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Shimura M, Higashi-Kuwata N, Fujiwara A, Taniguchi M, Ichinose T, Hamano F, Uematsu M, Inoue T, Matsuyama S, Suzuki T, Ghosh AK, Shindou H, Shimuzu T, Mitsuya H. A lipid index for risk of hyperlipidemia caused by anti-retroviral drugs. Antiviral Res 2024; 223:105819. [PMID: 38272319 DOI: 10.1016/j.antiviral.2024.105819] [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: 11/29/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024]
Abstract
HIV-associated lipodystrophy has been reported in people taking anti-retroviral therapy (ART). Lipodystrophy can cause cardiovascular diseases, affecting the quality of life of HIV-infected individuals. In this study, we propose a pharmacological lipid index to estimate the risk of hyperlipidemia caused by anti-retroviral drugs. Lipid droplets were stained in cells treated with anti-retroviral drugs and cyclosporin A. Signal intensities of lipid droplets were plotted against the drug concentrations to obtain an isodose of 10 μM of cyclosporin A, which we call the Pharmacological Lipid Index (PLI). The PLI was then normalized by EC50. PLI/EC50 values were low in early proteinase inhibitors and the nucleoside reverse transcriptase inhibitor, d4T, indicating high risk of hyperlipidemia, which is consistent with previous findings of hyperlipidemia. In contrast, there are few reports of hyperlipidemia for drugs with high PLI/EC50 scores. Data suggests that PLI/EC50 is a useful index for estimating the risk of hyperlipidemia.
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Affiliation(s)
- Mari Shimura
- Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan; RIKEN SPring-8 Center, Sayo, Hyogo, Japan.
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Asuka Fujiwara
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Mai Taniguchi
- Inorganic Analysis Laboratories, Toray Research Center, Inc., Otsu, Shiga, Japan
| | - Takayuki Ichinose
- Inorganic Analysis Laboratories, Toray Research Center, Inc., Otsu, Shiga, Japan
| | - Fumie Hamano
- Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Department of Lipid Signaling, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Masaaki Uematsu
- Department of Lipid Signaling, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Takato Inoue
- Department of Materials Physics, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Satoshi Matsuyama
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan; Department of Materials Physics, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Takahiro Suzuki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Arun K Ghosh
- Department of Chemistry & Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Hideo Shindou
- Department of Lipid Life Science, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan; Department of Medical Lipid Science, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takao Shimuzu
- Department of Lipid Signaling, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan; Institute of Microbial Chemistry, Shinagawa-ku, Tokyo, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Diseases, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Center Institute, National Institutes of Health, Bethesda, MD, 20893, USA.
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2
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Mehmood K, Wilczek MP, DuShane JK, Parent MT, Mayberry CL, Wallace JN, Levasseur FL, Fong TM, Hess ST, Maginnis MS. Dynamics and Patterning of 5-Hydroxytryptamine 2 Subtype Receptors in JC Polyomavirus Entry. Viruses 2022; 14:v14122597. [PMID: 36560603 PMCID: PMC9782046 DOI: 10.3390/v14122597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
The organization and dynamics of plasma membrane receptors are a critical link in virus-receptor interactions, which finetune signaling efficiency and determine cellular responses during infection. Characterizing the mechanisms responsible for the active rearrangement and clustering of receptors may aid in developing novel strategies for the therapeutic treatment of viruses. Virus-receptor interactions are poorly understood at the nanoscale, yet they present an attractive target for the design of drugs and for the illumination of viral infection and pathogenesis. This study utilizes super-resolution microscopy and related techniques, which surpass traditional microscopy resolution limitations, to provide both a spatial and temporal assessment of the interactions of human JC polyomavirus (JCPyV) with 5-hydroxytrypamine 2 receptors (5-HT2Rs) subtypes during viral entry. JCPyV causes asymptomatic kidney infection in the majority of the population and can cause fatal brain disease, and progressive multifocal leukoencephalopathy (PML), in immunocompromised individuals. Using Fluorescence Photoactivation Localization Microscopy (FPALM), the colocalization of JCPyV with 5-HT2 receptor subtypes (5-HT2A, 5-HT2B, and 5-HT2C) during viral attachment and viral entry was analyzed. JCPyV was found to significantly enhance the clustering of 5-HT2 receptors during entry. Cluster analysis of infected cells reveals changes in 5-HT2 receptor cluster attributes, and radial distribution function (RDF) analyses suggest a significant increase in the aggregation of JCPyV particles colocalized with 5-HT2 receptor clusters in JCPyV-infected samples. These findings provide novel insights into receptor patterning during viral entry and highlight improved technologies for the future development of therapies for JCPyV infection as well as therapies for diseases involving 5-HT2 receptors.
