1
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Gnyliukh N, Johnson A, Nagel MK, Monzer A, Babić D, Hlavata A, Alotaibi SS, Isono E, Loose M, Friml J. Role of the dynamin-related protein 2 family and SH3P2 in clathrin-mediated endocytosis in Arabidopsis thaliana. J Cell Sci 2024; 137:jcs261720. [PMID: 38506228 DOI: 10.1242/jcs.261720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 03/21/2024] Open
Abstract
Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development through controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scission machinery in plants, but the precise roles of these proteins in this process are not fully understood. Here, we characterised the roles of the plant dynamin-related protein 2 (DRP2) family (hereafter DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to recruiters of dynamins, such as endophilin and amphiphysin, in CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the sh3p123 triple mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggest that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that, despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME.
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Affiliation(s)
- Nataliia Gnyliukh
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Alexander Johnson
- Division of Anatomy, Centre for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Aline Monzer
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - David Babić
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Annamaria Hlavata
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Saqer S Alotaibi
- Department of Biotechnology, College of Science, Taif University, Taif 21944, Saudi Arabia
| | - Erika Isono
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
| | - Martin Loose
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
| | - Jiří Friml
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
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2
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Gada KD, Kamuene JM, Kawano T, Plant LD. Imaging Membrane Proteins Using Total Internal Reflection Fluorescence Microscopy (TIRFM) in Mammalian Cells. Bio Protoc 2023; 13:e4614. [PMID: 36845531 PMCID: PMC9947549 DOI: 10.21769/bioprotoc.4614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
The cell surfaceome is of vital importance across physiology, developmental biology, and disease states alike. The precise identification of proteins and their regulatory mechanisms at the cell membrane has been challenging and is typically determined using confocal microscopy, two-photon microscopy, or total internal reflection fluorescence microscopy (TIRFM). Of these, TIRFM is the most precise, as it harnesses the generation of a spatially delimited evanescent wave at the interface of two surfaces with distinct refractive indices. The limited penetration of the evanescent wave illuminates a narrow specimen field, which facilitates the localization of fluorescently tagged proteins at the cell membrane but not inside of the cell. In addition to constraining the depth of the image, TIRFM also significantly enhances the signal-to-noise ratio, which is particularly valuable in the study of live cells. Here, we detail a protocol for micromirror TIRFM analysis of optogenetically activated protein kinase C-ε in HEK293-T cells, as well as data analysis to demonstrate the translocation of this construct to the cell-surface following optogenetic activation. Graphic abstract.
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Affiliation(s)
- Kirin D. Gada
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, USA
| | - Jordie M. Kamuene
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, USA
| | - Takeharu Kawano
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, USA
| | - Leigh D. Plant
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, USA
- Center for Drug Discovery, Northeastern University, Boston, USA
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3
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Suzuki KGN. Single-Molecule Imaging of Ganglioside Probes in Living Cell Plasma Membranes. Methods Mol Biol 2023; 2613:215-27. [PMID: 36587082 DOI: 10.1007/978-1-0716-2910-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Gangliosides play a variety of physiological roles and are one of the most important lipid raft constituents. However, their dynamic behaviors have scarcely been investigated in living cells because of the lack of fluorescent probes that behave like their parental molecules. Recently, fluorescent ganglioside probes that mimic native ganglioside behaviors have been developed. In this chapter, I discuss the recent advances in research related to the lateral localization and dynamic behaviors of gangliosides in the plasma membranes of living cells.
