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Hu J, Zeng Z, Chen X, Zhang M, Hu Z, Gu M, Wang X, Gao R, Hu S, Chen Y, Liu X, Peng D, Liu X. Phosphorylation of PB2 at serine 181 restricts viral replication and virulence of the highly pathogenic H5N1 avian influenza virus in mice. Virol Sin 2024; 39:97-112. [PMID: 38103645 PMCID: PMC10877443 DOI: 10.1016/j.virs.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/12/2023] [Indexed: 12/19/2023] Open
Abstract
Influenza A virus (IAV) continues to pose a pandemic threat to public health, resulting a high mortality rate annually and during pandemic years. Posttranslational modification of viral protein plays a substantial role in regulating IAV infection. Here, based on immunoprecipitation (IP)-based mass spectrometry (MS) and purified virus-coupled MS, a total of 89 phosphorylation sites distributed among 10 encoded viral proteins of IAV were identified, including 60 novel phosphorylation sites. Additionally, for the first time, we provide evidence that PB2 can also be acetylated at site K187. Notably, the PB2 S181 phosphorylation site was consistently identified in both IP-based MS and purified virus-based MS. Both S181 and K187 are exposed on the surface of the PB2 protein and are highly conserved in various IAV strains, suggesting their fundamental importance in the IAV life cycle. Bioinformatic analysis results demonstrated that S181E/A and K187Q/R mimic mutations do not significantly alter the PB2 protein structure. While continuous phosphorylation mimicked by the PB2 S181E mutation substantially decreases viral fitness in mice, PB2 K187Q mimetic acetylation slightly enhances viral virulence in mice. Mechanistically, PB2 S181E substantially impairs viral polymerase activity and viral replication, remarkably dampens protein stability and nuclear accumulation of PB2, and significantly weakens IAV-induced inflammatory responses. Therefore, our study further enriches the database of phosphorylation and acetylation sites of influenza viral proteins, laying a foundation for subsequent mechanistic studies. Meanwhile, the unraveled antiviral effect of PB2 S181E mimetic phosphorylation may provide a new target for the subsequent study of antiviral drugs.
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Affiliation(s)
- Jiao Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Zixiong Zeng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Xia Chen
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Manyu Zhang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Zenglei Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, 225009, China
| | - Min Gu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Ruyi Gao
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Yu Chen
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Xiaowen Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Daxin Peng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, 225009, China.
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2
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Lin D, Dong X, Xiao X, Xiang Z, Lei X, Wang J. Proteomic and phosphoproteomic analysis of responses to enterovirus A71 infection reveals novel targets for antiviral and viral replication. Antiviral Res 2023; 220:105761. [PMID: 37992763 DOI: 10.1016/j.antiviral.2023.105761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/06/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023]
Abstract
Hand, foot, and mouth disease (HFMD) is a common infectious disease in infants and children, especially those under five years of age. EV-A71 is a common pathogen that causes HFMD and the primary pathogen leading to severe or fatal HFMD, which is characterized by neurological complications. However, the underlying mechanisms of EV-A71 pathogenesis remain largely unknown. In this report, we used proteomic and phosphorylated proteomic methods to characterize the proteome and phosphoproteome profiles of EV-A71-infected human neuroblastoma SK-N-SH cells. More than 7744 host proteins and 10069 phosphorylation modification sites were successfully quantified. Among them, 974 proteins and 3648 phosphorylation modification sites were regulated significantly during EV-A71 infection. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that EV-A71 altered cell biological processes, including protein synthesis, RNA splicing and metabolism in SK-N-SH cells. Notably, based on the prediction of upregulated kinases during EV-A71 infection, we identified specific kinase inhibitors approved by the FDA, with ceralasertib, bosutinib, flavin mononucleotide, minocycline, pimasertib and acetylcysteine inhibiting EV-A71 infection. Finally, EV-A71 proteins were found to be phosphorylated during infection, with one site (S184 on 3D polymerase) observed to be crucial for viral replication because a S184A mutation knocked out viral replication. The results improve our understanding of the host response to EV-A71 infection of neuroblastoma cells and provide potential targets for developing anti-EV-A71 strategies.
