1
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Rodríguez-Salazar CA, van Tol S, Mailhot O, Gonzalez-Orozco M, Galdino GT, Warren AN, Teruel N, Behera P, Afreen KS, Zhang L, Juelich TL, Smith JK, Zylber MI, Freiberg AN, Najmanovich RJ, Giraldo MI, Rajsbaum R. Ebola virus VP35 interacts non-covalently with ubiquitin chains to promote viral replication. PLoS Biol 2024; 22:e3002544. [PMID: 38422166 PMCID: PMC10942258 DOI: 10.1371/journal.pbio.3002544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/15/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Ebolavirus (EBOV) belongs to a family of highly pathogenic viruses that cause severe hemorrhagic fever in humans. EBOV replication requires the activity of the viral polymerase complex, which includes the cofactor and Interferon antagonist VP35. We previously showed that the covalent ubiquitination of VP35 promotes virus replication by regulating interactions with the polymerase complex. In addition, VP35 can also interact non-covalently with ubiquitin (Ub); however, the function of this interaction is unknown. Here, we report that VP35 interacts with free (unanchored) K63-linked polyUb chains. Ectopic expression of Isopeptidase T (USP5), which is known to degrade unanchored polyUb chains, reduced VP35 association with Ub and correlated with diminished polymerase activity in a minigenome assay. Using computational methods, we modeled the VP35-Ub non-covalent interacting complex, identified the VP35-Ub interacting surface, and tested mutations to validate the interface. Docking simulations identified chemical compounds that can block VP35-Ub interactions leading to reduced viral polymerase activity. Treatment with the compounds reduced replication of infectious EBOV in cells and in vivo in a mouse model. In conclusion, we identified a novel role of unanchored polyUb in regulating Ebola virus polymerase function and discovered compounds that have promising anti-Ebola virus activity.
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Affiliation(s)
- Carlos A. Rodríguez-Salazar
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander von Humboldt, Armenia, Colombia
| | - Sarah van Tol
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Olivier Mailhot
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Maria Gonzalez-Orozco
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Gabriel T. Galdino
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Abbey N. Warren
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| | - Natalia Teruel
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Padmanava Behera
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| | - Kazi Sabrina Afreen
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
| | - Lihong Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Terry L. Juelich
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jennifer K. Smith
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - María Inés Zylber
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Alexander N. Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rafael J. Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Maria I. Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey, United States of America
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Li Y, Gao J, Wang D, Liu Z, Zhang H. TRIM4 Expression Related to Malignant Progression and Cisplatin Resistance in Osteosarcoma. Appl Biochem Biotechnol 2024; 196:233-244. [PMID: 37115387 DOI: 10.1007/s12010-023-04551-5] [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] [Accepted: 04/18/2023] [Indexed: 04/29/2023]
Abstract
Osteosarcoma (OS) is a high-grade intraosseous malignancy. Twenty to thirty percent of OS patients react poorly to standard therapy with a combination of surgical resection and chemotherapy. It is necessary to find molecules that play an important role in this. This study explored the role of TRIM4 in OS chemotherapy sensitivity and malignant progression. The expression of TRIM4 in OS tissues and cells was examined by RT-qPCR, immunohistochemical staining, and western blot. Specific siRNA was transfected into U2-OS and SAOS2 cells to target TRIM4. Cell biological behavior was examined by CCK-8, Transwell, and flow cytometry experiments. Cisplatin-resistant SAOS2 (SAOS2-Cis-R) cells were established, and the effect of TRIM4 expression on the cisplatin response of SAOS2 cells was tested. Knockdown of TRIM4 significantly inhibited the proliferation, migration, and invasion of U2-OS and SAOS2 cells and induced apoptosis. TRIM4 expression was significantly higher in chemotherapy-resistant OS tissues compared to chemotherapy-sensitive OS tissues. Furthermore, the expression of TRIM4 in SAOS2-Cis-R cells was significantly increased compared to parental SAOS2 cells. Moreover, overexpression of TRIM4 enhanced cisplatin resistance in parental SAOS2 cells, while the downregulation of TRIM4 expression enhanced cisplatin sensitivity of SAOS2-Cis-R cells. High TRIM4 expression might be associated with malignant progression and poor response to chemotherapy response of OS. Targeting TRIM4 may be beneficial for OS treatment or combination therapy.
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Affiliation(s)
- Yan Li
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China
| | - Jie Gao
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China
| | - Dong Wang
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China
| | - Zijin Liu
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China
| | - Huawu Zhang
- Department of Joint Surgery, Shandong Second Provincial General Hospital, No.4 Duanxing West Road, Huaiyin District, Jinan, 250022, People's Republic of China.