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Affiliation(s)
- Kashif Mehmood
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, USA
| | - Michael P. Wilczek
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, USA
| | - Jeanne K. DuShane
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, USA
| | - Matthew T. Parent
- Department of Physics & Astronomy, The University of Maine, Orono, ME 04469, USA
| | - Colleen L. Mayberry
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, USA
| | - Jaqulin N. Wallace
- Department of Physics & Astronomy, The University of Maine, Orono, ME 04469, USA
| | - Francois L. Levasseur
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, USA
| | - Tristan M. Fong
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, USA
| | - Samuel T. Hess
- Department of Physics & Astronomy, The University of Maine, Orono, ME 04469, USA
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, ME 04469, USA
- Correspondence: (S.T.H.); (M.S.M.)
| | - Melissa S. Maginnis
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME 04469, USA
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, ME 04469, USA
- Correspondence: (S.T.H.); (M.S.M.)
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3
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Pigot C, Brunel D, Dumur F. Indane-1,3-Dione: From Synthetic Strategies to Applications. Molecules 2022; 27:molecules27185976. [PMID: 36144711 PMCID: PMC9501146 DOI: 10.3390/molecules27185976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022] Open
Abstract
Indane-1,3-dione is a versatile building block used in numerous applications ranging from biosensing, bioactivity, bioimaging to electronics or photopolymerization. In this review, an overview of the different chemical reactions enabling access to this scaffold but also to the most common derivatives of indane-1,3-dione are presented. Parallel to this, the different applications in which indane-1,3-dione-based structures have been used are also presented, evidencing the versatility of this structure.
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Affiliation(s)
- Corentin Pigot
- Aix Marseille Univ, CNRS, ICR, UMR 7273, F-13397 Marseille, France
| | - Damien Brunel
- Aix Marseille Univ, CNRS, ICR, UMR 7273, F-13397 Marseille, France
| | - Frédéric Dumur
- Aix Marseille Univ, CNRS, ICR, UMR 7273, F-13397 Marseille, France
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4
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Mantilla MJ, Cabrera Díaz CE, Ariza-Aranguren G, de Cock H, Helms JB, Restrepo S, Jiménez E, Celis Ramírez AM. Back to the Basics: Two Approaches for the Identification and Extraction of Lipid Droplets from Malassezia pachydermatis CBS1879 and Malassezia globosa CBS7966. Curr Protoc 2021; 1:e122. [PMID: 33950584 DOI: 10.1002/cpz1.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Malassezia spp. are lipid-dependent yeasts that have been related to skin mycobiota and dermatological and systemic diseases. Study of lipid droplets (LDs) is relevant to elucidate the unknown role of these organelles in Malassezia and to gain a broader overview of lipid metabolism in Malassezia. Here, we standardized two protocols for the analysis of LDs in M. pachydermatis and M. globosa. The first describes co-staining for confocal laser-scanning fluorescence microscopy, and the second details extraction and purification of LDs. The double stain is achieved with three different neutral lipid fluorophores, namely Nile Red, BODIPY™ 493/503, and HCS LipidTOX™ Deep Red Neutral, in combination with Calcofluor White. For LD extraction, cell wall rupture is conducted using Trichoderma harzianum enzymes and cycles of vortexing with zirconium beads. LD purification is performed in a three-step ultracentrifugation process. These standardizations will contribute to the study of the dynamics, morphology, and composition of LDs in Malassezia. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Lipid droplet fluorescence staining Basic Protocol 2: Lipid droplet extraction and purification Support Protocol: Malassezia spp. culture conditions.
