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Holmes CM, Babasyan S, Eady N, Schnabel CL, Wagner B. Immune horses rapidly increase antileukoproteinase and lack type I interferon secretion during mucosal innate immune responses against equine herpesvirus type 1. Microbiol Spectr 2024; 12:e0109224. [PMID: 39162558 PMCID: PMC11448092 DOI: 10.1128/spectrum.01092-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/25/2024] [Indexed: 08/21/2024] Open
Abstract
Equine herpesvirus type 1 (EHV-1) is one of the most prevalent respiratory pathogens in horses with a high impact on animal health worldwide. Entry of the virus into epithelial cells of the upper respiratory tract and rapid local viral replication is followed by infection of local lymphoid tissues leading to cell-associated viremia and disease progression. Pre-existing mucosal immunity has previously been shown to reduce viral shedding and prevent viremia, consequently limiting severe disease manifestations. Here, nasopharyngeal transcriptomic profiling was used to identify differentially expressed genes following EHV-1 challenge in horses with different EHV-1 immune statuses. Immune horses (n = 4) did neither develop clinical disease nor viremia and did not shed virus after experimental infection, while non-immune horses (n = 4) did all the above. RNA sequencing was performed on nasopharyngeal samples pre- and 24 hours post-infection (24hpi). At 24hpi, 109 and 44 genes were upregulated in immune horses and non-immune horses, respectively, and three genes were explored in further detail. Antileukoproteinase (SLPI) gene expression increased 2.1-fold within 24 hours in immune horses in concert with protein secretion. Interferon (IFN)-induced proteins with tetratricopeptide repeats 2 (IFIT2) and 3 (IFIT3) were upregulated in non-immune horses, corresponding with nasal IFN-α secretion and viral replication. By contrast, neither IFIT expression nor IFN-α secretion was induced by EHV-1 infection of immune horses. Transcriptomic profiling offered a tool to identify, for the first time, the role of SLPI in innate immunity against EHV-1, and further emphasized the central role of the type I IFN response in the anti-viral defense of non-immune horses. IMPORTANCE Equine herpesvirus type 1 (EHV-1) remains a considerable concern in the equine industry, with yearly outbreaks resulting in morbidity, mortality, and economic losses. In addition to its importance in equine health, EHV-1 is a respiratory pathogen and an alphaherpesvirus, and it may serve as a model for other viruses with similar pathogenicity or phylogeny. Large animal models allow the collection of high-volume samples longitudinally, permitting in-depth investigation of immunological processes. This study was performed on bio-banked nasopharyngeal samples from an EHV-1 infection experiment, where clinical outcomes had previously been determined. Matched nucleic acid and protein samples throughout infection permitted longitudinal quantification of the protein or related proteins of selected differentially expressed genes detected during the transcriptomic screen. The results of this manuscript identified novel innate immune pathways of the upper respiratory tract during the first 24 hours of EHV-1 infection, offering a first look at the components of early mucosal immunity that are indicative of protection.
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Affiliation(s)
- Camille M Holmes
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Susanna Babasyan
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Naya Eady
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | - Bettina Wagner
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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2
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Ryan EM, Norinskiy MA, Bracken AK, Lueders EE, Chen X, Fu Q, Anderson ET, Zhang S, Abbasov ME. Activity-Based Acylome Profiling with N-(Cyanomethyl)- N-(phenylsulfonyl)amides for Targeted Lysine Acylation and Post-Translational Control of Protein Function in Cells. J Am Chem Soc 2024. [PMID: 39348182 DOI: 10.1021/jacs.4c09073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Lysine acylations are ubiquitous and structurally diverse post-translational modifications that vastly expand the functional heterogeneity of the human proteome. Hence, the targeted acylation of lysine residues has emerged as a strategic approach to exert biomimetic control over the protein function. However, existing strategies for targeted lysine acylation in cells often rely on genetic intervention, recruitment of endogenous acylation machinery, or nonspecific acylating agents and lack methods to quantify the magnitude of specific acylations on a global level. In this study, we develop activity-based acylome profiling (ABAP), a chemoproteomic strategy that exploits elaborate N-(cyanomethyl)-N-(phenylsulfonyl)amides and lysine-centric probes for site-specific introduction and proteome-wide mapping of posttranslational lysine acylations in human cells. Harnessing this framework, we quantify various artificial acylations and rediscover numerous endogenous lysine acylations. We validate site-specific acetylation of target lysines and establish a structure-activity relationship for N-(cyanomethyl)-N-(phenylsulfonyl)amides in proteins from diverse structural and functional classes. We identify paralog-selective chemical probes that acetylate conserved lysines within interferon-stimulated antiviral RNA-binding proteins, generating de novo proteoforms with obstructed RNA interactions. We further demonstrate that targeted acetylation of a key enzyme in retinoid metabolism engenders a proteoform with a conformational change in the protein structure, leading to a gain-of-function phenotype and reduced drug potency. These findings underscore the versatility of our strategy in biomimetic control over protein function through targeted delivery and global profiling of endogenous and artificial lysine acylations, potentially advancing therapeutic modalities and our understanding of biological processes orchestrated by these post-translational modifications.
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Affiliation(s)
- Elizabeth M Ryan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Michael A Norinskiy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Amy K Bracken
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Emma E Lueders
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Xueer Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Qin Fu
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Elizabeth T Anderson
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York 14853, United States
| | - Mikail E Abbasov
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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3
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Barik S. Suppression of Innate Immunity by the Hepatitis C Virus (HCV): Revisiting the Specificity of Host-Virus Interactive Pathways. Int J Mol Sci 2023; 24:16100. [PMID: 38003289 PMCID: PMC10671098 DOI: 10.3390/ijms242216100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The hepatitis C virus (HCV) is a major causative agent of hepatitis that may also lead to liver cancer and lymphomas. Chronic hepatitis C affects an estimated 2.4 million people in the USA alone. As the sole member of the genus Hepacivirus within the Flaviviridae family, HCV encodes a single-stranded positive-sense RNA genome that is translated into a single large polypeptide, which is then proteolytically processed to yield the individual viral proteins, all of which are necessary for optimal viral infection. However, cellular innate immunity, such as type-I interferon (IFN), promptly thwarts the replication of viruses and other pathogens, which forms the basis of the use of conjugated IFN-alpha in chronic hepatitis C management. As a countermeasure, HCV suppresses this form of immunity by enlisting diverse gene products, such as HCV protease(s), whose primary role is to process the large viral polyprotein into individual proteins of specific function. The exact number of HCV immune suppressors and the specificity and molecular mechanism of their action have remained unclear. Nonetheless, the evasion of host immunity promotes HCV pathogenesis, chronic infection, and carcinogenesis. Here, the known and putative HCV-encoded suppressors of innate immunity have been reviewed and analyzed, with a predominant emphasis on the molecular mechanisms. Clinically, the knowledge should aid in rational interventions and the management of HCV infection, particularly in chronic hepatitis.
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Affiliation(s)
- Sailen Barik
- EonBio, 3780 Pelham Drive, Mobile, AL 36619, USA
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4
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Zhang X, Xie T, Li X, Feng M, Mo G, Zhang Q, Zhang X. Transcriptome Sequencing Reveals That Intact Expression of the Chicken Endogenous Retrovirus chERV3 In Vitro Can Possibly Block the Key Innate Immune Pathway. Animals (Basel) 2023; 13:2720. [PMID: 37684986 PMCID: PMC10486640 DOI: 10.3390/ani13172720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Endogenous retroviruses (ERVs) are viral sequences that have integrated into the genomes of vertebrates. Our preliminary transcriptome sequencing analysis revealed that chERV3 is active and is located on chromosome 1:32602284-32615631. We hypothesized that chERV3 may have a role in the host innate immune response to viral infection. In this study, using reverse genetics, we constructed the puc57-chERV3 full-length reverse cloning plasmid in vitro. We measured the p27 content in culture supernatant by enzyme-linked immunosorbent assay (ELISA). Finally, transcriptome analysis was performed to analyze the function of chERV3 in innate immunity. The results showed that chERV3 may generate p27 viral particles. We found that compared to the negative control (NC) group (transfected with pMD18T-EGFP), the chERV3 group exhibited 2538 up-regulated differentially expressed genes (DEGs) and 1828 down-regulated DEGs at 24 hours (h) and 1752 up-regulated DEGs and 1282 down-regulated DEGs at 48 h. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the down-regulated DEGs were enriched mainly in immune-related processes such as the inflammatory response, innate immune response, and Toll-like receptor signaling pathway. GSEA showed that the Toll-like receptor signaling pathway was suppressed by chERV3 at both time points. We hypothesized that chERV3 can influence the activation of the innate immune pathway by blocking the Toll-like receptor signaling pathway to achieve immune evasion.
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Affiliation(s)
- Xi Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Tingting Xie
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiaoqi Li
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Guodong Mo
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Qihong Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xiquan Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (X.Z.)
- Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
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5
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Whole genome assembly of the armored loricariid catfish Ancistrus triradiatus highlights herbivory signatures. Mol Genet Genomics 2022; 297:1627-1642. [PMID: 36006456 PMCID: PMC9596584 DOI: 10.1007/s00438-022-01947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/12/2022] [Indexed: 11/01/2022]
Abstract
The catfish Ancistrus triradiatus belongs to the species-rich family Loricariidae. Loricariids display remarkable traits such as herbivory, a benthic lifestyle, the absence of scales but the presence of dermal bony plates. They are exported as ornamental fish worldwide, with escaped fishes becoming a threat locally. Although genetic and phylogenetic studies are continuously increasing and developmental genetic investigations are underway, no genome assembly has been formally proposed for Loricariidae yet. We report a high-quality genome assembly of Ancistrus triradiatus using long and short reads, and a newly assembled transcriptome. The genome assembly is composed of 9530 scaffolds, including 85.6% of ray-finned fish BUSCOs, and 26,885 predicted protein-coding genes. The genomic GC content is higher than in other catfishes, reflecting the higher metabolism associated with herbivory. The examination of the SCPP gene family indicates that the genes presumably triggering scale loss when absent, are present in the scaleless A. triradiatus, questioning their explanatory role. The analysis of the opsin gene repertoire revealed that gene losses associated to the nocturnal lifestyle of catfishes were not entirely found in A. triradiatus, as the UV-sensitive opsin 5 is present. Finally, most gene family expansions were related to immunity except the gamma crystallin gene family which controls pupil shape and sub-aquatic vision. Thus, the genome of A. triradiatus reveals that fish herbivory may be related to the photic zone habitat, conditions metabolism, photoreception and visual functions. This genome is the first for the catfish suborder Loricarioidei and will serve as backbone for future genetic, developmental and conservation studies.