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3
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Wang W, Götte B, Guo R, Pyle AM. The E3 ligase Riplet promotes RIG-I signaling independent of RIG-I oligomerization. Nat Commun 2023; 14:7308. [PMID: 37951994 PMCID: PMC10640585 DOI: 10.1038/s41467-023-42982-0] [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: 03/27/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
RIG-I is an essential innate immune receptor that responds to infection by RNA viruses. The RIG-I signaling cascade is mediated by a series of post-translational modifications, the most important of which is ubiquitination of the RIG-I Caspase Recruitment Domains (CARDs) by E3 ligase Riplet. This is required for interaction between RIG-I and its downstream adapter protein MAVS, but the mechanism of action remains unclear. Here we show that Riplet is required for RIG-I signaling in the presence of both short and long dsRNAs, establishing that Riplet activation does not depend upon RIG-I filament formation on long dsRNAs. Likewise, quantitative Riplet-RIG-I affinity measurements establish that Riplet interacts with RIG-I regardless of whether the receptor is bound to RNA. To understand this, we solved high-resolution cryo-EM structures of RIG-I/RNA/Riplet complexes, revealing molecular interfaces that control Riplet-mediated activation and enabling the formulation of a unified model for the role of Riplet in signaling.
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Affiliation(s)
- Wenshuai Wang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA
| | - Benjamin Götte
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Rong Guo
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA.
- Howard Hughes Medical Institute, Yale University, New Haven, CT, 06520, USA.
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4
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Rodríguez-Salazar CA, van Tol S, Mailhot O, Galdino G, Teruel N, Zhang L, Warren AN, González-Orozco M, Freiberg AN, Najmanovich RJ, Giraldo MI, Rajsbaum R. Ebola Virus VP35 Interacts Non-Covalently with Ubiquitin Chains to Promote Viral Replication Creating New Therapeutic Opportunities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549057. [PMID: 37503276 PMCID: PMC10369991 DOI: 10.1101/2023.07.14.549057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ebolavirus (EBOV) belongs to a family of highly pathogenic viruses that cause severe hemorrhagic fever in humans. EBOV replication requires the activity of the viral polymerase complex, which includes the co-factor and Interferon antagonist VP35. We previously showed that the covalent ubiquitination of VP35 promotes virus replication by regulating interactions with the polymerase complex. In addition, VP35 can also interact non-covalently with ubiquitin (Ub); however, the function of this interaction is unknown. Here, we report that VP35 interacts with free (unanchored) K63-linked polyUb chains. Ectopic expression of Isopeptidase T (USP5), which is known to degrade unanchored polyUb chains, reduced VP35 association with Ub and correlated with diminished polymerase activity in a minigenome assay. Using computational methods, we modeled the VP35-Ub non-covalent interacting complex, identified the VP35-Ub interacting surface and tested mutations to validate the interface. Docking simulations identified chemical compounds that can block VP35-Ub interactions leading to reduced viral polymerase activity that correlated with reduced replication of infectious EBOV. In conclusion, we identified a novel role of unanchored polyUb in regulating Ebola virus polymerase function and discovered compounds that have promising anti-Ebola virus activity.
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Affiliation(s)
- Carlos A. Rodríguez-Salazar
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
- Molecular Biology and Virology Laboratory, Faculty of Medicine and Health Sciences, Corporación Universitaria Empresarial Alexander von Humboldt, Armenia 630003, Colombia
| | - Sarah van Tol
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Olivier Mailhot
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Gabriel Galdino
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Natalia Teruel
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - Lihong Zhang
- Department of Pathology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Abbey N. Warren
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey 07103
| | - María González-Orozco
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Alexander N. Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Rafael J. Najmanovich
- Department of Pharmacology and Physiology, Faculty of Medicine, Université de Montréal, Montreal, Canada
| | - María I. Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
| | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston 77555, Texas, USA
- Center for Virus-Host-Innate Immunity and Department of Medicine; Rutgers Biomedical and Health Sciences, Institute for Infectious and Inflammatory Diseases, Rutgers University, Newark, New Jersey 07103
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5
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Avian Influenza NS1 Proteins Inhibit Human, but Not Duck, RIG-I Ubiquitination and Interferon Signaling. J Virol 2022; 96:e0077622. [PMID: 36069546 PMCID: PMC9517716 DOI: 10.1128/jvi.00776-22] [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: 12/12/2022] Open
Abstract
The nonstructural protein 1 (NS1) of influenza A viruses is an important virulence factor that controls host cell immune responses. In human cells, NS1 proteins inhibit the induction of type I interferon by several mechanisms, including potentially, by preventing the activation of the retinoic acid-inducible gene I (RIG-I) receptor by the ubiquitin ligase tripartite motif-containing protein 25 (TRIM25). It is unclear whether the inhibition of human TRIM25 is a universal function of all influenza A NS1 proteins or is strain dependent. It is also unclear if NS1 proteins similarly target the TRIM25 of mallard ducks, a natural reservoir host of avian influenza viruses with a long coevolutionary history and unique disease dynamics. To answer these questions, we compared the ability of five different NS1 proteins to interact with human and duck TRIM25 using coimmunoprecipitation and microscopy and assessed the consequence of this on RIG-I ubiquitination and signaling in both species. We show that NS1 proteins from low-pathogenic and highly pathogenic avian influenza viruses potently inhibit RIG-I ubiquitination and reduce interferon promoter activity and interferon-beta protein secretion in transfected human cells, while the NS1 of the mouse-adapted PR8 strain does not. However, all the NS1 proteins, when cloned into recombinant viruses, suppress interferon in infected alveolar cells. In contrast, avian NS1 proteins do not suppress duck RIG-I ubiquitination and interferon promoter activity, despite interacting with duck TRIM25. IMPORTANCE Influenza A viruses are a major cause of human and animal disease. Periodically, avian influenza viruses from wild waterfowl, such as ducks, pass through intermediate agricultural hosts and emerge into the human population as zoonotic diseases with high mortality rates and epidemic potential. Because of their coevolution with influenza A viruses, ducks are uniquely resistant to influenza disease compared to other birds, animals, and humans. Here, we investigate a mechanism of influenza A virus interference in an important antiviral signaling pathway that is orthologous in humans and ducks. We show that NS1 proteins from four avian influenza strains can block the coactivation and signaling of the human RIG-I antiviral receptor, while none block the coactivation and signaling of duck RIG-I. Understanding host-pathogen dynamics in the natural reservoir will contribute to our understanding of viral disease mechanisms, viral evolution, and the pressures that drive it, which benefits global surveillance and outbreak prevention.