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Affiliation(s)
- Dandan Lin
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China
| | - Xiaojing Dong
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China
| | - Xia Xiao
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China
| | - Zichun Xiang
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China; State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Xiaobo Lei
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China; State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China.
| | - Jianwei Wang
- NHC Key Laboratory of System Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, PR China.
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Liu L, Madhugiri R, Saul VV, Bacher S, Kracht M, Pleschka S, Schmitz ML. Phosphorylation of the PA subunit of influenza polymerase at Y393 prevents binding of the 5'-termini of RNA and polymerase function. Sci Rep 2023; 13:7042. [PMID: 37120635 PMCID: PMC10148841 DOI: 10.1038/s41598-023-34285-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/27/2023] [Indexed: 05/01/2023] Open
Abstract
The influenza A virus (IAV) polymerase is a multifunctional machine that can adopt alternative configurations to perform transcription and replication of the viral RNA genome in a temporally ordered manner. Although the structure of polymerase is well understood, our knowledge of its regulation by phosphorylation is still incomplete. The heterotrimeric polymerase can be regulated by posttranslational modifications, but the endogenously occurring phosphorylations at the PA and PB2 subunits of the IAV polymerase have not been studied. Mutation of phosphosites in PB2 and PA subunits revealed that PA mutants resembling constitutive phosphorylation have a partial (S395) or complete (Y393) defect in the ability to synthesize mRNA and cRNA. As PA phosphorylation at Y393 prevents binding of the 5' promoter of the genomic RNA, recombinant viruses harboring such a mutation could not be rescued. These data show the functional relevance of PA phosphorylations to control the activity of viral polymerase during the influenza infectious cycle.
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Affiliation(s)
- Lu Liu
- Institute of Biochemistry, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Ramakanth Madhugiri
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Vera Vivian Saul
- Institute of Biochemistry, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Susanne Bacher
- Institute of Biochemistry, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus Liebig University, Member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen, Giessen, Germany
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus Liebig University Giessen, Member of the German Center for Lung Research (DZL), Giessen, Germany.
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4
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Phosphorylation of Influenza A Virus Matrix Protein 1 at Threonine 108 Controls Its Multimerization State and Functional Association with the STRIPAK Complex. mBio 2023; 14:e0323122. [PMID: 36602306 PMCID: PMC9973344 DOI: 10.1128/mbio.03231-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The influenza A virus (IAV)-encoded matrix protein 1 (M1) acts as a master regulator of virus replication and fulfills multiple structural and regulatory functions in different cell compartments. Therefore, the spatiotemporal regulation of M1 is achieved by different mechanisms, including its structural and pH-dependent flexibility, differential association with cellular factors, and posttranslational modifications. Here, we investigated the function of M1 phosphorylation at the evolutionarily conserved threonine 108 (T108) and found that its mutation to a nonphosphorylatable alanine prohibited virus replication. Absent T108, phosphorylation led to strongly increased self-association of M1 at the cell membrane and consequently prohibited its ability to enter the nucleus and to contribute to viral ribonucleoprotein nuclear export. M1 T108 phosphorylation also controls the binding affinity to the cellular STRIPAK (striatin-interacting phosphatases and kinases) complex, which contains different kinases and the phosphatase PP2A to shape phosphorylation-dependent signaling networks. IAV infection led to the redistribution of the STRIPAK scaffolding subunits STRN and STRN3 from the cell membrane to cytosolic and perinuclear clusters, where it colocalized with M1. Inactivation of the STRIPAK complex resulted in compromised M1 polymerization and IAV replication. IMPORTANCE Influenza viruses pose a major threat to human health and cause annual epidemics and occasional pandemics. Many virus-encoded proteins exert various functions in different subcellular compartments, as exemplified by the M1 protein, but the molecular mechanisms endowing the multiplicity of functions remain incompletely understood. Here, we report that phosphorylation of M1 at T108 is essential for virus replication and controls its propensity for self-association and nuclear localization. This phosphorylation also controls binding affinity of the M1 protein to the STRIPAK complex, which contributes to M1 polymerization and virus replication.
