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Bai G, Zeng X, Zhang L, Wang Y, Ma B. Computational investigation of the inhibitory interaction of IRF3 and SARS-CoV-2 accessory protein ORF3b. Biochem Biophys Res Commun 2024; 712-713:149945. [PMID: 38640732 DOI: 10.1016/j.bbrc.2024.149945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
ORF3b is one of the SARS-CoV-2 accessory proteins. Previous experimental study suggested that ORF3b prevents IRF3 translocating to nucleus. However, the biophysical mechanism of ORF3b-IRF3 interaction is elusive. Here, we explored the conformation ensemble of ORF3b using all-atom replica exchange molecular dynamics simulation. Disordered ORF3b has mixed α-helix, β-turn and loop conformers. The potential ORF3b-IRF3 binding modes were searched by docking representative ORF3b conformers with IRF3, and 50 ORF3b-IRF3 complex poses were screened using molecular dynamics simulations ranging from 500 to 1000 ns. We found that ORF3b binds IRF3 predominantly on its CBP binding and phosphorylated pLxIS motifs, with CBP binding site has the highest binding affinity. The ORF3b-IRF3 binding residues are highly conserved in SARS-CoV-2. Our results provided biophysics insights into ORF3b-IRF3 interaction and explained its interferon antagonism mechanism.
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Affiliation(s)
- Ganggang Bai
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xincheng Zeng
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linghao Zhang
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanjing Wang
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody (MOE), School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Dalskov L, Narita R, Andersen LL, Jensen N, Assil S, Kristensen K, Mikkelsen JG, Fujita T, Mogensen TH, Paludan SR, Hartmann R. Characterization of distinct molecular interactions responsible for IRF3 and IRF7 phosphorylation and subsequent dimerization. Nucleic Acids Res 2020; 48:11421-11433. [PMID: 33205822 PMCID: PMC7672473 DOI: 10.1093/nar/gkaa873] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/24/2020] [Accepted: 10/05/2020] [Indexed: 01/01/2023] Open
Abstract
IRF3 and IRF7 are critical transcription factors in the innate immune response. Their activation is controlled by phosphorylation events, leading to the formation of homodimers that are transcriptionally active. Phosphorylation occurs when IRF3 is recruited to adaptor proteins via a positively charged surface within the regulatory domain of IRF3. This positively charged surface also plays a crucial role in forming the active homodimer by interacting with the phosphorylated sites stabilizing the homodimer. Here, we describe a distinct molecular interaction that is responsible for adaptor docking and hence phosphorylation as well as a separate interaction responsible for the formation of active homodimer. We then demonstrate that IRF7 can be activated by both MAVS and STING in a manner highly similar to that of IRF3 but with one key difference. Regulation of IRF7 appears more tightly controlled; while a single phosphorylation event is sufficient to activate IRF3, at least two phosphorylation events are required for IRF7 activation.
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Affiliation(s)
- Louise Dalskov
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Ryo Narita
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Line L Andersen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Nanna Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Sonia Assil
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | | | - Takashi Fujita
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606–8507, Japan
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital Skejby, 8200 Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Rune Hartmann
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
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3
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Angeletti M, Hsu WLN, Majo N, Moriyama H, Moriyama EN, Zhang L. Adaptations of Interferon Regulatory Factor 3 with Transition from Terrestrial to Aquatic Life. Sci Rep 2020; 10:4508. [PMID: 32161340 PMCID: PMC7066157 DOI: 10.1038/s41598-020-61365-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/10/2020] [Indexed: 01/19/2023] Open
Abstract
Interferon regulatory factor 3 (IRF3) and IRF7 are closely related IRF members and the major factors for the induction of interferons, a key component in vertebrate innate immunity. However, there is limited knowledge regarding the evolution and adaptation of those IRFs to the environments. Two unique motifs in IRF3 and 7 were identified. One motif, GASSL, is highly conserved throughout the evolution of IRF3 and 7 and located in the signal response domain. Another motif, DPHK, is in the DNA-binding domain. The ancestral protein of IRF3 and 7 seemed to possess the DPHK motif. In the ray-finned fish lineage, while the DPHK is maintained in IRF7, the motif in IRF3 is changed to NPHK with a D → N amino acid substitution. The D → N substitution are also found in amphibian IRF3 but not in amphibian IRF7. Terrestrial animals such as reptiles and mammals predominantly use DPHK sequences in both IRF3 and 7. However, the D → N substitution in IRF3 DPHK is again found in cetaceans such as whales and dolphins as well as in marsupials. These observations suggest that the D → N substitutions in the IRF3 DPHK motif is likely to be associated with vertebrate's adaptations to aquatic environments and other environmental changes.
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Affiliation(s)
- Monica Angeletti
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Wan-Ling Nicole Hsu
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
- Department of Biostatistics, University of Washington, Washington, USA
| | - Nashaat Majo
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Etsuko N Moriyama
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Luwen Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Nebraska Center for Virology, University of Nebraska, Lincoln, NE, 68583, USA.