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4
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Riachy L, Ferrand T, Chasserot-Golaz S, Galas L, Alexandre S, Montero-Hadjadje M. Advanced Imaging Approaches to Reveal Molecular Mechanisms Governing Neuroendocrine Secretion. Neuroendocrinology 2023; 113:107-119. [PMID: 34915491 DOI: 10.1159/000521457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/09/2021] [Indexed: 11/19/2022]
Abstract
Identification of the molecular mechanisms governing neuroendocrine secretion and resulting intercellular communication is one of the great challenges of cell biology to better understand organism physiology and neurosecretion disruption-related pathologies such as hypertension, neurodegenerative, or metabolic diseases. To visualize molecule distribution and dynamics at the nanoscale, many imaging approaches have been developed and are still emerging. In this review, we provide an overview of the pioneering studies using transmission electron microscopy, atomic force microscopy, total internal reflection microscopy, and super-resolution microscopy in neuroendocrine cells to visualize molecular mechanisms driving neurosecretion processes, including exocytosis and associated fusion pores, endocytosis and associated recycling vesicles, and protein-protein or protein-lipid interactions. Furthermore, the potential and the challenges of these different advanced imaging approaches for application in the study of neuroendocrine cell biology are discussed, aiming to guide researchers to select the best approach for their specific purpose around the crucial but not yet fully understood neurosecretion process.
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Affiliation(s)
- Lina Riachy
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
| | - Thomas Ferrand
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
| | - Sylvette Chasserot-Golaz
- Institut des Neurosciences Cellulaires et Intégratives, Centre National de la Recherche Scientifique, Strasbourg University, Strasbourg, France
| | - Ludovic Galas
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Stéphane Alexandre
- Polymères, Biopolymères, Surfaces Laboratory, CNRS, Normandie University, UNIROUEN, UMR 6270, Rouen, France
| | - Maité Montero-Hadjadje
- Laboratoire de Différenciation et Communication Neuronale et Neuroendocrine, Institut de Recherche et d'Innovation Biomédicale de Normandie, Normandie University, UNIROUEN, INSERM, U1239, Rouen, France
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5
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Huet-Calderwood C, Rivera-Molina F, Toomre D, Calderwood DA. Use of Ecto-Tagged Integrins to Monitor Integrin Exocytosis and Endocytosis. Methods Mol Biol 2023; 2608:17-38. [PMID: 36653699 PMCID: PMC9999384 DOI: 10.1007/978-1-0716-2887-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Controlled exocytosis and endocytosis of integrin adhesion receptors is required for normal cell adhesion, migration, and signaling. In this chapter, we describe the design of functional β1 integrins carrying extracellular fluorescent or chemically traceable tags (ecto-tag) and methods for their use to image β1 integrin trafficking in cells. We provide approaches to generate cells in which endogenous β1 integrins are replaced by ecto-tagged integrins containing a pH-sensitive fluorophore pHluorin or a HaloTag and describe strategies using photobleaching, selective extracellular/intracellular labeling, and chase, quenching, and blocking to reveal β1 integrin exocytosis, endocytosis, and recycling by live total internal reflection fluorescence (TIRF) microscopy.
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Affiliation(s)
- Clotilde Huet-Calderwood
- Departments of Pharmacology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| | - Felix Rivera-Molina
- Departments of Cell Biology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| | - Derek Toomre
- Departments of Cell Biology, Yale University School of Medicine, Yale University, New Haven, CT, USA
| | - David A Calderwood
- Departments of Pharmacology, Yale University School of Medicine, Yale University, New Haven, CT, USA.
- Departments of Cell Biology, Yale University School of Medicine, Yale University, New Haven, CT, USA.
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6
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De Oliveira PA, Moreno E, Casajuana-Martin N, Casadó-Anguera V, Cai NS, Camacho-Hernandez GA, Zhu H, Bonifazi A, Hall MD, Weinshenker D, Newman AH, Logothetis DE, Casadó V, Plant LD, Pardo L, Ferré S. Preferential Gs protein coupling of the galanin Gal 1 receptor in the µ-opioid-Gal 1 receptor heterotetramer. Pharmacol Res 2022; 182:106322. [PMID: 35750299 PMCID: PMC9462584 DOI: 10.1016/j.phrs.2022.106322] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/18/2022] [Accepted: 06/19/2022] [Indexed: 12/25/2022]
Abstract
Recent studies have proposed that heteromers of µ-opioid receptors (MORs) and galanin Gal1 receptors (Gal1Rs) localized in the mesencephalon mediate the dopaminergic effects of opioids. The present study reports converging evidence, using a peptide-interfering approach combined with biophysical and biochemical techniques, including total internal reflection fluorescence microscopy, for a predominant homodimeric structure of MOR and Gal1R when expressed individually, and for their preference to form functional heterotetramers when co-expressed. Results show that a heteromerization-dependent change in the Gal1R homodimeric interface leads to a switch in G-protein coupling from inhibitory Gi to stimulatory Gs proteins. The MOR-Gal1R heterotetramer, which is thus bound to Gs via the Gal1R homodimer and Gi via the MOR homodimer, provides the framework for a canonical Gs-Gi antagonist interaction at the adenylyl cyclase level. These novel results shed light on the intense debate about the oligomeric quaternary structure of G protein-coupled receptors, their predilection for heteromer formation, and the resulting functional significance.
