1
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Pokorny L, Burden JJ, Albrecht D, Bamford R, Leigh KE, Sridhar P, Knowles TJ, Modis Y, Mercer J. The vaccinia chondroitin sulfate binding protein drives host membrane curvature to facilitate fusion. EMBO Rep 2024; 25:1310-1325. [PMID: 38321165 PMCID: PMC10933376 DOI: 10.1038/s44319-023-00040-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 02/08/2024] Open
Abstract
Cellular attachment of viruses determines their cell tropism and species specificity. For entry, vaccinia, the prototypic poxvirus, relies on four binding proteins and an eleven-protein entry fusion complex. The contribution of the individual virus binding proteins to virion binding orientation and membrane fusion is unclear. Here, we show that virus binding proteins guide side-on virion binding and promote curvature of the host membrane towards the virus fusion machinery to facilitate fusion. Using a membrane-bleb model system together with super-resolution and electron microscopy we find that side-bound vaccinia virions induce membrane invagination in the presence of low pH. Repression or deletion of individual binding proteins reveals that three of four contribute to binding orientation, amongst which the chondroitin sulfate binding protein, D8, is required for host membrane bending. Consistent with low-pH dependent macropinocytic entry of vaccinia, loss of D8 prevents virion-associated macropinosome membrane bending, disrupts fusion pore formation and infection. Our results show that viral binding proteins are active participants in successful virus membrane fusion and illustrate the importance of virus protein architecture for successful infection.
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Affiliation(s)
- Laura Pokorny
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- MRC-LMCB, University College London, London, WC1E 6BT, UK
| | - Jemima J Burden
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - David Albrecht
- MRC-LMCB, University College London, London, WC1E 6BT, UK
| | - Rebecca Bamford
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- MRC-LMCB, University College London, London, WC1E 6BT, UK
| | - Kendra E Leigh
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy J Knowles
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Jason Mercer
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
- MRC-LMCB, University College London, London, WC1E 6BT, UK.
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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; 14:2597. [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
| | - 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
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3
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Mendes A, Heil HS, Coelho S, Leterrier C, Henriques R. Mapping molecular complexes with super-resolution microscopy and single-particle analysis. Open Biol 2022; 12:220079. [PMID: 35892200 PMCID: PMC9326279 DOI: 10.1098/rsob.220079] [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] [Indexed: 12/25/2022] Open
Abstract
Understanding the structure of supramolecular complexes provides insight into their functional capabilities and how they can be modulated in the context of disease. Super-resolution microscopy (SRM) excels in performing this task by resolving ultrastructural details at the nanoscale with molecular specificity. However, technical limitations, such as underlabelling, preclude its ability to provide complete structures. Single-particle analysis (SPA) overcomes this limitation by combining information from multiple images of identical structures and producing an averaged model, effectively enhancing the resolution and coverage of image reconstructions. This review highlights important studies using SRM-SPA, demonstrating how it broadens our knowledge by elucidating features of key biological structures with unprecedented detail.
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Affiliation(s)
| | | | - Simao Coelho
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras, Portugal,MRC Laboratory for Molecular Cell Biology, University College London, London, UK
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4
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Bidgood SR, Samolej J, Novy K, Collopy A, Albrecht D, Krause M, Burden JJ, Wollscheid B, Mercer J. Poxviruses package viral redox proteins in lateral bodies and modulate the host oxidative response. PLoS Pathog 2022; 18:e1010614. [PMID: 35834477 PMCID: PMC9282662 DOI: 10.1371/journal.ppat.1010614] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 05/24/2022] [Indexed: 01/23/2023] Open
Abstract
All poxviruses contain a set of proteinaceous structures termed lateral bodies (LB) that deliver viral effector proteins into the host cytosol during virus entry. To date, the spatial proteotype of LBs remains unknown. Using the prototypic poxvirus, vaccinia virus (VACV), we employed a quantitative comparative mass spectrometry strategy to determine the poxvirus LB proteome. We identified a large population of candidate cellular proteins, the majority being mitochondrial, and 15 candidate viral LB proteins. Strikingly, one-third of these are VACV redox proteins whose LB residency could be confirmed using super-resolution microscopy. We show that VACV infection exerts an anti-oxidative effect on host cells and that artificial induction of oxidative stress impacts early and late gene expression as well as virion production. Using targeted repression and/or deletion viruses we found that deletion of individual LB-redox proteins was insufficient for host redox modulation suggesting there may be functional redundancy. In addition to defining the spatial proteotype of VACV LBs, these findings implicate poxvirus redox proteins as potential modulators of host oxidative anti-viral responses and provide a solid starting point for future investigations into the role of LB resident proteins in host immunomodulation.