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4
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Krishnan R, Kurcheti PP, Mushtaq Z, K J, Naik T V. Interferon-regulatory factors, IRF3 and IRF7 in Asian seabass, Lates calcarifer: Characterization, ontogeny and transcriptional modulation upon challenge with nervous necrosis virus. Fish Shellfish Immunol 2019; 89:468-476. [PMID: 30940578 DOI: 10.1016/j.fsi.2019.03.073] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/11/2019] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Interferon regulatory factor (IRF) 3 and IRF7 are key regulators of type I interferon (IFN) gene expression for the antiviral immune response. In the present study, interferon regulatory factor 3 and 7 from Asian seabass, namely AsIRF3 and AsIRF7 were cloned and characterized. The full-length cDNA sequence of IRF3 and IRF7 consisted of 2965 and 2343 bp respectively. AsIRF3 and AsIRF7 were true orthologes of vertebrate IRF3/7 and showed similar domain organization, with an N-terminal DBD which consisted five tryptophan residues in IRF3 and four in IRF7, a C-terminal IRF3 domain and a serine rich region. Both IRF3 and 7 constitutively expressed during the ontogenesis and in all tissues of healthy fish. The expression of both genes was up-regulated following NNV challenge with obvious transcript abundance in brain heart and kidney. Ectopic expression of AsIRF3 and AsIRF7 displayed activation of ISRE/NF-κB promoters and modulation of interferon, ISGs and pro-inflammatory cytokine gene expression. These observations indicated that IRF3 and IRF7 play an important role in Asian seabass's antiviral defense and the RIG-IRF-IFN axis is conserved in the species.
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Affiliation(s)
- Rahul Krishnan
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400061, India; Present Address: Department of Aqualife Medicine, Chonnam National University, Republic of Korea
| | - Pani Prasad Kurcheti
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400061, India.
| | - Zahoor Mushtaq
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Jeena K
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Vismai Naik T
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400061, India
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5
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Li Z, Chen J, Li P, Li XY, Lu L, Li S. Functional characterization of dark sleeper (Odontobutis obscura) IRF3 in IFN regulation. Fish Shellfish Immunol 2019; 89:411-419. [PMID: 30978449 DOI: 10.1016/j.fsi.2019.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 03/29/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
The dark sleeper, Odontobutis obscura (O. obscura), is a commercially important species of freshwater sleeper native to East Asia. However, its molecular biology system is unexplored, including the interferon (IFN) signaling pathway, which is crucial to the antiviral response. In this study, we characterised the IFN regulation pattern of dark sleeper interferon regulatory factor 3 (OdIRF3), supplementing evidence of the conservation of this classical pathway in fish. First, the open reading frame (ORF) of OdIRF3 was cloned from the liver tissue by Rapid amplification of cDNA ends (RACE). Amino acid sequence analysis suggested that OdIRF3 is homologous with other fish IRF3 and that the N-terminal DNA-binding domain (DBD) and the C-terminal IRF-association domain (IAD) are conserved. Then, the cellular distribution demonstrated that OdIRF3 is located in the cytoplasm region and transfers into the nuclear region under stimulation. For the function identification, OdIRF3 activated several types of IFN promoters and induced downstream interferon stimulated genes (ISGs) expression. Finally, the overexpression of OdIRF3 significantly decreased viral proliferation. Taken together, these data systematically characterised the sequence, cellular location, and function in IFN expression of OdIRF3, shedding light on the molecular biology mechanism of the dark sleeper.
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Affiliation(s)
- Zhuocong Li
- University of Chinese Academy of Sciences, Beijing, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jian Chen
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Pei Li
- Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Longfeng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
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6
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Wong HH, Fung TS, Fang S, Huang M, Le MT, Liu DX. Accessory proteins 8b and 8ab of severe acute respiratory syndrome coronavirus suppress the interferon signaling pathway by mediating ubiquitin-dependent rapid degradation of interferon regulatory factor 3. Virology 2017; 515:165-175. [PMID: 29294448 PMCID: PMC7112132 DOI: 10.1016/j.virol.2017.12.028] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/22/2017] [Accepted: 12/25/2017] [Indexed: 12/28/2022]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) is an inefficient inducer of interferon (IFN) response. It expresses various proteins that effectively circumvent IFN production at different levels via distinct mechanisms. Through the construction of recombinant IBV expressing proteins 8a, 8b and 8ab encoded by SARS-CoV ORF8, we demonstrate that expression of 8b and 8ab enables the corresponding recombinant viruses to partially overcome the inhibitory actions of IFN activation to achieve higher replication efficiencies in cells. We also found that proteins 8b and 8ab could physically interact with IRF3. Overexpression of 8b and 8ab resulted in the reduction of poly (I:C)-induced IRF3 dimerization and inhibition of the IFN-β signaling pathway. This counteracting effect was partially mediated by protein 8b/8ab-induced degradation of IRF3 in a ubiquitin-proteasome-dependent manner. Taken together, we propose that SARS-CoV may exploit the unique functions of proteins 8b and 8ab as novel mechanisms to overcome the effect of IFN response during virus infection. Recombinant IBV expressing SARS-CoV protein 8b or 8ab replicates better than wild type in cells pre-treated with poly(I:C). 8b interacts with the IAD domain of IRF3. Overexpression of 8b or 8ab reduces poly(I:C)-induced IRF3 dimerization and interferon induction. 8b and 8ab induce degradation of IRF3 in a ubiquitin-proteasome-dependent manner. 8b and 8ab suppress interferon response induced by constitutively active IRF3.
