizes the impacts of important epigenetic marks on viral RNAs, including N6-methyladenosine (m6A), 5-methylcytidine (m5C), 2ʹ-O-methylation (2ʹ-O-Methyl), and a few uncanonical nucleotides (A-to-I editing, pseudouridine), on antiviral innate immunity and relevant signaling pathways, while highlighting the significance of antiviral innate immune responses during virus infection.
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Affiliation(s)
- Jie Tong
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Wuchao Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Yuran Chen
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Qiaoling Yuan
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Ning-Ning Qin
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Guosheng Qu
- College of Life Sciences, Hebei University, Baoding, China.,Institute of Life Sciences and Green Development, Hebei University, Baoding, China
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18
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Woo SJ, Choi HJ, Park YH, Rengaraj D, Kim JK, Han JY. Amplification of immunity by engineering chicken MDA5 combined with the C terminal domain (CTD) of RIG-I. Appl Microbiol Biotechnol 2022; 106:1599-1613. [PMID: 35129655 DOI: 10.1007/s00253-022-11806-4] [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: 08/29/2021] [Revised: 12/24/2021] [Accepted: 01/26/2022] [Indexed: 11/24/2022]
Abstract
Innate immune system is triggered by pattern recognition receptors (PRRs) recognition. Retinoic acid-inducible gene 1 (RIG-I) is a major sensor that recognizes RNA ligands. However, chickens have no homologue of RIG-I; instead, they rely on melanoma differentiation-associated protein 5 (MDA5) to recognize RNA ligands, which renders chickens susceptible to infection by influenza A viruses (IAVs). Here, we engineered the cMDA5 viral RNA sensing domain (C-terminal domain, CTD) such that it functions similarly to human RIG-I (hRIG-I) by mutating histidine 925 into phenylalanine, a key residue for hRIG-I RNA binding loop function, or by swapping the CTD of cMDA5 with that of hRIG-I or duck RIG-I (dRIG-I). The engineered cMDA5 gene was expressed in cMDA5 knockout DF-1 cells, and interferon-beta (IFN-β) activity and expression of interferon-related genes were measured after transfection of cells with RNA ligands of hRIG-I or human MDA5 (hMDA5). We found that both mutant cMDA5 and engineered cMDA5 triggered significantly stronger interferon-mediated immune responses than wild-type cMDA5. Moreover, engineered cMDA5 reduced the IAV titer by 100-fold compared with that in control cells. Collectively, engineered cMDA5/RIG-I CTD significantly enhanced interferon-mediated immune responses, making them invaluable strategies for production of IAV-resistant chickens. KEY POINTS: • Mutant chicken MDA5 with critical residue of RIG-I (phenylalanine) enhanced immunity. • Engineered chicken MDA5 with CTD of RIG-I increased IFN-mediated immune responses. • Engineered chicken MDA5 reduced influenza A virus titers by up to 100-fold.
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Affiliation(s)
- Seung Je Woo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Hee Jung Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Young Hyun Park
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Deivendran Rengaraj
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Jin-Kyoo Kim
- Department of Microbiology, Changwon National University, Changwon, South Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea.
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19
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MDA5 disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA. Nat Commun 2021; 12:6668. [PMID: 34795277 PMCID: PMC8602431 DOI: 10.1038/s41467-021-27062-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022] Open
Abstract
Our innate immune responses to viral RNA are vital defenses. Long cytosolic double-stranded RNA (dsRNA) is recognized by MDA5. The ATPase activity of MDA5 contributes to its dsRNA binding selectivity. Mutations that reduce RNA selectivity can cause autoinflammatory disease. Here, we show how the disease-associated MDA5 variant M854K perturbs MDA5-dsRNA recognition. M854K MDA5 constitutively activates interferon signaling in the absence of exogenous RNA. M854K MDA5 lacks ATPase activity and binds more stably to synthetic Alu:Alu dsRNA. CryoEM structures of MDA5-dsRNA filaments at different stages of ATP hydrolysis show that the K854 sidechain forms polar bonds that constrain the conformation of MDA5 subdomains, disrupting key steps in the ATPase cycle- RNA footprint expansion and helical twist modulation. The M854K mutation inhibits ATP-dependent RNA proofreading via an allosteric mechanism, allowing MDA5 to form signaling complexes on endogenous RNAs. This work provides insights on how MDA5 recognizes dsRNA in health and disease.