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Affiliation(s)
- Susanna R. Bidgood
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Jerzy Samolej
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Karel Novy
- Swiss Federal Institute of Technology (ETH Zürich), Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), Zürich, Switzerland
| | - Abigail Collopy
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - David Albrecht
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Melanie Krause
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Jemima J. Burden
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Bernd Wollscheid
- Swiss Federal Institute of Technology (ETH Zürich), Department of Health Sciences and Technology (D-HEST), Institute of Translational Medicine (ITM), Zürich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Jason Mercer
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
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5
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Wang W, Heydarian H, Huijben TAPM, Stallinga S, Rieger B. Joint registration of multiple point clouds for fast particle fusion in localization microscopy. Bioinformatics 2022; 38:3281-3287. [PMID: 35552632 PMCID: PMC9191212 DOI: 10.1093/bioinformatics/btac320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/22/2022] [Accepted: 05/09/2022] [Indexed: 11/14/2022] Open
Abstract
SUMMARY We present a fast particle fusion method for particles imaged with single-molecule localization microscopy. The state-of-the-art approach based on all-to-all registration has proven to work well but its computational cost scales unfavorably with the number of particles N, namely as N2. Our method overcomes this problem and achieves a linear scaling of computational cost with N by making use of the Joint Registration of Multiple Point Clouds (JRMPC) method. Straightforward application of JRMPC fails as mostly locally optimal solutions are found. These usually contain several overlapping clusters that each consist of well-aligned particles, but that have different poses. We solve this issue by repeated runs of JRMPC for different initial conditions, followed by a classification step to identify the clusters, and a connection step to link the different clusters obtained for different initializations. In this way a single well-aligned structure is obtained containing the majority of the particles. RESULTS We achieve reconstructions of experimental DNA-origami datasets consisting of close to 400 particles within only 10 min on a CPU, with an image resolution of 3.2 nm. In addition, we show artifact-free reconstructions of symmetric structures without making any use of the symmetry. We also demonstrate that the method works well for poor data with a low density of labeling and for 3D data. AVAILABILITY AND IMPLEMENTATION The code is available for download from https://github.com/wexw/Joint-Registration-of-Multiple-Point-Clouds-for-Fast-Particle-Fusion-in-Localization-Microscopy. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wenxiu Wang
- Department of Imaging Physics, Delft University of Technology, Delft 2628CJ, The Netherlands
| | - Hamidreza Heydarian
- Department of Imaging Physics, Delft University of Technology, Delft 2628CJ, The Netherlands
| | - Teun A P M Huijben
- Department of Imaging Physics, Delft University of Technology, Delft 2628CJ, The Netherlands
| | - Sjoerd Stallinga
- Department of Imaging Physics, Delft University of Technology, Delft 2628CJ, The Netherlands
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft 2628CJ, The Netherlands
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6
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Robb NC. Virus morphology: Insights from super-resolution fluorescence microscopy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166347. [PMID: 35032594 PMCID: PMC8755447 DOI: 10.1016/j.bbadis.2022.166347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 01/06/2023]
Abstract
As epitomised by the COVID-19 pandemic, diseases caused by viruses are one of the greatest health and economic burdens to human society. Viruses are 'nanostructures', and their small size (typically less than 200 nm in diameter) can make it challenging to obtain images of their morphology and structure. Recent advances in fluorescence microscopy have given rise to super-resolution techniques, which have enabled the structure of viruses to be visualised directly at a resolution in the order of 20 nm. This mini-review discusses how recent state-of-the-art super-resolution imaging technologies are providing new nanoscale insights into virus structure.
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Affiliation(s)
- Nicole C Robb
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom.
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7
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Yakimovich A. Artificial Intelligence in Infection Biology. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Yakimovich A. Machine Learning and Artificial Intelligence for the Prediction of Host-Pathogen Interactions: A Viral Case. Infect Drug Resist 2021; 14:3319-3326. [PMID: 34456575 PMCID: PMC8385421 DOI: 10.2147/idr.s292743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/03/2021] [Indexed: 01/27/2023] Open
Abstract
The research of interactions between the pathogens and their hosts is key for understanding the biology of infection. Commencing on the level of individual molecules, these interactions define the behavior of infectious agents and the outcomes they elicit. Discovery of host-pathogen interactions (HPIs) conventionally involves a stepwise laborious research process. Yet, amid the global pandemic the urge for rapid discovery acceleration through the novel computational methodologies has become ever so poignant. This review explores the challenges of HPI discovery and investigates the efforts currently undertaken to apply the latest machine learning (ML) and artificial intelligence (AI) methodologies to this field. This includes applications to molecular and genetic data, as well as image and language data. Furthermore, a number of breakthroughs, obstacles, along with prospects of AI for host-pathogen interactions (HPI), are discussed.
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9
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Huijben TAPM, Heydarian H, Auer A, Schueder F, Jungmann R, Stallinga S, Rieger B. Detecting structural heterogeneity in single-molecule localization microscopy data. Nat Commun 2021; 12:3791. [PMID: 34145284 PMCID: PMC8213809 DOI: 10.1038/s41467-021-24106-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/02/2021] [Indexed: 11/28/2022] Open
Abstract
Particle fusion for single molecule localization microscopy improves signal-to-noise ratio and overcomes underlabeling, but ignores structural heterogeneity or conformational variability. We present a-priori knowledge-free unsupervised classification of structurally different particles employing the Bhattacharya cost function as dissimilarity metric. We achieve 96% classification accuracy on mixtures of up to four different DNA-origami structures, detect rare classes of origami occuring at 2% rate, and capture variation in ellipticity of nuclear pore complexes.
