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Huang Y, Urban C, Hubel P, Stukalov A, Pichlmair A. Protein turnover regulation is critical for influenza A virus infection. Cell Syst 2024:S2405-4712(24)00268-0. [PMID: 39368468 DOI: 10.1016/j.cels.2024.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 08/16/2024] [Accepted: 09/13/2024] [Indexed: 10/07/2024]
Abstract
The abundance of a protein is defined by its continuous synthesis and degradation, a process known as protein turnover. Here, we systematically profiled the turnover of proteins in influenza A virus (IAV)-infected cells using a pulse-chase stable isotope labeling by amino acids in cell culture (SILAC)-based approach combined with downstream statistical modeling. We identified 1,798 virus-affected proteins with turnover changes (tVAPs) out of 7,739 detected proteins (data available at pulsechase.innatelab.org). In particular, the affected proteins were involved in RNA transcription, splicing and nuclear transport, protein translation and stability, and energy metabolism. Many tVAPs appeared to be known IAV-interacting proteins that regulate virus propagation, such as KPNA6, PPP6C, and POLR2A. Notably, our analysis identified additional IAV host and restriction factors, such as the splicing factor GPKOW, that exhibit significant turnover rate changes while their total abundance is minimally affected. Overall, we show that protein turnover is a critical factor both for virus replication and antiviral defense.
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Affiliation(s)
- Yiqi Huang
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Christian Urban
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Philipp Hubel
- Core Facility Hohenheim, Universität Hohenheim, Stuttgart, Germany
| | - Alexey Stukalov
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany
| | - Andreas Pichlmair
- Institute of Virology, Technical University of Munich, School of Medicine, Munich, Germany; Institute of Virology, Helmholtz Munich, Munich, Germany; German Centre for Infection Research (DZIF), Partner Site, Munich, Germany.
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2
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Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024; 31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Proteins are responsible for most intracellular functions, which they perform as part of higher-order molecular complexes, located within defined subcellular niches. Localization is both dynamic and context specific and mislocalization underlies a multitude of diseases. It is thus vital to be able to measure the components of higher-order protein complexes and their subcellular location dynamically in order to fully understand cell biological processes. Here, we review the current range of highly complementary approaches that determine the subcellular organization of the proteome. We discuss the scale and resolution at which these approaches are best employed and the caveats that should be taken into consideration when applying them. We also look to the future and emerging technologies that are paving the way for a more comprehensive understanding of the functional roles of protein isoforms, which is essential for unraveling the complexities of cell biology and the development of disease treatments.
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Affiliation(s)
- Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Charlotte Hutchings
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kishor D Ingole
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Suyeon Kim
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Mehul V Makwana
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kieran J A McCaskie
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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3
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Maas-Bauer K, Stell AV, Yan KL, de Vega E, Vinnakota JM, Unger S, Núñez N, Norona J, Talvard-Balland N, Koßmann S, Schwan C, Miething C, Martens US, Shoumariyeh K, Nestor RP, Duquesne S, Hanke K, Rackiewicz M, Hu Z, El Khawanky N, Taromi S, Andrlova H, Faraidun H, Walter S, Pfeifer D, Follo M, Waldschmidt J, Melchinger W, Rassner M, Wehr C, Schmitt-Graeff A, Halbach S, Liao J, Häcker G, Brummer T, Dengjel J, Andrieux G, Grosse R, Tugues S, Blazar BR, Becher B, Boerries M, Zeiser R. ROCK1/2 signaling contributes to corticosteroid-refractory acute graft-versus-host disease. Nat Commun 2024; 15:446. [PMID: 38199985 PMCID: PMC10781952 DOI: 10.1038/s41467-024-44703-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Patients with corticosteroid-refractory acute graft-versus-host disease (aGVHD) have a low one-year survival rate. Identification and validation of novel targetable kinases in patients who experience corticosteroid-refractory-aGVHD may help improve outcomes. Kinase-specific proteomics of leukocytes from patients with corticosteroid-refractory-GVHD identified rho kinase type 1 (ROCK1) as the most significantly upregulated kinase. ROCK1/2 inhibition improved survival and histological GVHD severity in mice and was synergistic with JAK1/2 inhibition, without compromising graft-versus-leukemia-effects. ROCK1/2-inhibition in macrophages or dendritic cells prior to transfer reduced GVHD severity. Mechanistically, ROCK1/2 inhibition or ROCK1 knockdown interfered with CD80, CD86, MHC-II expression and IL-6, IL-1β, iNOS and TNF production in myeloid cells. This was accompanied by impaired T cell activation by dendritic cells and inhibition of cytoskeletal rearrangements, thereby reducing macrophage and DC migration. NF-κB signaling was reduced in myeloid cells following ROCK1/2 inhibition. In conclusion, ROCK1/2 inhibition interferes with immune activation at multiple levels and reduces acute GVHD while maintaining GVL-effects, including in corticosteroid-refractory settings.
