1
|
Zeng Y, Li Y, Zhang W, Lu H, Lin S, Zhang W, Xia L, Hu H, Song Y, Xu F. Proteome analysis develops novel plasma proteins classifier in predicting the mortality of COVID-19. Cell Prolif 2024; 57:e13617. [PMID: 38403992 PMCID: PMC11216943 DOI: 10.1111/cpr.13617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
COVID-19 has been a global concern for 3 years, however, consecutive plasma protein changes in the disease course are currently unclear. Setting the mortality within 28 days of admission as the main clinical outcome, plasma samples were collected from patients in discovery and independent validation groups at different time points during the disease course. The whole patients were divided into death and survival groups according to their clinical outcomes. Proteomics and pathway/network analyses were used to find the differentially expressed proteins and pathways. Then, we used machine learning to develop a protein classifier which can predict the clinical outcomes of the patients with COVID-19 and help identify the high-risk patients. Finally, a classifier including C-reactive protein, extracellular matrix protein 1, insulin-like growth factor-binding protein complex acid labile subunit, E3 ubiquitin-protein ligase HECW1 and phosphatidylcholine-sterol acyltransferase was determined. The prediction value of the model was verified with an independent patient cohort. This novel model can realize early prediction of 28-day mortality of patients with COVID-19, with the area under curve 0.88 in discovery group and 0.80 in validation group, superior to 4C mortality and E-CURB65 scores. In total, this work revealed a potential protein classifier which can assist in predicting the outcomes of COVID-19 patients and providing new diagnostic directions.
Collapse
Affiliation(s)
- Yifei Zeng
- Department of Infectious DiseasesSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Yufan Li
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Wanying Zhang
- Department of Infectious DiseasesSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Huidan Lu
- Department of Infectious DiseasesSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Siyi Lin
- Department of Infectious DiseasesSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Wenting Zhang
- Department of Infectious DiseasesSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Lexin Xia
- Department of Infectious DiseasesSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Huiqun Hu
- Department of Infectious DiseasesSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Yuanlin Song
- Shanghai Key Laboratory of Lung Inflammation and Injury, Department of Pulmonary Medicine, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Feng Xu
- Department of Infectious DiseasesSecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
- Key Laboratory of Multiple Organ Failure (Zhejiang University)Ministry of EducationHangzhouChina
- Research Center for Life Science and Human HealthBinjiang Institute of Zhejiang UniversityHangzhouChina
| |
Collapse
|
2
|
Hofstadter WA, Tsopurashvili E, Cristea IM. Viral regulation of organelle membrane contact sites. PLoS Biol 2024; 22:e3002529. [PMID: 38442090 PMCID: PMC10914265 DOI: 10.1371/journal.pbio.3002529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
At the core of organelle functions lies their ability and need to form dynamic organelle-organelle networks that drive intracellular communication and coordination of cellular pathways. These networks are facilitated by membrane contact sites (MCSs) that promote both intra-organelle and inter-organelle communication. Given their multiple functions, MCSs and the proteins that form them are commonly co-opted by viruses during infection to promote viral replication. This Essay discusses mechanisms acquired by diverse human viruses to regulate MCS functions in either proviral processes or host defense. It also examines techniques used for examining MCSs in the context of viral infections.
Collapse
Affiliation(s)
- William A. Hofstadter
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Elene Tsopurashvili
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
3
|
Osei D, Baumgart-Vogt E, Ahlemeyer B, Herden C. Tumor Necrosis Factor-α Receptor 1 Mediates Borna Disease Virus 1-Induced Changes in Peroxisomal and Mitochondrial Dynamics in Neurons. Int J Mol Sci 2024; 25:1849. [PMID: 38339126 PMCID: PMC10855776 DOI: 10.3390/ijms25031849] [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: 12/23/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Borna disease virus 1 (BoDV1) causes a persistent infection in the mammalian brain. Peroxisomes and mitochondria play essential roles in the cellular antiviral immune response, but the effect of BoDV1 infection on peroxisomal and mitochondrial dynamics and their respective antioxidant capacities is still not clear. Using different mouse lines-i.e., tumor necrosis factor-α transgenic (TNFTg; to pro-inflammatory status), TNF receptor-1 knockout (TNFR1ko), and TNFR2ko mice in comparison to wild-type (Wt) mice-we analyzed the abundances of both organelles and their main antioxidant enzymes, catalase and superoxide dismutase 2 (SOD2), in neurons of the hippocampal, cerebral, and cerebellar cortices. In TNFTg mice, a strong increase in mitochondrial (6.9-fold) and SOD2 (12.1-fold) abundances was detected; meanwhile, peroxisomal abundance increased slightly (1.5-fold), but that of catalase decreased (2.9-fold). After BoDV1 infection, a strong decrease in mitochondrial (2.1-6.5-fold), SOD2 (2.7-9.1-fold), and catalase (2.7-10.3-fold) abundances, but a slight increase in peroxisomes (1.3-1.6-fold), were detected in Wt and TNFR2ko mice, whereas no changes occurred in TNFR1ko mice. Our data suggest that the TNF system plays a crucial role in the biogenesis of both subcellular organelles. Moreover, TNFR1 signaling mediated the changes in peroxisomal and mitochondrial dynamics after BoDV1 infection, highlighting new mechanisms by which BoDV1 may achieve immune evasion and viral persistence.
Collapse
Affiliation(s)
- Dominic Osei
- Institute for Anatomy and Cell Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.O.); (E.B.-V.)
- Institute of Veterinary Pathology, Justus Liebig University Giessen, 35392 Giessen, Germany
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.O.); (E.B.-V.)
| | - Barbara Ahlemeyer
- Institute for Anatomy and Cell Biology, Justus Liebig University Giessen, 35392 Giessen, Germany; (D.O.); (E.B.-V.)
| | - Christiane Herden
- Institute of Veterinary Pathology, Justus Liebig University Giessen, 35392 Giessen, Germany
- Center for Mind, Brain and Behavior, Justus Liebig University Giessen, 35392 Giessen, Germany
| |
Collapse
|
4
|
Kumar R, Islinger M, Worthy H, Carmichael R, Schrader M. The peroxisome: an update on mysteries 3.0. Histochem Cell Biol 2024; 161:99-132. [PMID: 38244103 PMCID: PMC10822820 DOI: 10.1007/s00418-023-02259-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2023] [Indexed: 01/22/2024]
Abstract
Peroxisomes are highly dynamic, oxidative organelles with key metabolic functions in cellular lipid metabolism, such as the β-oxidation of fatty acids and the synthesis of myelin sheath lipids, as well as the regulation of cellular redox balance. Loss of peroxisomal functions causes severe metabolic disorders in humans. Furthermore, peroxisomes also fulfil protective roles in pathogen and viral defence and immunity, highlighting their wider significance in human health and disease. This has sparked increasing interest in peroxisome biology and their physiological functions. This review presents an update and a continuation of three previous review articles addressing the unsolved mysteries of this remarkable organelle. We continue to highlight recent discoveries, advancements, and trends in peroxisome research, and address novel findings on the metabolic functions of peroxisomes, their biogenesis, protein import, membrane dynamics and division, as well as on peroxisome-organelle membrane contact sites and organelle cooperation. Furthermore, recent insights into peroxisome organisation through super-resolution microscopy are discussed. Finally, we address new roles for peroxisomes in immune and defence mechanisms and in human disorders, and for peroxisomal functions in different cell/tissue types, in particular their contribution to organ-specific pathologies.
Collapse
Grants
- BB/W015420/1, BB/V018167/1, BB/T002255/1, BB/R016844/1 Biotechnology and Biological Sciences Research Council
- BB/W015420/1, BB/V018167/1, BB/T002255/1, BB/R016844/1 Biotechnology and Biological Sciences Research Council
- BB/W015420/1, BB/V018167/1, BB/T002255/1, BB/R016844/1 Biotechnology and Biological Sciences Research Council
- European Union’s Horizon 2020 research and innovation programme
- Deutsches Zentrum für Herz-Kreislaufforschung
- German Research Foundation
- Medical Faculty Mannheim, University of Heidelberg
Collapse
Affiliation(s)
- Rechal Kumar
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Markus Islinger
- Institute of Neuroanatomy, Medical Faculty Mannheim, Mannheim Centre for Translational Neuroscience, University of Heidelberg, 68167, Mannheim, Germany
| | - Harley Worthy
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Ruth Carmichael
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Michael Schrader
- Faculty of Health and Life Sciences, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| |
Collapse
|
5
|
Jiang H, Nair V, Sun Y, Ding C. The diverse roles of peroxisomes in the interplay between viruses and mammalian cells. Antiviral Res 2024; 221:105780. [PMID: 38092324 DOI: 10.1016/j.antiviral.2023.105780] [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: 07/30/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/26/2023]
Abstract
Peroxisomes are ubiquitous organelles found in eukaryotic cells that play a critical role in the oxidative metabolism of lipids and detoxification of reactive oxygen species (ROS). Recently, the role of peroxisomes in viral infections has been extensively studied. Although several studies have reported that peroxisomes exert antiviral activity, evidence indicates that viruses have also evolved diverse strategies to evade peroxisomal antiviral signals. In this review, we summarize the multiple roles of peroxisomes in the interplay between viruses and mammalian cells. Focus is given on the peroxisomal regulation of innate immune response, lipid metabolism, ROS production, and viral regulation of peroxisomal biosynthesis and degradation. Understanding the interactions between peroxisomes and viruses provides novel insights for the development of new antiviral strategies.
Collapse
Affiliation(s)
- Hui Jiang
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China
| | - Venugopal Nair
- Avian Oncogenic Viruses Group, UK-China Centre of Excellence in Avian Disease Research, The Pirbright Institute, Pirbright, Guildford, Surrey, United Kingdom
| | - Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China.
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu Province, China.
| |
Collapse
|
6
|
Pellegrino E, Aylan B, Bussi C, Fearns A, Bernard EM, Athanasiadi N, Santucci P, Botella L, Gutierrez MG. Peroxisomal ROS control cytosolic Mycobacterium tuberculosis replication in human macrophages. J Cell Biol 2023; 222:e202303066. [PMID: 37737955 PMCID: PMC10515436 DOI: 10.1083/jcb.202303066] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/27/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Peroxisomes are organelles involved in many metabolic processes including lipid metabolism, reactive oxygen species (ROS) turnover, and antimicrobial immune responses. However, the cellular mechanisms by which peroxisomes contribute to bacterial elimination in macrophages remain elusive. Here, we investigated peroxisome function in iPSC-derived human macrophages (iPSDM) during infection with Mycobacterium tuberculosis (Mtb). We discovered that Mtb-triggered peroxisome biogenesis requires the ESX-1 type 7 secretion system, critical for cytosolic access. iPSDM lacking peroxisomes were permissive to Mtb wild-type (WT) replication but were able to restrict an Mtb mutant missing functional ESX-1, suggesting a role for peroxisomes in the control of cytosolic but not phagosomal Mtb. Using genetically encoded localization-dependent ROS probes, we found peroxisomes increased ROS levels during Mtb WT infection. Thus, human macrophages respond to the infection by increasing peroxisomes that generate ROS primarily to restrict cytosolic Mtb. Our data uncover a peroxisome-controlled, ROS-mediated mechanism that contributes to the restriction of cytosolic bacteria.