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An anti-influenza combined therapy assessed by single cell RNA-sequencing. Commun Biol 2022; 5:1075. [PMID: 36216966 PMCID: PMC9549038 DOI: 10.1038/s42003-022-04013-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 09/20/2022] [Indexed: 11/08/2022] Open
Abstract
Influenza makes millions of people ill every year, placing a large burden on the healthcare system and the economy. To develop a treatment against influenza, we combined virucidal sialylated cyclodextrins with interferon lambda and demonstrated, in human airway epithelia, that the two compounds inhibit the replication of a clinical H1N1 strain more efficiently when administered together rather than alone. We investigated the mechanism of action of the combined treatment by single cell RNA-sequencing analysis and found that both the single and combined treatments impair viral replication to different extents across distinct epithelial cell types. We showed that each cell type comprises multiple sub-types, whose proportions are altered by H1N1 infection, and assessed the ability of the treatments to restore them. To the best of our knowledge this is the first study investigating the effectiveness of an antiviral therapy against influenza virus by single cell transcriptomic studies. When combined with interferon lambda, virucidal sialylated cyclodextrins inhibit the replication of a clinical H1N1 influenza strain in ex vivo human airway epithelia more efficiently than when delivered alone.
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6
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Liu L, Weiß A, Saul VV, Schermuly RT, Pleschka S, Schmitz ML. Comparative kinase activity profiling of pathogenic influenza A viruses reveals new anti- and pro-viral protein kinases. J Gen Virol 2022; 103. [PMID: 35771598 DOI: 10.1099/jgv.0.001762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Constant evolution of influenza A viruses (IAVs) leads to the occurrence of new virus strains, which can cause epidemics and occasional pandemics. Here we compared two medically relevant IAVs, namely A/Hamburg/4/09 (H1N1pdm09) of the 2009 pandemic and the highly pathogenic avian IAV human isolate A/Thailand/1(KAN-1)/2004 (H5N1), for their ability to trigger intracellular phosphorylation patterns using a highly sensitive peptide-based kinase activity profiling approach. Virus-dependent tyrosine phosphorylations of substrate peptides largely overlap between the two viruses and are also strongly overrepresented in comparison to serine/threonine peptide phosphorylations. Both viruses trigger phosphorylations with distinct kinetics by overlapping and different kinases from which many form highly interconnected networks. As approximately half of the kinases forming a signalling hub have no known function for the IAV life cycle, we interrogated selected members of this group for their ability to interfere with IAV replication. These experiments revealed negative regulation of H1N1pdm09 and H5N1 replication by NUAK [novel (nua) kinase] kinases and by redundant ephrin A (EphA) receptor tyrosine kinases.