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Affiliation(s)
- Hui Hui Wong
- South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, and Integrative Microbiology Research Centre, Guangzhou 510642, Guangdong, People's Republic of China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore
| | - To Sing Fung
- South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, and Integrative Microbiology Research Centre, Guangzhou 510642, Guangdong, People's Republic of China
| | - Shouguo Fang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore; Agricultural School, Yangtze University, 266 Jingmilu, Jingzhou City, Hubei Province 434025, China
| | - Mei Huang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - My Tra Le
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore
| | - Ding Xiang Liu
- South China Agricultural University, Guangdong Province Key Laboratory Microbial Signals & Disease Co, and Integrative Microbiology Research Centre, Guangzhou 510642, Guangdong, People's Republic of China; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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7
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Huang L, Xiong T, Yu H, Zhang Q, Zhang K, Li C, Hu L, Zhang Y, Zhang L, Liu Q, Wang S, He X, Bu Z, Cai X, Cui S, Li J, Weng C. Encephalomyocarditis virus 3C protease attenuates type I interferon production through disrupting the TANK-TBK1-IKKε-IRF3 complex. Biochem J 2017; 474:2051-2065. [PMID: 28487378 PMCID: PMC5465970 DOI: 10.1042/bcj20161037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 05/07/2017] [Accepted: 05/09/2017] [Indexed: 01/01/2023]
Abstract
TRAF family member-associated NF-κB activator (TANK) is a scaffold protein that assembles into the interferon (IFN) regulator factor 3 (IRF3)-phosphorylating TANK-binding kinase 1 (TBK1)-(IκB) kinase ε (IKKε) complex, where it is involved in regulating phosphorylation of the IRF3 and IFN production. However, the functions of TANK in encephalomyocarditis virus (EMCV) infection-induced type I IFN production are not fully understood. Here, we demonstrated that, instead of stimulating type I IFN production, the EMCV-HB10 strain infection potently inhibited Sendai virus- and polyI:C-induced IRF3 phosphorylation and type I IFN production in HEK293T cells. Mechanistically, EMCV 3C protease (EMCV 3C) cleaved TANK and disrupted the TANK-TBK1-IKKε-IRF3 complex, which resulted in the reduction in IRF3 phosphorylation and type I IFN production. Taken together, our findings demonstrate that EMCV adopts a novel strategy to evade host innate immune responses through cleavage of TANK.
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Affiliation(s)
- Li Huang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Tao Xiong
- College of Life Sciences, Yangtze University, Jingzhou 434100, China
| | - Huibin Yu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Quan Zhang
- College of Life Sciences, Yangtze University, Jingzhou 434100, China
| | - Kunli Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Changyao Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Liang Hu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Yuanfeng Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Lijie Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Qinfang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Shengnan Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Xijun He
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Zhigao Bu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Shangjin Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiangnan Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Changjiang Weng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
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Shu C, Chu Q, Bi D, Wang Y, Xu T. Identification and functional characterization of miiuy croaker IRF3 as an inducible protein involved regulation of IFN response. Fish Shellfish Immunol 2016; 54:499-506. [PMID: 27142934 DOI: 10.1016/j.fsi.2016.04.136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/25/2016] [Accepted: 04/29/2016] [Indexed: 06/05/2023]
Abstract
IFN regulatory factor (IRF) 3 as an important member of IRF family, is required for the host antiviral response. In mammals, IRF3 is known to be a critical player in regulating the transcription of IFN and IFN-stimulated genes (ISGs). However, only a few studies investigated the characteristics of IRF3 genes in fish. In this study, IRF3 from miiuy croaker was identified and characterized in bioinformatics and functions. Miiuy croaker IRF3 had conserved DBD, IAD and SRD domains with other vertebrates IRF3 genes, also miiuy croaker IRF3 had relatively conserved gene synteny and gene structures with other fish IRF3 genes. Evolutionary analysis showed IRF3 genes in mammals underwent positive selection, while IRF3 in fish underwent purifying selection. Expression analysis showed miiuy croaker IRF3 was expressed in all tested tissues and up-regulated expressed in infected liver and kidney; and up-regulated expression of miiuy croaker IRF3 was observed in head kidney macrophages which stimulated with poly(I:C) indicating that miiuy croaker IRF3 participated in the immune response to defense against poly(I:C) infection. Furthermore, luciferase reporter assay showed that overexpression of miiuy croaker IRF3 can activate the production of ISRE and IFNα, suggesting that miiuy croaker IRF3 acted as transcription activators in immune responses and maybe activate IFN signaling pathway. Immunofluorescence assay showed miiuy craoker IRF3 was localized in the cytoplasm in Hela cells. Overall, we systematically and comprehensively analyzed the bioinformatics and functions of miiuy croaker IRF3, which provided further insights into the transcriptional regulation of IRF3 gene in fish and valuable information for the study of evolution of IRF3 genes.