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Affiliation(s)
- Teun A P M Huijben
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Hamidreza Heydarian
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Alexander Auer
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sjoerd Stallinga
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands.
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10
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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: 13] [Impact Index Per Article: 4.3] [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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11
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Touizer E, Sieben C, Henriques R, Marsh M, Laine RF. Application of Super-Resolution and Advanced Quantitative Microscopy to the Spatio-Temporal Analysis of Influenza Virus Replication. Viruses 2021; 13:233. [PMID: 33540739 PMCID: PMC7912985 DOI: 10.3390/v13020233] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 02/07/2023] Open
Abstract
With an estimated three to five million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society, and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance, how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated, providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are providing new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.
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Affiliation(s)
- Emma Touizer
- Division of Infection and Immunity, University College London, London WC1E 6AE, UK;
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Christian Sieben
- Department of Cell Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (R.H.); (M.M.)
- The Francis Crick Institute, London NW1 1AT, UK
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12
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Yakimovich A. Artificial Intelligence in Infection Biology. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_105-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Groves NS, Bruns MM, van Engelenburg SB. A Quantitative Live-Cell Superresolution Imaging Framework for Measuring the Mobility of Single Molecules at Sites of Virus Assembly. Pathogens 2020; 9:pathogens9110972. [PMID: 33233482 PMCID: PMC7700196 DOI: 10.3390/pathogens9110972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
The insurgence of superresolution microscopy into the fields of virology and microbiology has begun to enable the mapping of molecular assemblies critical for host–pathogen interfaces that organize on a scale below the resolution limit of the light microscope. It is, however, challenging to completely understand the molecular interactions between host and pathogen from strictly time-invariant observations. Herein, we describe a method using simultaneous dual-color superresolution microscopy to gain both structural and dynamic information about HIV-1 assembly. Specifically, we demonstrate the reconstruction of single virus assembly sites using live-cell photo-activated localization microscopy (PALM) while concurrently assessing the sub-viral mobility of the HIV-1 envelope glycoprotein during interaction with the viral lattice. We propose that our method is broadly applicable to elucidating pathogen and host protein–protein interactions through quantification of the dynamics of these proteins at the nanoscale.
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14
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Gray RDM, Albrecht D, Beerli C, Huttunen M, Cohen GH, White IJ, Burden JJ, Henriques R, Mercer J. Nanoscale polarization of the entry fusion complex of vaccinia virus drives efficient fusion. Nat Microbiol 2019; 4:1636-1644. [PMID: 31285583 DOI: 10.1038/s41564-019-0488-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 05/14/2019] [Indexed: 01/29/2023]
Abstract
To achieve efficient binding and subsequent fusion, most enveloped viruses encode between one and five proteins1. For many viruses, the clustering of fusion proteins-and their distribution on virus particles-is crucial for fusion activity2,3. Poxviruses, the most complex mammalian viruses, dedicate 15 proteins to binding and membrane fusion4. However, the spatial organization of these proteins and how this influences fusion activity is unknown. Here, we show that the membrane of vaccinia virus is organized into distinct functional domains that are critical for the efficiency of membrane fusion. Using super-resolution microscopy and single-particle analysis, we found that the fusion machinery of vaccinia virus resides exclusively in clusters at virion tips. Repression of individual components of the fusion complex disrupts fusion-machinery polarization, consistent with the reported loss of fusion activity5. Furthermore, we show that displacement of functional fusion complexes from virion tips disrupts the formation of fusion pores and infection kinetics. Our results demonstrate how the protein architecture of poxviruses directly contributes to the efficiency of membrane fusion, and suggest that nanoscale organization may be an intrinsic property of these viruses to assure successful infection.
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Affiliation(s)
- Robert D M Gray
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
- CoMPLEX, University College London, London, UK
| | - David Albrecht
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Corina Beerli
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Moona Huttunen
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Gary H Cohen
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian J White
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Jemima J Burden
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
- Department of Cell and Developmental Biology, University College London, London, UK.
| | - Jason Mercer
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
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15
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Abstract
Artur Yakimovich works in the field of computational virology and applies machine learning algorithms to study host-pathogen interactions. In this mSphere of Influence article, he reflects on two papers “Holographic Deep Learning for Rapid Optical Screening of Anthrax Spores” by Jo et al. (Y. Jo, S. Park, J. Jung, J. Artur Yakimovich works in the field of computational virology and applies machine learning algorithms to study host-pathogen interactions. In this mSphere of Influence article, he reflects on two papers “Holographic Deep Learning for Rapid Optical Screening of Anthrax Spores” by Jo et al. (Y. Jo, S. Park, J. Jung, J. Yoon, et al., Sci Adv 3:e1700606, 2017, https://doi.org/10.1126/sciadv.1700606) and “Bacterial Colony Counting with Convolutional Neural Networks in Digital Microbiology Imaging” by Ferrari and colleagues (A. Ferrari, S. Lombardi, and A. Signoroni, Pattern Recognition 61:629–640, 2017, https://doi.org/10.1016/j.patcog.2016.07.016). Here he discusses how these papers made an impact on him by showcasing that artificial intelligence algorithms can be equally applicable to both classical infection biology techniques and cutting-edge label-free imaging of pathogens.