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6
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Hu X, Li H, Lin Y, Wang Z, Feng H, Zhou M, Shi L, Cao H, Ren Y. Genomic deciphering of sex determination and unique immune system of a potential model species rare minnow ( Gobiocypris rarus). SCIENCE ADVANCES 2022; 8:eabl7253. [PMID: 35108042 PMCID: PMC8809535 DOI: 10.1126/sciadv.abl7253] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Gobiocypris rarus is sensitive to environmental pollution, especially to heavy metal and grass carp reovirus (GCRV). Hence, it has potential utility as a biological monitor. Genetic deciphering of its unique immune system will advance our understanding of its unique adaptive strategies, which provide cues for its better application. A de novo genome of rare minnow was obtained, and its sex determination mechanism is ZZ/ZW. We identified several specific mutation genes and specific lost genes of rare minnow, and these might be related to the sensitivity of rare minnow to environmental stimuli. We also analyzed the gene expression level of different organs/tissues and found that several IFIT genes may play key roles in GCRV resistance. In addition, knockout of the gene PCDH10L indicates that PCDH10L affects Pb2+-induced mortality in rare minnow. Rare minnow is ready for genetic manipulation and shows potential as an emerging experimental model.
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Affiliation(s)
- Xudong Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Yusheng Lin
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongkai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
| | - Haohao Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Man Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixia Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author. (Y.R.); (H.C.)
| | - Yandong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an 710072, China
- Corresponding author. (Y.R.); (H.C.)
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7
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Mou CY, Li S, Lu LF, Wang Y, Yu P, Li Z, Tong JF, Zhang QY, Wang ZW, Zhang XJ, Wang GX, Zhou L, Gui JF. Divergent Antiviral Mechanisms of Two Viperin Homeologs in a Recurrent Polyploid Fish. Front Immunol 2021; 12:702971. [PMID: 34531856 PMCID: PMC8438203 DOI: 10.3389/fimmu.2021.702971] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 12/03/2022] Open
Abstract
Polyploidy and subsequent diploidization provide genomic opportunities for evolutionary innovations and adaptation. The researches on duplicated gene evolutionary fates in recurrent polyploids have seriously lagged behind that in paleopolyploids with diploidized genomes. Moreover, the antiviral mechanisms of Viperin remain largely unclear in fish. Here, we elaborate the distinct antiviral mechanisms of two viperin homeologs (Cgviperin-A and Cgviperin-B) in auto-allo-hexaploid gibel carp (Carassius gibelio). First, Cgviperin-A and Cgviperin-B showed differential and biased expression patterns in gibel carp adult tissues. Subsequently, using co-immunoprecipitation (Co-IP) screening analysis, both CgViperin-A and CgViperin-B were found to interact with crucian carp (C. auratus) herpesvirus (CaHV) open reading frame 46 right (ORF46R) protein, a negative herpesvirus regulator of host interferon (IFN) production, and to promote the proteasomal degradation of ORF46R via decreasing K63-linked ubiquitination. Additionally, CgViperin-B also mediated ORF46R degradation through autophagosome pathway, which was absent in CgViperin-A. Moreover, we found that the N-terminal α-helix domain was necessary for the localization of CgViperin-A and CgViperin-B at the endoplasmic reticulum (ER), and the C-terminal domain of CgViperin-A and CgViperin-B was indispensable for the interaction with degradation of ORF46R. Therefore, the current findings clarify the divergent antiviral mechanisms of the duplicated viperin homeologs in a recurrent polyploid fish, which will shed light on the evolution of teleost duplicated genes.
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Affiliation(s)
- Cheng-Yan Mou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Long-Feng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Jin-Feng Tong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Guang-Xin Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Hubei Hongshan Laboratory, Chinese Academy of Sciences, Wuhan, China
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8
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Zhang N, Shi H, Yan M, Liu G. IFIT5 Negatively Regulates the Type I IFN Pathway by Disrupting TBK1-IKKε-IRF3 Signalosome and Degrading IRF3 and IKKε. THE JOURNAL OF IMMUNOLOGY 2021; 206:2184-2197. [PMID: 33858962 DOI: 10.4049/jimmunol.2001033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/24/2021] [Indexed: 12/11/2022]
Abstract
IFN-induced protein with tetratricopeptide repeats (IFITs), known as canonical IFN-stimulated genes (ISGs), play critical roles in regulating immune responses against pathogens and maintaining homeostasis. How the IFIT5 regulates innate immune responses is rarely reported and remains enigmatic. In this study, we discover that human IFIT5 (hIFIT5) functions as a negative regulator of the type I IFN (IFN) pathway in HEK293T cell lines. Our data illustrated that hIFIT5 inhibited the promotor activities of IFN-β induced by IRF3 and its upstream factors but not by IRF3-5D (activated form of IRF3), suggesting that IRF3 might be a target of hIFIT5. Further investigations revealed that hIFIT5 downregulated the phosphorylation of IRF3 and IKKε and blocked the IRF3 nuclear translocation. Moreover, hIFIT5 impaired the IRF3-TBK1-IKKε complex, accompanied by IRF3 and IKKε degradation. In conclusion, these findings indicate that hIFIT5 is a negative modulator in the type I IFN signaling pathway, opening additional avenues for preventing hyperactivation and maintaining immunity homeostasis.
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Affiliation(s)
- Na Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Han Shi
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Miaomiao Yan
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Guangliang Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
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9
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Jacquet S, Pontier D, Etienne L. Rapid Evolution of HERC6 and Duplication of a Chimeric HERC5/6 Gene in Rodents and Bats Suggest an Overlooked Role of HERCs in Mammalian Immunity. Front Immunol 2021; 11:605270. [PMID: 33391270 PMCID: PMC7775381 DOI: 10.3389/fimmu.2020.605270] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Studying the evolutionary diversification of mammalian antiviral defenses is of main importance to better understand our innate immune repertoire. The small HERC proteins are part of a multigene family, including HERC5 and HERC6, which have probably diversified through complex evolutionary history in mammals. Here, we performed mammalian-wide phylogenetic and genomic analyses of HERC5 and HERC6, using 83 orthologous sequences from bats, rodents, primates, artiodactyls, and carnivores—the top five representative groups of mammalian evolution. We found that HERC5 has been under weak and differential positive selection in mammals, with only primate HERC5 showing evidences of pathogen-driven selection. In contrast, HERC6 has been under strong and recurrent adaptive evolution in mammals, suggesting past and widespread genetic arms-races with viral pathogens. Importantly, the rapid evolution of mammalian HERC6 spacer domain suggests that it might be a host-pathogen interface, targeting viral proteins and/or being the target of virus antagonists. Finally, we identified a HERC5/6 chimeric gene that arose from independent duplication in rodent and bat lineages and encodes for a conserved HERC5 N-terminal domain and divergent HERC6 spacer and HECT domains. This duplicated chimeric gene highlights adaptations that potentially contribute to rodent and bat immunity. Our findings open new research avenues on the functions of HERC6 and HERC5/6 in mammals, and on their implication in antiviral innate immunity.
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Affiliation(s)
- Stéphanie Jacquet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France.,CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France.,LabEx Ecofect, Université de Lyon, Lyon, France
| | - Dominique Pontier
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France.,LabEx Ecofect, Université de Lyon, Lyon, France
| | - Lucie Etienne
- CIRI-Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France.,LabEx Ecofect, Université de Lyon, Lyon, France
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10
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Mears HV, Sweeney TR. Mouse Ifit1b is a cap1-RNA-binding protein that inhibits mouse coronavirus translation and is regulated by complexing with Ifit1c. J Biol Chem 2020; 295:17781-17801. [PMID: 33454014 PMCID: PMC7762956 DOI: 10.1074/jbc.ra120.014695] [Citation(s) in RCA: 2] [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: 06/04/2020] [Revised: 09/18/2020] [Accepted: 10/19/2020] [Indexed: 11/24/2022] Open
Abstract
Knockout mouse models have been extensively used to study the antiviral activity of IFIT (interferon-induced protein with tetratricopeptide repeats). Human IFIT1 binds to cap0 (m7GpppN) RNA, which lacks methylation on the first and second cap-proximal nucleotides (cap1, m7GpppNm, and cap2, m7GpppNmNm, respectively). These modifications are signatures of "self" in higher eukaryotes, whereas unmodified cap0-RNA is recognized as foreign and, therefore, potentially harmful to the host cell. IFIT1 inhibits translation at the initiation stage by competing with the cap-binding initiation factor complex, eIF4F, restricting infection by certain viruses that possess "nonself" cap0-mRNAs. However, in mice and other rodents, the IFIT1 orthologue has been lost, and the closely related Ifit1b has been duplicated twice, yielding three paralogues: Ifit1, Ifit1b, and Ifit1c. Although murine Ifit1 is similar to human IFIT1 in its cap0-RNA-binding selectivity, the roles of Ifit1b and Ifit1c are unknown. Here, we found that Ifit1b preferentially binds to cap1-RNA, whereas binding is much weaker to cap0- and cap2-RNA. In murine cells, we show that Ifit1b can modulate host translation and restrict WT mouse coronavirus infection. We found that Ifit1c acts as a stimulatory cofactor for both Ifit1 and Ifit1b, promoting their translation inhibition. In this way, Ifit1c acts in an analogous fashion to human IFIT3, which is a cofactor to human IFIT1. This work clarifies similarities and differences between the human and murine IFIT families to facilitate better design and interpretation of mouse models of human infection and sheds light on the evolutionary plasticity of the IFIT family.