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Affiliation(s)
- Lu Liu
- Institute of Biochemistry, Justus-Liebig-University Giessen (Germany), Member of the German Center for Lung Research, Germany.,Institute of Medical Virology, Justus Liebig University Giessen, Germany
| | - Astrid Weiß
- Department of Internal Medicine, Cardio-Pulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus-Liebig-University Giessen, Germany
| | - Vera Vivian Saul
- Institute of Biochemistry, Justus-Liebig-University Giessen (Germany), Member of the German Center for Lung Research, Germany
| | - Ralph Theo Schermuly
- Department of Internal Medicine, Cardio-Pulmonary Institute (CPI), Member of the German Center for Lung Research (DZL), Justus-Liebig-University Giessen, Germany
| | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Germany.,German Center for Infection Research (DZIF), partner site Giessen, Germany
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus-Liebig-University Giessen (Germany), Member of the German Center for Lung Research, Germany
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Lata S, Mishra R, Arya RP, Arora P, Lahon A, Banerjea AC, Sood V. Where all the Roads Meet? A Crossover Perspective on Host Factors Regulating SARS-CoV-2 infection. J Mol Biol 2022; 434:167403. [PMID: 34914966 PMCID: PMC8666384 DOI: 10.1016/j.jmb.2021.167403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/18/2021] [Accepted: 12/07/2021] [Indexed: 01/11/2023]
Abstract
COVID-19 caused by SARS-CoV-2 is the latest pandemic which has thrown the world into an unprecedented social and economic uncertainties along with huge loss to humanity. Identification of the host factors regulating the replication of SARS-CoV-2 in human host may help in the development of novel anti-viral therapies to combat the viral infection and spread. Recently, some research groups used genome-wide CRISPR/Cas screening to identify the host factors critical for the SARS-CoV-2 replication and infection. A comparative analysis of these significant host factors (p < 0.05) identified fifteen proteins common in these studies. Apart from ACE2 (receptor for SARS-CoV-2 attachment), other common host factors were CSNK2B, GDI2, SLC35B2, DDX51, VPS26A, ARPP-19, C1QTNF7, ALG6, LIMA1, COG3, COG8, BCOR, LRRN2 and TLR9. Additionally, viral interactome of these host factors revealed that many of them were associated with several SARS-CoV-2 proteins as well. Interestingly, some of these host factors have already been shown to be critical for the pathogenesis of other viruses suggesting their crucial role in virus-host interactions. Here, we review the functions of these host factors and their role in other diseases with special emphasis on viral diseases.
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Affiliation(s)
- Sneh Lata
- Virology Laboratory, National Institute of Immunology, New Delhi, India
| | - Ritu Mishra
- Virology Laboratory, National Institute of Immunology, New Delhi, India
| | - Ravi P. Arya
- KSBS, Indian Institute of Technology, New Delhi, India
| | - Pooja Arora
- Hansraj College, University of Delhi, New Delhi, India
| | | | - Akhil C. Banerjea
- Institute of Advanced Virology, Kerala, India,Corresponding authors
| | - Vikas Sood
- Biochemistry Department, Jamia Hamdard, New Delhi, India,Corresponding authors
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Gerlt V, Mayr J, Del Sarto J, Ludwig S, Boergeling Y. Cellular Protein Phosphatase 2A Regulates Cell Survival Mechanisms in Influenza A Virus Infection. Int J Mol Sci 2021; 22:ijms222011164. [PMID: 34681823 PMCID: PMC8540457 DOI: 10.3390/ijms222011164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
Influenza A viruses (IAVs) are respiratory pathogens that are able to hijack multiple cellular mechanisms to drive their replication. Consequently, several viral and cellular proteins undergo posttranslational modifications such as dynamic phosphorylation/dephosphorylation. In eukaryotic cells, dephosphorylation is mainly catalyzed by protein phosphatase 2A (PP2A). While the function of kinases in IAV infection is quite well studied, only little is known about the role of PP2A in IAV replication. Here, we show, by using knockdown and inhibition approaches of the catalytic subunit PP2Ac, that this phosphatase is important for efficient replication of several IAV subtypes. This could neither be attributed to alterations in the antiviral immune response nor to changes in transcription or translation of viral genes. Interestingly, decreased PP2Ac levels resulted in a significantly reduced cell viability after IAV infection. Comprehensive kinase activity profiling identified an enrichment of process networks related to apoptosis and indicated a synergistic action of hyper-activated PI3K/Akt, MAPK/JAK-STAT and NF-kB signaling pathways, collectively resulting in increased cell death. Taken together, while IAV seems to effectively tap leftover PP2A activity to ensure efficient viral replication, reduced PP2Ac levels fail to orchestrate cell survival mechanisms to protect infected cells from early cell death.