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16
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Krokowski S, Atwal S, Lobato-Márquez D, Chastanet A, Carballido-López R, Salje J, Mostowy S. Shigella MreB promotes polar IcsA positioning for actin tail formation. J Cell Sci 2019; 132:jcs.226217. [PMID: 30992346 PMCID: PMC6526709 DOI: 10.1242/jcs.226217] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/01/2019] [Indexed: 01/17/2023] Open
Abstract
Pathogenic Shigella bacteria are a paradigm to address key issues of cell and infection biology. Polar localisation of the Shigella autotransporter protein IcsA is essential for actin tail formation, which is necessary for the bacterium to travel from cell-to-cell; yet how proteins are targeted to the bacterial cell pole is poorly understood. The bacterial actin homologue MreB has been extensively studied in broth culture using model organisms including Escherichia coli, Bacillus subtilis and Caulobacter crescentus, but has never been visualised in rod-shaped pathogenic bacteria during infection of host cells. Here, using single-cell analysis of intracellular Shigella, we discover that MreB accumulates at the cell pole of bacteria forming actin tails, where it colocalises with IcsA. Pharmacological inhibition of host cell actin polymerisation and genetic deletion of IcsA is used to show, respectively, that localisation of MreB to the cell poles precedes actin tail formation and polar localisation of IcsA. Finally, by exploiting the MreB inhibitors A22 and MP265, we demonstrate that MreB polymerisation can support actin tail formation. We conclude that Shigella MreB promotes polar IcsA positioning for actin tail formation, and suggest that understanding the bacterial cytoskeleton during host–pathogen interactions can inspire development of new therapeutic regimes for infection control. This article has an associated First Person interview with the first author of the paper. Summary: The pathogen Shigella forms actin tails to move through the cytosol of infected cells. We show that the bacterial actin homologue MreB can help to position the autotransporter protein IcsA for such actin tail formation.
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Affiliation(s)
- Sina Krokowski
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK.,Department of Immunology & Infection, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Sharanjeet Atwal
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7JT, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400 PHRI 07103, Thailand.,Public Health Research Institute, Rutgers Biomedical and Health Science, Newark, New Jersey NJ 07103, USA
| | - Damián Lobato-Márquez
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK.,Department of Immunology & Infection, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Arnaud Chastanet
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Rut Carballido-López
- MICALIS Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jeanne Salje
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7JT, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400 PHRI 07103, Thailand.,Public Health Research Institute, Rutgers Biomedical and Health Science, Newark, New Jersey NJ 07103, USA
| | - Serge Mostowy
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK .,Department of Immunology & Infection, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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17
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Laine RF, Tosheva KL, Gustafsson N, Gray RDM, Almada P, Albrecht D, Risa GT, Hurtig F, Lindås AC, Baum B, Mercer J, Leterrier C, Pereira PM, Culley S, Henriques R. NanoJ: a high-performance open-source super-resolution microscopy toolbox. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2019; 52:163001. [PMID: 33191949 PMCID: PMC7655149 DOI: 10.1088/1361-6463/ab0261] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 01/09/2019] [Accepted: 01/28/2019] [Indexed: 05/18/2023]
Abstract
Super-resolution microscopy (SRM) has become essential for the study of nanoscale biological processes. This type of imaging often requires the use of specialised image analysis tools to process a large volume of recorded data and extract quantitative information. In recent years, our team has built an open-source image analysis framework for SRM designed to combine high performance and ease of use. We named it NanoJ-a reference to the popular ImageJ software it was developed for. In this paper, we highlight the current capabilities of NanoJ for several essential processing steps: spatio-temporal alignment of raw data (NanoJ-Core), super-resolution image reconstruction (NanoJ-SRRF), image quality assessment (NanoJ-SQUIRREL), structural modelling (NanoJ-VirusMapper) and control of the sample environment (NanoJ-Fluidics). We expect to expand NanoJ in the future through the development of new tools designed to improve quantitative data analysis and measure the reliability of fluorescent microscopy studies.
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Affiliation(s)
- Romain F Laine
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Kalina L Tosheva
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Nils Gustafsson
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- Centre for Mathematics and Physics in Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United Kingdom
| | - Robert D M Gray
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- Centre for Mathematics and Physics in Life Sciences and Experimental Biology (CoMPLEX), University College London, London, United Kingdom
| | - Pedro Almada
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - David Albrecht
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Gabriel T Risa
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Fredrik Hurtig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Jason Mercer
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Christophe Leterrier
- CNRS, INP, Institute of Neurophysiopathology, NeuroCyto, Aix-Marseille University, Marseille, France
| | - Pedro M Pereira
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
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18
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Almada P, Pereira PM, Culley S, Caillol G, Boroni-Rueda F, Dix CL, Charras G, Baum B, Laine RF, Leterrier C, Henriques R. Automating multimodal microscopy with NanoJ-Fluidics. Nat Commun 2019. [PMID: 30874553 DOI: 10.1101/320416] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows. Here, we present a robust, open-source approach for treating, labelling and imaging live or fixed cells in automated sequences. NanoJ-Fluidics is based on low-cost Lego hardware controlled by ImageJ-based software, making high-content, multimodal imaging easy to implement on any microscope with high reproducibility. We demonstrate its capacity on event-driven, super-resolved live-to-fixed and multiplexed STORM/DNA-PAINT experiments.