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Affiliation(s)
- Maria Juliana Mantilla
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | | | - Gabriela Ariza-Aranguren
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
| | - Hans de Cock
- Microbiology, Department of Biology, Faculty of Science, Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - J Bernd Helms
- Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología (LAMFU), Chemical and Food Engineering Department, Universidad de Los Andes, Bogotá, Colombia
| | - Elizabeth Jiménez
- Applied Biochemistry Research Group (GIBA), Department of Chemistry, Universidad de Los Andes, Bogotá, Colombia
| | - Adriana Marcela Celis Ramírez
- Grupo de Investigación Celular y Molecular de Microorganismos Patógenos (CeMoP), Department of Biological Sciences, Universidad de Los Andes, Bogotá, Colombia
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5
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Hepatitis C virus infection restricts human LINE-1 retrotransposition in hepatoma cells. PLoS Pathog 2021; 17:e1009496. [PMID: 33872335 PMCID: PMC8084336 DOI: 10.1371/journal.ppat.1009496] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/29/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022] Open
Abstract
LINE-1 (L1) retrotransposons are autonomous transposable elements that can affect gene expression and genome integrity. Potential consequences of exogenous viral infections for L1 activity have not been studied to date. Here, we report that hepatitis C virus (HCV) infection causes a significant increase of endogenous L1-encoded ORF1 protein (L1ORF1p) levels and translocation of L1ORF1p to HCV assembly sites at lipid droplets. HCV replication interferes with retrotransposition of engineered L1 reporter elements, which correlates with HCV RNA-induced formation of stress granules and can be partially rescued by knockdown of the stress granule protein G3BP1. Upon HCV infection, L1ORF1p localizes to stress granules, associates with HCV core in an RNA-dependent manner and translocates to lipid droplets. While HCV infection has a negative effect on L1 mobilization, L1ORF1p neither restricts nor promotes HCV infection. In summary, our data demonstrate that HCV infection causes an increase of endogenous L1 protein levels and that the observed restriction of retrotransposition of engineered L1 reporter elements is caused by sequestration of L1ORF1p in HCV-induced stress granules. Members of the Long Interspersed Nuclear Element 1 (LINE-1, L1) class of retrotransposons account for ~17% of the human genome and include ~100–150 intact L1 loci that are still functional. L1 mobilization is known to affect genomic integrity, thereby leading to disease-causing mutations, but little is known about the impact of exogenous viral infections on L1 and vice versa. While L1 retrotransposition is controlled by various mechanisms including CpG methylation, hypomethylation of L1 has been observed in hepatocellular carcinoma tissues of hepatitis C virus (HCV)-infected patients. Here, we demonstrate molecular interactions between HCV and L1 elements. HCV infection stably increases cellular levels of the L1-encoded ORF1 protein (L1ORF1p). HCV core and L1ORF1p interact in ribonucleoprotein complexes that traffic to lipid droplets. Despite its redistribution to HCV assembly sites, L1ORF1p is dispensable for HCV infection. In contrast, retrotransposition of engineered L1 reporter elements is restricted by HCV, correlating with an increased formation of L1ORF1p-containing cytoplasmic stress granules. Thus, our data provide first insights into the molecular interplay of endogenous transposable elements and exogenous viruses that might contribute to disease progression in vivo.
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Arista-Romero M, Pujals S, Albertazzi L. Towards a Quantitative Single Particle Characterization by Super Resolution Microscopy: From Virus Structures to Antivirals Design. Front Bioeng Biotechnol 2021; 9:647874. [PMID: 33842446 PMCID: PMC8033170 DOI: 10.3389/fbioe.2021.647874] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
In the last year the COVID19 pandemic clearly illustrated the potential threat that viruses pose to our society. The characterization of viral structures and the identification of key proteins involved in each step of the cycle of infection are crucial to develop treatments. However, the small size of viruses, invisible under conventional fluorescence microscopy, make it difficult to study the organization of protein clusters within the viral particle. The applications of super-resolution microscopy have skyrocketed in the last years, converting this group into one of the leading techniques to characterize viruses and study the viral infection in cells, breaking the diffraction limit by achieving resolutions up to 10 nm using conventional probes such as fluorescent dyes and proteins. There are several super-resolution methods available and the selection of the right one it is crucial to study in detail all the steps involved in the viral infection, quantifying and creating models of infection for relevant viruses such as HIV-1, Influenza, herpesvirus or SARS-CoV-1. Here we review the use of super-resolution microscopy (SRM) to study all steps involved in the viral infection and antiviral design. In light of the threat of new viruses, these studies could inspire future assays to unveil the viral mechanism of emerging viruses and further develop successful antivirals against them.