Collapse
Affiliation(s)
- Enrica Pellegrino
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Beren Aylan
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Claudio Bussi
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Antony Fearns
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Elliott M. Bernard
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Natalia Athanasiadi
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Pierre Santucci
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | - Laure Botella
- Host-pathogen interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK
| | | |
Collapse
|
7
|
Martin de Fourchambault E, Callens N, Saliou JM, Fourcot M, Delos O, Barois N, Thorel Q, Ramirez S, Bukh J, Cocquerel L, Bertrand-Michel J, Marot G, Sebti Y, Dubuisson J, Rouillé Y. Hepatitis C virus alters the morphology and function of peroxisomes. Front Microbiol 2023; 14:1254728. [PMID: 37808318 PMCID: PMC10551450 DOI: 10.3389/fmicb.2023.1254728] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
Despite the introduction of effective treatments for hepatitis C in clinics, issues remain regarding the liver disease induced by chronic hepatitis C virus (HCV) infection. HCV is known to disturb the metabolism of infected cells, especially lipid metabolism and redox balance, but the mechanisms leading to HCV-induced pathogenesis are still poorly understood. In an APEX2-based proximity biotinylation screen, we identified ACBD5, a peroxisome membrane protein, as located in the vicinity of HCV replication complexes. Confocal microscopy confirmed the relocation of peroxisomes near HCV replication complexes and indicated that their morphology and number are altered in approximately 30% of infected Huh-7 cells. Peroxisomes are small versatile organelles involved among other functions in lipid metabolism and ROS regulation. To determine their importance in the HCV life cycle, we generated Huh-7 cells devoid of peroxisomes by inactivating the PEX5 and PEX3 genes using CRISPR/Cas9 and found that the absence of peroxisomes had no impact on replication kinetics or infectious titers of HCV strains JFH1 and DBN3a. The impact of HCV on peroxisomal functions was assessed using sub-genomic replicons. An increase of ROS was measured in peroxisomes of replicon-containing cells, correlated with a significant decrease of catalase activity with the DBN3a strain. In contrast, HCV replication had little to no impact on cytoplasmic and mitochondrial ROS, suggesting that the redox balance of peroxisomes is specifically impaired in cells replicating HCV. Our study provides evidence that peroxisome function and morphology are altered in HCV-infected cells.
Collapse
Affiliation(s)
- Esther Martin de Fourchambault
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U 1019 – UMR9017 – CIIL – Center for Infection and Immunity of Lille, Lille, France
| | - Nathalie Callens
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U 1019 – UMR9017 – CIIL – Center for Infection and Immunity of Lille, Lille, France
| | - Jean-Michel Saliou
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UAR CNRS 2014 - US Inserm 41 - PLBS, Lille, France
| | - Marie Fourcot
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UAR CNRS 2014 - US Inserm 41 - PLBS, Lille, France
| | - Oceane Delos
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
- I2MC, Université de Toulouse, Inserm, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Nicolas Barois
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U 1019 – UMR9017 – CIIL – Center for Infection and Immunity of Lille, Lille, France
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UAR CNRS 2014 - US Inserm 41 - PLBS, Lille, France
| | - Quentin Thorel
- Université de Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, Lille, France
| | - Santseharay Ramirez
- Faculty of Health and Medical Sciences, Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Faculty of Health and Medical Sciences, Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital Hvidovre and Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Laurence Cocquerel
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U 1019 – UMR9017 – CIIL – Center for Infection and Immunity of Lille, Lille, France
| | - Justine Bertrand-Michel
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
- I2MC, Université de Toulouse, Inserm, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Guillemette Marot
- Université de Lille, Inria, CHU Lille, ULR 2694 - METRICS: Évaluation des technologies de santé et des pratiques médicales, Lille, France
| | - Yasmine Sebti
- Université de Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011 - EGID, Lille, France
| | - Jean Dubuisson
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U 1019 – UMR9017 – CIIL – Center for Infection and Immunity of Lille, Lille, France
| | - Yves Rouillé
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U 1019 – UMR9017 – CIIL – Center for Infection and Immunity of Lille, Lille, France
| |
Collapse
|
8
|
Gu Y, Alam S, Oliferenko S. Peroxisomal compartmentalization of amino acid biosynthesis reactions imposes an upper limit on compartment size. Nat Commun 2023; 14:5544. [PMID: 37684233 PMCID: PMC10491753 DOI: 10.1038/s41467-023-41347-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
Cellular metabolism relies on just a few redox cofactors. Selective compartmentalization may prevent competition between metabolic reactions requiring the same cofactor. Is such compartmentalization necessary for optimal cell function? Is there an optimal compartment size? Here we probe these fundamental questions using peroxisomal compartmentalization of the last steps of lysine and histidine biosynthesis in the fission yeast Schizosaccharomyces japonicus. We show that compartmentalization of these NAD+ dependent reactions together with a dedicated NADH/NAD+ recycling enzyme supports optimal growth when an increased demand for anabolic reactions taxes cellular redox balance. In turn, compartmentalization constrains the size of individual organelles, with larger peroxisomes accumulating all the required enzymes but unable to support both biosynthetic reactions at the same time. Our reengineering and physiological experiments indicate that compartmentalized biosynthetic reactions are sensitive to the size of the compartment, likely due to scaling-dependent changes within the system, such as enzyme packing density.
Collapse
Affiliation(s)
- Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
| | - Sara Alam
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
- Medical Research Council London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
| |
Collapse
|
9
|
Roczkowsky A, Limonta D, Fernandes JP, Branton WG, Clarke M, Hlavay B, Noyce RS, Joseph JT, Ogando NS, Das SK, Elaish M, Arbour N, Evans DH, Langdon K, Hobman TC, Power C. COVID-19 Induces Neuroinflammation and Suppresses Peroxisomes in the Brain. Ann Neurol 2023; 94:531-546. [PMID: 37190821 DOI: 10.1002/ana.26679] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023]
Abstract
OBJECTIVE Peroxisome injury occurs in the central nervous system (CNS) during multiple virus infections that result in neurological disabilities. We investigated host neuroimmune responses and peroxisome biogenesis factors during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection using a multiplatform strategy. METHODS Brain tissues from coronavirus disease 2019 (COVID-19) (n = 12) and other disease control (ODC) (n = 12) patients, as well as primary human neural cells and Syrian hamsters, infected with a clinical variant of SARS-CoV-2, were investigated by droplet digital polymerase chain reaction (ddPCR), quantitative reverse transcriptase PCR (RT-qPCR), and immunodetection methods. RESULTS SARS-CoV-2 RNA was detected in the CNS of 4 patients with COVID-19 with viral protein (NSP3 and spike) immunodetection in the brainstem. Olfactory bulb, brainstem, and cerebrum from patients with COVID-19 showed induction of pro-inflammatory transcripts (IL8, IL18, CXCL10, NOD2) and cytokines (GM-CSF and IL-18) compared to CNS tissues from ODC patients (p < 0.05). Peroxisome biogenesis factor transcripts (PEX3, PEX5L, PEX11β, and PEX14) and proteins (PEX3, PEX14, PMP70) were suppressed in the CNS of COVID-19 compared to ODC patients (p < 0.05). SARS-CoV-2 infection of hamsters revealed viral RNA detection in the olfactory bulb at days 4 and 7 post-infection while inflammatory gene expression was upregulated in the cerebrum of infected animals by day 14 post-infection (p < 0.05). Pex3 transcript levels together with catalase and PMP70 immunoreactivity were suppressed in the cerebrum of SARS-CoV-2 infected animals (p < 0.05). INTERPRETATION COVID-19 induced sustained neuroinflammatory responses with peroxisome biogenesis factor suppression despite limited brainstem SARS-CoV-2 neurotropism in humans. These observations offer insights into developing biomarkers and therapies, while also implicating persistent peroxisome dysfunction as a contributor to the neurological post-acute sequelae of COVID-19. ANN NEUROL 2023;94:531-546.
Collapse
Affiliation(s)
- A Roczkowsky
- Department of Medicine, University of Alberta, Edmonton, AB, USA
| | - D Limonta
- Department of Cell Biology, University of Alberta, Edmonton, AB, USA
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, USA
| | - J P Fernandes
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, USA
| | - W G Branton
- Department of Medicine, University of Alberta, Edmonton, AB, USA
| | - M Clarke
- Department of Medicine, University of Alberta, Edmonton, AB, USA
| | - B Hlavay
- Department of Medicine, University of Alberta, Edmonton, AB, USA
| | - R S Noyce
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, USA
| | - J T Joseph
- Department of Pathology, University of Calgary, Calgary, AB, USA
| | - N S Ogando
- Department of Medicine, University of Alberta, Edmonton, AB, USA
| | - S K Das
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB, USA
| | - M Elaish
- Department of Cell Biology, University of Alberta, Edmonton, AB, USA
| | - N Arbour
- Department of Neuroscience, University of Montreal, and CHUM, Montreal, QC, Canada
| | - D H Evans
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, USA
| | - K Langdon
- Department of Pathology, University of Calgary, Calgary, AB, USA
| | - T C Hobman
- Department of Cell Biology, University of Alberta, Edmonton, AB, USA
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, USA
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, USA
| | - C Power
- Department of Medicine, University of Alberta, Edmonton, AB, USA
- Department of Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, USA
| |
Collapse
|
10
|
Park JW, Tyl MD, Cristea IM. Orchestration of Mitochondrial Function and Remodeling by Post-Translational Modifications Provide Insight into Mechanisms of Viral Infection. Biomolecules 2023; 13:biom13050869. [PMID: 37238738 DOI: 10.3390/biom13050869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The regulation of mitochondria structure and function is at the core of numerous viral infections. Acting in support of the host or of virus replication, mitochondria regulation facilitates control of energy metabolism, apoptosis, and immune signaling. Accumulating studies have pointed to post-translational modification (PTM) of mitochondrial proteins as a critical component of such regulatory mechanisms. Mitochondrial PTMs have been implicated in the pathology of several diseases and emerging evidence is starting to highlight essential roles in the context of viral infections. Here, we provide an overview of the growing arsenal of PTMs decorating mitochondrial proteins and their possible contribution to the infection-induced modulation of bioenergetics, apoptosis, and immune responses. We further consider links between PTM changes and mitochondrial structure remodeling, as well as the enzymatic and non-enzymatic mechanisms underlying mitochondrial PTM regulation. Finally, we highlight some of the methods, including mass spectrometry-based analyses, available for the identification, prioritization, and mechanistic interrogation of PTMs.
Collapse
Affiliation(s)
- Ji Woo Park
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Matthew D Tyl
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544, USA
| |
Collapse
|
11
|
Ivanova T, Mariienko Y, Mehterov N, Kazakova M, Sbirkov Y, Todorova K, Hayrabedyan S, Sarafian V. Autophagy and SARS-CoV-2-Old Players in New Games. Int J Mol Sci 2023; 24:7734. [PMID: 37175443 PMCID: PMC10178552 DOI: 10.3390/ijms24097734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
At present it is well-defined that autophagy is a fundamental process essential for cell life but its pro-viral and anti-viral role has been stated out with the COVID pandemic. However, viruses in turn have evolved diverse adaptive strategies to cope with autophagy driven host defense, either by blocking or hijacking the autophagy machinery for their own benefit. The mechanisms underlying autophagy modulation are presented in the current review which summarizes the accumulated knowledge on the crosstalk between autophagy and viral infections, with a particular emphasizes on SARS-CoV-2. The different types of autophagy related to infections and their molecular mechanisms are focused in the context of inflammation. In particular, SARS-CoV-2 entry, replication and disease pathogenesis are discussed. Models to study autophagy and to formulate novel treatment approaches and pharmacological modulation to fight COVID-19 are debated. The SARS-CoV-2-autophagy interplay is presented, revealing the complex dynamics and the molecular machinery of autophagy. The new molecular targets and strategies to treat COVID-19 effectively are envisaged. In conclusion, our finding underline the importance of development new treatment strategies and pharmacological modulation of autophagy to fight COVID-19.