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Affiliation(s)
- Pedro Almada
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Pedro M Pereira
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Ghislaine Caillol
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, 13015, France
| | - Fanny Boroni-Rueda
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, 13015, France
| | - Christina L Dix
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
| | - Guillaume Charras
- London Centre for Nanotechnology, London, WC1H 0AH, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
| | - Romain F Laine
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
- The Francis Crick Institute, London, NW1 1AT, UK.
| | - Christophe Leterrier
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, 13015, France.
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
- The Francis Crick Institute, London, NW1 1AT, UK.
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19
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Almada P, Pereira PM, Culley S, Caillol G, Boroni-Rueda F, Dix CL, Charras G, Baum B, Laine RF, Leterrier C, Henriques R. Automating multimodal microscopy with NanoJ-Fluidics. Nat Commun 2019; 10:1223. [PMID: 30874553 PMCID: PMC6420627 DOI: 10.1038/s41467-019-09231-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 02/26/2019] [Indexed: 12/19/2022] Open
Abstract
Combining and multiplexing microscopy approaches is crucial to understand cellular events, but requires elaborate workflows. Here, we present a robust, open-source approach for treating, labelling and imaging live or fixed cells in automated sequences. NanoJ-Fluidics is based on low-cost Lego hardware controlled by ImageJ-based software, making high-content, multimodal imaging easy to implement on any microscope with high reproducibility. We demonstrate its capacity on event-driven, super-resolved live-to-fixed and multiplexed STORM/DNA-PAINT experiments.
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Affiliation(s)
- Pedro Almada
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Pedro M Pereira
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Ghislaine Caillol
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, 13015, France
| | - Fanny Boroni-Rueda
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, 13015, France
| | - Christina L Dix
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
| | - Guillaume Charras
- London Centre for Nanotechnology, London, WC1H 0AH, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
| | - Romain F Laine
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
- The Francis Crick Institute, London, NW1 1AT, UK.
| | - Christophe Leterrier
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, 13015, France.
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK.
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
- The Francis Crick Institute, London, NW1 1AT, UK.
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20
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Abstract
The eradication of smallpox is one of the greatest medical successes in history. Vaccinia virus was made famous by being the virus used in the live vaccine that enabled this feat. Nearly 40 years on from that success, this prototypical poxvirus continues to empower the exploration of fundamental biology and the potential to develop therapeutics against some of the major causes of death and disease in the modern world.
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Affiliation(s)
- Susanna R. Bidgood
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- * E-mail:
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21
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Müller TG, Sakin V, Müller B. A Spotlight on Viruses-Application of Click Chemistry to Visualize Virus-Cell Interactions. Molecules 2019; 24:molecules24030481. [PMID: 30700005 PMCID: PMC6385038 DOI: 10.3390/molecules24030481] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 01/03/2023] Open
Abstract
The replication of a virus within its host cell involves numerous interactions between viral and cellular factors, which have to be tightly controlled in space and time. The intricate interplay between viral exploitation of cellular pathways and the intrinsic host defense mechanisms is difficult to unravel by traditional bulk approaches. In recent years, novel fluorescence microscopy techniques and single virus tracking have transformed the investigation of dynamic virus-host interactions. A prerequisite for the application of these imaging-based methods is the attachment of a fluorescent label to the structure of interest. However, their small size, limited coding capacity and multifunctional proteins render viruses particularly challenging targets for fluorescent labeling approaches. Click chemistry in conjunction with genetic code expansion provides virologists with a novel toolbox for site-specific, minimally invasive labeling of virion components, whose potential has just recently begun to be exploited. Here, we summarize recent achievements, current developments and future challenges for the labeling of viral nucleic acids, proteins, glycoproteins or lipids using click chemistry in order to study dynamic processes in virus-cell interactions.
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Affiliation(s)
- Thorsten G Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Volkan Sakin
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany.
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22
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Abstract
Super-resolution microscopy enables the study of vaccinia architecture at subviral resolution with molecular specificity. Here, we outline how to use structured illumination microscopy (SIM) and stochastic optical reconstruction microscopy (STORM) to detect fluorescently tagged or immunolabeled viral proteins on purified virions. Tens to hundreds of individual virions can be imaged in a single field of view providing data for single-particle averaging or quantitative analysis of viral protein spatial organization.