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6
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Hage A, Bharaj P, van Tol S, Giraldo MI, Gonzalez-Orozco M, Valerdi KM, Warren AN, Aguilera-Aguirre L, Xie X, Widen SG, Moulton HM, Lee B, Johnson JR, Krogan NJ, García-Sastre A, Shi PY, Freiberg AN, Rajsbaum R. The RNA helicase DHX16 recognizes specific viral RNA to trigger RIG-I-dependent innate antiviral immunity. Cell Rep 2022; 38:110434. [PMID: 35263596 PMCID: PMC8903195 DOI: 10.1016/j.celrep.2022.110434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 11/02/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Type I interferons (IFN-I) are essential to establish antiviral innate immunity. Unanchored (or free) polyubiquitin (poly-Ub) has been shown to regulate IFN-I responses. However, few unanchored poly-Ub interactors are known. To identify factors regulated by unanchored poly-Ub in a physiological setting, we developed an approach to isolate unanchored poly-Ub from lung tissue. We identified the RNA helicase DHX16 as a potential pattern recognition receptor (PRR). Silencing of DHX16 in cells and in vivo diminished IFN-I responses against influenza virus. These effects extended to members of other virus families, including Zika and SARS-CoV-2. DHX16-dependent IFN-I production requires RIG-I and unanchored K48-poly-Ub synthesized by the E3-Ub ligase TRIM6. DHX16 recognizes a signal in influenza RNA segments that undergo splicing and requires its RNA helicase motif for direct, high-affinity interactions with specific viral RNAs. Our study establishes DHX16 as a PRR that partners with RIG-I for optimal activation of antiviral immunity requiring unanchored poly-Ub.
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Affiliation(s)
- Adam Hage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Preeti Bharaj
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sarah van Tol
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Maria I Giraldo
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Maria Gonzalez-Orozco
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Karl M Valerdi
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Abbey N Warren
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Leopoldo Aguilera-Aguirre
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hong M Moulton
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR 97331, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), University of California at San Francisco, San Francisco, CA 94158, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alexander N Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA; Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA.
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7
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How Influenza A Virus NS1 Deals with the Ubiquitin System to Evade Innate Immunity. Viruses 2021; 13:v13112309. [PMID: 34835115 PMCID: PMC8619935 DOI: 10.3390/v13112309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/14/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
Ubiquitination is a post-translational modification regulating critical cellular processes such as protein degradation, trafficking and signaling pathways, including activation of the innate immune response. Therefore, viruses, and particularly influenza A virus (IAV), have evolved different mechanisms to counteract this system to perform proper infection. Among IAV proteins, the non-structural protein NS1 is shown to be one of the main virulence factors involved in these viral hijackings. NS1 is notably able to inhibit the host's antiviral response through the perturbation of ubiquitination in different ways, as discussed in this review.