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Affiliation(s)
- Chang Shu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Qing Chu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Dekun Bi
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yanjin Wang
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
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9
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Liu S, Cai X, Wu J, Cong Q, Chen X, Li T, Du F, Ren J, Wu YT, Grishin NV, Chen ZJ. Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation. Science 2015; 347:aaa2630. [PMID: 25636800 DOI: 10.1126/science.aaa2630] [Citation(s) in RCA: 1135] [Impact Index Per Article: 126.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During virus infection, the adaptor proteins MAVS and STING transduce signals from the cytosolic nucleic acid sensors RIG-I and cGAS, respectively, to induce type I interferons (IFNs) and other antiviral molecules. Here we show that MAVS and STING harbor two conserved serine and threonine clusters that are phosphorylated by the kinases IKK and/or TBK1 in response to stimulation. Phosphorylated MAVS and STING then bind to a positively charged surface of interferon regulatory factor 3 (IRF3) and thereby recruit IRF3 for its phosphorylation and activation by TBK1. We further show that TRIF, an adaptor protein in Toll-like receptor signaling, activates IRF3 through a similar phosphorylation-dependent mechanism. These results reveal that phosphorylation of innate adaptor proteins is an essential and conserved mechanism that selectively recruits IRF3 to activate the type I IFN pathway.
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Affiliation(s)
- Siqi Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Xin Cai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Jiaxi Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Qian Cong
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Xiang Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. Howard Hughes Medical Institute (HHMI), University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Tuo Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Fenghe Du
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. Howard Hughes Medical Institute (HHMI), University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Junyao Ren
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - You-Tong Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Nick V Grishin
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. Howard Hughes Medical Institute (HHMI), University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Zhijian J Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA. Howard Hughes Medical Institute (HHMI), University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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10
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Huang B, Huang WS, Nie P. Cloning and expression analyses of interferon regulatory factor (IRF) 3 and 7 genes in European eel, Anguilla anguilla with the identification of genes involved in IFN production. Fish Shellfish Immunol 2014; 37:239-247. [PMID: 24565894 DOI: 10.1016/j.fsi.2014.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 02/08/2014] [Accepted: 02/12/2014] [Indexed: 06/03/2023]
Abstract
Interferon regulatory factor (IRF) 3 and IRF7 have been identified as regulators of type I interferon (IFN) gene expression in mammals. In the present study, the two genes were cloned and characterized in the European eel, Anguilla anguilla. The full-length cDNA sequence of IRF3 and IRF7 in the European eel, named as AaIRF3 and AaIRF7 consists of 2879 and 2419 bp respectively. Multiple alignments showed that the two IRFs have a highly conserved DNA binding domain (DBD) in the N terminus, with the characteristic motif containing five tryptophan residues, which is a feature present in their mammalian homologues. But, IRF7 has only four of the five residues in other species of fish. The expression of AaIRF3 and AaIRF7 both displayed an obvious dose-dependent manner following polyinosinic:polycytidylic acid (PolyI:C) challenge. In vivo expression analysis showed that the mRNA level of AaIRF3 and AaIRF7 was significantly up-regulated in response to PolyI:C stimulation in all examined tissues/organs except in muscle, with a lower level of increase observed in response to lipopolysaccharide (LPS) challenge and Edwardsiella tarda infection, indicating that AaIRF3 and AaIRF7 may be more likely involved in antiviral immune response. In addition, some pattern recognition receptors genes related with the production of type I IFNs and those genes in response to type I IFNs were identified in the European eel genome database, indicating a relatively conserved system in the production of type I IFN and its signalling in the European eel.
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Affiliation(s)
- Bei Huang
- College of Fisheries, Jimei University, 43 Yindou Road, Xiamen, Fujian Province 361021, China
| | - Wen Shu Huang
- College of Fisheries, Jimei University, 43 Yindou Road, Xiamen, Fujian Province 361021, China
| | - P Nie
- College of Fisheries, Jimei University, 43 Yindou Road, Xiamen, Fujian Province 361021, China.
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11
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Zhao Y, Brasier AR. Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways. Methods 2013; 61:313-22. [PMID: 23410677 PMCID: PMC3763905 DOI: 10.1016/j.ymeth.2013.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 01/30/2013] [Accepted: 02/01/2013] [Indexed: 01/12/2023] Open
Abstract
Quantitative measurement of the major regulatory proteins in signaling networks poses several technical challenges, including low abundance, the presence of post-translational modifications (PTMs), and the lack of suitable affinity detection reagents. Using the innate immune response (IIR) as a model signaling pathway, we illustrate the approach of stable isotope dilution (SID)-selected reaction monitoring (SRM)-mass spectrometry (MS) assays for quantification of low abundance signaling proteins. A work flow for SID-SRM-MS assay development is established for proteins with experimentally observed MS spectra and for those without. Using the interferon response factor (IRF)-3 transcription factor as an example, we illustrate the steps in high responding signature peptide identification, SID-SRM-MS assay optimization, and evaluation. SRM assays for normalization of IIR abundance to invariant housekeeping proteins are presented. We provide an example of SID-SRM assay development for post-translational modification (PTM) detection using an activating phospho-Ser modified NF-κB/RelA transcription factor, and describe challenges inherent in PTM-SID-SRM-MS assay development. Application of highly qualified quantitative, SID-SRM-MS assays will enable a systems-level approach to understanding the dynamics and kinetics of signaling in host cells, such as the IIR.