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Affiliation(s)
- Maria Arista-Romero
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Silvia Pujals
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
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Optical technologies for the detection of viruses like COVID-19: Progress and prospects. Biosens Bioelectron 2021; 178:113004. [PMID: 33497877 PMCID: PMC7832448 DOI: 10.1016/j.bios.2021.113004] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023]
Abstract
The outbreak of life-threatening pandemic like COVID-19 necessitated the development of novel, rapid and cost-effective techniques that facilitate detection of viruses like SARS-CoV-2. The presently popular approach of a collection of samples using the nasopharyngeal swab method and subsequent detection of RNA using the real-time polymerase chain reaction suffers from false-positive results and a longer diagnostic time scale. Alternatively, various optical techniques namely optical sensing, spectroscopy, and imaging shows a great promise in virus detection. Herein, a comprehensive review of the various photonics technologies employed for virus detection, particularly the SARS-CoV family, is discussed. The state-of-art research activities in utilizing the photonics tools such as near-infrared spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, fluorescence-based techniques, super-resolution microscopy, surface plasmon resonance-based detection, for virus detection accounted extensively with an emphasis on coronavirus detection. Further, an account of emerging photonics technologies of SARS-CoV-2 detection and future possibilities is also explained. The progress in the field of optical techniques for virus detection unambiguously show a great promise in the development of rapid photonics-based devices for COVID-19 detection.
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8
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Lassen S, Grüttner C, Nguyen-Dinh V, Herker E. Perilipin-2 is critical for efficient lipoprotein and hepatitis C virus particle production. J Cell Sci 2019; 132:jcs.217042. [PMID: 30559250 DOI: 10.1242/jcs.217042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 12/07/2018] [Indexed: 12/18/2022] Open
Abstract
In hepatocytes, PLIN2 is the major protein coating lipid droplets (LDs), an organelle the hepatitis C virus (HCV) hijacks for virion morphogenesis. We investigated the consequences of PLIN2 deficiency on LDs and on HCV infection. Knockdown of PLIN2 did not affect LD homeostasis, likely due to compensation by PLIN3, but severely impaired HCV particle production. PLIN2-knockdown cells had slightly larger LDs with altered protein composition, enhanced local lipase activity and higher β-oxidation capacity. Electron micrographs showed that, after PLIN2 knockdown, LDs and HCV-induced vesicular structures were tightly surrounded by ER-derived double-membrane sacs. Strikingly, the LD access for HCV core and NS5A proteins was restricted in PLIN2-deficient cells, which correlated with reduced formation of intracellular HCV particles that were less infectious and of higher density, indicating defects in maturation. PLIN2 depletion also reduced protein levels and secretion of ApoE due to lysosomal degradation, but did not affect the density of ApoE-containing lipoproteins. However, ApoE overexpression in PLIN2-deficient cells did not restore HCV spreading. Thus, PLIN2 expression is required for trafficking of core and NS5A proteins to LDs, and for formation of functional low-density HCV particles prior to ApoE incorporation.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Susan Lassen
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Cordula Grüttner
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Van Nguyen-Dinh
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Eva Herker
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany .,Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany
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Collot M, Bou S, Fam TK, Richert L, Mély Y, Danglot L, Klymchenko AS. Probing Polarity and Heterogeneity of Lipid Droplets in Live Cells Using a Push–Pull Fluorophore. Anal Chem 2018; 91:1928-1935. [DOI: 10.1021/acs.analchem.8b04218] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mayeul Collot
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Sophie Bou
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Tkhe Kyong Fam
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Ludovic Richert
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
| | - Lydia Danglot
- Institut Jacques Monod, University Paris Diderot, Sorbonne Paris Cité, CNRS UMR 7592, 75013 Paris, France
- Membrane Traffic in Healthy and Diseased Brain, INSERM U894, Institute of Psychiatry and Neuroscience of Paris, 102 rue de la Santé, 75 014 Paris, France
| | - Andrey S. Klymchenko
- Laboratoire de Biophotonique et Pathologies, Faculté de Pharmacie, UMR 7021 CNRS, Université de Strasbourg, 74, Route du Rhin, 67401 Cedex, Illkirch, France
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10
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Visualisation and analysis of hepatitis C virus non-structural proteins using super-resolution microscopy. Sci Rep 2018; 8:13604. [PMID: 30206266 PMCID: PMC6134135 DOI: 10.1038/s41598-018-31861-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 08/29/2018] [Indexed: 01/17/2023] Open
Abstract
Hepatitis C virus (HCV) RNA replication occurs in the cytosol of infected cells within a specialised membranous compartment. How the viral non-structural (NS) proteins are associated and organised within these structures remains poorly defined. We employed a super-resolution microscopy approach to visualise NS3 and NS5A in HCV infected cells. Using single molecule localisation microscopy, both NS proteins were resolved as clusters of localisations smaller than the diffraction-limited volume observed by wide-field. Analysis of the protein clusters identified a significant difference in size between the NS proteins. We also observed a reduction in NS5A cluster size following inhibition of RNA replication using daclatasvir, a phenotype which was maintained in the presence of the Y93H resistance associated substitution and not observed for NS3 clusters. These results provide insight into the NS protein organisation within hepatitis C virus RNA replication complexes and the mode of action of NS5A inhibitors.
