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Bodmer BS, Hoenen T, Wendt L. Molecular insights into the Ebola virus life cycle. Nat Microbiol 2024; 9:1417-1426. [PMID: 38783022 DOI: 10.1038/s41564-024-01703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/17/2024] [Indexed: 05/25/2024]
Abstract
Ebola virus and other orthoebolaviruses cause severe haemorrhagic fevers in humans, with very high case fatality rates. Their non-segmented single-stranded RNA genome encodes only seven structural proteins and a small number of non-structural proteins to facilitate the virus life cycle. The basics of this life cycle are well established, but recent advances have substantially increased our understanding of its molecular details, including the viral and host factors involved. Here we provide a comprehensive overview of our current knowledge of the molecular details of the orthoebolavirus life cycle, with a special focus on proviral host factors. We discuss the multistep entry process, viral RNA synthesis in specialized phase-separated intracellular compartments called inclusion bodies, the expression of viral proteins and ultimately the assembly of new virus particles and their release at the cell surface. In doing so, we integrate recent studies into the increasingly detailed model that has developed for these fundamental aspects of orthoebolavirus biology.
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Affiliation(s)
- Bianca S Bodmer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Thomas Hoenen
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany.
| | - Lisa Wendt
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
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2
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Davey R, Donahue C, Kesari A, Thakur N, Wang L, Hulsey-Stubbs S, Williams C, Kirby C, Leung D, Aryal U, Basler C, LaCount D. A protein-proximity screen reveals Ebola virus co-opts the mRNA decapping complex through the scaffold protein EDC4. RESEARCH SQUARE 2024:rs.3.rs-3838220. [PMID: 38352529 PMCID: PMC10862950 DOI: 10.21203/rs.3.rs-3838220/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
The interaction of host and Ebola virus (EBOV) proteins is required for establishing infection of the cell. To identify protein binding partners, a proximity-dependent protein interaction screen was performed for six EBOV proteins. Hits were computationally mapped onto a human protein-protein interactome and then annotated with viral proteins to reveal known and previously undescribed EBOV-host protein interactions and processes. Importantly, this approach efficiently arranged proteins into functional complexes associated with single viral proteins. Focused characterization of interactions between EBOV VP35 and the mRNA decapping complex demonstrated that VP35 binds the scaffold protein EDC4 through the C-terminal subdomain, with each protein found associated in EBOV-infected cells. Mechanistically, depletion of three components of the complex each similarly inhibited viral replication by reducing early viral RNA synthesis. Overall, we demonstrate successful identification of EBOV protein interaction with entire cellular machines, providing a deeper understanding of replication mechanism for therapeutic intervention.
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Vucetic A, Lafleur A, Côté M, Kobasa D, Chan M, Alvarez F, Piccirillo C, Dong G, Olivier M. Extracellular vesicle storm during the course of Ebola virus infection in primates. Front Cell Infect Microbiol 2023; 13:1275277. [PMID: 38035334 PMCID: PMC10684970 DOI: 10.3389/fcimb.2023.1275277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Ebola virus (EBOV) is an RNA virus of the Filoviridae family that is responsible for outbreaks of hemorrhagic fevers in primates with a lethality rate as high as 90%. EBOV primarily targets host macrophages leading to cell activation and systemic cytokine storm, and fatal infection is associated with an inhibited interferon response, and lymphopenia. The EBOV surface glycoprotein (GP) has been shown to directly induce T cell depletion and can be secreted outside the virion via extracellular vesicles (EVs), though most studies are limited to epithelial cells and underlying mechanisms remain poorly elucidated. Methods To assess the role of GP on EBOV-induced dysregulation of host immunity, we first utilized EBOV virus-like particles (VLPs) expressing VP40 and NP either alone (Bald-VLP) or in conjunction with GP (VLP-GP) to investigate early inflammatory responses in THP-1 macrophages and in a murine model. We then sought to decipher the role of non-classical inflammatory mediators such as EVs over the course of EBOV infection in two EBOV-infected rhesus macaques by isolating and characterizing circulatory EVs throughout disease progression using size exclusion chromatography, nanoparticle tracking-analysis, and LC-MS/MS. Results While all VLPs could induce inflammatory mediators and recruit small peritoneal macrophages, pro-inflammatory cytokine and chemokine gene expression was exacerbated by the presence of GP. Further, quantification of EVs isolated from infected rhesus macaques revealed that the concentration of vesicles peaked in circulation at the terminal stage, at which time EBOV GP could be detected in host-derived exosomes. Moreover, comparative proteomics conducted across EV populations isolated from serum at various time points before and after infection revealed differences in host-derived protein content that were most significantly pronounced at the endpoint of infection, including significant expression of mediators of TLR4 signaling. Discussion These results suggest a dynamic role for EVs in the modification of disease states in the context of EBOV. Overall, our work highlights the importance of viral factors, such as the GP, and host derived EVs in the inflammatory cascade and pathogenesis of EBOV, which can be collectively further exploited for novel antiviral development.