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Affiliation(s)
- Yingxin Zhao
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Departments of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Allan R. Brasier
- Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Departments of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Science, University of Texas Medical Branch, Galveston, TX, USA
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12
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Yao CL, Huang XN, Fan Z, Kong P, Wang ZY. Cloning and expression analysis of interferon regulatory factor (IRF) 3 and 7 in large yellow croaker, Larimichthys crocea. Fish Shellfish Immunol 2012; 32:869-878. [PMID: 22374413 DOI: 10.1016/j.fsi.2012.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/06/2012] [Accepted: 02/12/2012] [Indexed: 05/31/2023]
Abstract
The interferon regulatory factor (IRF)3 and IRF7 are considered to play essential roles in innate immune system's antiviral responses. In this report, the full-length cDNA and genomic structure and immune response characterizations of IRF3 and IRF7 were investigated in large yellow croaker, Larimichthys crocea. The full-length cDNA of L. crocea (Lc)IRF3 was of 2204 bp, including a 5'-terminal untranslated region (UTR) of 41 bp, a 3'-terminal UTR of 774 bp and an open reading frame (ORF) of 1389 bp encoding a polypeptide of 462 amino acids residues. The full-length cDNA of LcIRF7 was of 1979 bp, including a 5'-terminal UTR of 47 bp, a 3'-terminal UTR of 636 bp and an ORF of 1296 bp encoding a polypeptide of 431 amino acids. The putative amino acid sequence of both LcIRF3 and LcIRF7 contained a typical IRF domain at the N-terminal and an IRF3 domain at the C-terminal. Furthermore, we obtained 4517 nucleotides (nt) LcIRF3 genome sequence based on the full-length cDNA, which contained 11 exons and 10 introns. The full-length genome sequence of LcIRF7 was of 3991 nucleotides, including 9 exons and 8 introns. Quantitative real-time reverse transcription PCR analysis revealed a broad expression of LcIRF3 and LcIRF7 with the most predominant expression of LcIRF3 and LcIRF7 in the liver and in the gill, respectively. The expression levels of LcIRF3 and LcIRF7 after challenged with LPS, poly I:C and Vibrio parahaemolyticus were tested in blood, spleen and liver. The results showed that the highest relative expression of LcIRF3 was in the liver at 24 h after poly I:C injection with 90 times greater than that of the non-injection group (p < 0.05). Moreover, LcIRF3 transcription increased significantly at most time point in blood and spleen tissue after poly I:C stimulation compared with that of the control group. After LPS injection, the peak value of LcIRF7 was in the liver with 207 times (at 3 h) as much as that in the control group (p < 0.05). In addition, LcIRF7 expression was significantly induced by poly I:C injection in spleen. Both LcIRF3 and LcIRF7 transcripts did not show significant change after V. parahaemolyticus stimulation. These results indicated that IRF3 and IRF7 might play an important role in large yellow croaker's defense against viral and bacterial infection.
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Affiliation(s)
- Cui-Luan Yao
- Key Laboratory of Healthy Mariculture for East China Sea, Ministry of Agriculture/Fisheries College, Jimei University, Jimei, Xiamen, China.
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13
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Vandevenne P, Lebrun M, El Mjiyad N, Ote I, Di Valentin E, Habraken Y, Dortu E, Piette J, Sadzot-Delvaux C. The varicella-zoster virus ORF47 kinase interferes with host innate immune response by inhibiting the activation of IRF3. PLoS One 2011; 6:e16870. [PMID: 21347389 PMCID: PMC3036730 DOI: 10.1371/journal.pone.0016870] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 01/17/2011] [Indexed: 12/24/2022] Open
Abstract
The innate immune response constitutes the first line of host defence that limits viral spread and plays an important role in the activation of adaptive immune response. Viral components are recognized by specific host pathogen recognition receptors triggering the activation of IRF3. IRF3, along with NF-κB, is a key regulator of IFN-β expression. Until now, the role of IRF3 in the activation of the innate immune response during Varicella-Zoster Virus (VZV) infection has been poorly studied. In this work, we demonstrated for the first time that VZV rapidly induces an atypical phosphorylation of IRF3 that is inhibitory since it prevents subsequent IRF3 homodimerization and induction of target genes. Using a mutant virus unable to express the viral kinase ORF47p, we demonstrated that (i) IRF3 slower-migrating form disappears; (ii) IRF3 is phosphorylated on serine 396 again and recovers the ability to form homodimers; (iii) amounts of IRF3 target genes such as IFN-β and ISG15 mRNA are greater than in cells infected with the wild-type virus; and (iv) IRF3 physically interacts with ORF47p. These data led us to hypothesize that the viral kinase ORF47p is involved in the atypical phosphorylation of IRF3 during VZV infection, which prevents its homodimerization and subsequent induction of target genes such as IFN-β and ISG15.