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Affiliation(s)
- Kristina Maas-Bauer
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna-Verena Stell
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kai-Li Yan
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Enrique de Vega
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Janaki Manoja Vinnakota
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Susanne Unger
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Nicolas Núñez
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Johana Norona
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nana Talvard-Balland
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stefanie Koßmann
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carsten Schwan
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Cornelius Miething
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Uta S Martens
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg, Germany
| | - Khalid Shoumariyeh
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center - University of Freiburg, Freiburg, Germany
| | - Rosa P Nestor
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sandra Duquesne
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kathrin Hanke
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michal Rackiewicz
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Zehan Hu
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Nadia El Khawanky
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sanaz Taromi
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hana Andrlova
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hemin Faraidun
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Stefanie Walter
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dietmar Pfeifer
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marie Follo
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Johannes Waldschmidt
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Wolfgang Melchinger
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Rassner
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudia Wehr
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Sebastian Halbach
- German Cancer Consortium (DKTK), Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center - University of Freiburg, Freiburg, Germany
- IMMZ, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - James Liao
- Department of Medicine, University of Arizona, Tucson, USA
| | - Georg Häcker
- IMMH, University Hospital Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Tilman Brummer
- German Cancer Consortium (DKTK), Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center - University of Freiburg, Freiburg, Germany
- IMMZ, University of Freiburg, Faculty of Medicine, Freiburg, Germany
- Signaling Research Centres BIOSS and CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Joern Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robert Grosse
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg, Germany
- CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sonia Tugues
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Bruce R Blazar
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota, Minneapolis, MN, USA
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Melanie Boerries
- German Cancer Consortium (DKTK), Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center - University of Freiburg, Freiburg, Germany
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robert Zeiser
- Department of Medicine I, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- German Cancer Consortium (DKTK), Partner Site Freiburg, a partnership between German Cancer Research Center (DKFZ) and Medical Center - University of Freiburg, Freiburg, Germany.
- Signaling Research Centres BIOSS and CIBSS - Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
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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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5
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Li H, Zhang Y, Li C, Ning P, Sun H, Wei F. Tandem mass tag-based quantitative proteomics analysis reveals the new regulatory mechanism of progranulin in influenza virus infection. Front Microbiol 2023; 13:1090851. [PMID: 36713155 PMCID: PMC9877624 DOI: 10.3389/fmicb.2022.1090851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Progranulin (PGRN) plays an important role in influenza virus infection. To gain insight into the potential molecular mechanisms by which PGRN regulates influenza viral replication, proteomic analyzes of whole mouse lung tissue from wild-type (WT) versus (vs) PGRN knockout (KO) mice were performed to identify proteins regulated by the absence vs. presence of PGRN. Our results revealed that PGRN regulated the differential expression of ALOX15, CD14, CD5L, and FCER1g, etc., and also affected the lysosomal activity in influenza virus infection. Collectively these findings provide a panoramic view of proteomic changes resulting from loss of PGRN and thereby shedding light on the functions of PGRN in influenza virus infection.
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Affiliation(s)
- Haoning Li
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Yuying Zhang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Chengye Li
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Peng Ning
- College of Agriculture, Ningxia University, Yinchuan, China
| | - Hailiang Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Fanhua Wei
- College of Agriculture, Ningxia University, Yinchuan, China,*Correspondence: Fanhua Wei, ✉
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6
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Zhou A, Zhang W, Dong X, Liu M, Chen H, Tang B. The battle for autophagy between host and influenza A virus. Virulence 2022; 13:46-59. [PMID: 34967267 PMCID: PMC9794007 DOI: 10.1080/21505594.2021.2014680] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Influenza A virus (IAV) is an infectious pathogen, threatening the population and public safety with its epidemics. Therefore, it is essential to better understand influenza virus biology to develop efficient strategies against its pathogenicity. Autophagy is an important cellular process to maintain cellular homeostasis by cleaning up the hazardous substrates in lysosome. Accumulating research has also suggested that autophagy is a critical mechanism in host defense responses against IAV infection by degrading viral particles and activating innate or acquired immunity to induce viral clearance. However, IAV has conversely hijacked autophagy to strengthen virus infection by blocking autophagy maturation and further interfering host antiviral signalling to promote viral replication. Therefore, how the battle for autophagy between host and IAV is carried out need to be known. In this review, we describe the role of autophagy in host defence and IAV survival, and summarize the role of influenza proteins in subverting the autophagic process as well as then concentrate on how host utilize antiviral function of autophagy to prevent IAV infection.