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Affiliation(s)
- Andrea Vucetic
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Andrea Lafleur
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology and Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Darwyn Kobasa
- Special Pathogen Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mable Chan
- Special Pathogen Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Fernando Alvarez
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Federation of Clinical Immunology (FOCiS) Centres of Excellence in Translational Immunology (CETI), Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Ciriaco Piccirillo
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Federation of Clinical Immunology (FOCiS) Centres of Excellence in Translational Immunology (CETI), Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - George Dong
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Martin Olivier
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Federation of Clinical Immunology (FOCiS) Centres of Excellence in Translational Immunology (CETI), Research Institute of the McGill University Health Centre, Montréal, QC, Canada
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Wu Z, Wang L, Wang X, Sun Y, Li H, Zhang Z, Ren C, Zhang X, Li S, Lu J, Xu L, Yue X, Hong Y, Li Q, Zhu H, Gong Y, Gao C, Hu H, Gao L, Liang X, Ma C. cccDNA Surrogate MC-HBV-Based Screen Identifies Cohesin Complex as a Novel HBV Restriction Factor. Cell Mol Gastroenterol Hepatol 2022; 14:1177-1198. [PMID: 35987451 PMCID: PMC9579331 DOI: 10.1016/j.jcmgh.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV), existing as a stable minichromosome in the hepatocyte, is responsible for persistent HBV infection. Maintenance and sustained replication of cccDNA require its interaction with both viral and host proteins. However, the cccDNA-interacting host factors that limit HBV replication remain elusive. METHODS Minicircle HBV (MC-HBV), a recombinant cccDNA, was constructed based on chimeric intron and minicircle DNA technology. By mass spectrometry based on pull-down with biotinylated MC-HBV, the cccDNA-hepatocyte interaction profile was mapped. HBV replication was assessed in different cell models that support cccDNA formation. RESULTS MC-HBV supports persistent HBV replication and mimics the cccDNA minichromosome. The MC-HBV-based screen identified cohesin complex as a cccDNA binding host factor, leading to reduced HBV replication. Mechanistically, with the help of CCCTC-binding factor (CTCF), which has specific binding sites on cccDNA, cohesin loads on cccDNA and reshapes cccDNA confirmation to prevent RNA polymerase II enrichment. Interestingly, HBV X protein transcriptionally reduces structural maintenance of chromosomes complex expression to partially relieve the inhibitory role of the cohesin complex on HBV replication. CONCLUSIONS Our data not only provide a feasible approach to explore cccDNA-binding factors, but also identify cohesin/CTCF complex as a critical host restriction factor for cccDNA-driven HBV replication. These findings provide a novel insight into cccDNA-host interaction and targeted therapeutic intervention for HBV infection.