Collapse
Affiliation(s)
- Tsvetomira Ivanova
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
| | - Yuliia Mariienko
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
| | - Yordan Sbirkov
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
| | - Krassimira Todorova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Soren Hayrabedyan
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, 4000 Plovdiv, Bulgaria
| |
Collapse
|
12
|
Honsho M, Fujiki Y. Regulation of plasmalogen biosynthesis in mammalian cells and tissues. Brain Res Bull 2023; 194:118-123. [PMID: 36720320 DOI: 10.1016/j.brainresbull.2023.01.011] [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: 04/16/2022] [Revised: 01/08/2023] [Accepted: 01/27/2023] [Indexed: 01/29/2023]
Abstract
Plasmalogens are a unique family of cellular glycerophospholipids that contain a vinyl-ether bond. Synthesis of plasmalogens is initiated in peroxisomes and completed in the endoplasmic reticulum. The absence of plasmalogens in several organs of patients with deficiency in peroxisome biogenesis suggests that de novo synthesis of plasmalogens contributes significantly to plasmalogen homeostasis in humans. Plasmalogen biosynthesis is spatiotemporally regulated by a feedback mechanism that senses the amount of plasmalogens in the inner leaflet of the plasma membrane and regulates the stability of fatty acyl-CoA reductase 1 (FAR1), the rate-limiting enzyme for plasmalogen biosynthesis. Dysregulation of plasmalogen synthesis impairs cholesterol synthesis in cells and brain, resulting in the reduced expression of genes such as mRNA encoding myelin basic protein, a phenotype found in the cerebellum of plasmalogen-deficient mice. In this review, we summarize the current knowledge of molecular mechanisms underlying the regulation of plasmalogen biosynthesis and the link between plasmalogen homeostasis and cholesterol biosynthesis, and address the pathogenesis of impaired plasmalogen homeostasis in rodent and humans.
Collapse
Affiliation(s)
- Masanori Honsho
- Department of Neuroinflammation and Brain Fatigue Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Yukio Fujiki
- Institute of Rheological Functions of Food-Kyushu University Collaboration Program, Kyushu University, Fukuoka, Japan; Graduate School of Science, University of Hyogo, Hyogo, Japan.
| |
Collapse
|
13
|
Indari O, Ergün S, Karnati S, Chandra Jha H. Herpesviral interplay with peroxisome: An underexplored viral niche. Genes Dis 2023. [DOI: 10.1016/j.gendis.2023.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
|
14
|
Tao L, Dryden P, Lowe A, Wang G, Achuthkumar A, Chang T, Reese TA. WY14643 Increases Herpesvirus Replication and Inhibits IFNβ Production Independently of PPARα Expression. Microbiol Spectr 2023; 11:e0233722. [PMID: 36715509 PMCID: PMC10100363 DOI: 10.1128/spectrum.02337-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023] Open
Abstract
Peroxisome proliferator activated receptor (PPAR) agonists are commonly used to treat metabolic disorders in humans because they regulate fatty acid oxidation and cholesterol metabolism. In addition to their roles in controlling metabolism, PPAR agonists also regulate inflammation and are immunosuppressive in models of autoimmunity. We aimed to test whether activation of PPARα with clinically relevant ligands could impact gammaherpesvirus infection using murine gammaherpesvirus-68 (MHV68, MuHV-4). We found that PPAR agonists WY14643 and fenofibrate increased herpesvirus replication in vitro. In vivo, WY14643 increased viral replication and caused lethality in mice. Unexpectedly, these effects proved independent of PPARα. We found that WY14643 suppressed production of type I interferon after MHV68 infection in vitro and in vivo. Taken together, our data indicate that caution should be employed when using PPARα agonists in immuno-metabolic studies, as they can have off-target effects on viral replication through the inhibition of type I interferon production. IMPORTANCE PPAR agonists are used clinically to treat both metabolic and inflammatory disorders. Because viruses are known to rewire host metabolism to their own benefit, the intersection of immunity, metabolism, and virology is an important research area. Our article is an important contribution to this field for two reasons. First, it shows a role for PPARα agonists in altering virus replication. Second, it shows that PPARα agonists can affect virus replication in a manner independent of their predicted target. This knowledge is valuable for anyone seeking to use PPARα agonists as a research tool.
Collapse
Affiliation(s)
- Lili Tao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Phillip Dryden
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Alexandria Lowe
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Guoxun Wang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Amritha Achuthkumar
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tyron Chang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Tiffany A. Reese
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
15
|
Indari O, Rani A, Baral B, Ergün S, Bala K, Karnati S, Jha HC. Modulation of peroxisomal compartment by Epstein-Barr virus. Microb Pathog 2023; 174:105946. [PMID: 36526038 DOI: 10.1016/j.micpath.2022.105946] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Viruses utilize clever strategies of interacting with various cellular factors, to remodel an organelle function, for the establishment of successful infection. In recent decades, numerous studies revealed the exploitation of the peroxisomal compartment by viruses. Epstein-Barr virus (EBV) is a ubiquitous virus linked with various cancers and neurological disorders. Till now, there is no report regarding the impacts of EBV infection on peroxisomal compartment. Therefore, we investigate the modulation of peroxisomal proteins in EBV transformed cell lines and during acute EBV infection. EBV positive Burkitt lymphoma cells of different origins as EBV transformed cells along with EBV negative Burkitt lymphoma cells as a control were used in this study. For acute EBV infection experiments, we infected peripheral blood mononuclear cells with EBV for three days. Thereafter, analyzed the gene expression patterns of peroxisomal proteins using qPCR. In addition, quantification of lipid content was performed by using fluorescence microscopy and biochemical assay. Our results revealed that, the peroxisomal proteins were distinctly regulated in EBV transformed cells and during acute EBV infection. Interestingly, PEX19 was significantly upregulated in EBV infected cells. Further, in correlation with the altered expression of peroxisomes proteins involved in lipid metabolism, the EBV transformed cells showed lower lipid abundance. Conversely, the lipid levels were increased during acute EBV infection. Our study highlights the importance of investigating the manipulation of the peroxisomal compartment by putting forward various differentially expressed proteins upon EBV infection. This study provides a base for further investigation to delve deeper into EBV and peroxisomal interactions. The future research in this direction could provide involvement of novel signaling pathways to understand molecular changes during EBV mediated pathologies.
Collapse
Affiliation(s)
- Omkar Indari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Annu Rani
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Budhadev Baral
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Süleyman Ergün
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University Würzburg, Würzburg, 97070, Germany
| | - Kiran Bala
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Srikanth Karnati
- Institute of Anatomy and Cell Biology, Julius-Maximilians-University Würzburg, Würzburg, 97070, Germany.
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India.
| |
Collapse
|
16
|
Ferreira V, Ferreira AR, Ribeiro D. Peroxisomes and Viruses: Overview on Current Knowledge and Experimental Approaches. Methods Mol Biol 2023; 2643:271-294. [PMID: 36952192 DOI: 10.1007/978-1-0716-3048-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The general interest in the study of the interplay between peroxisomes and viruses has increased in recent years, with different reports demonstrating that distinct viruses modulate peroxisome-related mechanisms to either counteract the cellular antiviral response or support viral propagation. Nevertheless, mechanistical details are still scarce, and information is often incomplete. In this chapter, we present an overview of the current knowledge concerning the interplay between peroxisomes and different viruses. We furthermore present, compare, and discuss the most relevant experimental approaches and tools used in the different studies. Finally, we stress the importance of further, more detailed, and spatial-temporal analyses that encompass all the different phases of the viruses' infection cycles. These studies may lead to the discovery of novel peroxisome-related cellular mechanisms that can further be explored as targets for the development of novel antiviral therapies.
Collapse
Affiliation(s)
- Vanessa Ferreira
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Ana Rita Ferreira
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Daniela Ribeiro
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal.
| |
Collapse
|
17
|
Wanders RJA, Baes M, Ribeiro D, Ferdinandusse S, Waterham HR. The physiological functions of human peroxisomes. Physiol Rev 2023; 103:957-1024. [PMID: 35951481 DOI: 10.1152/physrev.00051.2021] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes are subcellular organelles that play a central role in human physiology by catalyzing a range of unique metabolic functions. The importance of peroxisomes for human health is exemplified by the existence of a group of usually severe diseases caused by an impairment in one or more peroxisomal functions. Among others these include the Zellweger spectrum disorders, X-linked adrenoleukodystrophy, and Refsum disease. To fulfill their role in metabolism, peroxisomes require continued interaction with other subcellular organelles including lipid droplets, lysosomes, the endoplasmic reticulum, and mitochondria. In recent years it has become clear that the metabolic alliance between peroxisomes and other organelles requires the active participation of tethering proteins to bring the organelles physically closer together, thereby achieving efficient transfer of metabolites. This review intends to describe the current state of knowledge about the metabolic role of peroxisomes in humans, with particular emphasis on the metabolic partnership between peroxisomes and other organelles and the consequences of genetic defects in these processes. We also describe the biogenesis of peroxisomes and the consequences of the multiple genetic defects therein. In addition, we discuss the functional role of peroxisomes in different organs and tissues and include relevant information derived from model systems, notably peroxisomal mouse models. Finally, we pay particular attention to a hitherto underrated role of peroxisomes in viral infections.
Collapse
Affiliation(s)
- Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Myriam Baes
- Laboratory of Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,United for Metabolic Diseases, Amsterdam, The Netherlands
| |
Collapse
|
18
|
Roczkowsky A, Doan MAL, Hlavay BA, Mamik MK, Branton WG, McKenzie BA, Saito LB, Schmitt L, Eitzen G, Di Cara F, Wuest M, Wuest F, Rachubinski R, Power C. Peroxisome Injury in Multiple Sclerosis: Protective Effects of 4-Phenylbutyrate in CNS-Associated Macrophages. J Neurosci 2022; 42:7152-7165. [PMID: 35940876 PMCID: PMC9480879 DOI: 10.1523/jneurosci.0312-22.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 06/14/2022] [Accepted: 07/30/2022] [Indexed: 11/21/2022] Open
Abstract
Multiple sclerosis (MS) is a progressive and inflammatory demyelinating disease of the CNS. Peroxisomes perform critical functions that contribute to CNS homeostasis. We investigated peroxisome injury and mitigating effects of peroxisome-restorative therapy on inflammatory demyelination in models of MS. Human autopsied CNS tissues (male and female), human cell cultures, and cuprizone-mediated demyelination mice (female) were examined by RT-PCR, Western blotting, and immunolabeling. The therapeutic peroxisome proliferator, 4-phenylbutyrate (4-PBA) was investigated in vitro and in vivo White matter from MS patients showed reduced peroxisomal transcript and protein levels, including PMP70, compared with non-MS controls. Cultured human neural cells revealed that human microglia contained abundant peroxisomal proteins. TNF-α-exposed microglia displayed reduced immunolabeling of peroxisomal proteins, PMP70 and PEX11β, which was prevented with 4-PBA. In human myeloid cells exposed to TNF-α or nigericin, suppression of PEX11β and catalase protein levels were observed to be dependent on NLRP3 expression. Hindbrains from cuprizone-exposed mice showed reduced Abcd1, Cat, and Pex5l transcript levels, with concurrent increased Nlrp3 and Il1b transcript levels, which was abrogated by 4-PBA. In the central corpus callosum, Iba-1 in CNS-associated macrophages and peroxisomal thiolase immunostaining after cuprizone exposure was increased by 4-PBA. 4-PBA prevented decreased myelin basic protein and neurofilament heavy chain immunoreactivity caused by cuprizone exposure. Cuprizone-induced neurobehavioral deficits were improved by 4-PBA treatment. Peroxisome injury in CNS-associated macrophages contributed to neuroinflammation and demyelination that was prevented by 4-PBA treatment. A peroxisome-targeted therapy might be valuable for treating inflammatory demyelination and neurodegeneration in MS.SIGNIFICANCE STATEMENT Multiple sclerosis (MS) is a common and disabling disorder of the CNS with no curative therapies for its progressive form. The present studies implicate peroxisome impairment in CNS-associated macrophages (CAMs), which include resident microglia and blood-derived macrophages, as an important contributor to inflammatory demyelination and neuroaxonal injury in MS. We also show that the inflammasome molecule NLRP3 is associated with peroxisome injury in vitro and in vivo, especially in CAMs. Treatment with the peroxisome proliferator 4-phenylbutyrate exerted protective effects with improved molecular, morphologic, and neurobehavioral outcomes that were associated with a neuroprotective CAM phenotype. These findings offer novel insights into the contribution of peroxisome injury in MS together with preclinical testing of a rational therapy for MS.