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Affiliation(s)
| | - Estefanía Moreno
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | - Nil Casajuana-Martin
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Autonomous University of Barcelona, Bellaterra, Spain
| | - Verònica Casadó-Anguera
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine, University of Barcelona, Barcelona, Spain
| | | | - Gisela Andrea Camacho-Hernandez
- Medicinal Chemistry Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Hu Zhu
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Alessandro Bonifazi
- Medicinal Chemistry Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Matthew D Hall
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - David Weinshenker
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Amy Hauck Newman
- Medicinal Chemistry Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Diomedes E Logothetis
- Departments of Pharmaceutical Sciences, Chemistry and Chemical Biology and Center for Drug Discovery, School of Pharmacy at the Bouvé College of Health Sciences and College of Science, Northeastern University, Boston, MA, USA
| | - Vicent Casadó
- Laboratory of Molecular Neuropharmacology, Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine, University of Barcelona, Barcelona, Spain.
| | - Leigh D Plant
- Departments of Pharmaceutical Sciences, Chemistry and Chemical Biology and Center for Drug Discovery, School of Pharmacy at the Bouvé College of Health Sciences and College of Science, Northeastern University, Boston, MA, USA.
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Autonomous University of Barcelona, Bellaterra, Spain.
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7
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Abstract
Due to the ultra-thin optical sectioning capability of exclusively illuminating space at the interface where total internal reflection occurs, the TIRF microscope has been indispensable for monitoring biological processes adjacent to the plasma membrane with excellent signal-to-noise ratio. Insulin-containing granules fuse with the plasma membrane to release contents within hundreds of milliseconds, which involves well-orchestrated assembly of SNARE complex and associated proteins. A video-rate multiple-color TIRF microscope offers the unique opportunity to visualize single secretory granule docking and fusion dynamics and can also map its regulators with high spatiotemporal resolution. Here, we describe the basic principles and practical implementation of a fast dual-color TIRF microscope, detailing a how-to guide on imaging and analysis of insulin granule dynamics in human β-cells.
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Affiliation(s)
- Fei Kang
- Department of Medicine, Temerty Faculty of Medicine of the University of Toronto and the Toronto General Hospital Research Institute, Toronto, ON, Canada.
| | - Herbert Y Gaisano
- Department of Medicine, Temerty Faculty of Medicine of the University of Toronto and the Toronto General Hospital Research Institute, Toronto, ON, Canada.
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8
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Gora RJ, de Jong B, van Hage P, Rhiemus MA, van Steenis F, van Noort J, Schmidt T, Schaaf MJM. Analysis of the H-Ras mobility pattern in vivo shows cellular heterogeneity inside epidermal tissue. Dis Model Mech 2021; 15:274496. [PMID: 34927194 PMCID: PMC8891639 DOI: 10.1242/dmm.049099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 12/14/2021] [Indexed: 12/04/2022] Open
Abstract
Developments in single-molecule microscopy (SMM) have enabled imaging individual proteins in biological systems, focusing on the analysis of protein mobility patterns inside cultured cells. In the present study, SMM was applied in vivo, using the zebrafish embryo model. We studied dynamics of the membrane protein H-Ras, its membrane-anchoring domain, C10H-Ras, and mutants, using total internal reflection fluorescence microscopy. Our results consistently confirm the presence of fast- and slow-diffusing subpopulations of molecules, which confine to microdomains within the plasma membrane. The active mutant H-RasV12 exhibits higher diffusion rates and is confined to larger domains than the wild-type H-Ras and its inactive mutant H-RasN17. Subsequently, we demonstrate that the structure and composition of the plasma membrane have an imperative role in modulating H-Ras mobility patterns. Ultimately, we establish that differences between cells within the same embryo largely contribute to the overall data variability. Our findings agree with a model in which the cell architecture and the protein activation state determine protein mobility, underlining the importance of SMM imaging for studying factors influencing protein dynamics in an intact living organism. This article has an associated First Person interview with the first author of the paper. Summary: Single-molecule microscopy analysis of factors altering the in vivo dynamics of H-Ras proteins in epidermal cells in living zebrafish embryos revealed that cell architecture and protein activation state determine protein mobility.