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Affiliation(s)
- Zhuanchang Wu
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Liyuan Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xin Wang
- College of Agriculture and Forestry, Linyi University, Linyi, Shandong, China
| | - Yang Sun
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Haoran Li
- College of Agriculture and Forestry, Linyi University, Linyi, Shandong, China
| | - Zhaoying Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Caiyue Ren
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xiaohui Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Shuangjie Li
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Jinghui Lu
- Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Leiqi Xu
- Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Xuetian Yue
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Yue Hong
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, China
| | - Qiang Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology, College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha, Hunan, China
| | - Yaoqin Gong
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Chengjiang Gao
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Huili Hu
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Genetics, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China,Correspondence Address correspondence to: Chunhong Ma, PhD, Key Laboratory for Experimental Teratology of Ministry of Education and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, 44 Wenhua Xi Road, Jinan, Shandong, 250012 China.
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Fang J, Pietzsch C, Tsaprailis G, Crynen G, Cho KF, Ting AY, Bukreyev A, de la Torre JC, Saphire EO. Functional interactomes of the Ebola virus polymerase identified by proximity proteomics in the context of viral replication. Cell Rep 2022; 38:110544. [PMID: 35320713 PMCID: PMC10496643 DOI: 10.1016/j.celrep.2022.110544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/26/2021] [Accepted: 03/01/2022] [Indexed: 11/21/2022] Open
Abstract
Ebola virus (EBOV) critically depends on the viral polymerase to replicate and transcribe the viral RNA genome in the cytoplasm of host cells, where cellular factors can antagonize or facilitate the virus life cycle. Here we leverage proximity proteomics and conduct a small interfering RNA (siRNA) screen to define the functional interactome of EBOV polymerase. As a proof of principle, we validate two cellular mRNA decay factors from 35 identified host factors: eukaryotic peptide chain release factor subunit 3a (eRF3a/GSPT1) and up-frameshift protein 1 (UPF1). Our data suggest that EBOV can subvert restrictions of cellular mRNA decay and repurpose GSPT1 and UPF1 to promote viral replication. Treating EBOV-infected human hepatocytes with a drug candidate that targets GSPT1 for degradation significantly reduces viral RNA load and particle production. Our work demonstrates the utility of proximity proteomics to capture the functional host interactome of the EBOV polymerase and to illuminate host-dependent regulation of viral RNA synthesis.
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Affiliation(s)
- Jingru Fang
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Colette Pietzsch
- Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Gogce Crynen
- Bioinformatics and Statistics Core, Scripps Research, Jupiter, FL 33458, USA
| | - Kelvin Frank Cho
- Cancer Biology Program, Stanford University, Stanford, CA 94305, USA
| | - Alice Y Ting
- Department of Genetics, Department of Biology, and Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Alexander Bukreyev
- Department of Pathology and Galveston National Laboratory, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA.
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Structural and Functional Aspects of Ebola Virus Proteins. Pathogens 2021; 10:pathogens10101330. [PMID: 34684279 PMCID: PMC8538763 DOI: 10.3390/pathogens10101330] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 01/14/2023] Open
Abstract
Ebola virus (EBOV), member of genus Ebolavirus, family Filoviridae, have a non-segmented, single-stranded RNA that contains seven genes: (a) nucleoprotein (NP), (b) viral protein 35 (VP35), (c) VP40, (d) glycoprotein (GP), (e) VP30, (f) VP24, and (g) RNA polymerase (L). All genes encode for one protein each except GP, producing three pre-proteins due to the transcriptional editing. These pre-proteins are translated into four products, namely: (a) soluble secreted glycoprotein (sGP), (b) Δ-peptide, (c) full-length transmembrane spike glycoprotein (GP), and (d) soluble small secreted glycoprotein (ssGP). Further, shed GP is released from infected cells due to cleavage of GP by tumor necrosis factor α-converting enzyme (TACE). This review presents a detailed discussion on various functional aspects of all EBOV proteins and their residues. An introduction to ebolaviruses and their life cycle is also provided for clarity of the available analysis. We believe that this review will help understand the roles played by different EBOV proteins in the pathogenesis of the disease. It will help in targeting significant protein residues for therapeutic and multi-protein/peptide vaccine development.