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11
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Microscopy in Infectious Disease Research-Imaging Across Scales. J Mol Biol 2018; 430:2612-2625. [PMID: 29908150 DOI: 10.1016/j.jmb.2018.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/03/2018] [Accepted: 06/08/2018] [Indexed: 12/18/2022]
Abstract
A comprehensive understanding of host-pathogen interactions requires quantitative assessment of molecular events across a wide range of spatiotemporal scales and organizational complexities. Due to recent technical developments, this is currently only achievable with microscopy. This article is providing a general perspective on the importance of microscopy in infectious disease research, with a focus on new imaging modalities that promise to have a major impact in biomedical research in the years to come. Every major technological breakthrough in light microscopy depends on, and is supported by, advancements in computing and information technologies. Bioimage acquisition and analysis based on machine learning will pave the way toward more robust, automated and objective implementation of new imaging modalities and in biomedical research in general. The combination of novel imaging technologies with machine learning and near-physiological model systems promises to accelerate discoveries and breakthroughs in our understanding of infectious diseases, from basic research all the way to clinical applications.
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12
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Hofmann S, Krajewski M, Scherer C, Scholz V, Mordhorst V, Truschow P, Schöbel A, Reimer R, Schwudke D, Herker E. Complex lipid metabolic remodeling is required for efficient hepatitis C virus replication. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:1041-1056. [PMID: 29885363 DOI: 10.1016/j.bbalip.2018.06.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/16/2018] [Accepted: 06/01/2018] [Indexed: 12/12/2022]
Abstract
The hepatitis C virus (HCV) life cycle is tightly linked to the host cell lipid metabolism with the endoplasmic reticulum-derived membranous web harboring viral RNA replication complexes and lipid droplets as virion assembly sites. To investigate HCV-induced changes in the lipid composition, we performed quantitative shotgun lipidomic studies of whole cell extracts and subcellular compartments. Our results indicate that HCV infection reduces the ratio of neutral to membrane lipids. While the amount of neutral lipids and lipid droplet morphology were unchanged, membrane lipids, especially cholesterol and phospholipids, accumulated in the microsomal fraction in HCV-infected cells. In addition, HCV-infected cells had a higher relative abundance of phosphatidylcholines and triglycerides with longer fatty acyl chains and a strikingly increased utilization of C18 fatty acids, most prominently oleic acid (FA [18:1]). Accordingly, depletion of fatty acid elongases and desaturases impaired HCV replication. Moreover, the analysis of free fatty acids revealed increased levels of polyunsaturated fatty acids (PUFAs) caused by HCV infection. Interestingly, inhibition of the PUFA synthesis pathway via knockdown of the rate-limiting Δ6-desaturase enzyme or by treatment with a high dose of a small-molecule inhibitor impaired viral progeny production, indicating that elevated PUFAs are needed for virion morphogenesis. In contrast, pretreatment with low inhibitor concentrations promoted HCV translation and/or early RNA replication. Taken together our results demonstrate the complex remodeling of the host cell lipid metabolism induced by HCV to enhance both virus replication and progeny production.
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Affiliation(s)
- Sarah Hofmann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Matthias Krajewski
- Division of Bioanalytical Chemistry, Research Center Borstel - Leibniz Lung Center, Parkallee 10, 23845 Borstel, Germany
| | - Christina Scherer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Verena Scholz
- Division of Bioanalytical Chemistry, Research Center Borstel - Leibniz Lung Center, Parkallee 10, 23845 Borstel, Germany
| | - Valerie Mordhorst
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Pavel Truschow
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Anja Schöbel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Rudolph Reimer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Research Center Borstel - Leibniz Lung Center, Parkallee 10, 23845 Borstel, Germany
| | - Eva Herker
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany.