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Affiliation(s)
- Ao Zhou
- Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, College of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, P.R. China
| | - Wenhua Zhang
- Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, College of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, P.R. China
| | - Xia Dong
- Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, College of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, P.R. China
| | - Mengyun Liu
- Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, College of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, P.R. China
| | - Hongbo Chen
- Hubei Provincial Center of Technology Innovation for Domestic Animal Breeding, College of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, P.R. China
| | - Bin Tang
- Department of Chemistry, School of Basic Medical College, Southwest Medical University, Luzhou, 646100, People’s Republic of China,CONTACT Bin Tang Department of Chemistry, School of Basic Medical College, Southwest Medical University, Luzhou, 646000, People’s Republic of China
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Diambra L, Alonso AM, Sookoian S, Pirola CJ. Single cell gene expression profiling of nasal ciliated cells reveals distinctive biological processes related to epigenetic mechanisms in patients with severe COVID-19. Comput Biol Med 2022; 148:105895. [PMID: 35926268 PMCID: PMC9338837 DOI: 10.1016/j.compbiomed.2022.105895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/21/2022] [Accepted: 07/16/2022] [Indexed: 01/08/2023]
Abstract
Objective To explore the molecular processes associated with cellular regulatory programs in patients with COVID-19, including gene activation or repression mediated by epigenetic mechanisms. We hypothesized that a comprehensive gene expression profiling of nasopharyngeal epithelial cells might expand our understanding of the pathogenic mechanisms of severe COVID-19. Methods We used single-cell RNA sequencing (scRNAseq) profiling of ciliated cells (n = 12,725) from healthy controls (SARS-CoV-2 negative n = 13) and patients with mild/moderate (n = 13) and severe (n = 14) COVID-19. ScRNAseq data at the patient level were used to perform gene set and pathway enrichment analyses. We prioritized candidate miRNA-target interactions and epigenetic mechanisms. Results We found that mild/moderate COVID-19 compared to healthy controls had upregulation of gene expression signatures associated with mitochondrial function, misfolded proteins, and membrane permeability. In addition, we found that compared to mild/moderate disease, severe COVID-19 had downregulation of epigenetic mechanisms, including DNA and histone H3K4 methylation and chromatin remodelling regulation. Furthermore, we found 11-ranked miRNAs that may explain miRNA-dependent regulation of histone methylation, some of which share seed sequences with SARS-CoV-2 miRNAs. Conclusion Our results may provide novel insights into the epigenetic mechanisms mediating the clinical course of SARS-CoV-2 infection.
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8
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Sura T, Gering V, Cammann C, Hammerschmidt S, Maaß S, Seifert U, Becher D. Streptococcus pneumoniae and Influenza A Virus Co-Infection Induces Altered Polyubiquitination in A549 Cells. Front Cell Infect Microbiol 2022; 12:817532. [PMID: 35281454 PMCID: PMC8908964 DOI: 10.3389/fcimb.2022.817532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
Epithelial cells are an important line of defense within the lung. Disruption of the epithelial barrier by pathogens enables the systemic dissemination of bacteria or viruses within the host leading to severe diseases with fatal outcomes. Thus, the lung epithelium can be damaged by seasonal and pandemic influenza A viruses. Influenza A virus infection induced dysregulation of the immune system is beneficial for the dissemination of bacteria to the lower respiratory tract, causing bacterial and viral co-infection. Host cells regulate protein homeostasis and the response to different perturbances, for instance provoked by infections, by post translational modification of proteins. Aside from protein phosphorylation, ubiquitination of proteins is an essential regulatory tool in virtually every cellular process such as protein homeostasis, host immune response, cell morphology, and in clearing of cytosolic pathogens. Here, we analyzed the proteome and ubiquitinome of A549 alveolar lung epithelial cells in response to infection by either Streptococcus pneumoniae D39Δcps or influenza A virus H1N1 as well as bacterial and viral co-infection. Pneumococcal infection induced alterations in the ubiquitination of proteins involved in the organization of the actin cytoskeleton and Rho GTPases, but had minor effects on the abundance of host proteins. H1N1 infection results in an anti-viral state of A549 cells. Finally, co-infection resembled the imprints of both infecting pathogens with a minor increase in the observed alterations in protein and ubiquitination abundance.
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Affiliation(s)
- Thomas Sura
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Vanessa Gering
- Friedrich Loeffler-Institute of Medical Microbiology-Virology, University Medicine Greifswald, Greifswald, Germany
| | - Clemens Cammann
- Friedrich Loeffler-Institute of Medical Microbiology-Virology, University Medicine Greifswald, Greifswald, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Ulrike Seifert
- Friedrich Loeffler-Institute of Medical Microbiology-Virology, University Medicine Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
- *Correspondence: Dörte Becher,
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9
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Multiomics Analysis of Endocytosis upon HBV Infection and Identification of SCAMP1 as a Novel Host Restriction Factor against HBV Replication. Int J Mol Sci 2022; 23:ijms23042211. [PMID: 35216324 PMCID: PMC8874515 DOI: 10.3390/ijms23042211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains a major global health problem and the primary cause of cirrhosis and hepatocellular carcinoma (HCC). HBV intrusion into host cells is prompted by virus–receptor interactions in clathrin-mediated endocytosis. Here, we report a comprehensive view of the cellular endocytosis-associated transcriptome, proteome and ubiquitylome upon HBV infection. In this study, we quantified 273 genes in the transcriptome and 190 endocytosis-associated proteins in the proteome by performing multi-omics analysis. We further identified 221 Lys sites in 77 endocytosis-associated ubiquitinated proteins. A weak negative correlation was observed among endocytosis-associated transcriptome, proteome and ubiquitylome. We found 33 common differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and Kub-sites. Notably, we reported the HBV-induced ubiquitination change of secretory carrier membrane protein (SCAMP1) for the first time, differentially expressed across all three omics data sets. Overexpression of SCAMP1 efficiently inhibited HBV RNAs/pgRNA and secreted viral proteins, whereas knockdown of SCAMP1 significantly increased viral production. Mechanistically, the EnhI/XP, SP1, and SP2 promoters were inhibited by SCAMP1, which accounts for HBV X and S mRNA inhibition. Overall, our study unveils the previously unknown role of SCAMP1 in viral replication and HBV pathogenesis and provides cumulative and novel information for a better understanding of endocytosis in response to HBV infection.