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8
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Atkinson SC, Heaton SM, Audsley MD, Kleifeld O, Borg NA. TRIM25 and DEAD-Box RNA Helicase DDX3X Cooperate to Regulate RIG-I-Mediated Antiviral Immunity. Int J Mol Sci 2021; 22:9094. [PMID: 34445801 PMCID: PMC8396550 DOI: 10.3390/ijms22169094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022] Open
Abstract
The cytoplasmic retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) initiate interferon (IFN) production and antiviral gene expression in response to RNA virus infection. Consequently, RLR signalling is tightly regulated by both host and viral factors. Tripartite motif protein 25 (TRIM25) is an E3 ligase that ubiquitinates multiple substrates within the RLR signalling cascade, playing both ubiquitination-dependent and -independent roles in RIG-I-mediated IFN induction. However, additional regulatory roles are emerging. Here, we show a novel interaction between TRIM25 and another protein in the RLR pathway that is essential for type I IFN induction, DEAD-box helicase 3X (DDX3X). In vitro assays and knockdown studies reveal that TRIM25 ubiquitinates DDX3X at lysine 55 (K55) and that TRIM25 and DDX3X cooperatively enhance IFNB1 induction following RIG-I activation, but the latter is independent of TRIM25's catalytic activity. Furthermore, we found that the influenza A virus non-structural protein 1 (NS1) disrupts the TRIM25:DDX3X interaction, abrogating both TRIM25-mediated ubiquitination of DDX3X and cooperative activation of the IFNB1 promoter. Thus, our results reveal a new interplay between two RLR-host proteins that cooperatively enhance IFN-β production. We also uncover a new and further mechanism by which influenza A virus NS1 suppresses host antiviral defence.
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Affiliation(s)
- Sarah C. Atkinson
- Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia; (S.C.A.); (M.D.A.)
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia;
| | - Steven M. Heaton
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia;
| | - Michelle D. Audsley
- Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia; (S.C.A.); (M.D.A.)
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia;
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel;
| | - Natalie A. Borg
- Immunity and Immune Evasion Laboratory, Chronic Infectious and Inflammatory Diseases Research, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia; (S.C.A.); (M.D.A.)
- Infection & Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia;
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9
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Xian H, Huang W, Sun T, Yang S, Zhang C, Wang J, Zhang Y, Cui J. Unanchored ubiquitin chain sustains RIG-I-induced interferon-I activation and controls selective gene expression. Sci Bull (Beijing) 2021; 66:794-802. [PMID: 36654136 DOI: 10.1016/j.scib.2020.11.003] [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: 08/26/2020] [Revised: 09/21/2020] [Accepted: 10/23/2020] [Indexed: 01/20/2023]
Abstract
Ubiquitination plays a crucial role in retinoic acid-inducible gene I (RIG-I)-induced antiviral responses. However, the precise regulatory mechanisms of RIG-I activity mediated by conjugated and unanchored ubiquitin chains remain to be determined. In this study, we discovered that T55 of RIG-I was required for its binding ability for the unanchored ubiquitin chains. Experimental and mathematical analysis showed that unanchored ubiquitin chains associated with RIG-I were essential for sustained activation of type I interferon (IFN) signaling. Transcriptomics study revealed that the binding of RIG-I with unanchored ubiquitin chains additionally regulated the expression of a subset of metabolic and cell fate decision genes. Moreover, we found that ubiquitin-specific peptidase 21 (USP21) and USP3 deubiquitinate conjugated and unanchored ubiquitin chains on RIG-I respectively. Taken together, characterization of the regulation mode and functions of conjugated ubiquitination and the unconjugated ubiquitin chain-binding of RIG-I may provide means to fine-tune RIG-I-mediated type I IFN signaling.
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Affiliation(s)
- Huifang Xian
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Wanming Huang
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Tingzhe Sun
- School of Life Sciences, Anqing Normal University, Anqing 246133, China
| | - Shuai Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chuanxia Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jun Wang
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yuxia Zhang
- Department of Gastroenterology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Jun Cui
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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10
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Hay-McCullough E, Morrison J. Contributions of Ubiquitin and Ubiquitination to Flaviviral Antagonism of Type I IFN. Viruses 2021; 13:v13050763. [PMID: 33925296 PMCID: PMC8145522 DOI: 10.3390/v13050763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022] Open
Abstract
Flaviviruses implement a broad range of antagonism strategies against the host antiviral response. A pivotal component of the early host response is production and signaling of type I interferon (IFN-I). Ubiquitin, a prevalent cellular protein-modifying molecule, is heavily involved in the cellular regulation of this and other immune response pathways. Viruses use ubiquitin and ubiquitin machinery to antagonize various steps of these pathways through diverse mechanisms. Here, we highlight ways in which flaviviruses use or inhibit ubiquitin to antagonize the antiviral IFN-I response.