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20
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Abstract
In vitro-transcribed RNAs are emerging as new biologics for therapeutic innovation, as exemplified by their application recently in SARS-CoV-2 vaccinations. RNAs prepared by in vitro transcription (IVT) allow transient expression of proteins of interest, conferring safety over DNA- or virus-mediated gene delivery systems. However, in vitro-transcribed RNAs should be used with caution because of their immunogenicity, which is in part triggered by double-stranded RNA (dsRNA) byproducts during IVT. Cellular innate immune response to dsRNA byproducts can lead to undesirable consequences, including suppression of protein synthesis and cell death, which in turn can detrimentally impact the efficacy of mRNA therapy. Thus, it is critical to understand the nature of IVT byproducts and the mechanisms by which they trigger innate immune responses.Our lab has been investigating the mechanisms by which the innate immune system discriminates between "self" and "nonself" RNA, with the focus on the cytoplasmic dsRNA receptors retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated 5 (MDA5). We have biochemically and structurally characterized critical events involving RNA discrimination and signal transduction by RIG-I or MDA5. We have used in vitro-transcribed RNAs as tools to investigate RNA specificity of RIG-I and MDA5, which required optimization of the IVT reaction and purification processes to eliminate the effect of IVT byproducts. In this Account, we summarize our current understanding of RIG-I and MDA5 and IVT reactions and propose future directions for improving IVT as a method to generate both research tools and therapeutics. Other critical proteins in cellular innate immune response to dsRNAs are also discussed. We arrange the contents in the following order: (i) innate immunity sensors for nonself RNA, including the RIG-I-like receptors (RLRs) in the cytosol and the toll-like receptors (TLRs) in the endosome, as well as cytoplasmic dsRNA-responding proteins, including protein kinase R (PKR) and 2',5'-oligoadenylate synthetases (OASes), illustrating the feature of protein-RNA binding and its consequences; (ii) the immunogenicity of IVT byproducts, specifically the generation of dsRNA molecules during IVT; and (iii) methods to reduce IVT RNA immunogenicity, including optimizations of RNA polymerases, reagents, and experimental conditions during IVT and subsequent purification.
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Affiliation(s)
- Xin Mu
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Tianjin University and Health-Biotech United Group Joint Laboratory of Innovative Drug Development and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States
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21
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Song B, Chen Y, Liu X, Yuan F, Tan EYJ, Lei Y, Song N, Han Y, Pascal BD, Griffin PR, Luo C, Wu B, Luo D, Zheng J. Ordered assembly of the cytosolic RNA-sensing MDA5-MAVS signaling complex via binding to unanchored K63-linked poly-ubiquitin chains. Immunity 2021; 54:2218-2230.e5. [PMID: 34644557 DOI: 10.1016/j.immuni.2021.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 05/05/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
The RNA sensor MDA5 recruits the signaling adaptor MAVS to initiate type I interferon signaling and downstream antiviral responses, a process that requires K63-linked polyubiquitin chains. Here, we examined the mechanisms whereby K63-polyUb chain regulate MDA5 activation. Only long unanchored K63-polyUbn (n ≥ 8) could mediate tetramerization of the caspase activation and recruitment domains of MDA5 (MDA5CARDs). Cryoelectron microscopy structures of a polyUb13-bound MDA5CARDs tetramer and a polyUb11-bound MDA5CARDs-MAVSCARD assembly revealed a tower-like formation, wherein eight Ubs tethered along the outer rim of the helical shell, bridging MDA5CARDs and MAVSCARD tetramers into proximity. ATP binding and hydrolysis promoted the stabilization of RNA-bound MDA5 prior to MAVS activation via allosteric effects on CARDs-polyUb complex. Abundant ATP prevented basal activation of apo MDA5. Our findings reveal the ordered assembly of a MDA5 signaling complex competent to recruit and activate MAVS and highlight differences with RIG-I in terms of CARD orientation and Ub sensing that suggest different abilities to induce antiviral responses.
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Affiliation(s)
- Bin Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yun Chen
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xin Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fei Yuan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Eddie Yong Jun Tan
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Yixuan Lei
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ning Song
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yinqi Han
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | - Patrick R Griffin
- The Scripps Research Institute, Department of Molecular Medicine, Jupiter, FL 33458, USA
| | - Cheng Luo
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Bin Wu
- NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore
| | - Jie Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
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22
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Li K, Zheng J, Wirawan M, Trinh NM, Fedorova O, Griffin PR, Pyle AM, Luo D. Insights into the structure and RNA-binding specificity of Caenorhabditis elegans Dicer-related helicase 3 (DRH-3). Nucleic Acids Res 2021; 49:9978-9991. [PMID: 34403472 PMCID: PMC8464030 DOI: 10.1093/nar/gkab712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022] Open
Abstract
DRH-3 is critically involved in germline development and RNA interference (RNAi) facilitated chromosome segregation via the 22G-siRNA pathway in Caenorhabditis elegans. DRH-3 has similar domain architecture to RIG-I-like receptors (RLRs) and belongs to the RIG-I-like RNA helicase family. The molecular understanding of DRH-3 and its function in endogenous RNAi pathways remains elusive. In this study, we solved the crystal structures of the DRH-3 N-terminal domain (NTD) and the C-terminal domains (CTDs) in complex with 5'-triphosphorylated RNAs. The NTD of DRH-3 adopts a distinct fold of tandem caspase activation and recruitment domains (CARDs) structurally similar to the CARDs of RIG-I and MDA5, suggesting a signaling function in the endogenous RNAi biogenesis. The CTD preferentially recognizes 5'-triphosphorylated double-stranded RNAs bearing the typical features of secondary siRNA transcripts. The full-length DRH-3 displays unique structural dynamics upon binding to RNA duplexes that differ from RIG-I or MDA5. These features of DRH-3 showcase the evolutionary divergence of the Dicer and RLR family of helicases.