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10
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Duan Z, Tang H, Wang Y, Zhao C, Zhou L, Han Y. The association of ribosomal protein L18 with Newcastle disease virus matrix protein enhances viral translation and replication. Avian Pathol 2021; 51:129-140. [PMID: 34859725 DOI: 10.1080/03079457.2021.2013435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ABSTRACTNumerous studies have shown that viruses can utilize or manipulate ribosomal proteins to achieve viral protein biosynthesis and replication. In our recent studies using proteomics analysis of virus-infected cells, we found that ribosomal protein L18 (RPL18) was the highest up-regulated differentially expressed protein, which was along with the increasingly expressed viral proteins later in Newcastle disease virus (NDV) infection. However, the association of RPL18 with viral protein biosynthesis and NDV replication remains unclear. In this study, we found that the expression and transcription levels of RPL18 was reduced early in NDV infection but increased later in NDV infection. In addition, the presence of cytoplasmic NDV matrix (M) protein was responsible for the increased expression of RPL18 in both virus-infected cells and plasmid-transfected cells. Moreover, cytoplasmic M protein increased RPL18 expression in a dose-dependent manner, even though they did not interact with each other. Furthermore, siRNA-mediated knockdown of RPL18 or overexpression of RPL18 dramatically reduced or enhanced NDV replication by decreasing or increasing viral protein translation rather than viral RNA synthesis and transcription. Taken together, these results suggested that the increased expression of RPL18 might be associated with the physical clumping together of the M protein, which in turn promoted viral protein biosynthesis and NDV replication, thus revealing for the first time the association of RPL18 with NDV M protein was important for viral translation and replication.
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Affiliation(s)
- Zhiqiang Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Hong Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Yanbi Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Caiqin Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Lei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
| | - Yifan Han
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China.,College of Animal Science, Guizhou University, Guiyang, China
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11
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Puchkova LV, Kiseleva IV, Polishchuk EV, Broggini M, Ilyechova EY. The Crossroads between Host Copper Metabolism and Influenza Infection. Int J Mol Sci 2021; 22:ijms22115498. [PMID: 34071094 PMCID: PMC8197124 DOI: 10.3390/ijms22115498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/15/2022] Open
Abstract
Three main approaches are used to combat severe viral respiratory infections. The first is preemptive vaccination that blocks infection. Weakened or dead viral particles, as well as genetic constructs carrying viral proteins or information about them, are used as an antigen. However, the viral genome is very evolutionary labile and changes continuously. Second, chemical agents are used during infection and inhibit the function of a number of viral proteins. However, these drugs lose their effectiveness because the virus can rapidly acquire resistance to them. The third is the search for points in the host metabolism the effect on which would suppress the replication of the virus but would not have a significant effect on the metabolism of the host. Here, we consider the possibility of using the copper metabolic system as a target to reduce the severity of influenza infection. This is facilitated by the fact that, in mammals, copper status can be rapidly reduced by silver nanoparticles and restored after their cancellation.