Collapse
Affiliation(s)
| | - Matthew A L Doan
- The Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | | | | | | | | | | | | | | | - Francesca Di Cara
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | | | | | | | - Christopher Power
- Departments of Medicine
- Medical Microbiology & Immunology
- The Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| |
Collapse
|
19
|
Weinhofer I, Buda A, Kunze M, Palfi Z, Traunfellner M, Hesse S, Villoria-Gonzalez A, Hofmann J, Hametner S, Regelsberger G, Moser AB, Eichler F, Kemp S, Bauer J, Kühl JS, Forss-Petter S, Berger J. Peroxisomal very long-chain fatty acid transport is targeted by herpesviruses and the antiviral host response. Commun Biol 2022; 5:944. [PMID: 36085307 PMCID: PMC9462615 DOI: 10.1038/s42003-022-03867-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Very long-chain fatty acids (VLCFA) are critical for human cytomegalovirus replication and accumulate upon infection. Here, we used Epstein-Barr virus (EBV) infection of human B cells to elucidate how herpesviruses target VLCFA metabolism. Gene expression profiling revealed that, despite a general induction of peroxisome-related genes, EBV early infection decreased expression of the peroxisomal VLCFA transporters ABCD1 and ABCD2, thus impairing VLCFA degradation. The mechanism underlying ABCD1 and ABCD2 repression involved RNA interference by the EBV-induced microRNAs miR-9-5p and miR-155, respectively, causing significantly increased VLCFA levels. Treatment with 25-hydroxycholesterol, an antiviral innate immune modulator produced by macrophages, restored ABCD1 expression and reduced VLCFA accumulation in EBV-infected B-lymphocytes, and, upon lytic reactivation, reduced virus production in control but not ABCD1-deficient cells. Finally, also other herpesviruses and coronaviruses target ABCD1 expression. Because viral infection might trigger neuroinflammation in X-linked adrenoleukodystrophy (X-ALD, inherited ABCD1 deficiency), we explored a possible link between EBV infection and cerebral X-ALD. However, neither immunohistochemistry of post-mortem brains nor analysis of EBV seropositivity in 35 X-ALD children supported involvement of EBV in the onset of neuroinflammation. Collectively, our findings indicate a previously unrecognized, pivotal role of ABCD1 in viral infection and host defence, prompting consideration of other viral triggers in cerebral X-ALD.
Collapse
Affiliation(s)
- Isabelle Weinhofer
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| | - Agnieszka Buda
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Zsofia Palfi
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Matthäus Traunfellner
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Sarah Hesse
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Andrea Villoria-Gonzalez
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Jörg Hofmann
- Institute of Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Simon Hametner
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Günther Regelsberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Ann B Moser
- Department of Neurogenetics, Hugo W. Moser Research Institute at Kennedy Krieger, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Florian Eichler
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Stephan Kemp
- Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Bauer
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Jörn-Sven Kühl
- Department of Pediatric Oncology, Hematology, and Hemostaseology, University Hospital Leipzig, Leipzig, Germany
| | - Sonja Forss-Petter
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
20
|
Dorninger F, Werner ER, Berger J, Watschinger K. Regulation of plasmalogen metabolism and traffic in mammals: The fog begins to lift. Front Cell Dev Biol 2022; 10:946393. [PMID: 36120579 PMCID: PMC9471318 DOI: 10.3389/fcell.2022.946393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022] Open
Abstract
Due to their unique chemical structure, plasmalogens do not only exhibit distinct biophysical and biochemical features, but require specialized pathways of biosynthesis and metabolization. Recently, major advances have been made in our understanding of these processes, for example by the attribution of the gene encoding the enzyme, which catalyzes the final desaturation step in plasmalogen biosynthesis, or by the identification of cytochrome C as plasmalogenase, which allows for the degradation of plasmalogens. Also, models have been presented that plausibly explain the maintenance of adequate cellular levels of plasmalogens. However, despite the progress, many aspects around the questions of how plasmalogen metabolism is regulated and how plasmalogens are distributed among organs and tissues in more complex organisms like mammals, remain unresolved. Here, we summarize and interpret current evidence on the regulation of the enzymes involved in plasmalogen biosynthesis and degradation as well as the turnover of plasmalogens. Finally, we focus on plasmalogen traffic across the mammalian body - a topic of major importance, when considering plasmalogen replacement therapies in human disorders, where deficiencies in these lipids have been reported. These involve not only inborn errors in plasmalogen metabolism, but also more common diseases including Alzheimer's disease and neurodevelopmental disorders.
Collapse
Affiliation(s)
- Fabian Dorninger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria,*Correspondence: Fabian Dorninger, ; Katrin Watschinger,
| | - Ernst R. Werner
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Katrin Watschinger
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria,*Correspondence: Fabian Dorninger, ; Katrin Watschinger,
| |
Collapse
|
21
|
Cook KC, Tsopurashvili E, Needham JM, Thompson SR, Cristea IM. Restructured membrane contacts rewire organelles for human cytomegalovirus infection. Nat Commun 2022; 13:4720. [PMID: 35953480 PMCID: PMC9366835 DOI: 10.1038/s41467-022-32488-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/30/2022] [Indexed: 12/24/2022] Open
Abstract
Membrane contact sites (MCSs) link organelles to coordinate cellular functions across space and time. Although viruses remodel organelles for their replication cycles, MCSs remain largely unexplored during infections. Here, we design a targeted proteomics platform for measuring MCS proteins at all organelles simultaneously and define functional virus-driven MCS alterations by the ancient beta-herpesvirus human cytomegalovirus (HCMV). Integration with super-resolution microscopy and comparisons to herpes simplex virus (HSV-1), Influenza A, and beta-coronavirus HCoV-OC43 infections reveals time-sensitive contact regulation that allows switching anti- to pro-viral organelle functions. We uncover a stabilized mitochondria-ER encapsulation structure (MENC). As HCMV infection progresses, MENCs become the predominant mitochondria-ER contact phenotype and sequentially recruit the tethering partners VAP-B and PTPIP51, supporting virus production. However, premature ER-mitochondria tethering activates STING and interferon response, priming cells against infection. At peroxisomes, ACBD5-mediated ER contacts balance peroxisome proliferation versus membrane expansion, with ACBD5 impacting the titers of each virus tested.
Collapse
Affiliation(s)
- Katelyn C Cook
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, US
| | - Elene Tsopurashvili
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, US
| | - Jason M Needham
- Department of Microbiology, University of Alabama Birmingham, Birmingham, AL, 35294, US
| | - Sunnie R Thompson
- Department of Microbiology, University of Alabama Birmingham, Birmingham, AL, 35294, US
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, US.
| |
Collapse
|
22
|
Liu P, Hu D, Yuan L, Lian Z, Yao X, Zhu Z, Li X. Metabolomics Analysis of PK-15 Cells with Pseudorabies Virus Infection Based on UHPLC-QE-MS. Viruses 2022; 14:v14061158. [PMID: 35746630 PMCID: PMC9229976 DOI: 10.3390/v14061158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 12/02/2022] Open
Abstract
Viruses depend on the metabolic mechanisms of the host to support viral replication. We utilize an approach based on ultra-high-performance liquid chromatography/Q Exactive HF-X Hybrid Quadrupole-Orbitrap Mass (UHPLC-QE-MS) to analyze the metabolic changes in PK-15 cells induced by the infections of the pseudorabies virus (PRV) variant strain and Bartha K61 strain. Infections with PRV markedly changed lots of metabolites, when compared to the uninfected cell group. Additionally, most of the differentially expressed metabolites belonged to glycerophospholipid metabolism, sphingolipid metabolism, purine metabolism, and pyrimidine metabolism. Lipid metabolites account for the highest proportion (around 35%). The results suggest that those alterations may be in favor of virion formation and genome amplification to promote PRV replication. Different PRV strains showed similar results. An understanding of PRV-induced metabolic reprogramming will provide valuable information for further studies on PRV pathogenesis and the development of antiviral therapy strategies.
Collapse
Affiliation(s)
- Panrao Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (P.L.); (D.H.); (L.Y.); (Z.L.); (X.Y.); (Z.Z.)
| | - Danhe Hu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (P.L.); (D.H.); (L.Y.); (Z.L.); (X.Y.); (Z.Z.)
| | - Lili Yuan
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (P.L.); (D.H.); (L.Y.); (Z.L.); (X.Y.); (Z.Z.)
| | - Zhengmin Lian
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (P.L.); (D.H.); (L.Y.); (Z.L.); (X.Y.); (Z.Z.)
| | - Xiaohui Yao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (P.L.); (D.H.); (L.Y.); (Z.L.); (X.Y.); (Z.Z.)
| | - Zhenbang Zhu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (P.L.); (D.H.); (L.Y.); (Z.L.); (X.Y.); (Z.Z.)
| | - Xiangdong Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (P.L.); (D.H.); (L.Y.); (Z.L.); (X.Y.); (Z.Z.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-514-8797-9036
| |
Collapse
|
23
|
Nicotine Affects Multiple Biological Processes in EpiDermTM Organotypic Tissues and Keratinocyte Monolayers. ATMOSPHERE 2022. [DOI: 10.3390/atmos13050810] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Dermal exposure to nicotine is common due to the widespread use of tobacco products. Here, we assessed the effects of nicotine at concentrations found in thirdhand smoke (THS) contaminated environments and electronic cigarette (EC) spills or leaks on a 3D human skin model (EpiDermTM) and on submerged keratinocyte cultures. Air liquid interface treatment of EpiDermTM with 10 or 400 μg/mL of nicotine for 24 h followed by proteomics analysis showed altered pathways related to inflammation, protein synthesis, cell–cell adhesion, apoptosis, and mitochondrial function. Submerged cultured keratinocytes were used to validate the proteomics data and further characterize the response of skin cells to nicotine. Mitochondrial phenotype changed from networked to punctate in keratinocytes treated with 10 or 400 μg/mL of nicotine for 48 h and 24 h, respectively. After 72 h, all concentrations of nicotine caused a significant decrease in the networked phenotype. In Western blots, keratinocytes exposed to 400 μg/mL of nicotine had a significant decrease in mitofusin 2, while mitofusin 1 decreased after 72 h. The shift from networked to punctate mitochondria correlated with a decrease in mitofusin 1/2, a protein needed to establish and maintain the networked phenotype. Mitochondrial changes were reversible after a 24 h recovery period. Peroxisomes exposed to 400 μg/mL of nicotine for 24 h became enlarged and were fewer in number. Nicotine concentrations in THS and EC spills altered the proteome profile in EpiDermTM and damaged organelles including mitochondria and peroxisomes, which are involved in ROS homeostasis. These changes may exacerbate skin infections, inhibit wound healing, and cause oxidative damage to cells in the skin.