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Affiliation(s)
- Kuohan Li
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
| | - Jie Zheng
- The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Melissa Wirawan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
| | - Nguyen Mai Trinh
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Anna M Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive 636921, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive 636921, Singapore
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23
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Bhowmik D, Du M, Tian Y, Ma S, Wu J, Chen Z, Yin Q, Zhu F. Cooperative DNA binding mediated by KicGAS/ORF52 oligomerization allows inhibition of DNA-induced phase separation and activation of cGAS. Nucleic Acids Res 2021; 49:9389-9403. [PMID: 34387695 PMCID: PMC8450086 DOI: 10.1093/nar/gkab689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/21/2021] [Accepted: 08/08/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) is a key DNA sensor that detects aberrant cytosolic DNA arising from pathogen invasions or genotoxic stresses. Upon binding to DNA, cGAS is activated and catalyzes the synthesis of cyclic GMP-AMP (cGAMP), which induces potent antimicrobial and antitumor responses. Kaposi sarcoma-associated herpesvirus (KSHV) is a human DNA tumor virus that causes Kaposi sarcoma and several other malignancies. We previously reported that KSHV inhibitor of cGAS (KicGAS) encoded by ORF52, inhibits cGAS enzymatic activity, but the underlying mechanisms remained unclear. To define the inhibitory mechanisms, here we performed in-depth biochemical and functional characterizations of KicGAS, and mapped its functional domains. We found KicGAS self-oligomerizes and binds to double stranded DNA cooperatively. This self-oligomerization is essential for its DNA binding and cGAS inhibition. Interestingly, KicGAS forms liquid droplets upon binding to DNA, which requires collective multivalent interactions with DNA mediated by both structured and disordered domains coordinated through the self-oligomerization of KicGAS. We also observed that KicGAS inhibits the DNA-induced phase separation and activation of cGAS. Our findings reveal a novel mechanism by which DNA viruses target the host protein phase separation for suppression of the host sensing of viral nucleic acids.
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Affiliation(s)
- Debipreeta Bhowmik
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Mingjian Du
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX75390-9148, USA
| | - Yuan Tian
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Siming Ma
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jianjun Wu
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Zhijian Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX75390-9148, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
| | - Qian Yin
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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24
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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: 83] [Impact Index Per Article: 27.7] [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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25
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Gosu V, Sasidharan S, Saudagar P, Lee HK, Shin D. Computational Insights into the Structural Dynamics of MDA5 Variants Associated with Aicardi-Goutières Syndrome and Singleton-Merten Syndrome. Biomolecules 2021; 11:biom11081251. [PMID: 34439917 PMCID: PMC8393256 DOI: 10.3390/biom11081251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/15/2021] [Accepted: 08/16/2021] [Indexed: 11/26/2022] Open
Abstract
Melanoma differentiation-associated protein 5 (MDA5) is a crucial RIG-I-like receptor RNA helicase enzyme encoded by IFIH1 in humans. Single nucleotide polymorphisms in the IFIH1 results in fatal genetic disorders such as Aicardi–Goutières syndrome and Singleton–Merten syndrome, and in increased risk of type I diabetes in humans. In this study, we chose four different amino acid substitutions of the MDA5 protein responsible for genetic disorders: MDA5L372F, MDA5A452T, MDA5R779H, and MDA5R822Q and analyzed their structural and functional relationships using molecular dynamic simulations. Our results suggest that the mutated complexes are relatively more stable than the wild-type MDA5. The radius of gyration, interaction energies, and intra-hydrogen bond analysis indicated the stability of mutated complexes over the wild type, especially MDA5L372F and MDA5R822Q. The dominant motions exhibited by the wild-type and mutant complexes varied significantly. Moreover, the betweenness centrality of the wild-type and mutant complexes showed shared residues for intra-signal propagation. The observed results indicate that the mutations lead to a gain of function, as reported in previous studies, due to increased interaction energies and stability between RNA and MDA5 in mutated complexes. These findings are expected to deepen our understanding of MDA5 variants and may assist in the development of relevant therapeutics against the disorders.
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Affiliation(s)
- Vijayakumar Gosu
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, Korea;
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India; (S.S.); (P.S.)
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology, Warangal 506004, Telangana, India; (S.S.); (P.S.)
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, Korea;
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence: (H.L.); (D.S.)
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea
- Correspondence: (H.L.); (D.S.)
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26
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de Oliveira Mann CC, Hornung V. Molecular mechanisms of nonself nucleic acid recognition by the innate immune system. Eur J Immunol 2021; 51:1897-1910. [PMID: 34138462 DOI: 10.1002/eji.202049116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/13/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022]
Abstract
Nucleic acids (NAs) represent one of the most important classes of molecules recognized by the innate immune system. However, NAs are not limited to pathogens, but are also present within the host. As such, the immune system has evolved an elaborate set of pathogen recognition receptors (PRRs) that employ various strategies to recognize distinct types of NAs, while reliably distinguishing between self and nonself. The here-employed strategies encompass the positioning of NA-sensing PRRs in certain subcellular compartments that potentially come in contact with pathogens but not host NAs, the existence of counterregulatory measures that keep endogenous NAs below a certain threshold, and also the specific identification of certain nonself patterns. Here, we review recent advances in the molecular mechanisms of NA recognition by TLRs, RLRs, and the cGAS-STING axis. We highlight the differences in NA-PRR interfaces that confer specificity and selectivity toward an NA ligand, as well as the NA-dependent induced conformational changes required for signal transduction.