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11
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Bufalieri F, Caimano M, Lospinoso Severini L, Basili I, Paglia F, Sampirisi L, Loricchio E, Petroni M, Canettieri G, Santoro A, D’Angelo L, Infante P, Di Marcotullio L. The RNA-Binding Ubiquitin Ligase MEX3A Affects Glioblastoma Tumorigenesis by Inducing Ubiquitylation and Degradation of RIG-I. Cancers (Basel) 2020; 12:cancers12020321. [PMID: 32019099 PMCID: PMC7072305 DOI: 10.3390/cancers12020321] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma multiforme (GB) is the most malignant primary brain tumor in humans, with an overall survival of approximatively 15 months. The molecular heterogeneity of GB, as well as its rapid progression, invasiveness and the occurrence of drug-resistant cancer stem cells, limits the efficacy of the current treatments. In order to develop an innovative therapeutic strategy, it is mandatory to identify and characterize new molecular players responsible for the GB malignant phenotype. In this study, the RNA-binding ubiquitin ligase MEX3A was selected from a gene expression analysis performed on publicly available datasets, to assess its biological and still-unknown activity in GB tumorigenesis. We find that MEX3A is strongly up-regulated in GB specimens, and this correlates with very low protein levels of RIG-I, a tumor suppressor involved in differentiation, apoptosis and innate immune response. We demonstrate that MEX3A binds RIG-I and induces its ubiquitylation and proteasome-dependent degradation. Further, the genetic depletion of MEX3A leads to an increase of RIG-I protein levels and results in the suppression of GB cell growth. Our findings unveil a novel molecular mechanism involved in GB tumorigenesis and suggest MEX3A and RIG-I as promising therapeutic targets in GB.
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Affiliation(s)
- Francesca Bufalieri
- Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161 Rome, Italy; (F.B.); (M.C.); (L.L.S.); (I.B.); (M.P.); (G.C.)
| | - Miriam Caimano
- Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161 Rome, Italy; (F.B.); (M.C.); (L.L.S.); (I.B.); (M.P.); (G.C.)
| | - Ludovica Lospinoso Severini
- Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161 Rome, Italy; (F.B.); (M.C.); (L.L.S.); (I.B.); (M.P.); (G.C.)
| | - Irene Basili
- Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161 Rome, Italy; (F.B.); (M.C.); (L.L.S.); (I.B.); (M.P.); (G.C.)
| | - Francesco Paglia
- Dipartimento di Neurologia e Psichiatria, Neurochirurgia, Sapienza University, Viale dell’Università 30, 00185 Rome, Italy; (F.P.); (L.S.); (A.S.); (L.D.)
| | - Luigi Sampirisi
- Dipartimento di Neurologia e Psichiatria, Neurochirurgia, Sapienza University, Viale dell’Università 30, 00185 Rome, Italy; (F.P.); (L.S.); (A.S.); (L.D.)
| | - Elena Loricchio
- Center for Life Nano Science (CLNS@Sapienza), Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Marialaura Petroni
- Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161 Rome, Italy; (F.B.); (M.C.); (L.L.S.); (I.B.); (M.P.); (G.C.)
| | - Gianluca Canettieri
- Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161 Rome, Italy; (F.B.); (M.C.); (L.L.S.); (I.B.); (M.P.); (G.C.)
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti-Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161 Rome, Italy
| | - Antonio Santoro
- Dipartimento di Neurologia e Psichiatria, Neurochirurgia, Sapienza University, Viale dell’Università 30, 00185 Rome, Italy; (F.P.); (L.S.); (A.S.); (L.D.)
| | - Luca D’Angelo
- Dipartimento di Neurologia e Psichiatria, Neurochirurgia, Sapienza University, Viale dell’Università 30, 00185 Rome, Italy; (F.P.); (L.S.); (A.S.); (L.D.)
| | - Paola Infante
- Center for Life Nano Science (CLNS@Sapienza), Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Correspondence: (P.I.); (L.D.M.); Tel.: +39-06-49255132 (P.I.); +39-06-49255657 (L.D.M.); Fax: +39-06-49255660 (L.D.M.)
| | - Lucia Di Marcotullio
- Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161 Rome, Italy; (F.B.); (M.C.); (L.L.S.); (I.B.); (M.P.); (G.C.)
- Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti-Department of Molecular Medicine, Sapienza University, Viale Regina Elena 291, 00161 Rome, Italy
- Correspondence: (P.I.); (L.D.M.); Tel.: +39-06-49255132 (P.I.); +39-06-49255657 (L.D.M.); Fax: +39-06-49255660 (L.D.M.)