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Affiliation(s)
- Ludmila V. Puchkova
- International Research Laboratory of Trace Elements Metabolism, ADTS Institute, RC AFMLCS, ITMO University, 197101 St. Petersburg, Russia;
| | - Irina V. Kiseleva
- Department of Virology, Institute of Experimental Medicine, 197376 St. Petersburg, Russia;
| | | | - Massimo Broggini
- Istituto di Ricerche Farmacologiche “Mario Negri”, IRCCS, 20156 Milan, Italy;
| | - Ekaterina Yu. Ilyechova
- International Research Laboratory of Trace Elements Metabolism, ADTS Institute, RC AFMLCS, ITMO University, 197101 St. Petersburg, Russia;
- Department of Molecular Genetics, Institute of Experimental Medicine, 197376 St. Petersburg, Russia
- Correspondence: ; Tel.: +7-921-760-5274
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12
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Christopher JA, Stadler C, Martin CE, Morgenstern M, Pan Y, Betsinger CN, Rattray DG, Mahdessian D, Gingras AC, Warscheid B, Lehtiö J, Cristea IM, Foster LJ, Emili A, Lilley KS. Subcellular proteomics. NATURE REVIEWS. METHODS PRIMERS 2021; 1:32. [PMID: 34549195 PMCID: PMC8451152 DOI: 10.1038/s43586-021-00029-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/15/2021] [Indexed: 12/11/2022]
Abstract
The eukaryotic cell is compartmentalized into subcellular niches, including membrane-bound and membrane-less organelles. Proteins localize to these niches to fulfil their function, enabling discreet biological processes to occur in synchrony. Dynamic movement of proteins between niches is essential for cellular processes such as signalling, growth, proliferation, motility and programmed cell death, and mutations causing aberrant protein localization are associated with a wide range of diseases. Determining the location of proteins in different cell states and cell types and how proteins relocalize following perturbation is important for understanding their functions, related cellular processes and pathologies associated with their mislocalization. In this Primer, we cover the major spatial proteomics methods for determining the location, distribution and abundance of proteins within subcellular structures. These technologies include fluorescent imaging, protein proximity labelling, organelle purification and cell-wide biochemical fractionation. We describe their workflows, data outputs and applications in exploring different cell biological scenarios, and discuss their main limitations. Finally, we describe emerging technologies and identify areas that require technological innovation to allow better characterization of the spatial proteome.
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Affiliation(s)
- Josie A. Christopher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Charlotte Stadler
- Department of Protein Sciences, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Claire E. Martin
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Marcel Morgenstern
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Yanbo Pan
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Cora N. Betsinger
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David G. Rattray
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Diana Mahdessian
- Department of Protein Sciences, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bettina Warscheid
- Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS and CIBSS Signaling Research Centers, University of Freiburg, Freiburg, Germany
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Kathryn S. Lilley
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
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13
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Zhang J, Zhang W, Ren L, He Y, Mei Z, Feng J, Shi T, Zhang H, Song Z, Jie Z. Astragaloside IV attenuates IL-1β secretion by enhancing autophagy in H1N1 infection. FEMS Microbiol Lett 2021; 367:5766227. [PMID: 32108899 DOI: 10.1093/femsle/fnaa007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 01/11/2020] [Indexed: 12/12/2022] Open
Abstract
Excessive secretion of inflammatory factors (cytokine storm) plays a significant role in H1N1-induced acute pneumonia, and autophagy acts as a cell-intrinsic mechanism to regulate inflammation. Astragaloside IV (AS-IV), originating from the astragalus root, possesses multiple pharmacological activities, such as anti-inflammation. However, the influences of AS-IV on H1N1-induced autophagy and inflammation have remained elusive. It has been reported that H1N1 infection leads to the accumulation of autophagosomes but obstructs autophagosomes incorporating into lysosomes, whereas the present study showed that AS-IV enhanced autophagy activation in H1N1 infection. Furthermore, we found that AS-IV promoted H1N1-triggered formation of autophagosomes and autolysosomes. Additionally, it was noted that AS-IV did not affect viral replication, mRNA level of interleukin-1 beta (IL-1β) and pro-IL-1β protein level, but significantly decreased secretion of IL-1β, and chloroquine (CQ, as an inhibitor of autophagy) increased secretion of IL-1β in H1N1 infection. In conclusion, AS-IV stimulates the formation of autophagosomes and the fusion of autophagosomes and lysosomes in H1N1 infection and may lead to decreased IL-1β secretion.
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Affiliation(s)
- Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China
| | - Wanju Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Lehao Ren
- Department of Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yanchao He
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China
| | - Zhoufang Mei
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China
| | - Jingjing Feng
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China
| | - Tianyun Shi
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China
| | - Huiying Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhigang Song
- Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China
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14
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Vavougios GD, Nday C, Pelidou SH, Zarogiannis SG, Gourgoulianis KI, Stamoulis G, Doskas T. Double hit viral parasitism, polymicrobial CNS residency and perturbed proteostasis in Alzheimer's disease: A data driven, in silico analysis of gene expression data. Mol Immunol 2020; 127:124-135. [PMID: 32971399 DOI: 10.1016/j.molimm.2020.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/25/2020] [Accepted: 08/30/2020] [Indexed: 01/04/2023]
Abstract
The aim of this study was to determine the interaction of peripheral immunity vs. the CNS in the setting of AD pathogenesis at the transcriptomic level in a data driven manner. For this purpose, publicly available gene expression data from the GEO Datasets repository. We performed differential gene expression and functional enrichment analyses were performed on the five retrieved studies: (a) three hippocampal cortex (HC) studies (b) one study of peripheral blood mononuclear cells (PBMC) and (c) one involving neurofibrillary tangle - containing neurons of the entorhinal cortex (NFT EC). Subsequently, BLAST was used to determine protein conservation between human proteins vs. microbial, whereas putative protein / oligopeptide antigenicity were determined via RANKPep. Gene ontology and pathway analyses revealed significantly enriched viral parasitism pathways in both PBMC and NFT - EC datasets, mediated by ribosomal protein families and epigenetic regulators. Among these, a salient viral pathway referred to Influenza A infection. NFT - EC annotations included leukocyte chemotaxis and immune response pathways. All datasets were significantly enriched for infectious pathways, as well as pathways involved in impaired proteostasis and non - phagocytic cell phagosomal cascades. In conclusion, our in silico analysis outlined an ad hoc model of AD pathophysiology in which double hit (PBMC and NFT-EC) viral parasitism is mediated by eukaryotic translational hijacking, and may be further implicated by impaired immune responses. Overall, our results overlap with the antimicrobial protection hypothesis of AD pathogenesis and support the notion of a pathogen - driven etiology.