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Affiliation(s)
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
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27
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Kaur G, Iyer LM, Burroughs AM, Aravind L. Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans. eLife 2021; 10:70394. [PMID: 34061031 PMCID: PMC8195603 DOI: 10.7554/elife.70394] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/23/2021] [Indexed: 12/12/2022] Open
Abstract
Several homologous domains are shared by eukaryotic immunity and programmed cell-death systems and poorly understood bacterial proteins. Recent studies show these to be components of a network of highly regulated systems connecting apoptotic processes to counter-invader immunity, in prokaryotes with a multicellular habit. However, the provenance of key adaptor domains, namely those of the Death-like and TRADD-N superfamilies, a quintessential feature of metazoan apoptotic systems, remained murky. Here, we use sensitive sequence analysis and comparative genomics methods to identify unambiguous bacterial homologs of the Death-like and TRADD-N superfamilies. We show the former to have arisen as part of a radiation of effector-associated α-helical adaptor domains that likely mediate homotypic interactions bringing together diverse effector and signaling domains in predicted bacterial apoptosis- and counter-invader systems. Similarly, we show that the TRADD-N domain defines a key, widespread signaling bridge that links effector deployment to invader-sensing in multicellular bacterial and metazoan counter-invader systems. TRADD-N domains are expanded in aggregating marine invertebrates and point to distinctive diversifying immune strategies probably directed both at RNA and retroviruses and cellular pathogens that might infect such communities. These TRADD-N and Death-like domains helped identify several new bacterial and metazoan counter-invader systems featuring underappreciated, common functional principles: the use of intracellular invader-sensing lectin-like (NPCBM and FGS), transcription elongation GreA/B-C, glycosyltransferase-4 family, inactive NTPase (serving as nucleic acid receptors), and invader-sensing GTPase switch domains. Finally, these findings point to the possibility of multicellular bacteria-stem metazoan symbiosis in the emergence of the immune/apoptotic systems of the latter.
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Affiliation(s)
- Gurmeet Kaur
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Lakshminarayan M Iyer
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - A Maxwell Burroughs
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - L Aravind
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
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28
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Abstract
Double-stranded RNA (dsRNA) is produced both by virus and host. Its recognition by the melanoma differentiation-associated gene 5 (MDA5) initiates type I interferon responses. How can a host distinguish self-transcripts from nonself to ensure that responses are targeted correctly? Here, I discuss a role for MDA5 helicase in inducing Z-RNA formation by Alu inverted repeat (AIR) elements. These retroelements have highly conserved sequences that favor Z-formation, creating a site for the dsRNA-specific deaminase enzyme ADAR1 to dock. The subsequent editing destabilizes the dsRNA, ending further interaction with MDA5 and terminating innate immune responses directed against self. By enabling self-recognition, Alu retrotransposons, once invaders, now are genetic elements that keep immune responses in check. I also discuss the possible but less characterized roles of the other helicases in modulating innate immune responses, focusing on DExH-box helicase 9 (DHX9) and Mov10 RISC complex RNA helicase (MOV10). DHX9 and MOV10 function differently from MDA5, but still use nucleic acid structure, rather than nucleotide sequence, to define self. Those genetic elements encoding the alternative conformations involved, referred to as flipons, enable helicases to dynamically shape a cell's repertoire of responses. In the case of MDA5, Alu flipons switch off the dsRNA-dependent responses against self. I suggest a number of genetic systems in which to study interactions between flipons and helicases further.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, Charlestown, Massachusetts, United States of America
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29
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ISG15-dependent activation of the sensor MDA5 is antagonized by the SARS-CoV-2 papain-like protease to evade host innate immunity. Nat Microbiol 2021; 6:467-478. [PMID: 33727702 DOI: 10.1038/s41564-021-00884-1] [Citation(s) in RCA: 156] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 02/24/2021] [Indexed: 12/30/2022]
Abstract
Activation of the RIG-I-like receptors, retinoic-acid inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5), establishes an antiviral state by upregulating interferon (IFN)-stimulated genes (ISGs). Among these is ISG15, the mechanistic roles of which in innate immunity still remain enigmatic. In the present study, we report that ISG15 conjugation is essential for antiviral IFN responses mediated by the viral RNA sensor MDA5. ISGylation of the caspase activation and recruitment domains of MDA5 promotes its oligomerization and thereby triggers activation of innate immunity against a range of viruses, including coronaviruses, flaviviruses and picornaviruses. The ISG15-dependent activation of MDA5 is antagonized through direct de-ISGylation mediated by the papain-like protease of SARS-CoV-2, a recently emerged coronavirus that has caused the COVID-19 pandemic. Our work demonstrates a crucial role for ISG15 in the MDA5-mediated antiviral response, and also identifies a key immune evasion mechanism of SARS-CoV-2, which may be targeted for the development of new antivirals and vaccines to combat COVID-19.
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30
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Donsbach P, Klostermeier D. Regulation of RNA helicase activity: principles and examples. Biol Chem 2021; 402:529-559. [PMID: 33583161 DOI: 10.1515/hsz-2020-0362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
RNA helicases are a ubiquitous class of enzymes involved in virtually all processes of RNA metabolism, from transcription, mRNA splicing and export, mRNA translation and RNA transport to RNA degradation. Although ATP-dependent unwinding of RNA duplexes is their hallmark reaction, not all helicases catalyze unwinding in vitro, and some in vivo functions do not depend on duplex unwinding. RNA helicases are divided into different families that share a common helicase core with a set of helicase signature motives. The core provides the active site for ATP hydrolysis, a binding site for non-sequence-specific interaction with RNA, and in many cases a basal unwinding activity. Its activity is often regulated by flanking domains, by interaction partners, or by self-association. In this review, we summarize the regulatory mechanisms that modulate the activities of the helicase core. Case studies on selected helicases with functions in translation, splicing, and RNA sensing illustrate the various modes and layers of regulation in time and space that harness the helicase core for a wide spectrum of cellular tasks.