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Affiliation(s)
- Harriet V Mears
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.
| | - Trevor R Sweeney
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.
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11
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Lei K, Zhang L, He Y, Sun H, Tong W, Xu Y, Jin L. Immune-associated biomarkers for early diagnosis of Parkinson's disease based on hematological lncRNA-mRNA co-expression. Biosci Rep 2020; 40:BSR20202921. [PMID: 33245101 PMCID: PMC7753636 DOI: 10.1042/bsr20202921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/22/2020] [Accepted: 11/26/2020] [Indexed: 02/07/2023] Open
Abstract
Early stage diagnosis of Parkinson's disease (PD) is challenging without significant motor symptoms. The identification of effective molecular biomarkers as a hematological indication of PD may help improve the diagnostic timeliness and accuracy. In this paper, we analyzed and compared the blood samples of PD and control (CTR) patients to identify the disease-related changes and determine the putative biomarkers for PD diagnosis. Based on the RNA sequencing analysis, differentially expressed genes (DEGs) were identified, and the co-expression network of DEGs was constructed using the weighted correlation network analysis (WGCNA). The analysis leads to the identification of 87 genes that were exclusively regulated in the PD group, whereas 66 genes were significantly increased and 21 genes were significantly decreased in contrast to the control group. The results indicate that the core lncRNA-mRNA co-expression network greatly changes the immune response in PD patients. Specifically, the results showed that PWAR6, LINC00861, AC83843.1, IRF family, IFIT family and CaMK4 may play important roles in the immune system of PD. Based on the findings from this the present study, future research aims at identify novel therapeutic strategies for PD.
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Affiliation(s)
- Kecheng Lei
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta 30322, GA, U.S.A
| | - Liwen Zhang
- National Engineering Research Center for Biochip, ShanghaiBiochip Limited Corporation, Shanghai 201203, P.R. China
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai 200065, P.R. China
| | - Yijing He
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Hui Sun
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Weifang Tong
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
| | - Yichun Xu
- National Engineering Research Center for Biochip, ShanghaiBiochip Limited Corporation, Shanghai 201203, P.R. China
- Department of Pathology, Shanghai Tongji Hospital, Tongji Hospital Affiliated to Tongji University, Shanghai 200065, P.R. China
| | - Lingjing Jin
- Neurotoxin Research Center of Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Neurological Department of Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, P.R. China
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12
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Koks S, Wood DJ, Reimann E, Awiszus F, Lohmann CH, Bertrand J, Prans E, Maasalu K, Märtson A. The Genetic Variations Associated With Time to Aseptic Loosening After Total Joint Arthroplasty. J Arthroplasty 2020; 35:981-988. [PMID: 31791832 DOI: 10.1016/j.arth.2019.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/07/2019] [Accepted: 11/04/2019] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Total joint arthroplasty (TJA) is one of the most frequent surgical procedures performed in modern hospitals, and aseptic loosening is the most common indication for revision surgeries. We conducted a systemic exploration of potential genetic determinants for early aseptic loosening. METHODS Data from 423 patients undergoing TJA were collected and analyzed. Three analytical groups were formed based on joint arthroplasty status. Group 1 were TJA patients without symptoms of aseptic loosening of at least 1 year, group 2 were patients with primary TJA, and group 3 were patients receiving revision surgery because of aseptic loosening. Genome-wide genotyping comparing genotype frequencies between patients with and without aseptic loosening (group 3 vs groups 1 and 2) was conducted. A case-control association analysis and linear modeling were applied to identify the impact of the identified genes on implant survival with time to the revision as an outcome measure. RESULTS We identified 52 single-nucleotide polymorphisms (SNPs) with a genome-wide suggestive P value less than 10-5 to be associated with the implant loosening. The most remarkable odds ratios (OR) were found with the variations in the IFIT2/IFIT3 (OR, 21.6), CERK (OR, 12.6), and PAPPA (OR, 14.0) genes. Variations in the genotypes of 4 SNPs-rs115871127, rs16823835, rs13275667, and rs2514486-predicted variability in the time to aseptic loosening. The time to aseptic loosening varied from 8 to 16 years depending on the genotype, indicating a substantial effect of genetic variance. CONCLUSION Development of the aseptic loosening is associated with several genetic variations and we identified at least 4 SNPs with a significant effect on the time for loosening. These data could help to develop a personalized approach for TJA and loosening management.
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Affiliation(s)
- Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia; The Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - David J Wood
- Department of Surgery, The University of Western Australia, Nedlands, WA, Australia
| | - Ene Reimann
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Friedemann Awiszus
- Department of Orthopaedic Surgery, Otto-von-Guericke University, Magdeburg, Germany
| | - Christoph H Lohmann
- Department of Orthopaedic Surgery, Otto-von-Guericke University, Magdeburg, Germany
| | - Jessica Bertrand
- Department of Orthopaedic Surgery, Otto-von-Guericke University, Magdeburg, Germany
| | - Ele Prans
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Katre Maasalu
- Department of Traumatology and Orthopaedics, University of Tartu, Tartu, Estonia; Clinic of Traumatology and Orthopaedics, Tartu University Hospital, Tartu, Estonia
| | - Aare Märtson
- Department of Traumatology and Orthopaedics, University of Tartu, Tartu, Estonia; Clinic of Traumatology and Orthopaedics, Tartu University Hospital, Tartu, Estonia
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13
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Komissarov AB, Sergeeva MV, Mozhaeva EV, Eshchenko NV, Vasilieva A, Vasilyev KA, Medvedev SP, Malakhova AA, Balakhonova EA, Malanin S, Grigoryeva TV, Zhuravlev ES, Semenov DV, Richter V, Stepanov G. Increase in Sensitivity of HEK293FT Cells to Influenza Infection by CRISPR-Cas9-Mediated Knockout of IRF7 Transcription Factor. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019060232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Pidugu VK, Pidugu HB, Wu MM, Liu CJ, Lee TC. Emerging Functions of Human IFIT Proteins in Cancer. Front Mol Biosci 2019; 6:148. [PMID: 31921891 PMCID: PMC6930875 DOI: 10.3389/fmolb.2019.00148] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
Interferon-induced protein with tetratricopeptide repeats (IFIT) genes are prominent interferon-stimulated genes (ISGs). The human IFIT gene family consists of four genes named IFIT1, IFIT2, IFIT3, and IFIT5. The expression of IFIT genes is very low in most cell types, whereas their expression is greatly enhanced by interferon treatment, viral infection, and pathogen-associated molecular patterns (PAMPs). The proteins encoded by IFIT genes have multiple tetratricopeptide repeat (TPR) motifs. IFIT proteins do not have any known enzymatic roles. However, they execute a variety of cellular functions by mediating protein-protein interactions and forming multiprotein complexes with cellular and viral proteins through their multiple TPR motifs. The versatile tertiary structure of TPR motifs in IFIT proteins enables them to be involved in distinct biological functions, including host innate immunity, antiviral immune response, virus-induced translation initiation, replication, double-stranded RNA signaling, and PAMP recognition. The current understanding of the IFIT proteins and their role in cellular signaling mechanisms is limited to the antiviral immune response and innate immunity. However, recent studies on IFIT protein functions and their involvement in various molecular signaling mechanisms have implicated them in cancer progression and metastasis. In this article, we focused on critical molecular, biological and oncogenic functions of human IFIT proteins by reviewing their prognostic significance in health and cancer. Research suggests that IFIT proteins could be novel therapeutic targets for cancer therapy.
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Affiliation(s)
| | | | - Meei-Maan Wu
- Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chung-Ji Liu
- Department of Oral and Maxillofacial Surgery, Mackay Memorial Hospital, Taipei, Taiwan
| | - Te-Chang Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Institute of Pharmacology, National Yang-Ming University, Taipei, Taiwan
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15
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Anjum FR, Rahman SU, Aslam MA, Qureshi AS. Comprehensive network map of transcriptional activation of chicken type I IFNs and IFN-stimulated genes. Comp Immunol Microbiol Infect Dis 2019; 68:101407. [PMID: 31877494 DOI: 10.1016/j.cimid.2019.101407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 12/04/2019] [Accepted: 12/16/2019] [Indexed: 01/04/2023]
Abstract
Chicken type I interferons (type I IFNs) are key antiviral players of the chicken immune system and mediate the first line of defense against viral pathogens infecting the avian species. Recognition of viral pathogens by specific pattern recognition receptors (PRRs) induce chicken type I IFNs expression followed by their subsequent interaction to IFN receptors and induction of a variety of IFN stimulated antiviral proteins. These antiviral effectors establish the antiviral state in neighboring cells and thus protect the host from infection. Three subtypes of chicken type I IFNs; chIFN-α, chIFN-β, and a recently discovered chIFN-κ have been identified and characterized in chicken. Chicken type I IFNs are activated by various host cell pathways and constitute a major antiviral innate defense in chicken. This review will help to understand the chicken type 1 IFNs, host cellular pathways that are involved in activation of chicken type I IFNs and IFN stimulated antiviral effectors along with the gaps in knowledge which will be important for future investigation. These findings will help us to comprehend the role of chicken type I IFNs and to develop different strategies for controlling viral infection in poultry.