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12
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Choudhury NR, Heikel G, Michlewski G. TRIM25 and its emerging RNA-binding roles in antiviral defense. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1588. [PMID: 31990130 DOI: 10.1002/wrna.1588] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/25/2022]
Abstract
The innate immune system is the body's first line of defense against viruses, with pattern recognition receptors (PRRs) recognizing molecules unique to viruses and triggering the expression of interferons and other anti-viral cytokines, leading to the formation of an anti-viral state. The tripartite motif containing 25 (TRIM25) is an E3 ubiquitin ligase thought to be a key component in the activation of signaling by the PRR retinoic acid-inducible gene I protein (RIG-I). TRIM25 has recently been identified as an RNA-binding protein, raising the question of whether its RNA-binding activity is important for its role in innate immunity. Here, we review TRIM25's mechanisms and pathways in noninfected and infected cells. We also introduce models that explain how TRIM25 binding to RNA could modulate its functions and play part in the antiviral response. These findings have opened new lines of investigations into functional and molecular roles of TRIM25 and other E3 ubiquitin ligases in cell biology and control of pathogenic infections. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
| | - Gregory Heikel
- Infection Medicine, University of Edinburgh, Edinburgh, UK
| | - Gracjan Michlewski
- Infection Medicine, University of Edinburgh, Edinburgh, UK.,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Zhejiang, People's Republic of China
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13
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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: 218] [Impact Index Per Article: 43.6] [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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14
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Tong J, Li T, Bo L, Li W, Li Y, Zhang Y. Porous Nitrogen Self‐Doped Carbon Wrapped Iron Phosphide Hollow Spheres as Efficient Bifunctional Electrocatalysts for Water Splitting. ChemElectroChem 2019. [DOI: 10.1002/celc.201900513] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jinhui Tong
- Key Laboratory of Polymer Materials of Gansu Province Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education College of Chemistry and Chemical EngineeringNorthwest Normal University Lanzhou, Gansu 730070 China
| | - Tao Li
- Key Laboratory of Polymer Materials of Gansu Province Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education College of Chemistry and Chemical EngineeringNorthwest Normal University Lanzhou, Gansu 730070 China
| | - Lili Bo
- College of ScienceGansu Agricultural University Lanzhou 730070 China
| | - Wenyan Li
- Key Laboratory of Polymer Materials of Gansu Province Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education College of Chemistry and Chemical EngineeringNorthwest Normal University Lanzhou, Gansu 730070 China
| | - Yuliang Li
- Key Laboratory of Polymer Materials of Gansu Province Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education College of Chemistry and Chemical EngineeringNorthwest Normal University Lanzhou, Gansu 730070 China
| | - Yi Zhang
- Key Laboratory of Polymer Materials of Gansu Province Key Laboratory of Eco-Environment-Related Polymer Materials Ministry of Education College of Chemistry and Chemical EngineeringNorthwest Normal University Lanzhou, Gansu 730070 China
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15
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Zheng Y, Gao C. E3 ubiquitin ligases, the powerful modulator of innate antiviral immunity. Cell Immunol 2019; 340:103915. [PMID: 31054776 DOI: 10.1016/j.cellimm.2019.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/26/2019] [Accepted: 04/03/2019] [Indexed: 12/27/2022]
Abstract
During viral infection, the innate immune system represents the first defense line of the human body. The pathogen associated molecular patterns (PAMPs) from the viruses are recognized by pattern recognition receptors (PRRs) of the host cell, especially from those of the immune cells. Sensing of PAMPs by PRRs elicits an elegant signal transduction system, ultimately leading to the production of type I interferons (IFNs) and proinflammatory cytokines. Ubiquitination, with its versatile functions, plays a central role in modulating almost every single step of this signaling cascade. Ubiquitin ligases, which catalyze different types of ubiquitination correlating with multiple functions, are the key participant in fine-tuning antiviral signal transduction. In this review, we focus on summarizing the ubiquitin ligases that regulate the key signaling molecules in antiviral innate immunity.
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Affiliation(s)
- Yi Zheng
- State Key Laboratory of Microbial Technology, Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, The School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China
| | - Chengjiang Gao
- State Key Laboratory of Microbial Technology, Key Laboratory of Infection and Immunity of Shandong Province & Department of Immunology, The School of Basic Medical Sciences, Shandong University, Jinan, Shandong 250012, China.
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16
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Abstract
When a virus infects a host cell, it hijacks the biosynthetic capacity of the cell to produce virus progeny, a process that may take less than an hour or more than a week. The overall time required for a virus to reproduce depends collectively on the rates of multiple steps in the infection process, including initial binding of the virus particle to the surface of the cell, virus internalization and release of the viral genome within the cell, decoding of the genome to make viral proteins, replication of the genome, assembly of progeny virus particles, and release of these particles into the extracellular environment. For a large number of virus types, much has been learned about the molecular mechanisms and rates of the various steps. However, in only relatively few cases during the last 50 years has an attempt been made-using mathematical modeling-to account for how the different steps contribute to the overall timing and productivity of the infection cycle in a cell. Here we review the initial case studies, which include studies of the one-step growth behavior of viruses that infect bacteria (Qβ, T7, and M13), human immunodeficiency virus, influenza A virus, poliovirus, vesicular stomatitis virus, baculovirus, hepatitis B and C viruses, and herpes simplex virus. Further, we consider how such models enable one to explore how cellular resources are utilized and how antiviral strategies might be designed to resist escape. Finally, we highlight challenges and opportunities at the frontiers of cell-level modeling of virus infections.