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Affiliation(s)
- Vanessa Gerlt
- Institute of Virology Muenster, University of Muenster, 48149 Muenster, Germany; (V.G.); (J.M.); (J.D.S.); (S.L.)
| | - Juliane Mayr
- Institute of Virology Muenster, University of Muenster, 48149 Muenster, Germany; (V.G.); (J.M.); (J.D.S.); (S.L.)
| | - Juliana Del Sarto
- Institute of Virology Muenster, University of Muenster, 48149 Muenster, Germany; (V.G.); (J.M.); (J.D.S.); (S.L.)
- Department of Neurology, Institute of Translational Neurology, Medical Faculty, University Hospital Muenster, 48149 Muenster, Germany
| | - Stephan Ludwig
- Institute of Virology Muenster, University of Muenster, 48149 Muenster, Germany; (V.G.); (J.M.); (J.D.S.); (S.L.)
| | - Yvonne Boergeling
- Institute of Virology Muenster, University of Muenster, 48149 Muenster, Germany; (V.G.); (J.M.); (J.D.S.); (S.L.)
- Correspondence:
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9
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Applied Proteomics in 'One Health'. Proteomes 2021; 9:proteomes9030031. [PMID: 34208880 PMCID: PMC8293331 DOI: 10.3390/proteomes9030031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022] Open
Abstract
‘One Health’ summarises the idea that human health and animal health are interdependent and bound to the health of ecosystems. The purpose of proteomics methodologies and studies is to determine proteins present in samples of interest and to quantify changes in protein expression during pathological conditions. The objectives of this paper are to review the application of proteomics technologies within the One Health concept and to appraise their role in the elucidation of diseases and situations relevant to One Health. The paper develops in three sections. Proteomics Applications in Zoonotic Infections part discusses proteomics applications in zoonotic infections and explores the use of proteomics for studying pathogenetic pathways, transmission dynamics, diagnostic biomarkers and novel vaccines in prion, viral, bacterial, protozoan and metazoan zoonotic infections. Proteomics Applications in Antibiotic Resistance part discusses proteomics applications in mechanisms of resistance development and discovery of novel treatments for antibiotic resistance. Proteomics Applications in Food Safety part discusses the detection of allergens, exposure of adulteration, identification of pathogens and toxins, study of product traits and characterisation of proteins in food safety. Sensitive analysis of proteins, including low-abundant ones in complex biological samples, will be achieved in the future, thus enabling implementation of targeted proteomics in clinical settings, shedding light on biomarker research and promoting the One Health concept.
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10
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Boergeling Y, Brunotte L, Ludwig S. Dynamic phospho-modification of viral proteins as a crucial regulatory layer of influenza A virus replication and innate immune responses. Biol Chem 2021; 402:1493-1504. [PMID: 34062629 DOI: 10.1515/hsz-2021-0241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023]
Abstract
Influenza viruses are small RNA viruses with a genome of about 13 kb. Because of this limited coding capacity, viral proteins have evolved to fulfil multiple functions in the infected cell. This implies that there must be mechanisms allowing to dynamically direct protein action to a distinct activity in a spatio-temporal manner. Furthermore, viruses exploit many cellular processes, which also have to be dynamically regulated during the viral replication cycle. Phosphorylation and dephosphorylation of proteins are fundamental for the control of many cellular responses. There is accumulating evidence that this mechanism represents a so far underestimated level of regulation in influenza virus replication. Here, we focus on the current knowledge of dynamics of phospho-modifications in influenza virus replication and show recent examples of findings underlining the crucial role of phosphorylation in viral transport processes as well as activation and counteraction of the innate immune response.