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Affiliation(s)
| | - Sajjad Ur Rahman
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | | | - Anas Sarwar Qureshi
- Department of Anatomy, Faculty of Veterinary Science, University of Agriculture, Faisalabad, Pakistan
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16
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Xu M, Liu PP, Li H. Innate Immune Signaling and Its Role in Metabolic and Cardiovascular Diseases. Physiol Rev 2019; 99:893-948. [PMID: 30565509 DOI: 10.1152/physrev.00065.2017] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The innate immune system is an evolutionarily conserved system that senses and defends against infection and irritation. Innate immune signaling is a complex cascade that quickly recognizes infectious threats through multiple germline-encoded cell surface or cytoplasmic receptors and transmits signals for the deployment of proper countermeasures through adaptors, kinases, and transcription factors, resulting in the production of cytokines. As the first response of the innate immune system to pathogenic signals, inflammatory responses must be rapid and specific to establish a physical barrier against the spread of infection and must subsequently be terminated once the pathogens have been cleared. Long-lasting and low-grade chronic inflammation is a distinguishing feature of type 2 diabetes and cardiovascular diseases, which are currently major public health problems. Cardiometabolic stress-induced inflammatory responses activate innate immune signaling, which directly contributes to the development of cardiometabolic diseases. Additionally, although the innate immune elements are highly conserved in higher-order jawed vertebrates, lower-grade jawless vertebrates lack several transcription factors and inflammatory cytokine genes downstream of the Toll-like receptors (TLRs) and retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) pathways, suggesting that innate immune signaling components may additionally function in an immune-independent way. Notably, recent studies from our group and others have revealed that innate immune signaling can function as a vital regulator of cardiometabolic homeostasis independent of its immune function. Therefore, further investigation of innate immune signaling in cardiometabolic systems may facilitate the discovery of new strategies to manage the initiation and progression of cardiometabolic disorders, leading to better treatments for these diseases. In this review, we summarize the current progress in innate immune signaling studies and the regulatory function of innate immunity in cardiometabolic diseases. Notably, we highlight the immune-independent effects of innate immune signaling components on the development of cardiometabolic disorders.
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Affiliation(s)
- Meng Xu
- Department of Cardiology, Renmin Hospital of Wuhan University , Wuhan , China ; Medical Research Center, Zhongnan Hospital of Wuhan University , Wuhan , China ; Animal Experiment Center, Wuhan University , Wuhan , China ; Division of Cardiology, Department of Medicine, University of Ottawa Heart Institute, Ottawa, Ontario , Canada
| | - Peter P Liu
- Department of Cardiology, Renmin Hospital of Wuhan University , Wuhan , China ; Medical Research Center, Zhongnan Hospital of Wuhan University , Wuhan , China ; Animal Experiment Center, Wuhan University , Wuhan , China ; Division of Cardiology, Department of Medicine, University of Ottawa Heart Institute, Ottawa, Ontario , Canada
| | - Hongliang Li
- Department of Cardiology, Renmin Hospital of Wuhan University , Wuhan , China ; Medical Research Center, Zhongnan Hospital of Wuhan University , Wuhan , China ; Animal Experiment Center, Wuhan University , Wuhan , China ; Division of Cardiology, Department of Medicine, University of Ottawa Heart Institute, Ottawa, Ontario , Canada
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17
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Mears HV, Sweeney TR. Better together: the role of IFIT protein-protein interactions in the antiviral response. J Gen Virol 2018; 99:1463-1477. [PMID: 30234477 DOI: 10.1099/jgv.0.001149] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The interferon-induced proteins with tetratricopeptide repeats (IFITs) are a family of antiviral proteins conserved throughout all vertebrates. IFIT1 binds tightly to non-self RNA, particularly capped transcripts lacking methylation on the first cap-proximal nucleotide, and inhibits their translation by out-competing the cellular translation initiation apparatus. This exerts immense selection pressure on cytoplasmic RNA viruses to maintain mechanisms that protect their messenger RNA from IFIT1 recognition. However, it is becoming increasingly clear that protein-protein interactions are necessary for optimal IFIT function. Recently, IFIT1, IFIT2 and IFIT3 have been shown to form a functional complex in which IFIT3 serves as a central scaffold to regulate and/or enhance the antiviral functions of the other two components. Moreover, IFITs interact with other cellular proteins to expand their contribution to regulation of the host antiviral response by modulating innate immune signalling and apoptosis. Here, we summarize recent advances in our understanding of the IFIT complex and review how this impacts on the greater role of IFIT proteins in the innate antiviral response.
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Affiliation(s)
- Harriet V Mears
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Trevor R Sweeney
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
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18
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Fleith RC, Mears HV, Leong XY, Sanford TJ, Emmott E, Graham SC, Mansur DS, Sweeney TR. IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA. Nucleic Acids Res 2018; 46:5269-5285. [PMID: 29554348 PMCID: PMC6007307 DOI: 10.1093/nar/gky191] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/28/2018] [Accepted: 03/05/2018] [Indexed: 12/21/2022] Open
Abstract
Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed during the cell-intrinsic immune response to viral infection. IFIT1 inhibits translation by binding directly to the 5' end of foreign RNAs, particularly those with non-self cap structures, precluding the recruitment of the cap-binding eukaryotic translation initiation factor 4F and ribosome recruitment. The presence of IFIT1 imposes a requirement on viruses that replicate in the cytoplasm to maintain mechanisms to avoid its restrictive effects. Interaction of different IFIT family members is well described, but little is known of the molecular basis of IFIT association or its impact on function. Here, we reconstituted different complexes of IFIT1, IFIT2 and IFIT3 in vitro, which enabled us to reveal critical aspects of IFIT complex assembly. IFIT1 and IFIT3 interact via a YxxxL motif present in the C-terminus of each protein. IFIT2 and IFIT3 homodimers dissociate to form a more stable heterodimer that also associates with IFIT1. We show for the first time that IFIT3 stabilizes IFIT1 protein expression, promotes IFIT1 binding to a cap0 Zika virus reporter mRNA and enhances IFIT1 translation inhibition. This work reveals molecular aspects of IFIT interaction and provides an important missing link between IFIT assembly and function.
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Affiliation(s)
- Renata C Fleith
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, Florianópolis, Brazil
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Harriet V Mears
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Xin Yun Leong
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Thomas J Sanford
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Edward Emmott
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Stephen C Graham
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Daniel S Mansur
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Parasitology, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Trevor R Sweeney
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
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19
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Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses. Sci Rep 2018; 8:6794. [PMID: 29717152 PMCID: PMC5931624 DOI: 10.1038/s41598-018-24905-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 04/12/2018] [Indexed: 12/24/2022] Open
Abstract
The intracellular actions of interferon (IFN)-regulated proteins, including IFN-induced proteins with tetratricopeptide repeats (IFITs), attribute a major component of the protective antiviral host defense. Here we applied genomics approaches to annotate the chicken IFIT locus and currently identified a single IFIT (chIFIT5) gene. The profound transcriptional level of this effector of innate immunity was mapped within its unique cis-acting elements. This highly virus- and IFN-responsive chIFIT5 protein interacted with negative sense viral RNA structures that carried a triphosphate group on its 5' terminus (ppp-RNA). This interaction reduced the replication of RNA viruses in lentivirus-mediated IFIT5-stable chicken fibroblasts whereas CRISPR/Cas9-edited chIFIT5 gene knockout fibroblasts supported the replication of RNA viruses. Finally, we generated mosaic transgenic chicken embryos stably expressing chIFIT5 protein or knocked-down for endogenous chIFIT5 gene. Replication kinetics of RNA viruses in these transgenic chicken embryos demonstrated the antiviral potential of chIFIT5 in ovo. Taken together, these findings propose that IFIT5 specifically antagonize RNA viruses by sequestering viral nucleic acids in chickens, which are unique in innate immune sensing and responses to viruses of both poultry and human health significance.
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20
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Rohaim MA, Santhakumar D, Naggar RFE, Iqbal M, Hussein HA, Munir M. Chickens Expressing IFIT5 Ameliorate Clinical Outcome and Pathology of Highly Pathogenic Avian Influenza and Velogenic Newcastle Disease Viruses. Front Immunol 2018; 9:2025. [PMID: 30271403 PMCID: PMC6149294 DOI: 10.3389/fimmu.2018.02025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/16/2018] [Indexed: 12/18/2022] Open
Abstract
Innate antiviral immunity establishes first line of defense against invading pathogens through sensing their molecular structures such as viral RNA. This antiviral potential of innate immunity is mainly attributed to a myriad of IFN-stimulated genes (ISGs). Amongst well-characterized ISGs, we have previously shown that antiviral potential of chicken IFN-induced proteins with tetratricopeptides repeats 5 (chIFIT5) is determined by its interaction potential with 5'ppp containing viral RNA. Here, we generated transgenic chickens using avian sarcoma-leukosis virus (RCAS)-based gene transfer system that constitutively and stably express chIFIT5. The transgenic chickens infected with clinical dose (EID50 104 for HPAIV and 105 EID50 for vNDV) of high pathogenicity avian influenza virus (HPAIV; H5N1) or velogenic strain of Newcastle disease virus (vNDV; Genotype VII) showed marked resistance against infections. While transgenic chickens failed to sustain a lethal dose of these viruses (EID50 105 for HPAIV and 106 EID50 for vNDV), a delayed and lower level of clinical disease and mortality, reduced virus shedding and tissue damage was observed compared to non-transgenic control chickens. These observations suggest that stable expression of chIFIT5 alone is potentially insufficient in providing sterile protection against these highly virulent viruses; however, it is sufficient to ameliorate the clinical outcome of these RNA viruses. These findings propose the potential of innate immune genes in conferring genetic resistance in chickens against highly pathogenic and zoonotic viral pathogens causing sever disease in both animals and humans.
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Affiliation(s)
- Mohammed A Rohaim
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.,The Pirbright Institute, Woking, United Kingdom.,Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Diwakar Santhakumar
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Rania F El Naggar
- Department of Virology, Faculty of Veterinary Medicine, University of Sadat City, Sadat, Egypt
| | - Munir Iqbal
- The Pirbright Institute, Woking, United Kingdom
| | - Hussein A Hussein
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
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Zhang QM, Zhao X, Li Z, Wu M, Gui JF, Zhang YB. Alternative Splicing Transcripts of Zebrafish LGP2 Gene Differentially Contribute to IFN Antiviral Response. THE JOURNAL OF IMMUNOLOGY 2017; 200:688-703. [PMID: 29203516 DOI: 10.4049/jimmunol.1701388] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/05/2017] [Indexed: 01/08/2023]
Abstract
In mammals, RIG-I like receptors (RLRs) RIG-I and melanoma differentiation-associated gene 5 (MDA5) sense cytosolic viral RNA, leading to IFN antiviral response; however, LGP2 exhibits controversial functions. The same happens to fish LGP2. In this study we report that three zebrafish LGP2 splicing transcripts, a full-length LGP2, and two truncating variants, LGP2v1 and LGP2v2, play distinct roles during IFN antiviral response. Overexpression of the full-length LGP2 not only potentiates IFN response through the RLR pathway, in the absence or presence of poly(I:C) at limited concentrations, but also inhibits IFN response by relative high concentrations of poly(I:C) through functional attenuation of signaling factors involved in the RLR pathway; however, LGP2v1 and LGP2v2 only retain the inhibitory role. Consistently, LGP2 but not LGP2v1 and LGP2v2 confers protection on fish cells against spring viremia of carp virus (SVCV) infection and at limited expression levels, LGP2 exerts more significant protection than either RIG-I or MDA5. Further data suggest that in the early phase of SVCV infection, LGP2 functions as a positive regulator but along with SVCV replicating in cells up to a certain titer, which leads to a far more robust expression of IFN, LGP2 switches to a negative role. These in vitro results suggest an ingenious mechanism where the three zebrafish LGP2 splicing transcripts work cooperatively to shape IFN antiviral responses.