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Affiliation(s)
- Robert Gray
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
| | - David Albrecht
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
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23
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Marzook NB, Newsome TP. Construction and Isolation of Recombinant Vaccinia Virus Expressing Fluorescent Proteins. Methods Mol Biol 2019; 2023:73-92. [PMID: 31240671 DOI: 10.1007/978-1-4939-9593-6_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Vaccinia virus recombinants that express fluorescent proteins have a variety of applications such as the identification of infected cells, efficient screening for genetically modified strains, and molecular characterization of virus replication and spread. The detection of fluorescent proteins and viral-fluorescent fusion proteins by fluorescence microscopy is noninvasive and can be used to describe protein localization in live cells and track the intracellular movement of virus particles. This chapter describes a number of approaches for the construction of plasmids and subsequent generation and isolation of fluorescent recombinant viruses.
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Affiliation(s)
- N Bishara Marzook
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia
| | - Timothy P Newsome
- The University of Sydney, School of Life and Environmental Sciences, Sydney, NSW, Australia.
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24
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Krokowski S, Lobato-Márquez D, Chastanet A, Pereira PM, Angelis D, Galea D, Larrouy-Maumus G, Henriques R, Spiliotis ET, Carballido-López R, Mostowy S. Septins Recognize and Entrap Dividing Bacterial Cells for Delivery to Lysosomes. Cell Host Microbe 2018; 24:866-874.e4. [PMID: 30543779 PMCID: PMC6299245 DOI: 10.1016/j.chom.2018.11.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 08/14/2018] [Accepted: 11/05/2018] [Indexed: 12/31/2022]
Abstract
The cytoskeleton occupies a central role in cellular immunity by promoting bacterial sensing and antibacterial functions. Septins are cytoskeletal proteins implicated in various cellular processes, including cell division. Septins also assemble into cage-like structures that entrap cytosolic Shigella, yet how septins recognize bacteria is poorly understood. Here, we discover that septins are recruited to regions of micron-scale membrane curvature upon invasion and division by a variety of bacterial species. Cardiolipin, a curvature-specific phospholipid, promotes septin recruitment to highly curved membranes of Shigella, and bacterial mutants lacking cardiolipin exhibit less septin cage entrapment. Chemically inhibiting cell separation to prolong membrane curvature or reducing Shigella cell growth respectively increases and decreases septin cage formation. Once formed, septin cages inhibit Shigella cell division upon recruitment of autophagic and lysosomal machinery. Thus, recognition of dividing bacterial cells by the septin cytoskeleton is a powerful mechanism to restrict the proliferation of intracellular bacterial pathogens.
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Affiliation(s)
- Sina Krokowski
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; Department of Immunology & Infection, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Damián Lobato-Márquez
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; Department of Immunology & Infection, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Arnaud Chastanet
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas 78350, France
| | - Pedro Matos Pereira
- Quantitative Imaging and NanoBiophysics Group, MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Dimitrios Angelis
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Dieter Galea
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Gerald Larrouy-Maumus
- Faculty of Natural Sciences, Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Ricardo Henriques
- Quantitative Imaging and NanoBiophysics Group, MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Elias T Spiliotis
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Rut Carballido-López
- MICALIS, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas 78350, France
| | - Serge Mostowy
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK; Department of Immunology & Infection, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK.
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25
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Combined expansion microscopy with structured illumination microscopy for analyzing protein complexes. Nat Protoc 2018; 13:1869-1895. [PMID: 30072723 DOI: 10.1038/s41596-018-0023-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 05/09/2018] [Indexed: 12/19/2022]
Abstract
Biologists have long been fascinated with the organization and function of intricate protein complexes. Therefore, techniques for precisely imaging protein complexes and the location of proteins within these complexes are critically important and often require multidisciplinary collaboration. A challenge in these explorations is the limited resolution of conventional light microscopy. However, a new microscopic technique has circumvented this resolution limit by making the biological sample larger, thus allowing for super-resolution of the enlarged structure. This 'expansion' is accomplished by embedding the sample in a hydrogel that, when exposed to water, uniformly expands. Here, we present a protocol that transforms thick expansion microscopy (ExM) hydrogels into sections that are physically expanded four times, creating samples that are compatible with the super-resolution technique structured illumination microscopy (SIM). This super-resolution ExM method (ExM-SIM) allows the analysis of the three-dimensional (3D) organization of multiprotein complexes at ~30-nm lateral (xy) resolution. This protocol details the steps necessary for analysis of protein localization using ExM-SIM, including antibody labeling, hydrogel preparation, protease digestion, post-digestion antibody labeling, hydrogel embedding with tissue-freezing medium (TFM), cryosectioning, expansion, image alignment, and particle averaging. We have used this approach for 3D mapping of in situ protein localization in the Drosophila synaptonemal complex (SC), but it can be readily adapted to study thick tissues such as brain and organs in various model systems. This procedure can be completed in 5 d.