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Pal M, Muñoz-Hernandez H, Bjorklund D, Zhou L, Degliesposti G, Skehel JM, Hesketh EL, Thompson RF, Pearl LH, Llorca O, Prodromou C. Structure of the TELO2-TTI1-TTI2 complex and its function in TOR recruitment to the R2TP chaperone. Cell Rep 2021; 36:109317. [PMID: 34233195 PMCID: PMC8278493 DOI: 10.1016/j.celrep.2021.109317] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/15/2021] [Accepted: 06/07/2021] [Indexed: 11/28/2022] Open
Abstract
The R2TP (RUVBL1-RUVBL2-RPAP3-PIH1D1) complex, in collaboration with heat shock protein 90 (HSP90), functions as a chaperone for the assembly and stability of protein complexes, including RNA polymerases, small nuclear ribonucleoprotein particles (snRNPs), and phosphatidylinositol 3-kinase (PI3K)-like kinases (PIKKs) such as TOR and SMG1. PIKK stabilization depends on an additional complex of TELO2, TTI1, and TTI2 (TTT), whose structure and function are poorly understood. The cryoelectron microscopy (cryo-EM) structure of the human R2TP-TTT complex, together with biochemical experiments, reveals the mechanism of TOR recruitment to the R2TP-TTT chaperone. The HEAT-repeat TTT complex binds the kinase domain of TOR, without blocking its activity, and delivers TOR to the R2TP chaperone. In addition, TTT regulates the R2TP chaperone by inhibiting RUVBL1-RUVBL2 ATPase activity and by modulating the conformation and interactions of the PIH1D1 and RPAP3 components of R2TP. Taken together, our results show how TTT couples the recruitment of TOR to R2TP with the regulation of this chaperone system.
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Affiliation(s)
- Mohinder Pal
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Hugo Muñoz-Hernandez
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Dennis Bjorklund
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Lihong Zhou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Gianluca Degliesposti
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Emma L Hesketh
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW1E 6BT, UK.
| | - Oscar Llorca
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain.
| | - Chrisostomos Prodromou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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Zhou L, Han YF, Yuan C, Duan ZQ. Screening and bioinformatics analysis of cellular proteins interacting with chicken bromodomain-containing protein 2 in DF-1 cells. Br Poult Sci 2021; 62:810-819. [PMID: 34152239 DOI: 10.1080/00071668.2021.1943311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
1. Bromodomain-containing protein 2 (BRD2) is an important member of the BET protein family, which can specifically bind histone acetylated lysine to participate in gene transcriptional regulation, chromatin remodelling, cell proliferation and apoptosis. The following investigation of cellular proteins interacting with chBRD2 will be helpful in understanding the new functions of chBRD2 and the mechanism of NDV replication.2. The recombinant eukaryotic expression vector pEGFP-chBRD2 and empty vector pEGFP-C1 were transfected into DF-1 cells to overexpress GFP-chBRD2 and GFP, respectively. GO annotation, KEGG pathway, and protein-protein interaction network were used to analyse the cellular proteins interacting with chBRD2. In addition, one targeted protein was selected to verify its interaction with chBRD2 using fluorescent co-localisation and Co-IP.3. A total of 225 cellular proteins were identified that potentially interact with chBRD2. GO analysis showed that these play key roles in gene transcriptional regulation, cell cycle and development, immunity and viral infection. Further KEGG pathway analysis showed that these proteins were mainly involved in genetic information processing, immune system, cellular processes and translation. In addition, one targeted cellular protein chicken matrin 3 (chMATR3) was also identified as chBRD2 complex using both fluorescence co-localisation and Co-IP analysis.4. This study presents the interactome data of chBRD2 protein in DF-1 cells, which provides new information to understand the functions of chBRD2 and new targets for further investigating the replication and pathogenesis of NDV.