Collapse
|
24
|
Ferreira AR, Gouveia A, Magalhães AC, Valença I, Marques M, Kagan JC, Ribeiro D. Human Cytomegalovirus vMIA Inhibits MAVS Oligomerization at Peroxisomes in an MFF-Dependent Manner. Front Cell Dev Biol 2022; 10:871977. [PMID: 35445031 PMCID: PMC9014249 DOI: 10.3389/fcell.2022.871977] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/04/2022] [Indexed: 11/21/2022] Open
Abstract
Upon intracellular recognition of viral RNA, RIG-I-like proteins interact with MAVS at peroxisomes and mitochondria, inducing its oligomerization and the downstream production of direct antiviral effectors. The human cytomegalovirus (HCMV) is able to specifically evade this antiviral response, via its antiapoptotic protein vMIA. Besides suppressing the programmed cell death of infected cells, vMIA inhibits the antiviral signalling at mitochondria by inducing the organelle’s fragmentation, consequently hindering the interaction between MAVS and the endoplasmic reticulum protein STING. Here we demonstrate that vMIA interferes with the peroxisomal antiviral signalling via a distinct mechanism that is independent of the organelle’s morphology and does not affect STING. vMIA interacts with MAVS at peroxisomes and inhibits its oligomerization, restraining downstream signalling, in an MFF-dependent manner. This study also demonstrates that vMIA is totally dependent on the organelle’s fission machinery to induce peroxisomal fragmentation, while this dependency is not observed at mitochondria. Furthermore, although we demonstrate that vMIA is also able to inhibit MAVS oligomerization at mitochondria, our results indicate that this process, such as the whole vMIA-mediated inhibition of the mitochondrial antiviral response, is independent of MFF. These observed differences in the mechanisms of action of vMIA towards both organelles, likely reflect their intrinsic differences and roles throughout the viral infection. This study uncovers specific molecular mechanisms that may be further explored as targets for antiviral therapy and highlights the relevance of peroxisomes as platforms for antiviral signalling against HCMV.
Collapse
Affiliation(s)
- Ana Rita Ferreira
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Ana Gouveia
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Ana Cristina Magalhães
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Isabel Valença
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Mariana Marques
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Jonathan C Kagan
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| |
Collapse
|
25
|
Host Cells Actively Resist Porcine Reproductive and Respiratory Syndrome Virus Infection via the IRF8-MicroRNA-10a-SRP14 Regulatory Pathway. J Virol 2022; 96:e0000322. [PMID: 35293774 DOI: 10.1128/jvi.00003-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) play an important role in the virus-host interaction. Our previous work has indicated that the expression level of miR-10a increased in porcine alveolar macrophages (PAMs) during porcine reproductive and respiratory syndrome virus (PRRSV) infection and further inhibited viral replication through downregulates the expression of host molecule signal-recognition particle 14 (SRP14) protein. However, the molecular mechanism of miR-10a increased after PRRSV infection remains unknown. In the present study, transcription factor interferon regulatory factor 8 (IRF8) was identified as a negative regulator of miR-10a. PRRSV infection decreases the expression level of IRF8 in PAMs, leading to upregulating miR-10a expression to play an anti-PRRSV role. Meanwhile, this work first proved that IRF8 promoted PRRSV replication in an miR-10a-dependent manner. Further, we explained that SRP14, the target gene of miR-10a, promotes the synthesis of the PRRSV genome by interacting with the viral components Nsp2, thus facilitating PRRSV replication. In conclusion, we identified a novel IRF8-miR-10a-SRP14 regulatory pathway against PRRSV infection, which provides new insights into virus-host interactions and suggests potential new antiviral strategies to control PRRSV. IMPORTANCE Porcine reproductive and respiratory syndrome virus (PRRSV) has rapidly spread to the global pig industry and caused incalculable economic damage since first discovered in the 1980s. However, conventional vaccines do not provide satisfactory protection. Understanding the molecular mechanisms of host resistance to PRRSV infection is necessary to develop safe and effective strategies to control PRRSV. During viral infection, miRNAs play vital roles in regulating the expression of viral or host genes at the posttranscriptional level. The significance of our study is that we revealed the transcriptional regulation mechanism of the antiviral molecule miR-10a after PRRSV infection. Moreover, our research also explained the mechanism of host molecule SRP14, the target gene of miR-10a regulating PRRSV replication. Thus, we report a novel regulatory pathway of IRF8-miR-10a-SRP14 against PRRSV infection, which provides new insights into virus-host interactions and suggests potential new control measures for future PRRSV outbreaks.
Collapse
|
26
|
Oom AL, Stoneham CA, Lewinski MK, Richards A, Wozniak JM, Shams-Ud-Doha K, Gonzalez DJ, Krogan NJ, Guatelli J. Comparative Analysis of T-Cell Spatial Proteomics and the Influence of HIV Expression. Mol Cell Proteomics 2022; 21:100194. [PMID: 35017099 PMCID: PMC8956815 DOI: 10.1016/j.mcpro.2022.100194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/29/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022] Open
Abstract
As systems biology approaches to virology have become more tractable, highly studied viruses such as HIV can now be analyzed in new unbiased ways, including spatial proteomics. We employed here a differential centrifugation protocol to fractionate Jurkat T cells for proteomic analysis by mass spectrometry; these cells contain inducible HIV-1 genomes, enabling us to look for changes in the spatial proteome induced by viral gene expression. Using these proteomics data, we evaluated the merits of several reported machine learning pipelines for classification of the spatial proteome and identification of protein translocations. From these analyses, we found that classifier performance in this system was organelle dependent, with Bayesian t-augmented Gaussian mixture modeling outperforming support vector machine learning for mitochondrial and endoplasmic reticulum proteins but underperforming on cytosolic, nuclear, and plasma membrane proteins by QSep analysis. We also observed a generally higher performance for protein translocation identification using a Bayesian model, Bayesian analysis of differential localization experiments, on row-normalized data. Comparative Bayesian analysis of differential localization experiment analysis of cells induced to express the WT viral genome versus cells induced to express a genome unable to express the accessory protein Nef identified known Nef-dependent interactors such as T-cell receptor signaling components and coatomer complex. Finally, we found that support vector machine classification showed higher consistency and was less sensitive to HIV-dependent noise. These findings illustrate important considerations for studies of the spatial proteome following viral infection or viral gene expression and provide a reference for future studies of HIV-gene-dropout viruses.
Collapse
Affiliation(s)
- Aaron L Oom
- Biomedical Sciences Doctoral Program, University of California San Diego, La Jolla, California, USA; School of Medicine, University of California San Diego, La Jolla, California, USA; Veterans Medical Research Foundation, La Jolla, California, USA; VA San Diego Healthcare System, La Jolla, California, USA.
| | - Charlotte A Stoneham
- School of Medicine, University of California San Diego, La Jolla, California, USA; Veterans Medical Research Foundation, La Jolla, California, USA; VA San Diego Healthcare System, La Jolla, California, USA
| | - Mary K Lewinski
- School of Medicine, University of California San Diego, La Jolla, California, USA; VA San Diego Healthcare System, La Jolla, California, USA
| | - Alicia Richards
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA; Institute for Virology and Immunology, J. David Gladstone Institutes, San Francisco, California, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Jacob M Wozniak
- Biomedical Sciences Doctoral Program, University of California San Diego, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Km Shams-Ud-Doha
- Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - David J Gonzalez
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA; Institute for Virology and Immunology, J. David Gladstone Institutes, San Francisco, California, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - John Guatelli
- Biomedical Sciences Doctoral Program, University of California San Diego, La Jolla, California, USA; School of Medicine, University of California San Diego, La Jolla, California, USA; Veterans Medical Research Foundation, La Jolla, California, USA; VA San Diego Healthcare System, La Jolla, California, USA
| |
Collapse
|
27
|
Tyl MD, Betsinger CN, Cristea IM. Virus-host protein interactions as footprints of human cytomegalovirus replication. Curr Opin Virol 2022; 52:135-147. [PMID: 34923282 PMCID: PMC8844139 DOI: 10.1016/j.coviro.2021.11.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 02/03/2023]
Abstract
Human cytomegalovirus (HCMV) is a pervasive β-herpesvirus that causes lifelong infection. The lytic replication cycle of HCMV is characterized by global organelle remodeling and dynamic virus-host interactions, both of which are necessary for productive HCMV replication. With the advent of new technologies for investigating protein-protein and protein-nucleic acid interactions, numerous critical interfaces between HCMV and host cells have been identified. Here, we review temporal and spatial virus-host interactions that support different stages of the HCMV replication cycle. Understanding how HCMV interacts with host cells during entry, replication, and assembly, as well as how it interfaces with host cell metabolism and immune responses promises to illuminate processes that underlie the biology of infection and the resulting pathologies.
Collapse
Affiliation(s)
- Matthew D. Tyl
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Cora N. Betsinger
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA,Corresponding author and lead contact: Ileana M. Cristea, 210 Lewis Thomas Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, Tel: 6092589417, Fax: 6092584575,
| |
Collapse
|
28
|
Farelo MA, Korrou-Karava D, Brooks KF, Russell TA, Maringer K, Mayerhofer PU. Dengue and Zika Virus Capsid Proteins Contain a Common PEX19-Binding Motif. Viruses 2022; 14:v14020253. [PMID: 35215846 PMCID: PMC8874546 DOI: 10.3390/v14020253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Flaviviruses such as dengue virus (DENV) and Zika virus (ZIKV) have evolved sophisticated mechanisms to suppress the host immune system. For instance, flavivirus infections were found to sabotage peroxisomes, organelles with an important role in innate immunity. The current model suggests that the capsid (C) proteins of DENV and ZIKV downregulate peroxisomes, ultimately resulting in reduced production of interferons by interacting with the host protein PEX19, a crucial chaperone in peroxisomal biogenesis. Here, we aimed to explore the importance of peroxisomes and the role of C interaction with PEX19 in the flavivirus life cycle. By infecting cells lacking peroxisomes we show that this organelle is required for optimal DENV replication. Moreover, we demonstrate that DENV and ZIKV C bind PEX19 through a conserved PEX19-binding motif, which is also commonly found in cellular peroxisomal membrane proteins (PMPs). However, in contrast to PMPs, this interaction does not result in the targeting of C to peroxisomes. Furthermore, we show that the presence of C results in peroxisome loss due to impaired peroxisomal biogenesis, which appears to occur by a PEX19-independent mechanism. Hence, these findings challenge the current model of how flavivirus C might downregulate peroxisomal abundance and suggest a yet unknown role of peroxisomes in flavivirus biology.
Collapse
Affiliation(s)
- Mafalda A. Farelo
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Despoina Korrou-Karava
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Katrina F. Brooks
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Tiffany A. Russell
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
| | - Kevin Maringer
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
- The Pirbright Institute, Pirbright GU24 0NF, UK
- Correspondence: (K.M.); (P.U.M.)
| | - Peter U. Mayerhofer
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK; (M.A.F.); (D.K.-K.); (K.F.B.); (T.A.R.)