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Affiliation(s)
- George D Vavougios
- Department of Neurology, Athens Naval Hospital, P.C. 115 21, Athens, Greece; Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, P.C, 41500, Larissa, Greece; Department of Computer Science and Telecommunications, University of Thessaly, Papasiopoulou 2 - 4, P.C. 35 131 Galaneika, Lamia, Greece.
| | - Christiane Nday
- Laboratory of Medical Physics, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, P.C. 5414, Thessaloniki, Greece
| | | | - Sotirios G Zarogiannis
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, Larissa, 41500, Greece
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, P.C, 41500, Larissa, Greece
| | - George Stamoulis
- Department of Electrical and Computer Engineering, University of Thessaly, 37 Glavani - 28th October Str, Deligiorgi Building, 4th floor, P.C. 382 21, Volos, Greece
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15
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TRIM Proteins and Their Roles in the Influenza Virus Life Cycle. Microorganisms 2020; 8:microorganisms8091424. [PMID: 32947942 PMCID: PMC7565951 DOI: 10.3390/microorganisms8091424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) has been recognized for regulating fundamental cellular processes, followed by induction of proteasomal degradation of target proteins, and triggers multiple signaling pathways that are crucial for numerous aspects of cellular physiology. Especially tripartite motif (TRIM) proteins, well-known E3 ubiquitin ligases, emerge as having critical roles in several antiviral signaling pathways against varying viral infections. Here we highlight recent advances in the study of antiviral roles of TRIM proteins toward influenza virus infection in terms of the modulation of pathogen recognition receptor (PRR)-mediated innate immune sensing, direct obstruction of influenza viral propagation, and participation in virus-induced autophagy.
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16
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Abstract
This review aims to reflect upon the major developments in PARP14 research from late 2017 to early 2020. In doing so, this report will focus on the continual elucidation of PARP14's function including an emerging role in viral replication. This is in addition to other functional developments in cancer and inflammation, along with reflecting upon the leads in inhibitor design, including the increased attention toward the macrodomain. This report will also include a brief recap on contemporary poly(ADP-ribose) polymerase inhibitors and reflect upon the development surrounding the other poly(ADP-ribose) polymerases to overall give a succinct update to assist the development of selective PARP14 inhibitors.
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Affiliation(s)
- Amanda L Tauber
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast 4229, Queensland, Australia
| | - Stephan M Levonis
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast 4229, Queensland, Australia
| | - Stephanie S Schweiker
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast 4229, Queensland, Australia
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17
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Miller CM, Selvam S, Fuchs G. Fatal attraction: The roles of ribosomal proteins in the viral life cycle. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1613. [PMID: 32657002 DOI: 10.1002/wrna.1613] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 12/30/2022]
Abstract
Upon viral infection of a host cell, each virus starts a program to generate many progeny viruses. Although viruses interact with the host cell in numerous ways, one critical step in the virus life cycle is the expression of viral proteins, which are synthesized by the host ribosomes in conjunction with host translation factors. Here we review different mechanisms viruses have evolved to effectively seize host cell ribosomes, the roles of specific ribosomal proteins and their posttranslational modifications on viral RNA translation, or the cellular response to infection. We further highlight ribosomal proteins with extra-ribosomal function during viral infection and put the knowledge of ribosomal proteins during viral infection into the larger context of ribosome-related diseases, known as ribosomopathies. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation.
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Affiliation(s)
- Clare M Miller
- Department of Biological Sciences, University at Albany, Albany, New York, USA
| | - Sangeetha Selvam
- Department of Biological Sciences, University at Albany, Albany, New York, USA
| | - Gabriele Fuchs
- Department of Biological Sciences, University at Albany, Albany, New York, USA.,The RNA Institute, University at Albany, Albany, New York, USA
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18
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Bogdanow B, Wang X, Eichelbaum K, Sadewasser A, Husic I, Paki K, Budt M, Hergeselle M, Vetter B, Hou J, Chen W, Wiebusch L, Meyer IM, Wolff T, Selbach M. The dynamic proteome of influenza A virus infection identifies M segment splicing as a host range determinant. Nat Commun 2019; 10:5518. [PMID: 31797923 PMCID: PMC6892822 DOI: 10.1038/s41467-019-13520-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 11/12/2019] [Indexed: 12/16/2022] Open
Abstract
Pandemic influenza A virus (IAV) outbreaks occur when strains from animal reservoirs acquire the ability to infect and spread among humans. The molecular basis of this species barrier is incompletely understood. Here we combine metabolic pulse labeling and quantitative proteomics to monitor protein synthesis upon infection of human cells with a human- and a bird-adapted IAV strain and observe striking differences in viral protein synthesis. Most importantly, the matrix protein M1 is inefficiently produced by the bird-adapted strain. We show that impaired production of M1 from bird-adapted strains is caused by increased splicing of the M segment RNA to alternative isoforms. Strain-specific M segment splicing is controlled by the 3' splice site and functionally important for permissive infection. In silico and biochemical evidence shows that avian-adapted M segments have evolved different conserved RNA structure features than human-adapted sequences. Thus, we identify M segment RNA splicing as a viral host range determinant.