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Affiliation(s)
- Yvonne Boergeling
- Institute of Virology and Interdisciplinary Center for Clinical Research (IZKF), Medical Faculty, University of Münster, Von-Esmarch-Str. 56, D-48149Münster, Germany
| | - Linda Brunotte
- Institute of Virology and Interdisciplinary Center for Clinical Research (IZKF), Medical Faculty, University of Münster, Von-Esmarch-Str. 56, D-48149Münster, Germany
| | - Stephan Ludwig
- Institute of Virology and Interdisciplinary Center for Clinical Research (IZKF), Medical Faculty, University of Münster, Von-Esmarch-Str. 56, D-48149Münster, Germany
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11
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Simanjuntak Y, Schamoni-Kast K, Grün A, Uetrecht C, Scaturro P. Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology. Viruses 2021; 13:668. [PMID: 33924391 PMCID: PMC8070632 DOI: 10.3390/v13040668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/01/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023] Open
Abstract
RNA viruses cause a wide range of human diseases that are associated with high mortality and morbidity. In the past decades, the rise of genetic-based screening methods and high-throughput sequencing approaches allowed the uncovering of unique and elusive aspects of RNA virus replication and pathogenesis at an unprecedented scale. However, viruses often hijack critical host functions or trigger pathological dysfunctions, perturbing cellular proteostasis, macromolecular complex organization or stoichiometry, and post-translational modifications. Such effects require the monitoring of proteins and proteoforms both on a global scale and at the structural level. Mass spectrometry (MS) has recently emerged as an important component of the RNA virus biology toolbox, with its potential to shed light on critical aspects of virus-host perturbations and streamline the identification of antiviral targets. Moreover, multiple novel MS tools are available to study the structure of large protein complexes, providing detailed information on the exact stoichiometry of cellular and viral protein complexes and critical mechanistic insights into their functions. Here, we review top-down and bottom-up mass spectrometry-based approaches in RNA virus biology with a special focus on the most recent developments in characterizing host responses, and their translational implications to identify novel tractable antiviral targets.
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Affiliation(s)
- Yogy Simanjuntak
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Kira Schamoni-Kast
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Alice Grün
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Charlotte Uetrecht
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
- European XFEL GmbH, 22869 Schenefeld, Germany
| | - Pietro Scaturro
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
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12
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Klann K, Tascher G, Münch C. Virus systems biology: Proteomics profiling of dynamic protein networks during infection. Adv Virus Res 2021; 109:1-29. [PMID: 33934824 DOI: 10.1016/bs.aivir.2020.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The host cell proteome undergoes a variety of dynamic changes during viral infection, elicited by the virus itself or host cell defense mechanisms. Studying these changes on a global scale by integrating functional and physical interactions within protein networks during infection is an important tool to understand pathology. Indeed, proteomics studies dissecting protein signaling cascades and interaction networks upon infection showed how global information can significantly improve understanding of disease mechanisms of diverse viral infections. Here, we summarize and give examples of different experimental designs, proteomics approaches and bioinformatics analyses that allow profiling proteome changes and host-pathogen interactions to gain a molecular systems view of viral infection.
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Affiliation(s)
- Kevin Klann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Frankfurt am Main, Germany; Cardio-Pulmonary Institute, Frankfurt am Main, Germany.
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13
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Zhang J, Peng Q, Zhao W, Sun W, Yang J, Liu N. Proteomics in Influenza Research: The Emerging Role of Posttranslational Modifications. J Proteome Res 2020; 20:110-121. [PMID: 33348980 DOI: 10.1021/acs.jproteome.0c00778] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especially in posttranslational regulation of a variety of key biological processes. Protein posttranslational modifications (PTMs) increase the diversity of functionality of the organismal proteome and affect almost all aspects of pathogen biology, primarily by regulating the structure, function, and localization of the modified proteins. Considerable technical achievements in mass spectrometry-based proteomics have been made in a large number of proteome-wide surveys of PTMs in many different organisms. Herein we specifically focus on the proteomic studies regarding a variety of PTMs that occur in both the influenza viruses, mainly influenza A viruses (IAVs), and their hosts, including phosphorylation, ubiquitination and ubiquitin-like modification, glycosylation, methylation, acetylation, and some types of acylation. Integration of these data sets provides a unique scenery of the global regulation and interplay of different PTMs during the interaction between IAVs and their hosts. Various techniques used to globally profiling these PTMs, mostly MS-based approaches, are discussed regarding their increasing roles in mechanical regulation of interaction between influenza viruses and their hosts.