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Affiliation(s)
- L Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountains Region, Ministry of Education (Guizhou University)/Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, Guiyang, China.,College of Animal Sciences, Guizhou University, Guiyang, China
| | - Y F Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountains Region, Ministry of Education (Guizhou University)/Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, Guiyang, China.,College of Animal Sciences, Guizhou University, Guiyang, China
| | - C Yuan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountains Region, Ministry of Education (Guizhou University)/Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, Guiyang, China.,College of Animal Sciences, Guizhou University, Guiyang, China
| | - Z Q Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountains Region, Ministry of Education (Guizhou University)/Key Laboratory of Animal Genetics, Breeding and Reproduction in Guizhou Province, Guiyang, China.,College of Animal Sciences, Guizhou University, Guiyang, China
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9
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Wang Y, Zhou J, Mackintosh SG, Du Y. RuvB-Like Protein 2 Interacts with the NS1 Protein of Influenza A Virus and Affects Apoptosis That Is Counterbalanced by Type I Interferons. Viruses 2021; 13:v13061038. [PMID: 34072766 PMCID: PMC8229658 DOI: 10.3390/v13061038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/12/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
The NS1 protein of influenza A virus (IAV) plays important roles in viral pathogenesis and host immune response. Through a proteomic approach, we have identified RuvB-like proteins 1 and 2 (RuvBL1 and RuvBL2) as interacting partners of the NS1 protein of IAVs. Infection of human lung A549 cells with A/PR/8/34 (PR8) virus resulted in reductions in the protein levels of RuvBL2 but not RuvBL1. Further studies with RuvBL2 demonstrated that the NS1-RuvBL2 interaction is RNA-independent, and RuvBL2 binds the RNA-binding domain of the NS1. Infection of interferon (IFN)-deficient Vero cells with wild-type or delNS1 PR8 virus reduced RuvBL2 protein levels and induced apoptosis; delNS1 virus caused more reductions in RuvBL2 protein levels and induced more apoptosis than did wild-type virus. Knockdown of RuvBL2 by siRNAs induced apoptosis and overexpression of RuvBL2 resulted in increased resistance to infection-induced apoptosis in Vero cells. These results suggest that a non-NS1 viral element or elements induce apoptosis by suppressing RuvBL2 protein levels, and the NS1 inhibits the non-NS1 viral element-induced apoptosis by maintaining RuvBL2 abundance in infected cells in the absence of IFN influence. In contrast to Vero cells, infection of IFN-competent A549 cells with PR8 virus caused reductions in RuvBL2 protein levels but did not induce apoptosis. Concomitantly, pretreatment of Vero cells with a recombinant IFN resulted in resistance to infection-induced apoptosis. These results demonstrate that the infection-induced, RuvBL2-regulated apoptosis in infected cells is counterbalanced by IFN survival signals. Our results reveal a novel mechanism underlying the infection-induced apoptosis that can be modulated by the NS1 and type I IFN signaling in IAV-infected cells.
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Affiliation(s)
- Yimeng Wang
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (J.Z.)
| | - Jianhong Zhou
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (J.Z.)
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Yuchun Du
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.W.); (J.Z.)
- Correspondence: ; Tel.: +1-479-575-6944
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10
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Bioinformatics analyses of significant genes, related pathways, and candidate diagnostic biomarkers and molecular targets in SARS-CoV-2/COVID-19. GENE REPORTS 2020; 21:100956. [PMID: 33553808 PMCID: PMC7854084 DOI: 10.1016/j.genrep.2020.100956] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection is a leading cause of pneumonia and death. The aim of this investigation is to identify the key genes in SARS-CoV-2 infection and uncover their potential functions. We downloaded the expression profiling by high throughput sequencing of GSE152075 from the Gene Expression Omnibus database. Normalization of the data from primary SARS-CoV-2 infected samples and negative control samples in the database was conducted using R software. Then, joint analysis of the data was performed. Pathway and Gene ontology (GO) enrichment analyses were performed, and the protein-protein interaction (PPI) network, target gene - miRNA regulatory network, target gene - TF regulatory network of the differentially expressed genes (DEGs) were constructed using Cytoscape software. Identification of diagnostic biomarkers was conducted using receiver operating characteristic (ROC) curve analysis. 994 DEGs (496 up regulated and 498 down regulated genes) were identified. Pathway and GO enrichment analysis showed up and down regulated genes mainly enriched in the NOD-like receptor signaling pathway, Ribosome, response to external biotic stimulus and viral transcription in SARS-CoV-2 infection. Down and up regulated genes were selected to establish the PPI network, modules, target gene - miRNA regulatory network, target gene - TF regulatory network revealed that these genes were involved in adaptive immune system, fluid shear stress and atherosclerosis, influenza A and protein processing in endoplasmic reticulum. In total, ten genes (CBL, ISG15, NEDD4, PML, REL, CTNNB1, ERBB2, JUN, RPS8 and STUB1) were identified as good diagnostic biomarkers. In conclusion, the identified DEGs, hub genes and target genes contribute to the understanding of the molecular mechanisms underlying the advancement of SARS-CoV-2 infection and they may be used as diagnostic and molecular targets for the treatment of patients with SARS-CoV-2 infection in the future.