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Affiliation(s)
- Qi-Min Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control of Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Xiang Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control of Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control of Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and
| | - Min Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control of Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control of Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yi-Bing Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control of Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; and .,University of Chinese Academy of Sciences, Beijing 10049, China
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22
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Torres-Odio S, Key J, Hoepken HH, Canet-Pons J, Valek L, Roller B, Walter M, Morales-Gordo B, Meierhofer D, Harter PN, Mittelbronn M, Tegeder I, Gispert S, Auburger G. Progression of pathology in PINK1-deficient mouse brain from splicing via ubiquitination, ER stress, and mitophagy changes to neuroinflammation. J Neuroinflammation 2017; 14:154. [PMID: 28768533 PMCID: PMC5541666 DOI: 10.1186/s12974-017-0928-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 07/26/2017] [Indexed: 12/18/2022] Open
Abstract
Background PINK1 deficiency causes the autosomal recessive PARK6 variant of Parkinson’s disease. PINK1 activates ubiquitin by phosphorylation and cooperates with the downstream ubiquitin ligase PARKIN, to exert quality control and control autophagic degradation of mitochondria and of misfolded proteins in all cell types. Methods Global transcriptome profiling of mouse brain and neuron cultures were assessed in protein-protein interaction diagrams and by pathway enrichment algorithms. Validation by quantitative reverse transcriptase polymerase chain reaction and immunoblots was performed, including human neuroblastoma cells and patient primary skin fibroblasts. Results In a first approach, we documented Pink1-deleted mice across the lifespan regarding brain mRNAs. The expression changes were always subtle, consistently affecting “intracellular membrane-bounded organelles”. Significant anomalies involved about 250 factors at age 6 weeks, 1300 at 6 months, and more than 3500 at age 18 months in the cerebellar tissue, including Srsf10, Ube3a, Mapk8, Creb3, and Nfkbia. Initially, mildly significant pathway enrichment for the spliceosome was apparent. Later, highly significant networks of ubiquitin-mediated proteolysis and endoplasmic reticulum protein processing occurred. Finally, an enrichment of neuroinflammation factors appeared, together with profiles of bacterial invasion and MAPK signaling changes—while mitophagy had minor significance. Immunohistochemistry showed pronounced cellular response of Iba1-positive microglia and GFAP-positive astrocytes; brain lipidomics observed increases of ceramides as neuroinflammatory signs at old age. In a second approach, we assessed PINK1 deficiency in the presence of a stressor. Marked dysregulations of microbial defense factors Ifit3 and Rsad2 were consistently observed upon five analyses: (1) Pink1−/− primary neurons in the first weeks after brain dissociation, (2) aged Pink1−/− midbrain with transgenic A53T-alpha-synuclein overexpression, (3) human neuroblastoma cells with PINK1-knockdown and murine Pink1−/− embryonal fibroblasts undergoing acute starvation, (4) triggering mitophagy in these cells with trifluoromethoxy carbonylcyanide phenylhydrazone (FCCP), and (5) subjecting them to pathogenic RNA-analogue poly(I:C). The stress regulation of MAVS, RSAD2, DDX58, IFIT3, IFIT1, and LRRK2 was PINK1 dependent. Dysregulation of some innate immunity genes was also found in skin fibroblast cells from PARK6 patients. Conclusions Thus, an individual biomarker with expression correlating to progression was not identified. Instead, more advanced disease stages involved additional pathways. Hence, our results identify PINK1 deficiency as an early modulator of innate immunity in neurons, which precedes late stages of neuroinflammation during alpha-synuclein spreading. Electronic supplementary material The online version of this article (doi:10.1186/s12974-017-0928-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sylvia Torres-Odio
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Jana Key
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Hans-Hermann Hoepken
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Júlia Canet-Pons
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Lucie Valek
- Institute of Clinical Pharmacology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Bastian Roller
- Edinger-Institute (Institute of Neurology), Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Michael Walter
- Institute for Medical Genetics, Eberhard-Karls-University of Tuebingen, 72076, Tuebingen, Germany
| | - Blas Morales-Gordo
- Department of Neurology, University Hospital San Cecilio, 18012, Granada, Spain
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Patrick N Harter
- Edinger-Institute (Institute of Neurology), Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Michel Mittelbronn
- Edinger-Institute (Institute of Neurology), Goethe University Medical School, 60590, Frankfurt am Main, Germany.,Luxembourg Centre of Neuropathology (LCNP), Luxembourg, Luxembourg.,Department of Pathology, Laboratoire National de Santé, Dudelange, Luxembourg.,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg, Luxembourg.,Department of Oncology, Luxembourg Institute of Health, NORLUX Neuro-Oncology Laboratory, Luxembourg, Luxembourg
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Suzana Gispert
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany.
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23
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Hwang JY, Ahn SJ, Kwon MG, Seo JS, Hwang SD, Son MH. Interferon-induced protein 56 (IFI56) is induced by VHSV infection but not by bacterial infection in olive flounder (Paralichthys olivaceus). FISH & SHELLFISH IMMUNOLOGY 2017; 66:382-389. [PMID: 28499966 DOI: 10.1016/j.fsi.2017.05.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/30/2017] [Accepted: 05/08/2017] [Indexed: 06/07/2023]
Abstract
Interferon-inducible protein 56 (IFI56, also known as ISG56/IFIT1, interferon-induced protein with tetratricopeptide repeats 1) is strongly induced in response to interferon and a potent inhibitor of viral replication and translational initiation. Here, we describe the identification of IFI56 (OfIFI56) in olive flounder, its characteristic features, and expression levels in various tissues before and after viral hemorrhagic septicemia virus (VHSV) infection. The full-length OfIFI56 sequence was identified from rapid amplification of cDNA ends PCR. The complete coding sequence of OfIFI56 is 1971 bp in length and encodes 431 amino acids. The putative OfIFI56 protein has multiple tetratricopeptide (TPR) motifs, which regulate diverse biological processes, such as organelle targeting, protein import, and vesicle fusion. Based on sequence analysis, the Larimichthys crocea IFI56 protein (61%) had the highest sequence homology to OfIFI56. In healthy olive flounder, OfIFI56 mRNA expression was detected in many tissues such as intestine, gill, head kidney, heart, spleen, and trunk kidney tissues. After VHSV challenge, OfIFI56 mRNA was significantly up-regulated in these tissues. Additionally, OfIFI56 expression was induced by poly I:C but not by Streptococcus parauberis and S. iniae infection or lipopolysaccharide injection in kidney and spleen tissues of olive flounder. These results demonstrate that piscine OfIFI56 expression is not induced by bacterial infection but is selectively induced by viral infection, especially VHSV, and that OfIFI56 may play an important role in the host response against VHSV infection.
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Affiliation(s)
- Jee Youn Hwang
- Aquatic Disease Control Division, National Institute of Fisheries Science (NIFS), 216 Gijanghaean-ro, Gijang-eup, Gijang-gun, Busan 46083, Republic of Korea.
| | - Sang Jung Ahn
- Fisheries R&D Management Center, Korea Institute of Marine Science & Technology Promotion (KIMST), Seoul 06775, Republic of Korea.
| | - Mun-Gyeong Kwon
- Aquatic Disease Control Division, National Institute of Fisheries Science (NIFS), 216 Gijanghaean-ro, Gijang-eup, Gijang-gun, Busan 46083, Republic of Korea.
| | - Jung Soo Seo
- Aquatic Disease Control Division, National Institute of Fisheries Science (NIFS), 216 Gijanghaean-ro, Gijang-eup, Gijang-gun, Busan 46083, Republic of Korea.
| | - Seong Don Hwang
- Aquatic Disease Control Division, National Institute of Fisheries Science (NIFS), 216 Gijanghaean-ro, Gijang-eup, Gijang-gun, Busan 46083, Republic of Korea.
| | - Maeng-Hyun Son
- Aquatic Disease Control Division, National Institute of Fisheries Science (NIFS), 216 Gijanghaean-ro, Gijang-eup, Gijang-gun, Busan 46083, Republic of Korea.
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24
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XU W, CHEN S. Genomics and genetic breeding in aquatic animals: progress and prospects. FRONTIERS OF AGRICULTURAL SCIENCE AND ENGINEERING 2017; 4:305. [DOI: 10.15302/j-fase-2017154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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25
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Liu QN, Xin ZZ, Chai XY, Jiang SH, Li CF, Zhang HB, Ge BM, Zhang DZ, Zhou CL, Tang BP. Characterization of immune-related genes in the yellow catfish Pelteobagrus fulvidraco in response to LPS challenge. FISH & SHELLFISH IMMUNOLOGY 2016; 56:248-254. [PMID: 27235365 DOI: 10.1016/j.fsi.2016.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/03/2016] [Accepted: 05/17/2016] [Indexed: 06/05/2023]
Abstract
Fish are considered an excellent model for studies in comparative immunology as they are a representative population of lower vertebrates linked to invertebrate evolution. To gain a better understanding of the immune response in fish, we constructed a subtractive cDNA library from the head kidney of lipopolysaccharide-stimulated yellow catfish (Pelteobagrus fulvidraco) using suppression subtractive hybridization (SSH). A total of 300 putative EST clones were identified which contained 95 genes, including 27 immune-related genes, 7 cytoskeleton-related genes, 3 genes involved in the cell cycle and apoptosis, 9 respiration and energy metabolism-related genes, 7 genes related to transport, 24 metabolism-related genes, 10 genes involved in stress responses, seven genes involved in regulation of transcription and translation and 59 unknown genes. Using real-time quantitative reverse transcription PCR, a subset of randomly selected genes involved in the immune response to lipopolysaccharide challenge were investigated to verify the reliability of the SSH data which identified 16 up-regulated genes. The genes identified in this study provide novel insight into the immune response in fish.