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Affiliation(s)
- Patricia Vandevenne
- GIGA-Research, Laboratory of Virology and Immunology, University of Liege, Liege, Belgium
| | - Marielle Lebrun
- GIGA-Research, Laboratory of Virology and Immunology, University of Liege, Liege, Belgium
| | - Nadia El Mjiyad
- Laboratory of Molecular Oncology (LOM), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Isabelle Ote
- GIGA-Research, Laboratory of Virology and Immunology, University of Liege, Liege, Belgium
| | - Emmanuel Di Valentin
- GIGA-Research, Laboratory of Virology and Immunology, University of Liege, Liege, Belgium
| | - Yvette Habraken
- GIGA-Research, Laboratory of Virology and Immunology, University of Liege, Liege, Belgium
| | - Estelle Dortu
- Department of Pathology, University of Liege, Liege, Belgium
| | - Jacques Piette
- GIGA-Research, Laboratory of Virology and Immunology, University of Liege, Liege, Belgium
| | - Catherine Sadzot-Delvaux
- GIGA-Research, Laboratory of Virology and Immunology, University of Liege, Liege, Belgium
- * E-mail:
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14
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Hu G, Yin X, Lou H, Xia J, Dong X, Zhang J, Liu Q. Interferon regulatory factor 3 (IRF-3) in Japanese flounder, Paralichthys olivaceus: sequencing, limited tissue distribution, inducible expression and induction of fish type I interferon promoter. Dev Comp Immunol 2011; 35:164-173. [PMID: 20837055 DOI: 10.1016/j.dci.2010.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Revised: 09/06/2010] [Accepted: 09/06/2010] [Indexed: 05/29/2023]
Abstract
Two cDNAs with different 3'-untranslated region (UTR) encoding an interferon regulatory factor 3 (IRF-3) were cloned from head kidney of Japanese flounder, Paralichthys olivaceus, by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) methods. Sequence analysis reveals that they were generated by alternative polyadenylation. The predicted protein consists of 467 amino acid residues which shares the highest identity of 50.7-57.6% to fish IRF-3 and possesses a DNA-binding domain (DBD), an IRF association domain (IAD) and a serine-rich domain (SRD) of vertebrate IRF-3. The presence of these domains along with phylogenetic analysis places it into the IRF-3 group of the IRF-3 subfamily. RT-PCR analysis revealed that flounder IRF-3 was expressed constitutively in limited tissue types including head kidney, spleen, kidney, heart, gill, intestine and liver. A quantitative real time PCR assay was employed to monitor expression of IRF-3, type I interferon (IFN) and Mx in flounder head kidney and gill. All three genes were up-regulated by polyinosinic:polycytidylic acid (polyI:C) and lymphocystis disease virus (LCDV) with an earlier but slight and less persistent increase in transcription levels seen for the IRF-3. Finally, flounder IRF-3 was proved to induce fish type I IFN promoter in FG9307 cells, a flounder gill cell line, by a luciferase assay. These results provide insights into the roles of fish IRF-3 in the antiviral immunity.
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Affiliation(s)
- Guobin Hu
- College of Marine Life Sciences, Ocean University of China, 5# Yushan Road, Qingdao 266003, China.
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15
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Takahasi K, Yoneyama M, Nishihori T, Hirai R, Kumeta H, Narita R, Gale M, Inagaki F, Fujita T. Nonself RNA-sensing mechanism of RIG-I helicase and activation of antiviral immune responses. Mol Cell 2008; 29:428-40. [PMID: 18242112 DOI: 10.1016/j.molcel.2007.11.028] [Citation(s) in RCA: 376] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 10/01/2007] [Accepted: 11/09/2007] [Indexed: 12/25/2022]
Abstract
A DExD/H protein, RIG-I, is critical in innate antiviral responses by sensing viral RNA. Here we show that RIG-I recognizes two distinct viral RNA patterns: double-stranded (ds) and 5'ppp single-stranded (ss) RNA. The binding of RIG-I with dsRNA or 5'ppp ssRNA in the presence of ATP produces a common structure, as suggested by protease digestion. Further analyses demonstrated that the C-terminal domain of RIG-I (CTD) recognizes these RNA patterns and CTD coincides with the autorepression domain. Structural analysis of CTD by NMR spectroscopy in conjunction with mutagenesis revealed that the basic surface of CTD with a characteristic cleft interacts with RIG-I ligands. Our results suggest that the bipartite structure of CTD regulates RIG-I on encountering viral RNA patterns.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- DEAD Box Protein 58
- DEAD-box RNA Helicases/chemistry
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Gene Expression Regulation
- Humans
- Immune System/physiology
- Interferon Regulatory Factor-3/chemistry
- Interferon Regulatory Factor-3/genetics
- Interferon Regulatory Factor-3/metabolism
- Interferons/immunology
- Mice
- Mice, Knockout
- Models, Molecular
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Nucleic Acid Conformation
- Oligonucleotides/chemistry
- Oligonucleotides/genetics
- Oligonucleotides/immunology
- Protein Binding
- Protein Conformation
- Protein Structure, Tertiary
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/immunology
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/immunology
- Receptors, Immunologic
- Sequence Alignment
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Affiliation(s)
- Kiyohiro Takahasi
- Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan