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Key Words
- Bioinformatics
- CBL, Cbl proto-oncogene
- DEGs, differentially expressed genes
- Diagnosis
- GO, Gene ontology
- ISG15, ISG15 ubiquitin like modifier
- Key genes
- NEDD4, NEDD4 E3 ubiquitin protein ligase
- PML, promyelocyticleukemia
- PPI, protein-protein interaction
- Pathways
- REL, REL proto-oncogene, NF-kB subunit
- ROC, receiver operating characteristic
- SARS-CoV-2 infection
- SARS-CoV-2, Severe acute respiratory syndrome corona virus 2
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The Cellular Protein CAD is Recruited into Ebola Virus Inclusion Bodies by the Nucleoprotein NP to Facilitate Genome Replication and Transcription. Cells 2020; 9:cells9051126. [PMID: 32370067 PMCID: PMC7290923 DOI: 10.3390/cells9051126] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022] Open
Abstract
Ebola virus (EBOV) is a zoonotic pathogen causing severe hemorrhagic fevers in humans and non-human primates with high case fatality rates. In recent years, the number and extent of outbreaks has increased, highlighting the importance of better understanding the molecular aspects of EBOV infection and host cell interactions to control this virus more efficiently. Many viruses, including EBOV, have been shown to recruit host proteins for different viral processes. Based on a genome-wide siRNA screen, we recently identified the cellular host factor carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD) as being involved in EBOV RNA synthesis. However, mechanistic details of how this host factor plays a role in the EBOV life cycle remain elusive. In this study, we analyzed the functional and molecular interactions between EBOV and CAD. To this end, we used siRNA knockdowns in combination with various reverse genetics-based life cycle modelling systems and additionally performed co-immunoprecipitation and co-immunofluorescence assays to investigate the influence of CAD on individual aspects of the EBOV life cycle and to characterize the interactions of CAD with viral proteins. Following this approach, we could demonstrate that CAD directly interacts with the EBOV nucleoprotein NP, and that NP is sufficient to recruit CAD into inclusion bodies dependent on the glutaminase (GLN) domain of CAD. Further, siRNA knockdown experiments indicated that CAD is important for both viral genome replication and transcription, while substrate rescue experiments showed that the function of CAD in pyrimidine synthesis is indeed required for those processes. Together, this suggests that NP recruits CAD into inclusion bodies via its GLN domain in order to provide pyrimidines for EBOV genome replication and transcription. These results define a novel mechanism by which EBOV hijacks host cell pathways in order to facilitate genome replication and transcription and provide a further basis for the development of host-directed broad-spectrum antivirals.