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Rösch K, Kwiatkowski M, Hofmann S, Schöbel A, Grüttner C, Wurlitzer M, Schlüter H, Herker E. Quantitative Lipid Droplet Proteome Analysis Identifies Annexin A3 as a Cofactor for HCV Particle Production. Cell Rep 2018; 16:3219-3231. [PMID: 27653686 DOI: 10.1016/j.celrep.2016.08.052] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 05/20/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022] Open
Abstract
Lipid droplets are vital to hepatitis C virus (HCV) infection as the putative sites of virion assembly, but morphogenesis and egress of virions remain ill defined. We performed quantitative lipid droplet proteome analysis of HCV-infected cells to identify co-factors of that process. Our results demonstrate that HCV disconnects lipid droplets from their metabolic function. Annexin A3 (ANXA3), a protein enriched in lipid droplet fractions, strongly impacted HCV replication and was characterized further: ANXA3 is recruited to lipid-rich fractions in HCV-infected cells by the viral core and NS5A proteins. ANXA3 knockdown does not affect HCV RNA replication but severely impairs virion production with lower specific infectivity and higher density of secreted virions. ANXA3 is essential for the interaction of viral envelope E2 with apolipoprotein E (ApoE) and for trafficking, but not lipidation, of ApoE in HCV-infected cells. Thus, we identified ANXA3 as a regulator of HCV maturation and egress.
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Affiliation(s)
- Kathrin Rösch
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Marcel Kwiatkowski
- Core Facility Mass Spectrometric Proteomics, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sarah Hofmann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Anja Schöbel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Cordula Grüttner
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Marcus Wurlitzer
- Core Facility Mass Spectrometric Proteomics, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Core Facility Mass Spectrometric Proteomics, Institute of Clinical Chemistry, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Eva Herker
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany.
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14
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Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
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15
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Gao M, Su H, Li S, Lin Y, Ling X, Qin A, Tang BZ. An easily accessible aggregation-induced emission probe for lipid droplet-specific imaging and movement tracking. Chem Commun (Camb) 2017; 53:921-924. [DOI: 10.1039/c6cc09471f] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An easily accessible aggregation-induced emission (AIE) probe is developed for LD-specific imaging and dynamic movement tracking with advantages of NIR two-photon excited red emission and fast cell permeability.
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Affiliation(s)
- Meng Gao
- State Key Laboratory of Luminescent Materials and Devices
- South China University of Technology
- Guangzhou 510640
- China
| | - Huifang Su
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction
- The Hong Kong University of Science & Technology
- Kowloon
- China
| | - Shiwu Li
- State Key Laboratory of Luminescent Materials and Devices
- South China University of Technology
- Guangzhou 510640
- China
| | - Yuhan Lin
- State Key Laboratory of Luminescent Materials and Devices
- South China University of Technology
- Guangzhou 510640
- China
| | - Xia Ling
- State Key Laboratory of Luminescent Materials and Devices
- South China University of Technology
- Guangzhou 510640
- China
| | - Anjun Qin
- State Key Laboratory of Luminescent Materials and Devices
- South China University of Technology
- Guangzhou 510640
- China
| | - Ben Zhong Tang
- State Key Laboratory of Luminescent Materials and Devices
- South China University of Technology
- Guangzhou 510640
- China
- Department of Chemistry and Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction
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16
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Gao M, Su H, Lin Y, Ling X, Li S, Qin A, Tang BZ. Photoactivatable aggregation-induced emission probes for lipid droplets-specific live cell imaging. Chem Sci 2016; 8:1763-1768. [PMID: 29780451 PMCID: PMC5933432 DOI: 10.1039/c6sc04842k] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/20/2016] [Indexed: 12/11/2022] Open
Abstract
Photoactivatable probes for lipid droplets (LDs)-specific live-cell imaging are powerful tools for investigating their biological functions through precise spatial and temporal control.
Photoactivatable probes for lipid droplets (LDs)-specific live-cell imaging are powerful tools for investigating their biological functions through precise spatial and temporal control. Ideal photoactivatable probes for LDs imaging require high concentration accumulation of fluorophores in LDs, simple synthetic procedures, and excellent photoactivation efficiency. However, it is difficult to overcome these challenges by conventional fluorophores due to aggregation-caused quenching (ACQ). In this study, a new class of photoactivatable and LDs-specific fluorescent probes was developed based on dihydro-2-azafluorenones, which can easily undergo photooxidative dehydrogenation reaction to afford 2-azafluorenones with aggregation-induced emission (AIE) properties. Dihydro-2-azafluorenones as photoactivatable and LDs-specific probes display significant advantages of excellent photoactivation efficiency and lack of self-quenching in the aggregated state, and are expected to have broad applications in study of biological functions of LDs' through light-controlled spatiotemporal imaging.