- Correspondence: (K.M.); (P.U.M.)
| |
Collapse
|
29
|
Pike DP, McGuffee RM, Geerling E, Albert CJ, Hoft DF, Shashaty MGS, Meyer NJ, Pinto AK, Ford DA. Plasmalogen Loss in Sepsis and SARS-CoV-2 Infection. Front Cell Dev Biol 2022; 10:912880. [PMID: 35784479 PMCID: PMC9242022 DOI: 10.3389/fcell.2022.912880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Plasmalogens are plasma-borne antioxidant phospholipid species that provide protection as cellular lipid components during cellular oxidative stress. In this study we investigated plasma plasmalogen levels in human sepsis as well as in rodent models of infection. In humans, levels of multiple plasmenylethanolamine molecular species were decreased in septic patient plasma compared to control subject plasma as well as an age-aligned control subject cohort. Additionally, lysoplasmenylcholine levels were significantly decreased in septic patients compared to the control cohorts. In contrast, plasma diacyl phosphatidylethanolamine and phosphatidylcholine levels were elevated in septic patients. Lipid changes were also determined in rats subjected to cecal slurry sepsis. Plasma plasmenylcholine, plasmenylethanolamine, and lysoplasmenylcholine levels were decreased while diacyl phosphatidylethanolamine levels were increased in septic rats compared to control treated rats. Kidney levels of lysoplasmenylcholine as well as plasmenylethanolamine molecular species were decreased in septic rats. Interestingly, liver plasmenylcholine and plasmenylethanolamine levels were increased in septic rats. Since COVID-19 is associated with sepsis-like acute respiratory distress syndrome and oxidative stress, plasmalogen levels were also determined in a mouse model of COVID-19 (intranasal inoculation of K18 mice with SARS-CoV-2). 3 days following infection, lung infection was confirmed as well as cytokine expression in the lung. Multiple molecular species of lung plasmenylcholine and plasmenylethanolamine were decreased in infected mice. In contrast, the predominant lung phospholipid, dipalmitoyl phosphatidylcholine, was not decreased following SARS-CoV-2 infection. Additionally total plasmenylcholine levels were decreased in the plasma of SARS-CoV-2 infected mice. Collectively, these data demonstrate the loss of plasmalogens during both sepsis and SARS-CoV-2 infection. This study also indicates plasma plasmalogens should be considered in future studies as biomarkers of infection and as prognostic indicators for sepsis and COVID-19 outcomes.
Collapse
Affiliation(s)
- Daniel P Pike
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Reagan M McGuffee
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Elizabeth Geerling
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Carolyn J Albert
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Daniel F Hoft
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Department of Internal Medicine, Division of Infectious Diseases, Allergy and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - Michael G S Shashaty
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.,Center for Translational Lung Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Nuala J Meyer
- Pulmonary, Allergy, and Critical Care Division, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States.,Center for Translational Lung Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Amelia K Pinto
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States
| | - David A Ford
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, United States.,Center for Cardiovascular Research, Saint Louis University School of Medicine, St. Louis, MO, United States
| |
Collapse
|
30
|
Ferreira AR, Marques M, Ramos B, Kagan JC, Ribeiro D. Emerging roles of peroxisomes in viral infections. Trends Cell Biol 2021; 32:124-139. [PMID: 34696946 DOI: 10.1016/j.tcb.2021.09.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 01/01/2023]
Abstract
Peroxisomes, essential subcellular organelles that fulfill important functions in lipid and reactive oxygen species metabolism, have recently emerged as key players during viral infections. Their importance for the establishment of the cellular antiviral response has been highlighted by numerous reports of specific evasion of peroxisome-dependent signaling by different viruses. Recent data demonstrate that peroxisomes also assume important proviral functions. Here, we review and discuss the recent advances in the study of the diverse roles of peroxisomes during viral infections, from animal to plant viruses, and from basic to translational perspectives. We further discuss the future development of this emerging area and propose that peroxisome-related mechanisms represent a promising target for the development of novel antiviral strategies.
Collapse
Affiliation(s)
- Ana Rita Ferreira
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Mariana Marques
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Bruno Ramos
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED) and Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
| |
Collapse
|
31
|
He A, Dean JM, Lodhi IJ. Peroxisomes as cellular adaptors to metabolic and environmental stress. Trends Cell Biol 2021; 31:656-670. [PMID: 33674166 PMCID: PMC8566112 DOI: 10.1016/j.tcb.2021.02.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023]
Abstract
Peroxisomes are involved in multiple metabolic processes, including fatty acid oxidation, ether lipid synthesis, and reactive oxygen species (ROS) metabolism. Recent studies suggest that peroxisomes are critical mediators of cellular responses to various forms of stress, including oxidative stress, hypoxia, starvation, cold exposure, and noise. As dynamic organelles, peroxisomes can modulate their proliferation, morphology, and movement within cells, and engage in crosstalk with other organelles in response to external cues. Although peroxisome-derived hydrogen peroxide has a key role in cellular signaling related to stress, emerging studies suggest that other products of peroxisomal metabolism, such as acetyl-CoA and ether lipids, are also important for metabolic adaptation to stress. Here, we review molecular mechanisms through which peroxisomes regulate metabolic and environmental stress.
Collapse
Affiliation(s)
- Anyuan He
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA.
| | - John M Dean
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Irfan J Lodhi
- Division of Endocrinology, Metabolism and Lipid Research, Department of Medicine, Washington University School of Medicine, St Louis, MO 63110, USA.
| |
Collapse
|
32
|
Knoblach B, Ishida R, Hobman TC, Rachubinski RA. Peroxisomes exhibit compromised structure and matrix protein content in SARS-CoV-2-infected cells. Mol Biol Cell 2021; 32:1273-1282. [PMID: 34010015 PMCID: PMC8351553 DOI: 10.1091/mbc.e21-02-0074] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus that has triggered global health and economic crises. Here we report the effects of SARS-CoV-2 infection on peroxisomes of human cell lines Huh-7 and SK-N-SH. Peroxisomes undergo dramatic changes in morphology in SARS-CoV-2-infected cells. Rearrangement of peroxisomal membranes is followed by redistribution of peroxisomal matrix proteins to the cytosol, resulting in a dramatic decrease in the number of mature peroxisomes. The SARS-CoV-2 ORF14 protein was shown to interact physically with human PEX14, a peroxisomal membrane protein required for matrix protein import and peroxisome biogenesis. Given the important roles of peroxisomes in innate immunity, SARS-CoV-2 may directly target peroxisomes, resulting in loss of peroxisome structural integrity, matrix protein content and ability to function in antiviral signaling.
Collapse
Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Ray Ishida
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Tom C Hobman
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.,Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| |
Collapse
|
33
|
Mitochondria and Peroxisome Remodeling across Cytomegalovirus Infection Time Viewed through the Lens of Inter-ViSTA. Cell Rep 2021; 32:107943. [PMID: 32726614 DOI: 10.1016/j.celrep.2020.107943] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/20/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
Nearly all biological processes rely on the finely tuned coordination of protein interactions across cellular space and time. Accordingly, generating protein interactomes has become routine in biological studies, yet interpreting these datasets remains computationally challenging. Here, we introduce Inter-ViSTA (Interaction Visualization in Space and Time Analysis), a web-based platform that quickly builds animated protein interaction networks and automatically synthesizes information on protein abundances, functions, complexes, and subcellular localizations. Using Inter-ViSTA with proteomics and molecular virology, we define virus-host interactions for the human cytomegalovirus (HCMV) anti-apoptotic protein, pUL37x1. We find that spatiotemporal controlled interactions underlie pUL37x1 functions, facilitating the pro-viral remodeling of mitochondria and peroxisomes during infection. Reciprocal isolations, microscopy, and genetic manipulations further characterize these associations, revealing the interplay between pUL37x1 and the MIB complex, which is critical for mitochondrial integrity. At the peroxisome, we show that pUL37x1 activates PEX11β to regulate fission, a key aspect of virus assembly and spread.
Collapse
|
34
|
Mechanisms and Functions of Pexophagy in Mammalian Cells. Cells 2021; 10:cells10051094. [PMID: 34063724 PMCID: PMC8147788 DOI: 10.3390/cells10051094] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 12/17/2022] Open
Abstract
Peroxisomes play essential roles in diverse cellular metabolism functions, and their dynamic homeostasis is maintained through the coordination of peroxisome biogenesis and turnover. Pexophagy, selective autophagic degradation of peroxisomes, is a major mechanism for removing damaged and/or superfluous peroxisomes. Dysregulation of pexophagy impairs the physiological functions of peroxisomes and contributes to the progression of many human diseases. However, the mechanisms and functions of pexophagy in mammalian cells remain largely unknown compared to those in yeast. This review focuses on mammalian pexophagy and aims to advance the understanding of the roles of pexophagy in human health and diseases. Increasing evidence shows that ubiquitination can serve as a signal for pexophagy, and ubiquitin-binding receptors, substrates, and E3 ligases/deubiquitinases involved in pexophagy have been described. Alternatively, pexophagy can be achieved in a ubiquitin-independent manner. We discuss the mechanisms of these ubiquitin-dependent and ubiquitin-independent pexophagy pathways and summarize several inducible conditions currently used to study pexophagy. We highlight several roles of pexophagy in human health and how its dysregulation may contribute to diseases.
Collapse
|
35
|
AGMO Inhibitor Reduces 3T3-L1 Adipogenesis. Cells 2021; 10:cells10051081. [PMID: 34062826 PMCID: PMC8147360 DOI: 10.3390/cells10051081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/20/2022] Open
Abstract
Alkylglycerol monooxygenase (AGMO) is a tetrahydrobiopterin (BH4)-dependent enzyme with major expression in the liver and white adipose tissue that cleaves alkyl ether glycerolipids. The present study describes the disclosure and biological characterization of a candidate compound (Cp6), which inhibits AGMO with an IC50 of 30–100 µM and 5–20-fold preference of AGMO relative to other BH4-dependent enzymes, i.e., phenylalanine-hydroxylase and nitric oxide synthase. The viability and metabolic activity of mouse 3T3-L1 fibroblasts, HepG2 human hepatocytes and mouse RAW264.7 macrophages were not affected up to 10-fold of the IC50. However, Cp6 reversibly inhibited the differentiation of 3T3-L1 cells towards adipocytes, in which AGMO expression was upregulated upon differentiation. Cp6 reduced the accumulation of lipid droplets in adipocytes upon differentiation and in HepG2 cells exposed to free fatty acids. Cp6 also inhibited IL-4-driven differentiation of RAW264.7 macrophages towards M2-like macrophages, which serve as adipocyte progenitors in adipose tissue. Collectively, the data suggest that pharmacologic AGMO inhibition may affect lipid storage.
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Deng Y, Angelova A. Coronavirus-Induced Host Cubic Membranes and Lipid-Related Antiviral Therapies: A Focus on Bioactive Plasmalogens. Front Cell Dev Biol 2021; 9:630242. [PMID: 33791293 PMCID: PMC8006408 DOI: 10.3389/fcell.2021.630242] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Coronaviruses have lipid envelopes required for their activity. The fact that coronavirus infection provokes the formation of cubic membranes (CM) (denoted also as convoluted membranes) in host cells has not been rationalized in the development of antiviral therapies yet. In this context, the role of bioactive plasmalogens (vinyl ether glycerophospholipids) is not completely understood. These lipid species display a propensity for non-lamellar phase formation, facilitating membrane fusion, and modulate the activity of membrane-bound proteins such as enzymes and receptors. At the organism level, plasmalogen deficiency is associated with cardiometabolic disorders including obesity and type 2 diabetes in humans. A straight link is perceived with the susceptibility of such patients to SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) infection, the severity of illness, and the related difficulty in treatment. Based on correlations between the coronavirus-induced modifications of lipid metabolism in host cells, plasmalogen deficiency in the lung surfactant of COVID-19 patients, and the alterations of lipid membrane structural organization and composition including the induction of CM, we emphasize the key role of plasmalogens in the coronavirus (SARS-CoV-2, SARS-CoV, or MERS-CoV) entry and replication in host cells. Considering that plasmalogen-enriched lung surfactant formulations may improve the respiratory process in severe infected individuals, plasmalogens can be suggested as an anti-viral prophylactic, a lipid biomarker in SARS-CoV and SARS-CoV-2 infections, and a potential anti-viral therapeutic component of lung surfactant development for COVID-19 patients.