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Lin AE, Diehl WE, Cai Y, Finch CL, Akusobi C, Kirchdoerfer RN, Bollinger L, Schaffner SF, Brown EA, Saphire EO, Andersen KG, Kuhn JH, Luban J, Sabeti PC. Reporter Assays for Ebola Virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111. Viruses 2020; 12:E105. [PMID: 31952352 PMCID: PMC7019320 DOI: 10.3390/v12010105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 01/17/2023] Open
Abstract
For highly pathogenic viruses, reporter assays that can be rapidly performed are critically needed to identify potentially functional mutations for further study under maximal containment (e.g., biosafety level 4 [BSL-4]). The Ebola virus nucleoprotein (NP) plays multiple essential roles during the viral life cycle, yet few tools exist to study the protein under BSL-2 or equivalent containment. Therefore, we adapted reporter assays to measure NP oligomerization and virion-like particle (VLP) production in live cells and further measured transcription and replication using established minigenome assays. As a proof-of-concept, we examined the NP-R111C substitution, which emerged during the 2013‒2016 Western African Ebola virus disease epidemic and rose to high frequency. NP-R111C slightly increased NP oligomerization and VLP budding but slightly decreased transcription and replication. By contrast, a synthetic charge-reversal mutant, NP-R111E, greatly increased oligomerization but abrogated transcription and replication. These results are intriguing in light of recent structures of NP oligomers, which reveal that the neighboring residue, K110, forms a salt bridge with E349 on adjacent NP molecules. By developing and utilizing multiple reporter assays, we find that the NP-111 position mediates a complex interplay between NP's roles in protein structure, virion budding, and transcription and replication.
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Affiliation(s)
- Aaron E. Lin
- Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William E. Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Yingyun Cai
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Courtney L. Finch
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Chidiebere Akusobi
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02120, USA;
| | | | - Laura Bollinger
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Stephen F. Schaffner
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elizabeth A. Brown
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kristian G. Andersen
- Department of Immunology and Microbial Sciences, The Scripps Research Institute, La Jolla, CA 92037, USA;
- Scripps Translational Science Institute, La Jolla, CA 92037, USA
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA; (Y.C.); (C.L.F.); (L.B.); (J.H.K.)
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; (W.E.D.); (J.L.)
| | - Pardis C. Sabeti
- Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA
- Department of Organismic and Evolutionary Biology, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA; (S.F.S.); (E.A.B.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Cloutier P, Poitras C, Faubert D, Bouchard A, Blanchette M, Gauthier MS, Coulombe B. Upstream ORF-Encoded ASDURF Is a Novel Prefoldin-like Subunit of the PAQosome. J Proteome Res 2019; 19:18-27. [PMID: 31738558 DOI: 10.1021/acs.jproteome.9b00599] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The PAQosome is an 11-subunit chaperone involved in the biogenesis of several human protein complexes. We show that ASDURF, a recently discovered upstream open reading frame (uORF) in the 5' UTR of ASNSD1 mRNA, encodes the 12th subunit of the PAQosome. ASDURF displays significant structural homology to β-prefoldins and assembles with the five known subunits of the prefoldin-like module of the PAQosome to form a heterohexameric prefoldin-like complex. A model of the PAQosome prefoldin-like module is presented. The data presented here provide an example of a eukaryotic uORF-encoded polypeptide whose function is not limited to cis-acting translational regulation of downstream coding sequence and highlights the importance of including alternative ORF products in proteomic studies.