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16
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Joo CH, Shin YC, Gack M, Wu L, Levy D, Jung JU. Inhibition of interferon regulatory factor 7 (IRF7)-mediated interferon signal transduction by the Kaposi's sarcoma-associated herpesvirus viral IRF homolog vIRF3. J Virol 2007; 81:8282-92. [PMID: 17522209 PMCID: PMC1951281 DOI: 10.1128/jvi.00235-07] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2007] [Accepted: 05/05/2007] [Indexed: 11/20/2022] Open
Abstract
Upon viral infection, the major defense mounted by the host immune system is activation of the interferon (IFN)-mediated antiviral pathway that is mediated by IFN regulatory factors (IRFs). In order to complete their life cycle, viruses must modulate the host IFN-mediated immune response. Kaposi's sarcoma-associated herpesvirus (KSHV), a human tumor-inducing herpesvirus, has developed a unique mechanism for antagonizing cellular IFN-mediated antiviral activity by incorporating viral homologs of the cellular IRFs, called vIRFs. Here, we report a novel immune evasion mechanism of KSHV vIRF3 to block cellular IRF7-mediated innate immunity in response to viral infection. KSHV vIRF3 specifically interacts with either the DNA binding domain or the central IRF association domain of IRF7, and this interaction leads to the inhibition of IRF7 DNA binding activity and, therefore, suppression of alpha interferon (IFN-alpha) production and IFN-mediated immunity. Remarkably, the central 40 amino acids of vIRF3, containing the double alpha helix motifs, are sufficient not only for binding to IRF7, but also for inhibiting IRF7 DNA binding activity. Consequently, the expression of the double alpha helix motif-containing peptide effectively suppresses IRF7-mediated IFN-alpha production. This demonstrates a remarkably efficient means of viral avoidance of host antiviral activity.
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Affiliation(s)
- Chul Hyun Joo
- Tumor Virology Division, New England Primate Research Center, Department of Microbiology and Molecular Genetics, Harvard Medical School, 1 Pine Hill Drive, Southborough, MA 01772, USA
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17
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Escalante CR, Nistal-Villán E, Shen L, García-Sastre A, Aggarwal AK. Structure of IRF-3 bound to the PRDIII-I regulatory element of the human interferon-beta enhancer. Mol Cell 2007; 26:703-16. [PMID: 17560375 DOI: 10.1016/j.molcel.2007.04.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 03/14/2007] [Accepted: 04/25/2007] [Indexed: 10/23/2022]
Abstract
Interferon regulatory factor 3 (IRF-3) is a key transcription factor in the assembly of the mammalian interferon-beta (IFN-beta) enhanceosome. We present here the structure of IRF-3 DNA binding domain in complex with the complete PRDIII-I regulatory element of the human IFN-beta enhancer. We show that four IRF-3 molecules bind in tandem to, variably spaced, consensus and nonconsensus IRF sites on the composite element. The ability of IRF-3 to bind these variable sites derives in part from two nonconserved arginines (Arg78 and Arg86) that partake in alternate protein-DNA contacts. We also show that the protein-DNA contacts are highly overlapped and that all four IRF sites are required for gene activation in vivo. In addition, we show that changing the nonconsensus IRF sites to consensus sites creates a more efficient enhancer in vivo. Together, the structure and accompanying biological data provide insights into the assembly of the IFN-beta enhanceosome in mammals.
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Affiliation(s)
- Carlos R Escalante
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
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18
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Dragan AI, Hargreaves VV, Makeyeva EN, Privalov PL. Mechanisms of activation of interferon regulator factor 3: the role of C-terminal domain phosphorylation in IRF-3 dimerization and DNA binding. Nucleic Acids Res 2007; 35:3525-34. [PMID: 17483521 PMCID: PMC1920236 DOI: 10.1093/nar/gkm142] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The interferon regulatory transcription factor (IRF-3) is activated by phosphorylation of Ser/Thr residues clustered in its C-terminal domain. Phosphorylation of these residues, which increases the negative charge of IRF-3, results in its dimerization and association with DNA, despite the increase in repulsive electrostatic interactions. To investigate this surprising effect, the dimerization of IRF-3 and two phosphomimetic mutants, 2D (S396D, S398D) and 5D (S396D, S398D, S402D, T404D and S405D), and their binding to single-site PRDI and double-site PRDIII-PRDI DNA sequences from the IFN-beta enhancer have been studied. It was found that: (a) the mutations in the C-terminal domain do not affect the state of the DNA-binding N-terminal domain or its ability to bind target DNA; (b) in the 5D-mutant, the local increase of negative charge in the C-terminal domain induces restructuring, resulting in the formation of a stable dimer; (c) dimerization of IRF-3 is the basis of its strong binding to PRDIII-PRDI sites since binding of 5D to the single PRDI site is similar to that of inactivated IRF-3. Analysis of the binding characteristics leads to the conclusion that binding of dimeric IRF-3 to the DNA with two tandem-binding sites, which are twisted by approximately 100 degrees relative to each other, requires considerable work to untwist and/or bend the DNA.