Collapse
Affiliation(s)
- Yuru Deng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Angelina Angelova
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay UMR 8612, Châtenay-Malabry, France
| |
Collapse
|
38
|
Scherer KM, Manton JD, Soh TK, Mascheroni L, Connor V, Crump CM, Kaminski CF. A fluorescent reporter system enables spatiotemporal analysis of host cell modification during herpes simplex virus-1 replication. J Biol Chem 2021; 296:100236. [PMID: 33380421 PMCID: PMC7948757 DOI: 10.1074/jbc.ra120.016571] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 01/12/2023] Open
Abstract
Herpesviruses are large and complex viruses that have a long history of coevolution with their host species. One important factor in the virus-host interaction is the alteration of intracellular morphology during viral replication with critical implications for viral assembly. However, the details of this remodeling event are not well understood, in part because insufficient tools are available to deconstruct this highly heterogeneous process. To provide an accurate and reliable method of investigating the spatiotemporal dynamics of virus-induced changes to cellular architecture, we constructed a dual-fluorescent reporter virus that enabled us to classify four distinct stages in the infection cycle of herpes simplex virus-1 at the single cell level. This timestamping method can accurately track the infection cycle across a wide range of multiplicities of infection. We used high-resolution fluorescence microscopy analysis of cellular structures in live and fixed cells in concert with our reporter virus to generate a detailed and chronological overview of the spatial and temporal reorganization during viral replication. The highly orchestrated and striking relocation of many organelles around the compartments of secondary envelopment during transition from early to late gene expression suggests that the reshaping of these compartments is essential for virus assembly. We furthermore find that accumulation of HSV-1 capsids in the cytoplasm is accompanied by fragmentation of the Golgi apparatus with potential impact on the late steps of viral assembly. We anticipate that in the future similar tools can be systematically applied for the systems-level analysis of intracellular morphology during replication of other viruses.
Collapse
Affiliation(s)
- Katharina M Scherer
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge, UK
| | - James D Manton
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge, UK; MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Timothy K Soh
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Luca Mascheroni
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge, UK
| | - Vivienne Connor
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Colin M Crump
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Clemens F Kaminski
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge, UK.
| |
Collapse
|
39
|
A cross-talk between epithelium and endothelium mediates human alveolar-capillary injury during SARS-CoV-2 infection. Cell Death Dis 2020; 11:1042. [PMID: 33293527 PMCID: PMC7721862 DOI: 10.1038/s41419-020-03252-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022]
Abstract
COVID-19, caused by SARS-CoV-2, is an acute and rapidly developing pandemic, which leads to a global health crisis. SARS-CoV-2 primarily attacks human alveoli and causes severe lung infection and damage. To better understand the molecular basis of this disease, we sought to characterize the responses of alveolar epithelium and its adjacent microvascular endothelium to viral infection under a co-culture system. SARS-CoV-2 infection caused massive virus replication and dramatic organelles remodeling in alveolar epithelial cells, alone. While, viral infection affected endothelial cells in an indirect manner, which was mediated by infected alveolar epithelium. Proteomics analysis and TEM examinations showed viral infection caused global proteomic modulations and marked ultrastructural changes in both epithelial cells and endothelial cells under the co-culture system. In particular, viral infection elicited global protein changes and structural reorganizations across many sub-cellular compartments in epithelial cells. Among the affected organelles, mitochondrion seems to be a primary target organelle. Besides, according to EM and proteomic results, we identified Daurisoline, a potent autophagy inhibitor, could inhibit virus replication effectively in host cells. Collectively, our study revealed an unrecognized cross-talk between epithelium and endothelium, which contributed to alveolar–capillary injury during SARS-CoV-2 infection. These new findings will expand our understanding of COVID-19 and may also be helpful for targeted drug development.
Collapse
|
40
|
Mast FD, Rachubinski RA, Aitchison JD. Peroxisome prognostications: Exploring the birth, life, and death of an organelle. J Cell Biol 2020; 219:133827. [PMID: 32211898 PMCID: PMC7054992 DOI: 10.1083/jcb.201912100] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Peroxisomes play a central role in human health and have biochemical properties that promote their use in many biotechnology settings. With a primary role in lipid metabolism, peroxisomes share a niche with lipid droplets within the endomembrane-secretory system. Notably, factors in the ER required for the biogenesis of peroxisomes also impact the formation of lipid droplets. The dynamic interface between peroxisomes and lipid droplets, and also between these organelles and the ER and mitochondria, controls their metabolic flux and their dynamics. Here, we review our understanding of peroxisome biogenesis to propose and reframe models for understanding how peroxisomes are formed in cells. To more fully understand the roles of peroxisomes and to take advantage of their many properties that may prove useful in novel therapeutics or biotechnology applications, we recast mechanisms controlling peroxisome biogenesis in a framework that integrates inference from these models with experimental data.
Collapse
Affiliation(s)
- Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA
| | | | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle WA.,Department of Pediatrics, University of Washington, Seattle, WA
| |
Collapse
|
41
|
Mahalingam SS, Shukla N, Farré JC, Zientara-Rytter K, Subramani S. Balancing the Opposing Principles That Govern Peroxisome Homeostasis. Trends Biochem Sci 2020; 46:200-212. [PMID: 33046344 DOI: 10.1016/j.tibs.2020.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/14/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
Despite major advances in our understanding of players and mechanisms involved in peroxisome biogenesis and peroxisome degradation, very few studies have focused on unraveling the multi-layered connections between, and the coordination of, these two opposing processes that regulate peroxisome homeostasis. The intersection between these processes also provides exciting avenues for future research. This review highlights the links between peroxisome biogenesis and degradation, incorporating an integrative approach that is critical not only for a mechanistic understanding, but also for manipulating the balance between these processes in relevant disease models.
Collapse
Affiliation(s)
- Shanmuga S Mahalingam
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Nandini Shukla
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Jean-Claude Farré
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Katarzyna Zientara-Rytter
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA.
| |
Collapse
|
42
|
Kennedy MA, Hofstadter WA, Cristea IM. TRANSPIRE: A Computational Pipeline to Elucidate Intracellular Protein Movements from Spatial Proteomics Data Sets. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1422-1439. [PMID: 32401031 PMCID: PMC7737664 DOI: 10.1021/jasms.0c00033] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein localization is paramount to protein function, and the intracellular movement of proteins underlies the regulation of numerous cellular processes. Given advances in spatial proteomics, the investigation of protein localization at a global scale has become attainable. Also becoming apparent is the need for dedicated analytical frameworks that allow the discovery of global intracellular protein movement events. Here, we describe TRANSPIRE, a computational pipeline that facilitates TRanslocation ANalysis of SPatIal pRotEomics data sets. TRANSPIRE leverages synthetic translocation profiles generated from organelle marker proteins to train a probabilistic Gaussian process classifier that predicts changes in protein distribution. This output is then integrated with information regarding co-translocating proteins and complexes and enriched gene ontology associations to discern the putative regulation and function of movement. We validate TRANSPIRE performance for predicting nuclear-cytoplasmic shuttling events. Analyzing an existing data set of nuclear and cytoplasmic proteomes during Kaposi Sarcoma-associated herpesvirus (KSHV)-induced cellular mRNA decay, we confirm that TRANSPIRE readily discerns expected translocations of RNA binding proteins. We next investigate protein translocations during infection with human cytomegalovirus (HCMV), a β-herpesvirus known to induce global organelle remodeling. We find that HCMV infection induces broad changes in protein localization, with over 800 proteins predicted to translocate during virus replication. Evident are protein movements related to HCMV modulation of host defense, metabolism, cellular trafficking, and Wnt signaling. For example, the low-density lipoprotein receptor (LDLR) translocates to the lysosome early in infection in conjunction with its degradation, which we validate by targeted mass spectrometry. Using microscopy, we also validate the translocation of the multifunctional kinase DAPK3, a movement that may contribute to HCMV activation of Wnt signaling.
Collapse
Affiliation(s)
- Michelle A Kennedy
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - William A Hofstadter
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| |
Collapse
|
43
|
Chen C, Li J, Qin X, Wang W. Peroxisomal Membrane Contact Sites in Mammalian Cells. Front Cell Dev Biol 2020; 8:512. [PMID: 32714927 PMCID: PMC7344225 DOI: 10.3389/fcell.2020.00512] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 05/28/2020] [Indexed: 12/11/2022] Open
Abstract
Peroxisomes participate in essential cellular metabolic processes, such as oxidation of fatty acids (FAs) and maintenance of reactive oxygen species (ROS) homeostasis. Peroxisomes must communicate with surrounding organelles to exchange information and metabolites. The formation of membrane contact sites (MCSs), where protein-protein or protein-lipid complexes tether the opposing membranes of two organelles, represents an essential means of organelle crosstalk. Peroxisomal MCS (PO-MCS) studies are emerging but are still in the early stages. In this review, we summarize the identified PO-MCSs with the ER, mitochondria, lipid droplets, and lysosomes in mammalian cells and discuss their tethering mechanisms and physiological roles. We also highlight several features of PO-MCSs that may help future studies.
Collapse
Affiliation(s)
- Chao Chen
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Li
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuhui Qin
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Wang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
44
|
Lee CH, Grey F. Systems Virology and Human Cytomegalovirus: Using High Throughput Approaches to Identify Novel Host-Virus Interactions During Lytic Infection. Front Cell Infect Microbiol 2020; 10:280. [PMID: 32587832 PMCID: PMC7298070 DOI: 10.3389/fcimb.2020.00280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022] Open
Abstract
Human Cytomegalovirus (HCMV) is a highly prevalent herpesvirus, persistently infecting between 30 and 100% of the population, depending on socio-economic status (Fields et al., 2013). HCMV remains an important clinical pathogen accounting for more than 60% of complications associated with solid organ transplant patients (Kotton, 2013; Kowalsky et al., 2013; Bruminhent and Razonable, 2014). It is also the leading cause of infectious congenital birth defects and has been linked to chronic inflammation and immune aging (Ballard et al., 1979; Griffith et al., 2016; Jergovic et al., 2019). There is currently no effective vaccine and HCMV antivirals have significant side effects. As current antivirals target viral genes, the virus can develop resistance, reducing drug efficacy. There is therefore an urgent need for new antiviral agents that are effective against HCMV, have better toxicity profiles and are less vulnerable to the emergence of resistant strains. Targeting of host factors that are critical to virus replication is a potential strategy for the development of novel antivirals that circumvent the development of viral resistance. Systematic high throughput approaches provide powerful methods for the identification of novel host-virus interactions. As well as contributing to our basic understanding of virus and cell biology, such studies provide potential targets for the development of novel antiviral agents. High-throughput studies, such as RNA sequencing, proteomics, and RNA interference screens, are useful tools to identify HCMV-induced global changes in host mRNA and protein expression levels and host factors important for virus replication. Here, we summarize new findings on HCMV lytic infection from high-throughput studies since 2014 and how screening approaches have evolved.