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Affiliation(s)
- Meng Gao
- Guangdong Innovative Research Team , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China .
| | - Huifang Su
- Department of Chemistry , Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , The Hong Kong University of Science & Technology , Clear Water Bay , Kowloon , Hong Kong , China .
| | - Yuhan Lin
- Guangdong Innovative Research Team , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China .
| | - Xia Ling
- Guangdong Innovative Research Team , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China .
| | - Shiwu Li
- Guangdong Innovative Research Team , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China .
| | - Anjun Qin
- Guangdong Innovative Research Team , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China .
| | - Ben Zhong Tang
- Guangdong Innovative Research Team , State Key Laboratory of Luminescent Materials & Devices , South China University of Technology , Guangzhou 510640 , China . .,Department of Chemistry , Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction , The Hong Kong University of Science & Technology , Clear Water Bay , Kowloon , Hong Kong , China .
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17
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Florian PE, Rouillé Y, Ruta S, Nichita N, Roseanu A. Recent advances in human viruses imaging studies. J Basic Microbiol 2016; 56:591-607. [DOI: 10.1002/jobm.201500575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/27/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Paula Ecaterina Florian
- Department of ; Ligand-Receptor Interactions; Institute of Biochemistry of the Romanian Academy; Bucharest Romania
| | - Yves Rouillé
- Center for Infection and Immunity of Lille (CIIL); Inserm U1019; CNRS UMR8204; Institut Pasteur de Lille; Université Lille Nord de France; Lille France
| | - Simona Ruta
- Department of Emergent Diseases; Stefan S. Nicolau Institute of Virology; Bucharest 030304 Romania
| | - Norica Nichita
- Department of Viral Glycoproteins; Institute of Biochemistry of the Romanian Academy; Bucharest Romania
| | - Anca Roseanu
- Department of ; Ligand-Receptor Interactions; Institute of Biochemistry of the Romanian Academy; Bucharest Romania
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18
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Daemen S, van Zandvoort MAMJ, Parekh SH, Hesselink MKC. Microscopy tools for the investigation of intracellular lipid storage and dynamics. Mol Metab 2015; 5:153-163. [PMID: 26977387 PMCID: PMC4770264 DOI: 10.1016/j.molmet.2015.12.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 12/19/2015] [Accepted: 12/27/2015] [Indexed: 12/01/2022] Open
Abstract
Background Excess storage of lipids in ectopic tissues, such as skeletal muscle, liver, and heart, seems to associate closely with metabolic abnormalities and cardiac disease. Intracellular lipid storage occurs in lipid droplets, which have gained attention as active organelles in cellular metabolism. Recent developments in high-resolution microscopy and microscopic spectroscopy have opened up new avenues to examine the physiology and biochemistry of intracellular lipids. Scope of review The aim of this review is to give an overview of recent technical advances in microscopy, and its application for the visualization, identification, and quantification of intracellular lipids, with special focus to lipid droplets. In addition, we attempt to summarize the probes currently available for the visualization of lipids. Major conclusions The continuous development of lipid probes in combination with the rapid development of microscopic techniques can provide new insights in the role and dynamics of intracellular lipids. Moreover, in situ identification of intracellular lipids is now possible and promises to add a new dimensionality to analysis of lipid biochemistry, and its relation to (patho)physiology.
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Key Words
- BODIPY, Boron-dipyrromethene
- CARS, coherent anti-stokes Raman scattering
- CLEM, correlative light electron microscopy
- CLSM, confocal laser scanning microscopy
- DIC, differential interference microscopy
- FA, fatty acid
- FIB-SEM, focused ion beam scanning electron microscopy
- FLIP, fluorescence loss in photobleaching
- FRAP, fluorescent recovery after photobleaching
- FRET, fluorescence resonance energy transfer
- Fluorescent lipid probes
- GFP, green fluorescent protein
- HCV, hepatitis C virus
- LD, lipid droplet
- Lipid droplets
- Live-cell imaging
- Metabolic disease
- NBD, nitro-benzoxadiazolyl
- PALM, photoactivation localization microscopy
- SBEM, serial block face scanning electron microscopy
- SIMS, Secondary Ion Mass Spectrometry
- SRS, Stimulated Raman Scattering
- STED, stimulated emission depletion
- STORM, stochastic optical reconstruction microscopy
- Super-resolution
- TAG, triacylglycerol
- TEM, transmission electron microscopy
- TOF-SIMS, time-of-flight SIMS
- TPLSM, two-photon laser scanning microscopy
- Vibrational microscopy
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Affiliation(s)
- Sabine Daemen
- Department of Human Movement Sciences and Human Biology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands.
| | - Marc A M J van Zandvoort
- Department of Genetics and Molecular Cell Biology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands; Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, Aachen, Germany.
| | - Sapun H Parekh
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz, Germany.
| | - Matthijs K C Hesselink
- Department of Human Movement Sciences and Human Biology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands.