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26
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Lynn H, Howell LM, Diefenbach RJ, Newsome TP. Phototracking Vaccinia Virus Transport Reveals Dynamics of Cytoplasmic Dispersal and a Requirement for A36R and F12L for Exit from the Site of Wrapping. Viruses 2018; 10:v10080390. [PMID: 30042325 PMCID: PMC6115981 DOI: 10.3390/v10080390] [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: 06/29/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 11/16/2022] Open
Abstract
The microtubule cytoskeleton is a primary organizer of viral infections for delivering virus particles to their sites of replication, establishing and maintaining subcellular compartments where distinct steps of viral morphogenesis take place, and ultimately dispersing viral progeny. One of the best characterized examples of virus motility is the anterograde transport of the wrapped virus form of vaccinia virus (VACV) from the trans-Golgi network (TGN) to the cell periphery by kinesin-1. Yet many aspects of this transport event are elusive due to the speed of motility and the challenges of imaging this stage at high resolution over extended time periods. We have established a novel imaging technology to track virus transport that uses photoconvertible fluorescent recombinant viruses to track subsets of virus particles from their site of origin and determine their destination. Here we image virus exit from the TGN and their rate of egress to the cell periphery. We demonstrate a role for kinesin-1 engagement in regulating virus exit from the TGN by removing A36 and F12 function, critical viral mediators of kinesin-1 recruitment to virus particles. Phototracking viral particles and components during infection is a powerful new imaging approach to elucidate mechanisms of virus replication.
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Affiliation(s)
- Helena Lynn
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Liam M Howell
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Russell J Diefenbach
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Timothy P Newsome
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
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27
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Banerjee S, Maurya S, Roy R. Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018; 43:519-540. [PMID: 30002270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule fluorescence methods remain a challenging yet information-rich set of techniques that allow one to probe the dynamics, stoichiometry and conformation of biomolecules one molecule at a time. Viruses are small (nanometers) in size, can achieve cellular infections with a small number of virions and their lifecycle is inherently heterogeneous with a large number of structural and functional intermediates. Single-molecule measurements that reveal the complete distribution of properties rather than the average can hence reveal new insights into virus infections and biology that are inaccessible otherwise. This article highlights some of the methods and recent applications of single-molecule fluorescence in the field of virology. Here, we have focused on new findings in virus-cell interaction, virus cell entry and transport, viral membrane fusion, genome release, replication, translation, assembly, genome packaging, egress and interaction with host immune proteins that underline the advantage of single-molecule approach to the question at hand. Finally, we discuss the challenges, outlook and potential areas for improvement and future use of single-molecule fluorescence that could further aid our understanding of viruses.
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Affiliation(s)
- Sunaina Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
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28
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Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018. [DOI: 10.1007/s12038-018-9769-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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29
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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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Witte R, Andriasyan V, Georgi F, Yakimovich A, Greber UF. Concepts in Light Microscopy of Viruses. Viruses 2018; 10:E202. [PMID: 29670029 PMCID: PMC5923496 DOI: 10.3390/v10040202] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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Affiliation(s)
- Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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Sieben C, Douglass KM, Guichard P, Manley S. Super-resolution microscopy to decipher multi-molecular assemblies. Curr Opin Struct Biol 2018; 49:169-176. [DOI: 10.1016/j.sbi.2018.03.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/16/2018] [Accepted: 03/17/2018] [Indexed: 12/12/2022]
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32
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Imaging, Tracking and Computational Analyses of Virus Entry and Egress with the Cytoskeleton. Viruses 2018; 10:v10040166. [PMID: 29614729 PMCID: PMC5923460 DOI: 10.3390/v10040166] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/27/2018] [Accepted: 03/28/2018] [Indexed: 12/27/2022] Open
Abstract
Viruses have a dual nature: particles are “passive substances” lacking chemical energy transformation, whereas infected cells are “active substances” turning-over energy. How passive viral substances convert to active substances, comprising viral replication and assembly compartments has been of intense interest to virologists, cell and molecular biologists and immunologists. Infection starts with virus entry into a susceptible cell and delivers the viral genome to the replication site. This is a multi-step process, and involves the cytoskeleton and associated motor proteins. Likewise, the egress of progeny virus particles from the replication site to the extracellular space is enhanced by the cytoskeleton and associated motor proteins. This overcomes the limitation of thermal diffusion, and transports virions and virion components, often in association with cellular organelles. This review explores how the analysis of viral trajectories informs about mechanisms of infection. We discuss the methodology enabling researchers to visualize single virions in cells by fluorescence imaging and tracking. Virus visualization and tracking are increasingly enhanced by computational analyses of virus trajectories as well as in silico modeling. Combined approaches reveal previously unrecognized features of virus-infected cells. Using select examples of complementary methodology, we highlight the role of actin filaments and microtubules, and their associated motors in virus infections. In-depth studies of single virion dynamics at high temporal and spatial resolutions thereby provide deep insight into virus infection processes, and are a basis for uncovering underlying mechanisms of how cells function.
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Laine RF, Goodfellow G, Young LJ, Travers J, Carroll D, Dibben O, Bright H, Kaminski CF. Structured illumination microscopy combined with machine learning enables the high throughput analysis and classification of virus structure. eLife 2018; 7:40183. [PMID: 30543181 PMCID: PMC6331195 DOI: 10.7554/elife.40183] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/10/2018] [Indexed: 02/02/2023] Open
Abstract
Optical super-resolution microscopy techniques enable high molecular specificity with high spatial resolution and constitute a set of powerful tools in the investigation of the structure of supramolecular assemblies such as viruses. Here, we report on a new methodology which combines Structured Illumination Microscopy (SIM) with machine learning algorithms to image and classify the structure of large populations of biopharmaceutical viruses with high resolution. The method offers information on virus morphology that can ultimately be linked with functional performance. We demonstrate the approach on viruses produced for oncolytic viriotherapy (Newcastle Disease Virus) and vaccine development (Influenza). This unique tool enables the rapid assessment of the quality of viral production with high throughput obviating the need for traditional batch testing methods which are complex and time consuming. We show that our method also works on non-purified samples from pooled harvest fluids directly from the production line.