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Affiliation(s)
- Anatoly I Dragan
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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19
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Yang K, Shi H, Qi R, Sun S, Tang Y, Zhang B, Wang C. Hsp90 regulates activation of interferon regulatory factor 3 and TBK-1 stabilization in Sendai virus-infected cells. Mol Biol Cell 2006; 17:1461-71. [PMID: 16394098 PMCID: PMC1382332 DOI: 10.1091/mbc.e05-09-0853] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Interferon regulatory factor 3 (IRF3) plays a crucial role in mediating cellular responses to virus intrusion. The protein kinase TBK1 is a key regulator inducing phosphorylation of IRF3. The regulatory mechanisms during IRF3 activation remain poorly characterized. In the present study, we have identified by yeast two-hybrid approach a specific interaction between IRF3 and chaperone heat-shock protein of 90 kDa (Hsp90). The C-terminal truncation mutant of Hsp90 is a strong dominant-negative inhibitor of IRF3 activation. Knockdown of endogenous Hsp90 by RNA interference attenuates IRF3 activation and its target gene expressions. Alternatively, Hsp90-specific inhibitor geldanamycin (GA) dramatically reduces expression of IRF3-regulated interferon-stimulated genes and abolishes the cytoplasm-to-nucleus translocation and DNA binding activity of IRF3 in Sendai virus-infected cells. Significantly, virus-induced IRF3 phosphorylation is blocked by GA, whereas GA does not affect the protein level of IRF3. In addition, TBK1 is found to be a client protein of Hsp90 in vivo. Treatment of 293 cells with GA interferes with the interaction of TBK1 and Hsp90, resulting in TBK1 destabilization and its subsequent proteasome-mediated degradation. Besides maintaining stability of TBK1, Hsp90 also forms a novel complex with TBK1 and IRF3, which brings TBK1 and IRF3 dynamically into proximity and facilitates signal transduction from TBK1 to IRF3. Our study uncovers an essential role of Hsp90 in the virus-induced activation of IRF3.
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Affiliation(s)
- Kai Yang
- Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
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20
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Abstract
Interferon regulatory factor (IRF) 3 plays a critical role in triggering the activation of interferon antiviral genes. The structure of IRF-3 in association with the CBP/p300 coactivator by in this issue of Structure illuminates the mechanism of IRF activation and the structural flexibilities inherent in CBP/p300.
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21
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Qin BY, Liu C, Srinath H, Lam SS, Correia JJ, Derynck R, Lin K. Crystal structure of IRF-3 in complex with CBP. Structure 2005; 13:1269-77. [PMID: 16154084 DOI: 10.1016/j.str.2005.06.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Revised: 05/06/2005] [Accepted: 06/10/2005] [Indexed: 10/25/2022]
Abstract
Transcriptional activation of interferon beta (IFN-beta), an antiviral cytokine, requires the assembly of IRF-3 and CBP/p300 at the promoter region of the IFN-beta gene. The crystal structure of IRF-3 in complex with CBP reveals that CBP interacts with a hydrophobic surface on IRF-3, which in latent IRF-3 is covered by its autoinhibitory elements. This structural organization suggests that virus-induced phosphoactivation of IRF-3 triggers unfolding of the autoinhibitory elements and exposes the same hydrophobic surface for CBP interaction. The structure also reveals that the interacting CBP segment can exist in drastically different conformations, depending on the identity of the associating transcription cofactor. The finding suggests a possible regulatory mechanism in CBP/p300, by which the interacting transcription factor can specify the coactivator's conformation and influence the transcriptional outcome.
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Affiliation(s)
- Bin Y Qin
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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22
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Scholle F, Mason PW. West Nile virus replication interferes with both poly(I:C)-induced interferon gene transcription and response to interferon treatment. Virology 2005; 342:77-87. [PMID: 16111732 DOI: 10.1016/j.virol.2005.07.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Revised: 06/06/2005] [Accepted: 07/16/2005] [Indexed: 10/25/2022]
Abstract
West Nile virus (WNV), the leading cause of viral encephalitis in the United States, is an arthropod-transmitted member of the family Flaviviridae. We have explored the interaction of this positive-strand RNA virus with signaling pathways involved in induction of the host's innate immune response. Phosphorylation of STAT-1 in response to interferon (IFN) treatment and the ability of IFN to establish an antiviral state were reduced in WNV replicon-bearing cell lines. Similarly, the activation of IRF3 and stimulation of IFN-beta transcription in response to the double-stranded RNA (dsRNA) mimetic poly(I:C) were inhibited in replicon-bearing and WNV-infected HeLa cells. In contrast, WNV replicons did not affect IRF3 activation by Sendai virus infection, suggesting that not all IRF3 activating pathways are inhibited by WNV. Taken together, these findings demonstrate that WNV replication in cultured cells interferes with both the response to IFN and synthesis of IFN-beta in response to dsRNA.
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Affiliation(s)
- Frank Scholle
- Department of Pathology, 3.206B Mary Moody Northen Pavilion, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0436, USA
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