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Affiliation(s)
- Pascal Donsbach
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
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31
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Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S. Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Mol Cell 2021; 81:599-613.e8. [PMID: 33373584 PMCID: PMC8183676 DOI: 10.1016/j.molcel.2020.11.047] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/17/2020] [Accepted: 11/23/2020] [Indexed: 01/28/2023]
Abstract
RNA helicases and E3 ubiquitin ligases mediate many critical functions in cells, but their actions have largely been studied in distinct biological contexts. Here, we uncover evolutionarily conserved rules of engagement between RNA helicases and tripartite motif (TRIM) E3 ligases that lead to their functional coordination in vertebrate innate immunity. Using cryoelectron microscopy and biochemistry, we show that RIG-I-like receptors (RLRs), viral RNA receptors with helicase domains, interact with their cognate TRIM/TRIM-like E3 ligases through similar epitopes in the helicase domains. Their interactions are avidity driven, restricting the actions of TRIM/TRIM-like proteins and consequent immune activation to RLR multimers. Mass spectrometry and phylogeny-guided biochemical analyses further reveal that similar rules of engagement may apply to diverse RNA helicases and TRIM/TRIM-like proteins. Our analyses suggest not only conserved substrates for TRIM proteins but also, unexpectedly, deep evolutionary connections between TRIM proteins and RNA helicases, linking ubiquitin and RNA biology throughout animal evolution.
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MESH Headings
- Cryoelectron Microscopy
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/metabolism
- DEAD Box Protein 58/ultrastructure
- Epitopes
- Evolution, Molecular
- HEK293 Cells
- Humans
- Immunity, Innate
- Interferon-Induced Helicase, IFIH1/genetics
- Interferon-Induced Helicase, IFIH1/metabolism
- Interferon-Induced Helicase, IFIH1/ultrastructure
- Models, Molecular
- Phylogeny
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Interaction Domains and Motifs
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Receptors, Immunologic/ultrastructure
- Tripartite Motif Proteins/genetics
- Tripartite Motif Proteins/metabolism
- Tripartite Motif Proteins/ultrastructure
- Ubiquitin-Protein Ligases/genetics
- Ubiquitin-Protein Ligases/metabolism
- Ubiquitin-Protein Ligases/ultrastructure
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Affiliation(s)
- Kazuki Kato
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sadeem Ahmad
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xin Mu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sehoon Park
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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32
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Duic I, Tadakuma H, Harada Y, Yamaue R, Deguchi K, Suzuki Y, Yoshimura SH, Kato H, Takeyasu K, Fujita T. Viral RNA recognition by LGP2 and MDA5, and activation of signaling through step-by-step conformational changes. Nucleic Acids Res 2021; 48:11664-11674. [PMID: 33137199 PMCID: PMC7672446 DOI: 10.1093/nar/gkaa935] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 10/03/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
Cytoplasmic RIG-I-like receptor (RLR) proteins in mammalian cells recognize viral RNA and initiate an antiviral response that results in IFN-β induction. Melanoma differentiation-associated protein 5 (MDA5) forms fibers along viral dsRNA and propagates an antiviral response via a signaling domain, the tandem CARD. The most enigmatic RLR, laboratory of genetics and physiology (LGP2), lacks the signaling domain but functions in viral sensing through cooperation with MDA5. However, it remains unclear how LGP2 coordinates fiber formation and subsequent MDA5 activation. We utilized biochemical and biophysical approaches to observe fiber formation and the conformation of MDA5. LGP2 facilitated MDA5 fiber assembly. LGP2 was incorporated into the fibers with an average inter-molecular distance of 32 nm, suggesting the formation of hetero-oligomers with MDA5. Furthermore, limited protease digestion revealed that LGP2 induces significant conformational changes on MDA5, promoting exposure of its CARDs. Although the fibers were efficiently dissociated by ATP hydrolysis, MDA5 maintained its active conformation to participate in downstream signaling. Our study demonstrated the coordinated actions of LGP2 and MDA5, where LGP2 acts as an MDA5 nucleator and requisite partner in the conversion of MDA5 to an active conformation. We revealed a mechanistic basis for LGP2-mediated regulation of MDA5 antiviral innate immune responses.