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19
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Superresolution imaging of viral protein trafficking. Med Microbiol Immunol 2015; 204:449-60. [PMID: 25724304 DOI: 10.1007/s00430-015-0395-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/13/2015] [Indexed: 12/25/2022]
Abstract
The endoplasmic reticulum (ER) membrane is closely apposed to the outer mitochondrial membrane (OMM), which facilitates communication between these organelles. These contacts, known as mitochondria-associated membranes (MAM), facilitate calcium signaling, lipid transfer, as well as antiviral and stress responses. How cellular proteins traffic to the MAM, are distributed therein, and interact with ER and mitochondrial proteins are subject of great interest. The human cytomegalovirus UL37 exon 1 protein or viral mitochondria-localized inhibitor of apoptosis (vMIA) is crucial for viral growth. Upon synthesis at the ER, vMIA traffics to the MAM and OMM, where it reprograms the organization and function of these compartments. vMIA significantly changes the abundance of cellular proteins at the MAM and OMM, including proteins that regulate calcium homeostasis and cell death. Through the use of superresolution imaging, we have shown that vMIA is distributed at the OMM in nanometer scale clusters. This is similar to the clusters reported for the mitochondrial calcium channel, VDAC, as well as electron transport chain, translocase of the OMM complex, and mitochondrial inner membrane organizing system components. Thus, aside from addressing how vMIA targets the MAM and regulates survival of infected cells, biochemical studies and superresolution imaging of vMIA offer insights into the formation, organization, and functioning of MAM. Here, we discuss these insights into trafficking, function, and organization of vMIA at the MAM and OMM and discuss how the use of superresolution imaging is contributing to the study of the formation and trafficking of viruses.
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20
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A comprehensive functional map of the hepatitis C virus genome provides a resource for probing viral proteins. mBio 2014; 5:e01469-14. [PMID: 25271282 PMCID: PMC4196222 DOI: 10.1128/mbio.01469-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pairing high-throughput sequencing technologies with high-throughput mutagenesis enables genome-wide investigations of pathogenic organisms. Knowledge of the specific functions of protein domains encoded by the genome of the hepatitis C virus (HCV), a major human pathogen that contributes to liver disease worldwide, remains limited to insight from small-scale studies. To enhance the capabilities of HCV researchers, we have obtained a high-resolution functional map of the entire viral genome by combining transposon-based insertional mutagenesis with next-generation sequencing. We generated a library of 8,398 mutagenized HCV clones, each containing one 15-nucleotide sequence inserted at a unique genomic position. We passaged this library in hepatic cells, recovered virus pools, and simultaneously assayed the abundance of mutant viruses in each pool by next-generation sequencing. To illustrate the validity of the functional profile, we compared the genetic footprints of viral proteins with previously solved protein structures. Moreover, we show the utility of these genetic footprints in the identification of candidate regions for epitope tag insertion. In a second application, we screened the genetic footprints for phenotypes that reflected defects in later steps of the viral life cycle. We confirmed that viruses with insertions in a region of the nonstructural protein NS4B had a defect in infectivity while maintaining genome replication. Overall, our genome-wide HCV mutant library and the genetic footprints obtained by high-resolution profiling represent valuable new resources for the research community that can direct the attention of investigators toward unidentified roles of individual protein domains. Our insertional mutagenesis library provides a resource that illustrates the effects of relatively small insertions on local protein structure and HCV viability. We have also generated complementary resources, including a website (http://hangfei.bol.ucla.edu) and a panel of epitope-tagged mutant viruses that should enhance the research capabilities of investigators studying HCV. Researchers can now detect epitope-tagged viral proteins by established antibodies, which will allow biochemical studies of HCV proteins for which antibodies are not readily available. Furthermore, researchers can now quickly look up genotype-phenotype relationships and base further mechanistic studies on the residue-by-residue information from the functional profile. More broadly, this approach offers a general strategy for the systematic functional characterization of viruses on the genome scale.
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