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Affiliation(s)
- Romain F Laine
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Gemma Goodfellow
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | - Laurence J Young
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
| | | | | | | | | | - Clemens F Kaminski
- Department of Chemical Engineering and BiotechnologyUniversity of CambridgeCambridgeUnited Kingdom
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Joensuu M, Martínez-Mármol R, Padmanabhan P, Glass NR, Durisic N, Pelekanos M, Mollazade M, Balistreri G, Amor R, Cooper-White JJ, Goodhill GJ, Meunier FA. Visualizing endocytic recycling and trafficking in live neurons by subdiffractional tracking of internalized molecules. Nat Protoc 2017; 12:2590-2622. [PMID: 29189775 DOI: 10.1038/nprot.2017.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Our understanding of endocytic pathway dynamics is restricted by the diffraction limit of light microscopy. Although super-resolution techniques can overcome this issue, highly crowded cellular environments, such as nerve terminals, can also dramatically limit the tracking of multiple endocytic vesicles such as synaptic vesicles (SVs), which in turn restricts the analytical dissection of their discrete diffusional and transport states. We recently introduced a pulse-chase technique for subdiffractional tracking of internalized molecules (sdTIM) that allows the visualization of fluorescently tagged molecules trapped in individual signaling endosomes and SVs in presynapses or axons with 30- to 50-nm localization precision. We originally developed this approach for tracking single molecules of botulinum neurotoxin type A, which undergoes activity-dependent internalization and retrograde transport in autophagosomes. This method was then adapted to localize the signaling endosomes containing cholera toxin subunit-B that undergo retrograde transport in axons and to track SVs in the crowded environment of hippocampal presynapses. We describe (i) the construction of a custom-made microfluidic device that enables control over neuronal orientation; (ii) the 3D printing of a perfusion system for sdTIM experiments performed on glass-bottom dishes; (iii) the dissection, culturing and transfection of hippocampal neurons in microfluidic devices; and (iv) guidance on how to perform the pulse-chase experiments and data analysis. In addition, we describe the use of single-molecule-tracking analytical tools to reveal the average and the heterogeneous single-molecule mobility behaviors. We also discuss alternative reagents and equipment that can, in principle, be used for sdTIM experiments and describe how to adapt sdTIM to image nanocluster formation and/or tubulation in early endosomes during sorting events. The procedures described in this protocol take ∼1 week.
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Affiliation(s)
- Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ramon Martínez-Mármol
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Pranesh Padmanabhan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Nick R Glass
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Nela Durisic
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew Pelekanos
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Mahdie Mollazade
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giuseppe Balistreri
- Division of General Microbiology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Rumelo Amor
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Justin J Cooper-White
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.,Division of General Microbiology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,School of Chemical Engineering, The University of Queensland, Brisbane, Queensland, Australia.,Materials Science and Engineering Division, CSIRO, Clayton, Victoria, Australia.,UQ Centre for Stem Cell Ageing and Regenerative Engineering, The University of Queensland, Brisbane, Queensland, Australia
| | - Geoffrey J Goodhill
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
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35
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Gray RDM, Mercer J, Henriques R. Open-source Single-particle Analysis for Super-resolution Microscopy with VirusMapper. J Vis Exp 2017. [PMID: 28448005 PMCID: PMC5564481 DOI: 10.3791/55471] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Super-resolution fluorescence microscopy is currently revolutionizing cell biology research. Its capacity to break the resolution limit of around 300 nm allows for the routine imaging of nanoscale biological complexes and processes. This increase in resolution also means that methods popular in electron microscopy, such as single-particle analysis, can readily be applied to super-resolution fluorescence microscopy. By combining this analytical approach with super-resolution optical imaging, it becomes possible to take advantage of the molecule-specific labeling capacity of fluorescence microscopy to generate structural maps of molecular elements within a metastable structure. To this end, we have developed a novel algorithm — VirusMapper — packaged as an easy-to-use, high-performance, and high-throughput ImageJ plugin. This article presents an in-depth guide to this software, showcasing its ability to uncover novel structural features in biological molecular complexes. Here, we present how to assemble compatible data and provide a step-by-step protocol on how to use this algorithm to apply single-particle analysis to super-resolution images.
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Affiliation(s)
- Robert D M Gray
- MRC Laboratory for Molecular Cell Biology, University College London; Centre for Mathematics and Physics in Life Sciences and Experimental Biology (CoMPLEX), University College London
| | - Jason Mercer
- MRC Laboratory for Molecular Cell Biology, University College London;
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology, University College London; Department of Cell and Developmental Biology, University College London;
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36
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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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