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Affiliation(s)
- Ivana Duic
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8397, Japan
| | - Hisashi Tadakuma
- Division of Protein Chemistry, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yoshie Harada
- Division of Protein Chemistry, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Ryo Yamaue
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8397, Japan
| | - Katashi Deguchi
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Yuki Suzuki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Shige H Yoshimura
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroki Kato
- Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8397, Japan.,Institute for Cardiovascular Immunology, University Hospital Bonn, University of Bonn, Bonn 53127, Germany
| | - Kunio Takeyasu
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - Takashi Fujita
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Molecular Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8397, Japan.,Institute for Cardiovascular Immunology, University Hospital Bonn, University of Bonn, Bonn 53127, Germany
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33
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Liu G, Lee JH, Parker ZM, Acharya D, Chiang JJ, van Gent M, Riedl W, Davis-Gardner ME, Wies E, Chiang C, Gack MU. ISG15-dependent Activation of the RNA Sensor MDA5 and its Antagonism by the SARS-CoV-2 papain-like protease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33140045 PMCID: PMC7605552 DOI: 10.1101/2020.10.26.356048] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Activation of the RIG-I-like receptors, RIG-I and MDA5, establishes an antiviral state by upregulating interferon (IFN)-stimulated genes (ISGs). Among these is ISG15 whose mechanistic roles in innate immunity still remain enigmatic. Here we report that ISGylation is essential for antiviral IFN responses mediated by the viral RNA sensor MDA5. ISG15 conjugation to the caspase activation and recruitment domains of MDA5 promotes the formation of higher-order assemblies of MDA5 and thereby triggers activation of innate immunity against a range of viruses including coronaviruses, flaviviruses and picornaviruses. The ISG15-dependent activation of MDA5 is antagonized through direct de-ISGylation mediated by the papain-like protease (PLpro) of SARS-CoV-2, a recently emerged coronavirus that causes the COVID-19 pandemic. Our work demonstrates a crucial role for ISG15 in the MDA5-mediated antiviral response, and also identifies a novel immune evasion mechanism of SARS-CoV-2, which may be targeted for the development of new antivirals and vaccines to combat COVID-19.
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Affiliation(s)
- GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Jung-Hyun Lee
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Zachary M Parker
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Dhiraj Acharya
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Jessica J Chiang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Michiel van Gent
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - William Riedl
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Effi Wies
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - Cindy Chiang
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic, FL 34987, USA.,Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
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Uehata T, Takeuchi O. RNA Recognition and Immunity-Innate Immune Sensing and Its Posttranscriptional Regulation Mechanisms. Cells 2020; 9:cells9071701. [PMID: 32708595 PMCID: PMC7407594 DOI: 10.3390/cells9071701] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/13/2022] Open
Abstract
RNA acts as an immunostimulatory molecule in the innate immune system to activate nucleic acid sensors. It functions as an intermediate, conveying genetic information to control inflammatory responses. A key mechanism for RNA sensing is discriminating self from non-self nucleic acids to initiate antiviral responses reliably, including the expression of type I interferon (IFN) and IFN-stimulated genes. Another important aspect of the RNA-mediated inflammatory response is posttranscriptional regulation of gene expression, where RNA-binding proteins (RBPs) have essential roles in various RNA metabolisms, including splicing, nuclear export, modification, and translation and mRNA degradation. Recent evidence suggests that the control of mRNA stability is closely involved in signal transduction and orchestrates immune responses. In this study, we review the current understanding of how RNA is sensed by host RNA sensing machinery and discuss self/non-self-discrimination in innate immunity focusing on mammalian species. Finally, we discuss how posttranscriptional regulation by RBPs shape immune reactions.
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35
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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: 21] [Impact Index Per Article: 5.3] [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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36
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Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 2020; 25:molecules25122881. [PMID: 32585844 PMCID: PMC7357161 DOI: 10.3390/molecules25122881] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.
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Rehwinkel J, Gack MU. RIG-I-like receptors: their regulation and roles in RNA sensing. Nat Rev Immunol 2020; 20:537-551. [PMID: 32203325 PMCID: PMC7094958 DOI: 10.1038/s41577-020-0288-3] [Citation(s) in RCA: 768] [Impact Index Per Article: 192.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 02/06/2023]
Abstract
Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are key sensors of virus infection, mediating the transcriptional induction of type I interferons and other genes that collectively establish an antiviral host response. Recent studies have revealed that both viral and host-derived RNAs can trigger RLR activation; this can lead to an effective antiviral response but also immunopathology if RLR activities are uncontrolled. In this Review, we discuss recent advances in our understanding of the types of RNA sensed by RLRs in the contexts of viral infection, malignancies and autoimmune diseases. We further describe how the activity of RLRs is controlled by host regulatory mechanisms, including RLR-interacting proteins, post-translational modifications and non-coding RNAs. Finally, we discuss key outstanding questions in the RLR field, including how our knowledge of RLR biology could be translated into new therapeutics. The RNA-sensing retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are important inducers of type I interferons and other antiviral immune mediators. Here, Jan Rehwinkel and Michaela Gack explain how members of the RLR family are regulated and reflect on the importance of the RLRs in viral infection, autoimmunity and cancer.
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Affiliation(s)
- Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
| | - Michaela U Gack
- Department of Microbiology, The University of Chicago, Chicago, IL, USA.
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Jones M, Beuron F, Borg A, Nans A, Earl CP, Briggs DC, Snijders AP, Bowles M, Morris EP, Linch M, McDonald NQ. Cryo-EM structures of the XPF-ERCC1 endonuclease reveal how DNA-junction engagement disrupts an auto-inhibited conformation. Nat Commun 2020; 11:1120. [PMID: 32111838 PMCID: PMC7048804 DOI: 10.1038/s41467-020-14856-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 02/05/2020] [Indexed: 12/31/2022] Open
Abstract
The structure-specific endonuclease XPF-ERCC1 participates in multiple DNA damage repair pathways including nucleotide excision repair (NER) and inter-strand crosslink repair (ICLR). How XPF-ERCC1 is catalytically activated by DNA junction substrates is not currently understood. Here we report cryo-electron microscopy structures of both DNA-free and DNA-bound human XPF-ERCC1. DNA-free XPF-ERCC1 adopts an auto-inhibited conformation in which the XPF helical domain masks the ERCC1 (HhH)2 domain and restricts access to the XPF catalytic site. DNA junction engagement releases the ERCC1 (HhH)2 domain to couple with the XPF-ERCC1 nuclease/nuclease-like domains. Structure-function data indicate xeroderma pigmentosum patient mutations frequently compromise the structural integrity of XPF-ERCC1. Fanconi anaemia patient mutations in XPF often display substantial in-vitro activity but are resistant to activation by ICLR recruitment factor SLX4. Our data provide insights into XPF-ERCC1 architecture and catalytic activation.