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Affiliation(s)
- Qiu-Ning Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Zhao-Zhe Xin
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Xin-Yue Chai
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Sen-Hao Jiang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Chao-Feng Li
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Hua-Bin Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Bao-Ming Ge
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Dai-Zhen Zhang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Chun-Lin Zhou
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China
| | - Bo-Ping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng 224051, PR China.
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26
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Feng H, Zhang QM, Zhang YB, Li Z, Zhang J, Xiong YW, Wu M, Gui JF. Zebrafish IRF1, IRF3, and IRF7 Differentially Regulate IFNΦ1 and IFNΦ3 Expression through Assembly of Homo- or Heteroprotein Complexes. THE JOURNAL OF IMMUNOLOGY 2016; 197:1893-904. [DOI: 10.4049/jimmunol.1600159] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 07/04/2016] [Indexed: 11/19/2022]
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27
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Li J, Chu Q, Xu T. A genome-wide survey of expansive NLR-C subfamily in miiuy croaker and characterization of the NLR-B30.2 genes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2016; 61:116-125. [PMID: 26979266 DOI: 10.1016/j.dci.2016.03.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/10/2016] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
NOD-like receptors (NLRs) are essential intracellular pattern-recognition receptors that respond to pathogens and regulate innate immunity. NLRs include three distinct subfamilies: NLR-A, NLR-B and NLR-C, thereinto, NLR-C as a large subfamily is unique to bony fish and little research about it has been done. In the current study, we identified the members of NLR-B and NLR-C subfamilies containing 2 and 48 genes respectively in miiuy croaker. Compared with other teleosts except for zebrafish, NLR-C subfamily genes occurred expansion in miiuy croaker. The gene expansions of NLR-C subfamily may illustrate adaptive genome evolution in response to specific aquatic environments. Structural analysis showed that the N-terminus of NLR-C subfamily receptors has different characteristics of the domains including RING domain, FISNA domain or PYRIN domain. Interestingly, the C-terminus of 18 NLR-C subfamily members contains an extra B30.2 domain (named NLR-B30.2 genes) which plays an important role in antiviral immune recognition. Simultaneously, molecular evolutionary analysis indicated that the positively sites in miiuy croaker are mainly located in NACHT domain which was the vital region for signal transduction in immune response. Significantly, pathogens challenge in spleen and macrophages demonstrated that NLR-B30.2 genes exhibited more sensitive response to virus than bacteria, suggesting these genes play enhanced roles in innate antiviral immunity, which may represent a new family used for antiviral infection.
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Affiliation(s)
- Jinrui Li
- 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
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
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28
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Henzy JE, Johnson WE. Phylogenetic sleuthing reveals pair of paralogous genes. eLife 2016; 5. [PMID: 27244557 PMCID: PMC4887199 DOI: 10.7554/elife.17224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 05/24/2016] [Indexed: 11/25/2022] Open
Abstract
The complex evolutionary history of the IFIT family of antiviral genes has been shaped by continuous interactions between mammalian hosts and their many viruses.
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Affiliation(s)
- Jamie E Henzy
- Biology Department, Boston College, Chestnut Hill, United States
| | - Welkin E Johnson
- Biology Department, Boston College, Chestnut Hill, United States
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29
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Daugherty MD, Schaller AM, Geballe AP, Malik HS. Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals. eLife 2016; 5. [PMID: 27240734 PMCID: PMC4887208 DOI: 10.7554/elife.14228] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/13/2016] [Indexed: 12/21/2022] Open
Abstract
IFIT (interferon-induced with tetratricopeptide repeats) proteins are critical mediators of mammalian innate antiviral immunity. Mouse IFIT1 selectively inhibits viruses that lack 2'O-methylation of their mRNA 5' caps. Surprisingly, human IFIT1 does not share this antiviral specificity. Here, we resolve this discrepancy by demonstrating that human and mouse IFIT1 have evolved distinct functions using a combination of evolutionary, genetic and virological analyses. First, we show that human IFIT1 and mouse IFIT1 (renamed IFIT1B) are not orthologs, but are paralogs that diverged >100 mya. Second, using a yeast genetic assay, we show that IFIT1 and IFIT1B proteins differ in their ability to be suppressed by a cap 2'O-methyltransferase. Finally, we demonstrate that IFIT1 and IFIT1B have divergent antiviral specificities, including the discovery that only IFIT1 proteins inhibit a virus encoding a cap 2'O-methyltransferase. These functional data, combined with widespread turnover of mammalian IFIT genes, reveal dramatic species-specific differences in IFIT-mediated antiviral repertoires.
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Affiliation(s)
- Matthew D Daugherty
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Aaron M Schaller
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Adam P Geballe
- Divisions of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States.,Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Microbiology, University of Washington School of Medicine, Seattle, United States.,Department of Medicine, University of Washington School of Medicine, Seattle, United States
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, United States
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30
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Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni JC, Soylemez O, Kondrashov F, Leptin M. Structure and evolutionary history of a large family of NLR proteins in the zebrafish. Open Biol 2016; 6:160009. [PMID: 27248802 PMCID: PMC4852459 DOI: 10.1098/rsob.160009] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/05/2016] [Indexed: 12/14/2022] Open
Abstract
Multicellular eukaryotes have evolved a range of mechanisms for immune recognition. A widespread family involved in innate immunity are the NACHT-domain and leucine-rich-repeat-containing (NLR) proteins. Mammals have small numbers of NLR proteins, whereas in some species, mostly those without adaptive immune systems, NLRs have expanded into very large families. We describe a family of nearly 400 NLR proteins encoded in the zebrafish genome. The proteins share a defining overall structure, which arose in fishes after a fusion of the core NLR domains with a B30.2 domain, but can be subdivided into four groups based on their NACHT domains. Gene conversion acting differentially on the NACHT and B30.2 domains has shaped the family and created the groups. Evidence of positive selection in the B30.2 domain indicates that this domain rather than the leucine-rich repeats acts as the pathogen recognition module. In an unusual chromosomal organization, the majority of the genes are located on one chromosome arm, interspersed with other large multigene families, including a new family encoding zinc-finger proteins. The NLR-B30.2 proteins represent a new family with diversity in the specific recognition module that is present in fishes in spite of the parallel existence of an adaptive immune system.
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Affiliation(s)
| | - Philipp H Schiffer
- Institut für Genetik, Universität zu Köln, Köln, Germany The European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Thomas Wiehe
- Institut für Genetik, Universität zu Köln, Köln, Germany
| | | | - John C Marioni
- Wellcome Trust Sanger Institute, Cambridge, UK The European Molecular Biology Laboratory, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
| | - Onuralp Soylemez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) 88 Dr. Aiguader, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Fyodor Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) 88 Dr. Aiguader, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, 08010 Barcelona, Spain
| | - Maria Leptin
- Institut für Genetik, Universität zu Köln, Köln, Germany The European Molecular Biology Laboratory, Heidelberg, Germany
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31
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Niess H, Camaj P, Mair R, Renner A, Zhao Y, Jäckel C, Nelson PJ, Jauch KW, Bruns CJ. Overexpression of IFN-induced protein with tetratricopeptide repeats 3 (IFIT3) in pancreatic cancer: cellular "pseudoinflammation" contributing to an aggressive phenotype. Oncotarget 2016; 6:3306-18. [PMID: 25650658 PMCID: PMC4413655 DOI: 10.18632/oncotarget.2494] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/16/2014] [Indexed: 12/20/2022] Open
Abstract
Inflammation contributes to important traits that cancer cells acquire during malignant progression. Gene array data recently identified upregulation of interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) in aggressive pancreatic cancer cells. IFIT3 belongs to the group of interferon stimulated genes (ISG), can be induced by several cellular stress stimuli and by its tetratricopeptide repeats interacts with a multitude of cellular proteins. Upregulation of IFIT3 was confirmed in the aggressive pancreatic cancer cell line L3.6pl compared with its less aggressive cell line of origin, COLO357FG. Transgenic induction of IFIT3 expression in COLO357FG resulted in greater mass of orthotopic tumors and higher prevalence of metastases. Several important traits that mediate malignancy were altered by IFIT3: increased VEGF and IL-6 secretion, chemoresistance and decreased starvation-induced apoptosis. IFIT3 showed binding to JNK and STAT1, the latter being an important inducer of IFIT3 expression. Despite still being alterable by “classical” IFN or NFκB signaling, our findings indicate constitutive - possibly auto-regulated - upregulation of IFIT3 in L3.6pl without presence of an adequate inflammatory stimulus. The transcription factor SOX9, which is linked to regulation of hypoxia-related genes, was identified as a key mediator of upregulation of the oncogene IFIT3 and thereby sustaining a “pseudoinflammatory” cellular condition.