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Affiliation(s)
- Jinming Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Qisheng Peng
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Weizheng Zhao
- Clinical Medical College, Jilin University, Changchun 130021, PR China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Jingbo Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
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14
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Dawson AR, Wilson GM, Freiberger EC, Mondal A, Coon JJ, Mehle A. Phosphorylation controls RNA binding and transcription by the influenza virus polymerase. PLoS Pathog 2020; 16:e1008841. [PMID: 32881973 PMCID: PMC7494117 DOI: 10.1371/journal.ppat.1008841] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/16/2020] [Accepted: 07/25/2020] [Indexed: 12/03/2022] Open
Abstract
The influenza virus polymerase transcribes and replicates the viral genome. The proper timing and balance of polymerase activity is important for successful replication. Genome replication is controlled in part by phosphorylation of NP that regulates assembly of the replication machinery. However, it remains unclear whether phosphorylation directly regulated polymerase activity. Here we identified polymerase phosphosites that control its function. Mutating phosphosites in the catalytic subunit PB1 altered polymerase activity and virus replication. Biochemical analyses revealed phosphorylation events that disrupted global polymerase function by blocking the NTP entry channel or preventing RNA binding. We also identified a regulatory site that split polymerase function by specifically suppressing transcription. These experiments show that host kinases phospho-regulate viral RNA synthesis directly by modulating polymerase activity and indirectly by controlling assembly of replication machinery. Further, they suggest polymerase phosphorylation may bias replication versus transcription at discrete times or locations during the infectious cycle. The influenza virus polymerase is a multifunctional enzyme directing viral gene expression and genome replication. Immediately following infection, the polymerase primarily performs transcription to make the viral mRNAs that program the replication cycle. The polymerase then shifts output to produce more copies of the viral genome at later stages of infection. The balance between transcription and replication is critical for successful infection. Here we identify phosphorylation sites within the viral polymerase and describe how these post-translational modifications control polymerase activity. Cellular kinases modify the viral polymerase. We identified a phosphorylation site in the catalytic subunit PB1 that selectively disables transcription, but not replication. We also describe a phosphorylation site in PB1 that disrupts binding to viral RNAs, disabling all activities of the polymerase. These modifications may establish polymerases with specialized function, and help regulate the balance between transcription and replication throughout the viral life cycle.