Collapse
Affiliation(s)
- Chen-Hsuin Lee
- Division of Infection and Immunity, Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Finn Grey
- Division of Infection and Immunity, Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
45
|
Abstract
Viruses manipulate cellular lipids and membranes at each stage of their life cycle. This includes lipid-receptor interactions, the fusion of viral envelopes with cellular membranes during endocytosis, the reorganization of cellular membranes to form replication compartments, and the envelopment and egress of virions. In addition to the physical interactions with cellular membranes, viruses have evolved to manipulate lipid signaling and metabolism to benefit their replication. This review summarizes the strategies that viruses use to manipulate lipids and membranes at each stage in the viral life cycle.
Collapse
Affiliation(s)
- Ellen Ketter
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, USA;
| | - Glenn Randall
- Department of Microbiology, The University of Chicago, Chicago, Illinois 60637, USA;
| |
Collapse
|
46
|
Temporal dynamics of protein complex formation and dissociation during human cytomegalovirus infection. Nat Commun 2020; 11:806. [PMID: 32041945 PMCID: PMC7010728 DOI: 10.1038/s41467-020-14586-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/10/2020] [Indexed: 12/23/2022] Open
Abstract
The co-evolution and co-existence of viral pathogens with their hosts for millions of years is reflected in dynamic virus-host protein-protein interactions (PPIs) that are intrinsic to the spread of infections. Here, we investigate the system-wide dynamics of protein complexes throughout infection with the herpesvirus, human cytomegalovirus (HCMV). Integrating thermal shift assays and mass spectrometry quantification with virology and microscopy, we monitor the temporal formation and dissociation of hundreds of functional protein complexes and the dynamics of host-host, virus-host, and virus-virus PPIs. We establish pro-viral roles for cellular protein complexes and translocating proteins. We show the HCMV receptor integrin beta 1 dissociates from extracellular matrix proteins, becoming internalized with CD63, which is necessary for virus production. Moreover, this approach facilitates characterization of essential viral proteins, such as pUL52. This study of temporal protein complex dynamics provides insights into mechanisms of HCMV infection and a resource for biological and therapeutic studies. Here, Hashimoto et al. apply mass spectrometry-based thermal proximity coaggregation to characterize the temporal dynamics of virus-host protein-protein interactions during human cytomegalovirus (HCMV) infection, uncovering proviral functions including the internalization of the HCMV receptor integrin beta 1 with CD63.
Collapse
|
47
|
Liu P, Yin Y, Gong Y, Qiu X, Sun Y, Tan L, Song C, Liu W, Liao Y, Meng C, Ding C. In Vitro and In Vivo Metabolomic Profiling after Infection with Virulent Newcastle Disease Virus. Viruses 2019; 11:v11100962. [PMID: 31635316 PMCID: PMC6832399 DOI: 10.3390/v11100962] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/26/2022] Open
Abstract
Newcastle disease (ND) is an acute, febrile, highly contagious disease caused by the virulent Newcastle disease virus (vNDV). The disease causes serious economic losses to the poultry industry. However, the metabolic changes caused by vNDV infection remain unclear. The objective of this study was to determine the metabolomic profiling after infection with vNDV. DF-1 cells infected with the vNDV strain Herts/33 and the lungs from Herts/33-infected specific pathogen-free (SPF) chickens were analyzed via ultra-high-performance liquid chromatography/quadrupole time-of-flight tandem mass spectrometry (UHPLC-QTOF-MS) in combination with multivariate statistical analysis. A total of 305 metabolites were found to have changed significantly after Herts/33 infection, and most of them belong to the amino acid and nucleotide metabolic pathway. It is suggested that the increased pools of amino acids and nucleotides may benefit viral protein synthesis and genome amplification to promote NDV infection. Similar results were also confirmed in vivo. Identification of these metabolites will provide information to further understand the mechanism of vNDV replication and pathogenesis.
Collapse
Affiliation(s)
- Panrao Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Yuncong Yin
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China.
| | - Yabin Gong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Xusheng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Yingjie Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Lei Tan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Cuiping Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Weiwei Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Chunchun Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China.
| |
Collapse
|
48
|
Wang LW, Wang Z, Ersing I, Nobre L, Guo R, Jiang S, Trudeau S, Zhao B, Weekes MP, Gewurz BE. Epstein-Barr virus subverts mevalonate and fatty acid pathways to promote infected B-cell proliferation and survival. PLoS Pathog 2019; 15:e1008030. [PMID: 31518366 PMCID: PMC6760809 DOI: 10.1371/journal.ppat.1008030] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 09/25/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023] Open
Abstract
Epstein-Barr virus (EBV) causes infectious mononucleosis and is associated with multiple human malignancies. EBV drives B-cell proliferation, which contributes to the pathogenesis of multiple lymphomas. Yet, knowledge of how EBV subverts host biosynthetic pathways to transform resting lymphocytes into activated lymphoblasts remains incomplete. Using a temporal proteomic dataset of EBV primary human B-cell infection, we identified that cholesterol and fatty acid biosynthetic pathways were amongst the most highly EBV induced. Epstein-Barr nuclear antigen 2 (EBNA2), sterol response element binding protein (SREBP) and MYC each had important roles in cholesterol and fatty acid pathway induction. Unexpectedly, HMG-CoA reductase inhibitor chemical epistasis experiments revealed that mevalonate pathway production of geranylgeranyl pyrophosphate (GGPP), rather than cholesterol, was necessary for EBV-driven B-cell outgrowth, perhaps because EBV upregulated the low-density lipoprotein receptor in newly infected cells for cholesterol uptake. Chemical and CRISPR genetic analyses highlighted downstream GGPP roles in EBV-infected cell small G protein Rab activation. Rab13 was highly EBV-induced in an EBNA3-dependent manner and served as a chaperone critical for latent membrane protein (LMP) 1 and 2A trafficking and target gene activation in newly infected and in lymphoblastoid B-cells. Collectively, these studies identify highlight multiple potential therapeutic targets for prevention of EBV-transformed B-cell growth and survival. EBV, the first human tumor virus identified, persistently infects >95% of adults worldwide. Upon infection of small, resting B-lymphocytes, EBV establishes a state of viral latency, where viral oncoproteins and non-coding RNAs activate host pathways to promote rapid B-cell proliferation. EBV’s growth-transforming properties are closely linked to the pathogenesis of multiple immunoblastic lymphomas, particularly in immunosuppressed hosts. While EBV oncogenes important for B-cell transformation have been identified, knowledge remains incomplete of how these EBV factors remodel cellular metabolism, a hallmark of human cancers. Using a recently established proteomic map of EBV-mediated B-cell growth transformation, we found that EBV induces biosynthetic pathways that convert acetyl-coenzyme A (acetyl-CoA) into isoprenoids, steroids, terpenoids, cholesterol, and long-chain fatty acids. Viral nuclear antigens cooperated with EBV-activated host transcription factors to upregulate rate-limiting enzymes of these biosynthetic pathways. The isoprenoid geranylgeranyl pyrophosphate was identified as a key product of the EBV-induced mevalonate pathway. Our studies highlighted GGPP roles in Rab protein activation, and Rab13 was identified as a highly EBV-upregulated GTPase critical for LMP1 and LMP2A trafficking and signaling. These studies identify multiple EBV-induced metabolic enzymes important for B-cell transformation, including potential therapeutic targets.
Collapse
Affiliation(s)
- Liang Wei Wang
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Zhonghao Wang
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Ina Ersing
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Luis Nobre
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Rui Guo
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Sizun Jiang
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Stephen Trudeau
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Bo Zhao
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin E. Gewurz
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
49
|
Di Cara F, Andreoletti P, Trompier D, Vejux A, Bülow MH, Sellin J, Lizard G, Cherkaoui-Malki M, Savary S. Peroxisomes in Immune Response and Inflammation. Int J Mol Sci 2019; 20:ijms20163877. [PMID: 31398943 PMCID: PMC6721249 DOI: 10.3390/ijms20163877] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/24/2019] [Accepted: 08/05/2019] [Indexed: 12/11/2022] Open
Abstract
The immune response is essential to protect organisms from infection and an altered self. An organism’s overall metabolic status is now recognized as an important and long-overlooked mediator of immunity and has spurred new explorations of immune-related metabolic abnormalities. Peroxisomes are essential metabolic organelles with a central role in the synthesis and turnover of complex lipids and reactive species. Peroxisomes have recently been identified as pivotal regulators of immune functions and inflammation in the development and during infection, defining a new branch of immunometabolism. This review summarizes the current evidence that has helped to identify peroxisomes as central regulators of immunity and highlights the peroxisomal proteins and metabolites that have acquired relevance in human pathologies for their link to the development of inflammation, neuropathies, aging and cancer. This review then describes how peroxisomes govern immune signaling strategies such as phagocytosis and cytokine production and their relevance in fighting bacterial and viral infections. The mechanisms by which peroxisomes either control the activation of the immune response or trigger cellular metabolic changes that activate and resolve immune responses are also described.
Collapse
Affiliation(s)
- Francesca Di Cara
- Department of Microbiology and Immunology, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Pierre Andreoletti
- Lab. Bio-PeroxIL EA7270, University of Bourgogne Franche-Comté, 6 Bd Gabriel, 21000 Dijon, France
| | - Doriane Trompier
- Lab. Bio-PeroxIL EA7270, University of Bourgogne Franche-Comté, 6 Bd Gabriel, 21000 Dijon, France
| | - Anne Vejux
- Lab. Bio-PeroxIL EA7270, University of Bourgogne Franche-Comté, 6 Bd Gabriel, 21000 Dijon, France
| | - Margret H Bülow
- Molecular Developmental Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Julia Sellin
- Molecular Developmental Biology, Life & Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Gérard Lizard
- Lab. Bio-PeroxIL EA7270, University of Bourgogne Franche-Comté, 6 Bd Gabriel, 21000 Dijon, France
| | - Mustapha Cherkaoui-Malki
- Lab. Bio-PeroxIL EA7270, University of Bourgogne Franche-Comté, 6 Bd Gabriel, 21000 Dijon, France
| | - Stéphane Savary
- Lab. Bio-PeroxIL EA7270, University of Bourgogne Franche-Comté, 6 Bd Gabriel, 21000 Dijon, France.
| |
Collapse
|
50
|
Cook KC, Moreno JA, Jean Beltran PM, Cristea IM. Peroxisome Plasticity at the Virus-Host Interface. Trends Microbiol 2019; 27:906-914. [PMID: 31331665 DOI: 10.1016/j.tim.2019.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/12/2019] [Accepted: 06/19/2019] [Indexed: 02/07/2023]
Abstract
Peroxisomes are multifunctional organelles with roles in cellular metabolism, cytotoxicity, and signaling. The plastic nature of these organelles allows them to respond to diverse biological processes, such as virus infections, by remodeling their biogenesis, morphology, and composition to enhance specific functions. During virus infections in humans, peroxisomes act as important immune signaling organelles, aiding the host by orchestrating antiviral signaling. However, more recently it was discovered that peroxisomes can also benefit the virus, facilitating virus-host interactions that rewire peroxisomes to support cellular processes for virus replication and spread. Here, we describe recent studies that uncovered this double-edged character of peroxisomes during infection, highlighting mechanisms that viruses have coevolved to take advantage of peroxisome plasticity. We also provide a perspective for future studies by comparing the established roles of peroxisomes in plant infections and discussing the promise of virology studies as a venue to reveal the uncharted biology of peroxisomes.
Collapse
Affiliation(s)
- Katelyn C Cook
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Jorge A Moreno
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Pierre M Jean Beltran
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
| |
Collapse
|