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Affiliation(s)
- Boris Bogdanow
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
- Structural Interactomics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Xi Wang
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Division of Theoretical Systems Biology, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Katrin Eichelbaum
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Anne Sadewasser
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
| | - Immanuel Husic
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Katharina Paki
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
| | - Matthias Budt
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
| | - Martha Hergeselle
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Barbara Vetter
- Labor für Pädiatrische Molekularbiologie, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Jingyi Hou
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
| | - Wei Chen
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Department of Biology, Southern University of Science and Technology, Xuanyuan Road 1088, 518055, Shenzhen, China
| | - Lüder Wiebusch
- Labor für Pädiatrische Molekularbiologie, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Irmtraud M Meyer
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany
- Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry, Thielallee 63, 14195, Berlin, Germany
| | - Thorsten Wolff
- Unit 17 "Influenza and other Respiratory Viruses", Robert Koch Institut, Seestrase 10, 13353, Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.
- Charité Universitätsmedizin Berlin, 10117, Berlin, Germany.
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19
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Wu H, Zhang S, Huo C, Zou S, Lian Z, Hu Y. iTRAQ-based proteomic and bioinformatic characterization of human mast cells upon infection by the influenza A virus strains H1N1 and H5N1. FEBS Lett 2019; 593:2612-2627. [PMID: 31271652 DOI: 10.1002/1873-3468.13523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/26/2019] [Accepted: 06/19/2019] [Indexed: 12/12/2022]
Abstract
Mast cells can support the replication of influenza A virus, although how this occurs is poorly understood. In the present study, using quantitative MS, we analyzed the proteome of human mast cells infected with different influenza A virus strains at 12 h post-infection. Forty-one differentially expressed proteins were identified in human mast cells upon infection by the virulent H5N1 (A/Chicken/Henan/1/04) virus compared to the seasonal H1N1 (A/WSN/33) virus. Bioinformatic analyses confirmed that H1N1 significantly regulates the RNA degradation pathway via up-regulation of CCR4-NOT transcription complex subunit 4, whereas apoptosis could be suppressed by H5N1 via down-regulation of the tumor protein p53 signaling pathway with P ≤ 0.05 at 12 h post-infection. The hypoxia-inducible factor-1 signaling pathway of human mast cells is more susceptible to infection by H5N1 than by H1N1 virus.
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Affiliation(s)
- Hongping Wu
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shouping Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Caiyun Huo
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shumei Zou
- National Institute for Viral Disease Control and Prevention, Collaboration Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, China
| | - Zhengxing Lian
- Beijing Key Laboratory of Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanxin Hu
- Key Laboratory of Animal Epidemiology of Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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20
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Liu J, Yang Z, Kong Y, He Y, Xu Y, Cao X. Antitumor activity of alantolactone in lung cancer cell lines NCI-H1299 and Anip973. J Food Biochem 2019; 43:e12972. [PMID: 31489665 DOI: 10.1111/jfbc.12972] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 05/13/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022]
Abstract
Alantolactone is a sesquiterpene lactone extracted from Inula helenium L. plants possessing many biological activities, including anti-inflammatory, antiproliferation, and antimicrobial. The inhibitory effects and the underlying mechanisms of alantolactone on lung cancer cells NCI-H1299 and Anip973 were investigated in this study. The results showed that alantolactone could decrease cell viability and induce cell apoptosis of NCI-H1299 and Anip973. After the cells were treated with alantolactone, the expression of Bcl-2 decreased, while the expression of Bax increased, the expression of MMP-9, MMP-7, and MMP-2 gradually decreased after alantolactone treatment. Furthermore, results showed that alantolactone could activate p38 MAPK pathway and suppress NF-κB pathway, which are involving in lung cancer development. These results indicated that alantolactone was a potential agent for lung cancer treatment. PRACTICAL APPLICATIONS: Lung cancer is one of the most common contributors of cancer death in the world. Chemoprevention and chemotherapy with natural substances are prospective methods for lung cancer treatment. In recent years, the anti-cancer activity of various sesquiterpene lactones has attracted a great deal of interest. Alantolactone is the major active sesquiterpene lactones isolated from Inula helenium L, which is used as a medicine in ancient Romans due to wide range of pharmacological activities. The results obtained from this study revealed the inhibitory effects of alantolactone on lung cancer cells and might provide some experimental basis for prevention and treatment of lung cancer with alantolactone.