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Affiliation(s)
- Philippe Cloutier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Christian Poitras
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Annie Bouchard
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Mathieu Blanchette
- School of Computer Science , McGill University , 3480 University Street , Montréal , Quebec H3A 0E9 , Canada
| | - Marie-Soleil Gauthier
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal , 110 Avenue des Pins Ouest , Montréal , Quebec H2W 1R7 , Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de Médecine , Université de Montréal , 2900 Boulevard Édouart-Montpetit , Montréal , Quebec H3T 1J4 , Canada
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Estrogen enhances human osteoblast survival and function via promotion of autophagy. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:1498-1507. [PMID: 31255720 DOI: 10.1016/j.bbamcr.2019.06.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/05/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022]
Abstract
Estrogen increases bone formation by promoting mineralization and prolonging the lifespan of osteoblasts. To understand the underlying molecular mechanism/s, we identified estrogen-regulated proteins at different stages of human osteoblast differentiation using differential proteomics approach. Among the identified proteins, we observed that estrogen upregulated RAB3GAP1 on day 1 and 5 of differentiation. RAB3GAP1 is critically involved in the process of autophagy, a eukaryotic degradative pathway essential for cell survival. We, therefore, investigated the effect of estrogen on autophagy in differentiating human osteoblasts and their precursors, the mesenchymal stem cells (MSCs). MSCs exhibited high autophagic flux which declined during osteoblast differentiation, resulting in high basal apoptosis in osteoblasts. Estrogen reduced apoptosis in differentiating osteoblasts by promoting autophagy, thus contributing towards their longer lifespan. Further, MSCs were resistant against starvation-induced apoptosis, whereas, differentiating osteoblasts showed significant susceptibility towards it. Estrogen, in addition to promoting mineralization, protected differentiating osteoblasts from starvation-induced apoptosis by increasing autophagic flux. Autophagic flux in RAB3GAP1 knockdown osteoblasts appeared diminished, and showed increased apoptosis even in nutrient-rich conditions, and exhibited significantly impaired mineralization. However, irrespective of the presence of estrogen, starvation further enhanced apoptosis in these cells. Furthermore, estrogen failed to promote mineralization in these osteoblasts. Our study illustrates that autophagy is essential for human osteoblast survival and mineralization, and osteoblasts are susceptible to apoptosis due to reduced autophagy during differentiation. Estrogen, via upregulation of RAB3GAP1, promotes autophagy in osteoblasts during differentiation thereby increasing their survival and mineralization capacity. Our study demonstrates the positive role of autophagy in bone homeostasis.
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Kovanich D, Saisawang C, Sittipaisankul P, Ramphan S, Kalpongnukul N, Somparn P, Pisitkun T, Smith DR. Analysis of the Zika and Japanese Encephalitis Virus NS5 Interactomes. J Proteome Res 2019; 18:3203-3218. [PMID: 31199156 DOI: 10.1021/acs.jproteome.9b00318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mosquito-borne flaviviruses, including dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV), are major human pathogens. Among the flaviviral proteins, the nonstructural protein 5 (NS5) is the largest, most conserved, and major enzymatic component of the viral replication complex. Disruption of the common key NS5-host protein-protein interactions critical for viral replication could aid in the development of broad-spectrum antiflaviviral therapeutics. Hundreds of NS5 interactors have been identified, but these are mostly DENV-NS5 interactors. To this end, we sought to investigate the JEV- and ZIKV-NS5 interactomes using EGFP immunoprecipitation with label-free quantitative mass spectrometry analysis. We report here a total of 137 NS5 interactors with a significant enrichment of spliceosomal and spliceosomal-associated proteins. The transcription complex Paf1C and phosphatase 6 were identified as common NS5-associated complexes. PAF1 was shown to play opposite roles in JEV and ZIKV infections. Additionally, we validated several NS5 targets and proposed their possible roles in infection. These include lipid-shuttling proteins OSBPL9 and OSBPL11, component of RNAP3 transcription factor TFIIIC, minichromosome maintenance, and cochaperone PAQosome. Mining this data set, our study expands the current interaction landscape of NS5 and uncovers several NS5 targets that are new to flavivirus biology.
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Affiliation(s)
- Duangnapa Kovanich
- Institute of Molecular Biosciences, Mahidol University , Nakhon Pathom , Thailand
| | - Chonticha Saisawang
- Institute of Molecular Biosciences, Mahidol University , Nakhon Pathom , Thailand
| | | | - Suwipa Ramphan
- Institute of Molecular Biosciences, Mahidol University , Nakhon Pathom , Thailand
| | - Nuttiya Kalpongnukul
- Center of Excellence in Systems Biology, Research affairs, Faculty of Medicine , Chulalongkorn University , Bangkok , Thailand
| | - Poorichaya Somparn
- Center of Excellence in Systems Biology, Research affairs, Faculty of Medicine , Chulalongkorn University , Bangkok , Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Research affairs, Faculty of Medicine , Chulalongkorn University , Bangkok , Thailand
| | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University , Nakhon Pathom , Thailand
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