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Affiliation(s)
- Morgan Jones
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT, London, UK
| | - Fabienne Beuron
- Structural Electron Microscopy, The Institute of Cancer Research, SW7 3RP, London, UK
| | - Aaron Borg
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, NW1 1AT, London, UK
| | - Andrea Nans
- Structural Biology of Cells and Viruses, Francis Crick Institute, NW1 1AT, London, UK
| | - Christopher P Earl
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT, London, UK
| | - David C Briggs
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT, London, UK
| | - Ambrosius P Snijders
- Mass Spectrometry Science Technology Platform, Francis Crick Institute, NW1 1AT, London, UK
| | - Maureen Bowles
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT, London, UK
| | - Edward P Morris
- Structural Electron Microscopy, The Institute of Cancer Research, SW7 3RP, London, UK
| | - Mark Linch
- Department of Oncology, University College London Cancer Institute, WC1E 6AG, London, England, UK
| | - Neil Q McDonald
- Signalling and Structural Biology Laboratory, Francis Crick Institute, NW1 1AT, London, UK.
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK.
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Zerbe CM, Mouser DJ, Cole JL. Oligomerization of RIG-I and MDA5 2CARD domains. Protein Sci 2020; 29:521-526. [PMID: 31697400 PMCID: PMC6954692 DOI: 10.1002/pro.3776] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/17/2019] [Accepted: 11/01/2019] [Indexed: 12/25/2022]
Abstract
The innate immune system is the first line of defense against invading pathogens. The retinoic acid-inducible gene I (RIG-I) like receptors (RLRs), RIG-I and melanoma differentiation-associated protein 5 (MDA5), are critical for host recognition of viral RNAs. These receptors contain a pair of N-terminal tandem caspase activation and recruitment domains (2CARD), an SF2 helicase core domain, and a C-terminal regulatory domain. Upon RLR activation, 2CARD associates with the CARD domain of MAVS, leading to the oligomerization of MAVS, downstream signaling and interferon induction. Unanchored K63-linked polyubiquitin chains (polyUb) interacts with the 2CARD domain, and in the case of RIG-I, induce tetramer formation. However, the nature of the MDA5 2CARD signaling complex is not known. We have used sedimentation velocity analytical ultracentrifugation to compare MDA5 2CARD and RIG-I 2CARD binding to polyUb and to characterize the assembly of MDA5 2CARD oligomers in the absence of polyUb. Multi-signal sedimentation velocity analysis indicates that Ub4 binds to RIG-I 2CARD with a 3:4 stoichiometry and cooperatively induces formation of an RIG-I 2CARD tetramer. In contrast, Ub4 and Ub7 interact with MDA5 2CARD weakly and form complexes with 1:1 and 2:1 stoichiometries but do not induce 2CARD oligomerization. In the absence of polyUb, MDA5 2CARD self-associates to forms large oligomers in a concentration-dependent manner. Thus, RIG-I and MDA5 2CARD assembly processes are distinct. MDA5 2CARD concentration-dependent self-association, rather than polyUb binding, drives oligomerization and MDA5 2CARD forms oligomers larger than tetramer. We propose a mechanism where MDA5 2CARD oligomers, rather than a stable tetramer, function to nucleate MAVS polymerization.
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Affiliation(s)
- Cassie M. Zerbe
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticut
| | - David J. Mouser
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticut
| | - James L. Cole
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticut
- Department of ChemistryUniversity of ConnecticutStorrsConnecticut
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40
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Jain M, Jantsch MF, Licht K. The Editor's I on Disease Development. Trends Genet 2019; 35:903-913. [PMID: 31648814 DOI: 10.1016/j.tig.2019.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing of RNA leads to deamination of adenosine to inosine. Inosine is interpreted as guanosine by the cellular machinery, thus altering the coding, folding, splicing, or transport of transcripts. A-to-I editing is tightly regulated. Altered editing has severe consequences for human health and can cause interferonopathies, neurological disorders, and cardiovascular disease, as well as impacting on cancer progression. ADAR1-mediated RNA editing plays an important role in antiviral immunity and is essential for distinguishing between endogenous and viral RNA, thereby preventing autoimmune disorders. Interestingly, A-to-I editing can be used not only to correct genomic mutations at the RNA level but also to modulate tumor antigenicity with large therapeutic potential. We highlight recent developments in the field, focusing on cancer and other human diseases.