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Affiliation(s)
- John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jacob Redovich
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA
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17
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Koliopoulos MG, Lethier M, van der Veen AG, Haubrich K, Hennig J, Kowalinski E, Stevens RV, Martin SR, Reis e Sousa C, Cusack S, Rittinger K. Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition. Nat Commun 2018; 9:1820. [PMID: 29739942 PMCID: PMC5940772 DOI: 10.1038/s41467-018-04214-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 04/13/2018] [Indexed: 02/04/2023] Open
Abstract
RIG-I is a viral RNA sensor that induces the production of type I interferon (IFN) in response to infection with a variety of viruses. Modification of RIG-I with K63-linked poly-ubiquitin chains, synthesised by TRIM25, is crucial for activation of the RIG-I/MAVS signalling pathway. TRIM25 activity is targeted by influenza A virus non-structural protein 1 (NS1) to suppress IFN production and prevent an efficient host immune response. Here we present structures of the human TRIM25 coiled-coil-PRYSPRY module and of complexes between the TRIM25 coiled-coil domain and NS1. These structures show that binding of NS1 interferes with the correct positioning of the PRYSPRY domain of TRIM25 required for substrate ubiquitination and provide a mechanistic explanation for how NS1 suppresses RIG-I ubiquitination and hence downstream signalling. In contrast, the formation of unanchored K63-linked poly-ubiquitin chains is unchanged by NS1 binding, indicating that RING dimerisation of TRIM25 is not affected by NS1.
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Affiliation(s)
- Marios G Koliopoulos
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mathilde Lethier
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | | | - Kevin Haubrich
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Eva Kowalinski
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Rebecca V Stevens
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Caetano Reis e Sousa
- Immunobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042, Grenoble, Cedex 9, France
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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18
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Courtois G, Fauvarque MO. The Many Roles of Ubiquitin in NF-κB Signaling. Biomedicines 2018; 6:E43. [PMID: 29642643 PMCID: PMC6027159 DOI: 10.3390/biomedicines6020043] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 12/24/2022] Open
Abstract
The nuclear factor κB (NF-κB) signaling pathway ubiquitously controls cell growth and survival in basic conditions as well as rapid resetting of cellular functions following environment changes or pathogenic insults. Moreover, its deregulation is frequently observed during cell transformation, chronic inflammation or autoimmunity. Understanding how it is properly regulated therefore is a prerequisite to managing these adverse situations. Over the last years evidence has accumulated showing that ubiquitination is a key process in NF-κB activation and its resolution. Here, we examine the various functions of ubiquitin in NF-κB signaling and more specifically, how it controls signal transduction at the molecular level and impacts in vivo on NF-κB regulated cellular processes.
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19
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Abstract
Innate immunity is traditionally thought of as the first line of defense against pathogens that enter the body. It is typically characterized as a rather weak defense mechanism, designed to restrict pathogen replication until the adaptive immune response generates a tailored response and eliminates the infectious agent. However, intensive research in recent years has resulted in better understanding of innate immunity as well as the discovery of many effector proteins, revealing its numerous powerful mechanisms to defend the host. Furthermore, this research has demonstrated that it is simplistic to strictly separate adaptive and innate immune functions since these two systems often work synergistically rather than sequentially. Here, we provide a broad overview of innate pattern recognition receptors in antiviral defense, with a focus on the TRIM family, and discuss their signaling pathways and mechanisms of action with special emphasis on the intracellular antibody receptor TRIM21.
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Affiliation(s)
| | - Leo C James
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
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20
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Li K, Zhong B. Regulation of Cellular Antiviral Signaling by Modifications of Ubiquitin and Ubiquitin-like Molecules. Immune Netw 2018; 18:e4. [PMID: 29503737 PMCID: PMC5833123 DOI: 10.4110/in.2018.18.e4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/12/2022] Open
Abstract
The initiation of cellular antiviral signaling depends on host pattern-recognition receptors (PRRs)-mediated recognition of viral nucleic acids that are known as classical pathogen-associated molecular patterns (PAMPs). PRRs recruit adaptor proteins and kinases to activate transcription factors and epigenetic modifiers to regulate transcription of hundreds of genes, the products of which collaborate to elicit antiviral responses. In addition, PRRs-triggered signaling induces activation of various inflammasomes which leads to the release of IL-1β and inflammation. Recent studies have demonstrated that PRRs-triggered signaling is critically regulated by ubiquitin and ubiquitin-like molecules. In this review, we first summarize an updated understanding of cellular antiviral signaling and virus-induced activation of inflammasome and then focus on the regulation of key components by ubiquitin and ubiquitin-like molecules.
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Affiliation(s)
- Kang Li
- Department of Immunology, Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China
| | - Bo Zhong
- Department of Immunology, Medical Research Institute, School of Medicine, Wuhan University, Wuhan 430071, China.,Department of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
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21
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Tan P, He L, Cui J, Qian C, Cao X, Lin M, Zhu Q, Li Y, Xing C, Yu X, Wang HY, Wang RF. Assembly of the WHIP-TRIM14-PPP6C Mitochondrial Complex Promotes RIG-I-Mediated Antiviral Signaling. Mol Cell 2017; 68:293-307.e5. [PMID: 29053956 DOI: 10.1016/j.molcel.2017.09.035] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 08/09/2017] [Accepted: 09/25/2017] [Indexed: 01/30/2023]
Abstract
Mitochondrial antiviral signaling platform protein (MAVS) acts as a central hub for RIG-I receptor proximal signal propagation. However, key components in the assembly of the MAVS mitochondrial platform that promote RIG-I mitochondrial localization and optimal activation are still largely undefined. Employing pooled RNAi and yeast two-hybrid screenings, we report that the mitochondrial adaptor protein tripartite motif (TRIM)14 provides a docking platform for the assembly of the mitochondrial signaling complex required for maximal activation of RIG-I-mediated signaling, consisting of WHIP and protein phosphatase PPP6C. Following viral infection, the ubiquitin-binding domain in WHIP bridges RIG-I with MAVS by binding to polyUb chains of RIG-I at lysine 164. The ATPase domain in WHIP contributes to stabilization of the RIG-I-dsRNA interaction. Moreover, phosphatase PPP6C is responsible for RIG-I dephosphorylation. Together, our findings define the WHIP-TRIM14-PPP6C mitochondrial signalosome required for RIG-I-mediated innate antiviral immunity.