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Affiliation(s)
- Anthony R. Dawson
- Department of Medical Microbiology & Immunology, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Gary M. Wilson
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Elyse C. Freiberger
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Arindam Mondal
- Department of Medical Microbiology & Immunology, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI, United States of America
| | - Andrew Mehle
- Department of Medical Microbiology & Immunology, University of Wisconsin–Madison, Madison, WI, United States of America
- * E-mail:
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15
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Mecate-Zambrano A, Sukumar S, Seebohm G, Ciminski K, Schreiber A, Anhlan D, Greune L, Wixler L, Grothe S, Stein NC, Schmidt MA, Langer K, Schwemmle M, Shi T, Ludwig S, Boergeling Y. Discrete spatio-temporal regulation of tyrosine phosphorylation directs influenza A virus M1 protein towards its function in virion assembly. PLoS Pathog 2020; 16:e1008775. [PMID: 32866218 PMCID: PMC7485975 DOI: 10.1371/journal.ppat.1008775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 09/11/2020] [Accepted: 07/02/2020] [Indexed: 01/09/2023] Open
Abstract
Small RNA viruses only have a very limited coding capacity, thus most viral proteins have evolved to fulfill multiple functions. The highly conserved matrix protein 1 (M1) of influenza A viruses is a prime example for such a multifunctional protein, as it acts as a master regulator of virus replication whose different functions have to be tightly regulated. The underlying mechanisms, however, are still incompletely understood. Increasing evidence points towards an involvement of posttranslational modifications in the spatio-temporal regulation of M1 functions. Here, we analyzed the role of M1 tyrosine phosphorylation in genuine infection by using recombinant viruses expressing M1 phosphomutants. Presence of M1 Y132A led to significantly decreased viral replication compared to wildtype and M1 Y10F. Characterization of phosphorylation dynamics by mass spectrometry revealed the presence of Y132 phosphorylation in M1 incorporated into virions that is most likely mediated by membrane-associated Janus kinases late upon infection. Molecular dynamics simulations unraveled a potential phosphorylation-induced exposure of the positively charged linker domain between helices 4 and 5, supposably acting as interaction platform during viral assembly. Consistently, M1 Y132A showed a defect in lipid raft localization due to reduced interaction with viral HA protein resulting in a diminished structural stability of viral progeny and the formation of filamentous particles. Importantly, reduced M1-RNA binding affinity resulted in an inefficient viral genome incorporation and the production of non-infectious virions that interferes with virus pathogenicity in mice. This study advances our understanding of the importance of dynamic phosphorylation as a so far underestimated level of regulation of multifunctional viral proteins and emphasizes the potential feasibility of targeting posttranslational modifications of M1 as a novel antiviral intervention.
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Affiliation(s)
- Angeles Mecate-Zambrano
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
- Cells in Motion Interfaculty Centre (CiM), University of Muenster, Muenster, Germany
| | - Swathi Sukumar
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
- Cells in Motion Interfaculty Centre (CiM), University of Muenster, Muenster, Germany
| | - Guiscard Seebohm
- Institute for Genetics of Heart Diseases (IfGH), Department of Cardiovascular Medicine, University Hospital Muenster, Muenster, Germany
| | - Kevin Ciminski
- Institute of Virology, Medical Center–University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - André Schreiber
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
- Cells in Motion Interfaculty Centre (CiM), University of Muenster, Muenster, Germany
| | - Darisuren Anhlan
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
| | - Lilo Greune
- Cells in Motion Interfaculty Centre (CiM), University of Muenster, Muenster, Germany
- Institute of Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Muenster, Muenster, Germany
| | - Ludmilla Wixler
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
| | - Stephanie Grothe
- Institute of Pharmaceutical Technology and Biopharmacy, University of Muenster, Muenster, Germany
| | - Nora Caroline Stein
- Institute of Pharmaceutical Technology and Biopharmacy, University of Muenster, Muenster, Germany
| | - M. Alexander Schmidt
- Cells in Motion Interfaculty Centre (CiM), University of Muenster, Muenster, Germany
- Institute of Infectiology, Center for Molecular Biology of Inflammation (ZMBE), University of Muenster, Muenster, Germany
| | - Klaus Langer
- Cells in Motion Interfaculty Centre (CiM), University of Muenster, Muenster, Germany
- Institute of Pharmaceutical Technology and Biopharmacy, University of Muenster, Muenster, Germany
| | - Martin Schwemmle
- Institute of Virology, Medical Center–University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tianlai Shi
- Immunology, Inflammation and Infectious Diseases (I3) DTA, Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Stephan Ludwig
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
- Cells in Motion Interfaculty Centre (CiM), University of Muenster, Muenster, Germany
- * E-mail:
| | - Yvonne Boergeling
- Institute of Virology Muenster, University of Muenster, Muenster, Germany
- Cells in Motion Interfaculty Centre (CiM), University of Muenster, Muenster, Germany
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