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Affiliation(s)
- Mamta Jain
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
| | - Michael F Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria.
| | - Konstantin Licht
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria
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41
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Streicher F, Jouvenet N. Stimulation of Innate Immunity by Host and Viral RNAs. Trends Immunol 2019; 40:1134-1148. [PMID: 31735513 DOI: 10.1016/j.it.2019.10.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/15/2019] [Accepted: 10/18/2019] [Indexed: 12/24/2022]
Abstract
The interferon (IFN) response, a major vertebrate defense mechanism against viral infections, is initiated by RIG-I-like receptor (RLR)-mediated recognition of viral replicative intermediates in the cytosol. RLR purification methods coupled to RNA sequencing have recently led to the characterization of viral nucleic acid features recognized by RLRs in infected cells. This work revealed that some cellular RNAs can bind to RLRs and stimulate the IFN response. We provide an overview of self and non-self RNAs that activate innate immunity, and discuss the cellular dysregulation that allows recognition of cellular RNAs by RLRs, including RNA mislocalization and downregulation of RNA-shielding proteins. These discussions are relevant because manipulating RLR activation presents opportunities for treating viral infections and autoimmune disorders.
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Affiliation(s)
- Felix Streicher
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3569, Paris, France; Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Nolwenn Jouvenet
- Unité de Génomique Virale et Vaccination, Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 3569, Paris, France.
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42
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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: 214] [Impact Index Per Article: 42.8] [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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43
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Mechanisms of Non-segmented Negative Sense RNA Viral Antagonism of Host RIG-I-Like Receptors. J Mol Biol 2019; 431:4281-4289. [PMID: 31202887 DOI: 10.1016/j.jmb.2019.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/29/2019] [Accepted: 06/05/2019] [Indexed: 12/25/2022]
Abstract
The pattern recognition receptors RIG-I-like receptors (RLRs) are critical molecules for cytosolic viral recognition and for subsequent activation of type I interferon production. The interferon signaling pathway plays a key role in viral detection and generating antiviral responses. Among the many pathogens, the non-segmented negative sense RNA viruses target the RLR pathway using a variety of mechanisms. Here, I review the current state of knowledge on the molecular mechanisms that allow non-segmented negative sense RNA virus recognition and antagonism of RLRs.
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Zhu XB, Zhuo LY, Yue M, Liu M, Zang F, Fan HZ, Wu JJ, Xia XS, Zhang AM, Yu RB, Huang P. Genetic variants in IFIH1 and DDX58 influence hepatitis C virus clearance in Chinese Han population. J Med Virol 2019; 91:1097-1103. [PMID: 30633820 DOI: 10.1002/jmv.25398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/26/2018] [Accepted: 01/05/2019] [Indexed: 12/17/2022]
Abstract
AIMS To investigate the association between two RIG-I-like receptor gene polymorphisms and hepatitis C virus (HCV) infection in Chinese Han population. METHODS The current study genotyped two selected SNPs (IFIH1 rs3747517 and DDX58 rs9695310) using TaqMan allelic discrimination assay to assess their association with the susceptibility and clinical outcome of HCV infection among 3065 participants (1545 non-HCV infection individuals, 568 spontaneous HCV clearance cases, and 952 persistent infection patients). RESULTS IFIH1 rs3747517 (dominant model: Adjusted odds ratio [OR] = 1.34, 95% confidence interval [CI] = 1.07-1.68; P = 0.009) and DDX58 rs9695310 (dominant model: Adjusted OR = 1.43, 95% CI = 1.15-1.78; P = 0.001) were associated with chronic hepatitis C (CHC). And the risk of CHC increased when people were carrying more unfavorable rs3747517-GA/AA and rs9695310-GC/CC genotypes from zero to two with the chronic rates of 56.72%, 59.38%, and 69.01%, respectively (Ptrend < 0.001). CONCLUSION Genetic variations at IFIH1 rs3747517 and DDX58 rs9695310 were independent predictors of chronic hepatitis C in Chinese Han population.
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Affiliation(s)
- Xiao-Bo Zhu
- Department of Pharmacy, The People's Hospital of Danyang, Danyang, China
| | - Ling-Yun Zhuo
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ming Yue
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mei Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feng Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hao-Zhi Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jing-Jing Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xue-Shan Xia
- Department of Bioengineering, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - A-Mei Zhang
- Department of Bioengineering, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Rong-Bin Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
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45
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Kasumba DM, Grandvaux N. Therapeutic Targeting of RIG-I and MDA5 Might Not Lead to the Same Rome. Trends Pharmacol Sci 2019; 40:116-127. [PMID: 30606502 PMCID: PMC7112877 DOI: 10.1016/j.tips.2018.12.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 12/12/2022]
Abstract
RIG-I and MDA5 receptors are key sensors of pathogen-associated molecular pattern (PAMP)-containing viral RNA and transduce downstream signals to activate an antiviral and immunomodulatory response. Fifteen years of research have put them at the center of an ongoing hunt for novel pharmacological pan-antivirals, vaccine adjuvants, and antitumor strategies. Current knowledge testifies to the redundant, but also distinct, functions mediated by RIG-I and MDA5, opening opportunities for the use of specific and potent nucleic acid agonists. We critically discuss the evidence and remaining knowledge gaps that have an impact on the choice and design of optimal RNA ligands to achieve an appropriate immunostimulatory response, with limited adverse effects, for prophylactic and therapeutic interventions against viruses and cancer in humans.
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Affiliation(s)
- Dacquin M. Kasumba
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC, Canada,Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Nathalie Grandvaux
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, QC, Canada; Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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An integrative protocol for the structure determination of the mouse ASC-PYD filament. Methods Enzymol 2019; 625:205-222. [DOI: 10.1016/bs.mie.2019.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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