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Affiliation(s)
- Jianli Liu
- Department of Biological Sciences, School of Life Science, Liaoning University, Shenyang, P.R. China
| | - Zhijun Yang
- Department of Biological Sciences, School of Life Science, Liaoning University, Shenyang, P.R. China
| | - Yuchi Kong
- Department of Biological Sciences, School of Life Science, Liaoning University, Shenyang, P.R. China
| | - Yin He
- Department of Biological Sciences, School of Life Science, Liaoning University, Shenyang, P.R. China
| | - Yongliang Xu
- Department of Biological Sciences, School of Life Science, Liaoning University, Shenyang, P.R. China
| | - Xiangyu Cao
- Department of Biological Sciences, School of Life Science, Liaoning University, Shenyang, P.R. China
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21
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Khandia R, Dadar M, Munjal A, Dhama K, Karthik K, Tiwari R, Yatoo MI, Iqbal HMN, Singh KP, Joshi SK, Chaicumpa W. A Comprehensive Review of Autophagy and Its Various Roles in Infectious, Non-Infectious, and Lifestyle Diseases: Current Knowledge and Prospects for Disease Prevention, Novel Drug Design, and Therapy. Cells 2019; 8:cells8070674. [PMID: 31277291 PMCID: PMC6678135 DOI: 10.3390/cells8070674] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/04/2019] [Accepted: 06/04/2019] [Indexed: 02/05/2023] Open
Abstract
Autophagy (self-eating) is a conserved cellular degradation process that plays important roles in maintaining homeostasis and preventing nutritional, metabolic, and infection-mediated stresses. Autophagy dysfunction can have various pathological consequences, including tumor progression, pathogen hyper-virulence, and neurodegeneration. This review describes the mechanisms of autophagy and its associations with other cell death mechanisms, including apoptosis, necrosis, necroptosis, and autosis. Autophagy has both positive and negative roles in infection, cancer, neural development, metabolism, cardiovascular health, immunity, and iron homeostasis. Genetic defects in autophagy can have pathological consequences, such as static childhood encephalopathy with neurodegeneration in adulthood, Crohn's disease, hereditary spastic paraparesis, Danon disease, X-linked myopathy with excessive autophagy, and sporadic inclusion body myositis. Further studies on the process of autophagy in different microbial infections could help to design and develop novel therapeutic strategies against important pathogenic microbes. This review on the progress and prospects of autophagy research describes various activators and suppressors, which could be used to design novel intervention strategies against numerous diseases and develop therapeutic drugs to protect human and animal health.
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Affiliation(s)
- Rekha Khandia
- Department of Genetics, Barkatullah University, Bhopal 462 026, Madhya Pradesh, India
| | - Maryam Dadar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31975/148, Iran
| | - Ashok Munjal
- Department of Genetics, Barkatullah University, Bhopal 462 026, Madhya Pradesh, India.
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India.
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai, Tamil Nadu 600051, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, Uttar Pradesh 281 001, India
| | - Mohd Iqbal Yatoo
- Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar 190025, Jammu and Kashmir, India
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N. L., CP 64849, Mexico
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, Uttar Pradesh, India
| | - Sunil K Joshi
- Department of Pediatrics, Division of Hematology, Oncology and Bone Marrow Transplantation, University of Miami School of Medicine, Miami, FL 33136, USA.
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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22
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Liu D, Lin J, Su J, Chen X, Jiang P, Huang K. Glutamine Deficiency Promotes PCV2 Infection through Induction of Autophagy via Activation of ROS-Mediated JAK2/STAT3 Signaling Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:11757-11766. [PMID: 30343565 DOI: 10.1021/acs.jafc.8b04704] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Porcine circovirus type 2 (PCV2) is an important pathogen in swine herds. We previously reported that glutamine (Gln) deficiency promoted PCV2 infection in vitro. Here, we established a Gln deficiency model in vivo and further investigated the detailed molecular mechanisms. In vivo and in vitro, Gln deficiency promoted PCV2 infection, which was evident through increased viral yields and PCV2 Cap protein synthesis. It also induced autophagy, as demonstrated by the increases in LC3-II conversion, SQSTM1 degradation, and GFP-LC3 dot accumulation. Autophagy inhibition abolished the effects of Gln deficiency on PCV2 infection. Inhibition of ROS generation alleviated the Gln deficiency-activated JAK2/STAT3 signaling pathway, thereby inhibiting autophagy induction. In vitro, the inhibition of STAT3 by an inhibitor or RNA interference blocked autophagy, thus reversing the effects of Gln deficiency on PCV2 infection. These results indicate that Gln deficiency activates autophagy by upregulating ROS-medicated JAK2/STAT3 signaling and thereby promoting PCV2 infection.
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