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Affiliation(s)
- Hanno Niess
- Department of Surgery, Medical Center of the Ludwig-Maximilians-University, Campus Grosshadern, Munich, Germany
| | - Peter Camaj
- Department of Surgery, Medical Center of the Otto-von-Guericke-University, Magdeburg, Germany
| | - Ruth Mair
- Department of Surgery, Medical Center of the Ludwig-Maximilians-University, Campus Grosshadern, Munich, Germany
| | - Andrea Renner
- Department of Surgery, Medical Center of the Ludwig-Maximilians-University, Campus Grosshadern, Munich, Germany
| | - Yue Zhao
- Department of Surgery, Medical Center of the Ludwig-Maximilians-University, Campus Grosshadern, Munich, Germany
| | - Carsten Jäckel
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universitaet Muenchen, Arbeitsgruppe Klinische Biochemie, Munich, Germany
| | - Peter J Nelson
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universitaet Muenchen, Arbeitsgruppe Klinische Biochemie, Munich, Germany
| | - Karl-Walter Jauch
- Department of Surgery, Medical Center of the Ludwig-Maximilians-University, Campus Grosshadern, Munich, Germany
| | - Christiane J Bruns
- Department of Surgery, Medical Center of the Otto-von-Guericke-University, Magdeburg, Germany
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32
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Human and Murine IFIT1 Proteins Do Not Restrict Infection of Negative-Sense RNA Viruses of the Orthomyxoviridae, Bunyaviridae, and Filoviridae Families. J Virol 2015; 89:9465-76. [PMID: 26157117 DOI: 10.1128/jvi.00996-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 06/28/2015] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED Interferon-induced protein with tetratricopeptide repeats 1 (IFIT1) is a host protein with reported cell-intrinsic antiviral activity against several RNA viruses. The proposed basis for the activity against negative-sense RNA viruses is the binding to exposed 5'-triphosphates (5'-ppp) on the genome of viral RNA. However, recent studies reported relatively low binding affinities of IFIT1 for 5'-ppp RNA, suggesting that IFIT1 may not interact efficiently with this moiety under physiological conditions. To evaluate the ability of IFIT1 to have an impact on negative-sense RNA viruses, we infected Ifit1(-/-) and wild-type control mice and primary cells with four negative-sense RNA viruses (influenza A virus [IAV], La Crosse virus [LACV], Oropouche virus [OROV], and Ebola virus) corresponding to three distinct families. Unexpectedly, a lack of Ifit1 gene expression did not result in increased infection by any of these viruses in cell culture. Analogously, morbidity, mortality, and viral burdens in tissues were identical between Ifit1(-/-) and control mice after infection with IAV, LACV, or OROV. Finally, deletion of the human IFIT1 protein in A549 cells did not affect IAV replication or infection, and reciprocally, ectopic expression of IFIT1 in HEK293T cells did not inhibit IAV infection. To explain the lack of antiviral activity against IAV, we measured the binding affinity of IFIT1 for RNA oligonucleotides resembling the 5' ends of IAV gene segments. The affinity for 5'-ppp RNA was approximately 10-fold lower than that for non-2'-O-methylated (cap 0) RNA oligonucleotides. Based on this analysis, we conclude that IFIT1 is not a dominant restriction factor against negative-sense RNA viruses. IMPORTANCE Negative-sense RNA viruses, including influenza virus and Ebola virus, have been responsible for some of the most deadly outbreaks in recent history. The host interferon response and induction of antiviral genes contribute to the control of infections by these viruses. IFIT1 is highly induced after virus infection and reportedly has antiviral activity against several RNA and DNA viruses. However, its role in restricting infection by negative-sense RNA viruses remains unclear. In this study, we evaluated the ability of IFIT1 to inhibit negative-sense RNA virus replication and pathogenesis both in vitro and in vivo. Detailed cell culture and animal studies demonstrated that IFIT1 is not a dominant restriction factor against three different families of negative-sense RNA viruses.
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Comparative Evolution of Duplicated Ddx3 Genes in Teleosts: Insights from Japanese Flounder, Paralichthys olivaceus. G3-GENES GENOMES GENETICS 2015; 5:1765-73. [PMID: 26109358 PMCID: PMC4528332 DOI: 10.1534/g3.115.018911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Following the two rounds of whole-genome duplication that occurred during deuterostome evolution, a third genome duplication event occurred in the stem lineage of ray-finned fishes. This teleost-specific genome duplication is thought to be responsible for the biological diversification of ray-finned fishes. DEAD-box polypeptide 3 (DDX3) belongs to the DEAD-box RNA helicase family. Although their functions in humans have been well studied, limited information is available regarding their function in teleosts. In this study, two teleost Ddx3 genes were first identified in the transcriptome of Japanese flounder (Paralichthys olivaceus). We confirmed that the two genes originated from teleost-specific genome duplication through synteny and phylogenetic analysis. Additionally, comparative analysis of genome structure, molecular evolution rate, and expression pattern of the two genes in Japanese flounder revealed evidence of subfunctionalization of the duplicated Ddx3 genes in teleosts. Thus, the results of this study reveal novel insights into the evolution of the teleost Ddx3 genes and constitute important groundwork for further research on this gene family.
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Zhang XJ, Zhang P, Li H. Interferon regulatory factor signalings in cardiometabolic diseases. Hypertension 2015; 66:222-47. [PMID: 26077571 DOI: 10.1161/hypertensionaha.115.04898] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/14/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Xiao-Jing Zhang
- From the Department of Cardiology, Renmin Hospital (X.-J.Z., P.Z., H.L.) and Cardiovascular Research Institute (X.-J.Z., P.Z., H.L.), Wuhan University, Wuhan, China; and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, PR China (X.-J.Z.)
| | - Peng Zhang
- From the Department of Cardiology, Renmin Hospital (X.-J.Z., P.Z., H.L.) and Cardiovascular Research Institute (X.-J.Z., P.Z., H.L.), Wuhan University, Wuhan, China; and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, PR China (X.-J.Z.)
| | - Hongliang Li
- From the Department of Cardiology, Renmin Hospital (X.-J.Z., P.Z., H.L.) and Cardiovascular Research Institute (X.-J.Z., P.Z., H.L.), Wuhan University, Wuhan, China; and State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, PR China (X.-J.Z.).
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35
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Hyde JL, Diamond MS. Innate immune restriction and antagonism of viral RNA lacking 2׳-O methylation. Virology 2015; 479-480:66-74. [PMID: 25682435 PMCID: PMC4424151 DOI: 10.1016/j.virol.2015.01.019] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/22/2015] [Indexed: 01/31/2023]
Abstract
N-7 and 2′-O methylation of host cell mRNA occurs in the nucleus and results in the generation of cap structures (cap 0, m7GpppN; cap 1, m7GpppNm) that control gene expression by modulating nuclear export, splicing, turnover, and protein synthesis. Remarkably, RNA cap modification also contributes to mammalian cell host defense as viral RNA lacking 2′-O methylation is sensed and inhibited by IFIT1, an interferon (IFN) stimulated gene (ISG). Accordingly, pathogenic viruses that replicate in the cytoplasm have evolved mechanisms to circumvent IFIT1 restriction and facilitate infection of mammalian cells. These include: (a) generating cap 1 structures on their RNA through cap-snatching or virally-encoded 2′-O methyltransferases, (b) using cap-independent means of translation, or (c) using RNA secondary structural motifs to antagonize IFIT1 binding. This review will discuss new insights as to how specific modifications at the 5′-end of viral RNA modulate host pathogen recognition responses to promote infection and disease.
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Affiliation(s)
- Jennifer L Hyde
- Departments of Medicine, Washington University School of Medicine, St Louis., MO 63110, USA
| | - Michael S Diamond
- Departments of Medicine, Washington University School of Medicine, St Louis., MO 63110, USA; Molecular Microbiology, Washington University School of Medicine, St Louis., MO 63110 USA; Pathology & Immunology, Washington University School of Medicine, St Louis., MO 63110, USA; The Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis., MO 63110, USA.
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36
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Feng H, Zhang YB, Zhang QM, Li Z, Zhang QY, Gui JF. Zebrafish IRF1 Regulates IFN Antiviral Response through Binding to IFNϕ1 and IFNϕ3 Promoters Downstream of MyD88 Signaling. THE JOURNAL OF IMMUNOLOGY 2014; 194:1225-38. [DOI: 10.4049/jimmunol.1402415] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Long H, Sun L. CsIFIT1, an interferon-induced protein with tetratricopeptide repeat, inhibits viral infection in tongue sole (Cynoglossus semilaevis). FISH & SHELLFISH IMMUNOLOGY 2014; 41:231-237. [PMID: 25218274 DOI: 10.1016/j.fsi.2014.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/18/2014] [Accepted: 09/02/2014] [Indexed: 06/03/2023]
Abstract
Interferon-induced protein with tetratricopeptide repeats (IFIT) is involved in antiviral immunity in mammalian cells. In fish, the function of this group of proteins is unknown. In this study, we report the identification of an IFIT homologue (named CsIFIT1) from tongue sole (Cynoglossus semilaevis) and examined its antiviral potential. CsIFIT1 is composed of 436 residues and shares 30.9%-58.7% overall sequence identities with the known IFITs of a number of teleost species. In silico analysis identified two tetratricopeptide repeats in CsIFIT1. Quantitative real time RT-PCR analysis showed that CsIFIT1 expression was most abundant in immune relevant organs and upregulated, in a time-dependent manner, by experimental infection with the fish viral pathogen megalocytivirus. When CsIFIT1 was overexpressed in tongue sole before megalocytivirus infection, viral replication in fish tissues was blocked to significant extents. Consistently, when CsIFIT1 expression in tongue sole was knocked down by siRNA, viral replication in fish tissues was significantly enhanced. Taken together, these results indicate that CsIFIT1 is likely a key factor of antiviral immunity and is required for optimal defense against viral infection.
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Affiliation(s)
- Hao Long
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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38
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Cellular visualization of macrophage pyroptosis and interleukin-1β release in a viral hemorrhagic infection in zebrafish larvae. J Virol 2014; 88:12026-40. [PMID: 25100833 DOI: 10.1128/jvi.02056-14] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Hemorrhagic viral diseases are distributed worldwide with important pathogens, such as dengue virus or hantaviruses. The lack of adequate in vivo infection models has limited the research on viral pathogenesis and the current understanding of the underlying infection mechanisms. Although hemorrhages have been associated with the infection of endothelial cells, other cellular types could be the main targets for hemorrhagic viruses. Our objective was to take advantage of the use of zebrafish larvae in the study of viral hemorrhagic diseases, focusing on the interaction between viruses and host cells. Cellular processes, such as transendothelial migration of leukocytes, virus-induced pyroptosis of macrophages. and interleukin-1β (Il-1β) release, could be observed in individual cells, providing a deeper knowledge of the immune mechanisms implicated in the disease. Furthermore, the application of these techniques to other pathogens will improve the current knowledge of host-pathogen interactions and increase the potential for the discovery of new therapeutic targets. Importance: Pathogenic mechanisms of hemorrhagic viruses are diverse, and most of the research regarding interactions between viruses and host cells has been performed in cell lines that might not be major targets during natural infections. Thus, viral pathogenesis research has been limited because of the lack of adequate in vivo infection models. The understanding of the relative pathogenic roles of the viral agent and the host response to the infection is crucial. This will be facilitated by the establishment of in vivo infection models using organisms such as zebrafish, which allows the study of the diseases in the context of a complete individual. The use of this animal model with other pathogens could improve the current knowledge on host-pathogen interactions and increase the potential for the discovery of new therapeutic targets against diverse viral diseases.