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Affiliation(s)
- Peng Tan
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Lian He
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, College of Life Sciences, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Chen Qian
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Xin Cao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Meng Lin
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Qingyuan Zhu
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yinyin Li
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Changsheng Xing
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Xiao Yu
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Helen Y Wang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Rong-Fu Wang
- Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA; Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.
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22
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Xian H, Xie W, Yang S, Liu Q, Xia X, Jin S, Sun T, Cui J. Stratified ubiquitination of RIG-I creates robust immune response and induces selective gene expression. SCIENCE ADVANCES 2017; 3:e1701764. [PMID: 28948228 PMCID: PMC5609842 DOI: 10.1126/sciadv.1701764] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/01/2017] [Indexed: 05/12/2023]
Abstract
The activation of retinoic acid-inducible gene I (RIG-I), an indispensable viral RNA sensor in mammals, is subtly regulated by ubiquitination. Although multiple ubiquitination sites at the amino terminus of RIG-I have been identified, their functional allocations in RIG-I activation remain elusive. We identified a stratified model for RIG-I amino-terminal ubiquitination, in which initiation at either Lys164 or Lys172 allows subsequent ubiquitination at other lysines, to trigger and amplify RIG-I activation. Experimental and mathematical modeling showed that multisite ubiquitination provides robustness in RIG-I-mediated type I interferon (IFN) signaling. Furthermore, the flexibly controlled ultrasensitivity and IFN activation intensity determine the specificity of the IFN-stimulated gene transcription and manipulate cell fate in antiviral immune response. Our work demonstrates that tunable type I IFN signaling can be regulated through multisite RIG-I ubiquitination and elucidates a new paradigm for dynamic regulation in RIG-I-mediated antiviral signaling.
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Affiliation(s)
- Huifang Xian
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Weihong Xie
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shuai Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Qingxiang Liu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Xiaojun Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Shouheng Jin
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Tingzhe Sun
- School of Life Sciences, Anqing Normal University, Anqing 246011, China
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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Zhao Q, Liu H, Yao C, Shuai J, Sun X. Effect of Dynamic Interaction between microRNA and Transcription Factor on Gene Expression. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2676282. [PMID: 27957492 PMCID: PMC5121577 DOI: 10.1155/2016/2676282] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/10/2016] [Indexed: 01/27/2023]
Abstract
MicroRNAs (miRNAs) are endogenous noncoding RNAs which participate in diverse biological processes in animals and plants. They are known to join together with transcription factors and downstream gene, forming a complex and highly interconnected regulatory network. To recognize a few overrepresented motifs which are expected to perform important elementary regulatory functions, we constructed a computational model of miRNA-mediated feedforward loops (FFLs) in which a transcription factor (TF) regulates miRNA and targets gene. Based on the different dynamic interactions between miRNA and TF on gene expression, four possible structural topologies of FFLs with two gate functions (AND gate and OR gate) are introduced. We studied the dynamic behaviors of these different motifs. Furthermore, the relationship between the response time and maximal activation velocity of miRNA was investigated. We found that the curve of response time shows nonmonotonic behavior in Co1 loop with OR gate. This may help us to infer the mechanism of miRNA binding to the promoter region. At last we investigated the influence of important parameters on the dynamic response of system. We identified that the stationary levels of target gene in all loops were insensitive to the initial value of miRNA.
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Affiliation(s)
- Qi Zhao
- Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China
- School of Mathematics, Liaoning University, Shenyang 110036, China
- Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning Province, Shenyang 110036, China
| | - Hongsheng Liu
- Research Center for Computer Simulating and Information Processing of Bio-Macromolecules of Liaoning Province, Shenyang 110036, China
- School of life science, Liaoning University, Shenyang 110036, China
| | - Chenggui Yao
- Department of Mathematics, Shaoxing University, Shaoxing 312000, China
| | - Jianwei Shuai
- Department of Physics, College of Physics Science and Technology, Xiamen University, Xiamen 361005, China
| | - Xiaoqiang Sun
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510000, China
- School of Mathematical and Computational Science, Sun Yat-Sen University, Guangzhou 510275, China
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