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39
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Broad and adaptable RNA structure recognition by the human interferon-induced tetratricopeptide repeat protein IFIT5. Proc Natl Acad Sci U S A 2014; 111:12025-30. [PMID: 25092312 DOI: 10.1073/pnas.1412842111] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Interferon (IFN) responses play key roles in cellular defense against pathogens. Highly expressed IFN-induced proteins with tetratricopeptide repeats (IFITs) are proposed to function as RNA binding proteins, but the RNA binding and discrimination specificities of IFIT proteins remain unclear. Here we show that human IFIT5 has comparable affinity for RNAs with diverse phosphate-containing 5'-ends, excluding the higher eukaryotic mRNA cap. Systematic mutagenesis revealed that sequence substitutions in IFIT5 can alternatively expand or introduce bias in protein binding to RNAs with 5' monophosphate, triphosphate, cap0 (triphosphate-bridged N7-methylguanosine), or cap1 (cap0 with RNA 2'-O-methylation). We defined the breadth of cellular ligands for IFIT5 by using a thermostable group II intron reverse transcriptase for RNA sequencing. We show that IFIT5 binds precursor and processed tRNAs, as well as other RNA polymerase III transcripts. Our findings establish the RNA recognition specificity of the human innate immune response protein IFIT5.
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40
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Pereiro P, Costa MM, Díaz-Rosales P, Dios S, Figueras A, Novoa B. The first characterization of two type I interferons in turbot (Scophthalmus maximus) reveals their differential role, expression pattern and gene induction. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 45:233-244. [PMID: 24680948 DOI: 10.1016/j.dci.2014.03.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 06/03/2023]
Abstract
Type I interferons (IFNs) are considered the main cytokines directing the antiviral immune response in vertebrates. These molecules are able to induce the transcription of interferon-stimulated genes (ISGs) which, using different blocking mechanisms, reduce the viral proliferation in the host. In addition, a contradictory role of these IFNs in the protection against bacterial challenges using murine models has been observed, increasing the survival or having a detrimental effect depending on the bacteria species. In teleosts, a variable number of type I IFNs has been described with different expression patterns, protective capabilities or gene induction profiles even for the different IFNs belonging to the same species. In this work, two type I IFNs (ifn1 and ifn2) have been characterized for the first time in turbot (Scophthalmus maximus), showing different properties. Whereas Ifn1 reflected a clear antiviral activity (over-expression of ISGs and protection against viral haemorrhagic septicaemia virus), Ifn2 was not able to induce this response, although both transcripts were up-regulated after viral challenge. On the other hand, turbot IFNs did not show any protective effect against the bacteria Aeromonas salmonicida, although they were induced after bacterial challenge. Both IFNs induced the expression of several immune genes, but the effect of Ifn2 was mainly limited to the site of administration (intramuscular injection). Interestingly, Ifn2 but not Ifn1 induced an increase in the expression level of interleukin-1 beta (il1b). Therefore, the role of Ifn2 could be more related with the immune regulation, being involved mainly in the inflammation process.
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Affiliation(s)
- P Pereiro
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - M M Costa
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - P Díaz-Rosales
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - S Dios
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - A Figueras
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain
| | - B Novoa
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208 Vigo, Spain.
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41
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Varela M, Diaz-Rosales P, Pereiro P, Forn-Cuní G, Costa MM, Dios S, Romero A, Figueras A, Novoa B. Interferon-induced genes of the expanded IFIT family show conserved antiviral activities in non-mammalian species. PLoS One 2014; 9:e100015. [PMID: 24950240 PMCID: PMC4065003 DOI: 10.1371/journal.pone.0100015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 05/21/2014] [Indexed: 12/24/2022] Open
Abstract
Interferon-induced proteins with tetratricopeptide repeats (IFITs) are involved in the protective response to viral infection, although the precise mechanism of IFITs for reducing viral proliferation is currently unknown. The interaction with the translation initiation factor eIF-3 or viral proteins and the sequestering of viral RNA have been proposed as potential antiviral functions for these proteins. In humans, four members of this family have been characterized. Nevertheless, information about these proteins in fish is almost non-existent. Exploiting the conservation of synteny between human and zebrafish genomes, we have identified ten members of the IFIT family located on four different chromosomes. The induction of these genes was examined both in vitro and in vivo after interferon (IFN) administration and rhabdovirus challenge. Whereas an induction of IFIT genes was observed after interferon treatments (IFNΦ1, IFNΦ2 and IFNΦ3), the viral infection did not affect these IFN-induced genes in vitro, and even reduced the IFN-induced expression of these genes. The response was largely different in vivo, with a broad up-regulation of IFIT genes after viral challenge. In addition, three selected IFITs were cloned in an expression vector and microinjected into zebrafish larvae to examine the protective effect of IFITs upon viral infection. Reduction in the mortality rate was observed confirming a conserved antiviral function in non-mammalian species.
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Affiliation(s)
- Mónica Varela
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | | | | | | | - Maria M. Costa
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | - Sonia Dios
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | | | | | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
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42
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IFIT1: A dual sensor and effector molecule that detects non-2'-O methylated viral RNA and inhibits its translation. Cytokine Growth Factor Rev 2014; 25:543-50. [PMID: 24909568 PMCID: PMC4234691 DOI: 10.1016/j.cytogfr.2014.05.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/12/2014] [Indexed: 02/08/2023]
Abstract
Our understanding of the antiviral actions of IFIT1, one of the most strongly induced interferon stimulated genes (ISGs), has advanced remarkably within the last few years. This review focuses on the recent cellular, biochemical, and structural discoveries that have provided new insight as to how IFIT1 functions as both a sensor and effector molecule of the cellular innate immune system. IFIT1 can detect viral RNA lacking 2′-O methylation on their cap structures or displaying a 5′-triphosphate moiety and inhibit their translation or sequester them from active replication. Because of these inhibitory actions, many viruses have evolved unique mechanisms to evade IFIT1 to facilitate replication, spread of infection, and disease pathogenesis.
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43
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Vladimer GI, Górna MW, Superti-Furga G. IFITs: Emerging Roles as Key Anti-Viral Proteins. Front Immunol 2014; 5:94. [PMID: 24653722 PMCID: PMC3948006 DOI: 10.3389/fimmu.2014.00094] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 02/23/2014] [Indexed: 12/25/2022] Open
Abstract
Interferon-induced proteins with tetratricopeptide repeats (IFITs) are a family of proteins, which are strongly induced downstream of type I interferon signaling. The molecular mechanism of IFIT anti-viral activity has been studied in some detail, including the recently discovered direct binding of viral nucleic acid, the binding to viral and host proteins, and the possible involvement in anti-viral immune signal propagation. The unique structures of some members of the IFIT family have been solved to reveal an internal pocket for non-sequence-specific, but conformation- and modification-specific, nucleic acid binding. This review will focus on recent discoveries, which link IFITs to the anti-viral response, intrinsic to the innate immune system.
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Affiliation(s)
- Gregory I Vladimer
- Laboratory of Giulio Superti-Furga, Center for Molecular Medicine of the Austrian Academy of Sciences , Vienna , Austria
| | - Maria W Górna
- Laboratory of Giulio Superti-Furga, Center for Molecular Medicine of the Austrian Academy of Sciences , Vienna , Austria
| | - Giulio Superti-Furga
- Laboratory of Giulio Superti-Furga, Center for Molecular Medicine of the Austrian Academy of Sciences , Vienna , Austria
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Kumar P, Sweeney TR, Skabkin MA, Skabkina OV, Hellen CUT, Pestova TV. Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5'-terminal regions of cap0-, cap1- and 5'ppp- mRNAs. Nucleic Acids Res 2013; 42:3228-45. [PMID: 24371270 PMCID: PMC3950709 DOI: 10.1093/nar/gkt1321] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Ribosomal recruitment of cellular mRNAs depends on binding of eIF4F to the mRNA's 5'-terminal 'cap'. The minimal 'cap0' consists of N7-methylguanosine linked to the first nucleotide via a 5'-5' triphosphate (ppp) bridge. Cap0 is further modified by 2'-O-methylation of the next two riboses, yielding 'cap1' (m7GpppNmN) and 'cap2' (m7GpppNmNm). However, some viral RNAs lack 2'-O-methylation, whereas others contain only ppp- at their 5'-end. Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed effectors of innate immunity that inhibit viral replication by incompletely understood mechanisms. Here, we investigated the ability of IFIT family members to interact with cap1-, cap0- and 5'ppp- mRNAs and inhibit their translation. IFIT1 and IFIT1B showed very high affinity to cap-proximal regions of cap0-mRNAs (K1/2,app ∼9 to 23 nM). The 2'-O-methylation abrogated IFIT1/mRNA interaction, whereas IFIT1B retained the ability to bind cap1-mRNA, albeit with reduced affinity (K1/2,app ∼450 nM). The 5'-terminal regions of 5'ppp-mRNAs were recognized by IFIT5 (K1/2,app ∼400 nM). The activity of individual IFITs in inhibiting initiation on a specific mRNA was determined by their ability to interact with its 5'-terminal region: IFIT1 and IFIT1B efficiently outcompeted eIF4F and abrogated initiation on cap0-mRNAs, whereas inhibition on cap1- and 5'ppp- mRNAs by IFIT1B and IFIT5 was weaker and required higher protein concentrations.
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Affiliation(s)
- Parimal Kumar
- Department of Cell Biology, SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY 11203, USA
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