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Affiliation(s)
- Radoslaw J Gora
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Babette de Jong
- Biological, Soft and Complex Systems, Leiden Institute of Physics, Leiden University, Bohrweg 2, 2333 CA, Leiden, the Netherlands
| | - Patrick van Hage
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Mary Ann Rhiemus
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Fjodor van Steenis
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - John van Noort
- Biological, Soft and Complex Systems, Leiden Institute of Physics, Leiden University, Bohrweg 2, 2333 CA, Leiden, the Netherlands
| | - Thomas Schmidt
- Biological, Soft and Complex Systems, Leiden Institute of Physics, Leiden University, Bohrweg 2, 2333 CA, Leiden, the Netherlands
| | - Marcel J M Schaaf
- Animal Sciences and Health Cluster, Institute of Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
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9
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Bally M, Block S, Höök F, Larson G, Parveen N, Rydell GE. Physicochemical tools for studying virus interactions with targeted cell membranes in a molecular and spatiotemporally resolved context. Anal Bioanal Chem 2021; 413:7157-7178. [PMID: 34490501 PMCID: PMC8421089 DOI: 10.1007/s00216-021-03510-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022]
Abstract
The objective of this critical review is to provide an overview of how emerging bioanalytical techniques are expanding our understanding of the complex physicochemical nature of virus interactions with host cell surfaces. Herein, selected model viruses representing both non-enveloped (simian virus 40 and human norovirus) and enveloped (influenza A virus, human herpes simplex virus, and human immunodeficiency virus type 1) viruses are highlighted. The technologies covered utilize a wide range of cell membrane mimics, from supported lipid bilayers (SLBs) containing a single purified host membrane component to SLBs derived from the plasma membrane of a target cell, which can be compared with live-cell experiments to better understand the role of individual interaction pairs in virus attachment and entry. These platforms are used to quantify binding strengths, residence times, diffusion characteristics, and binding kinetics down to the single virus particle and single receptor, and even to provide assessments of multivalent interactions. The technologies covered herein are surface plasmon resonance (SPR), quartz crystal microbalance with dissipation (QCM-D), dynamic force spectroscopy (DFS), total internal reflection fluorescence (TIRF) microscopy combined with equilibrium fluctuation analysis (EFA) and single particle tracking (SPT), and finally confocal microscopy using multi-labeling techniques to visualize entry of individual virus particles in live cells. Considering the growing scientific and societal needs for untangling, and interfering with, the complex mechanisms of virus binding and entry, we hope that this review will stimulate the community to implement these emerging tools and strategies in conjunction with more traditional methods. The gained knowledge will not only contribute to a better understanding of the virus biology, but may also facilitate the design of effective inhibitors to block virus entry.
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Affiliation(s)
- Marta Bally
- Department of Clinical Microbiology & Wallenberg Centre for Molecular Medicine, Umeå University, 901 85, Umeå, Sweden
| | - Stephan Block
- Department of Chemistry and Biochemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Fredrik Höök
- Department of Physics, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
| | - Göran Larson
- Department of Laboratory Medicine, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Bruna Stråket 16, 413 45, Gothenburg, Sweden.
| | - Nagma Parveen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Gustaf E Rydell
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, 413 46, Gothenburg, Sweden
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10
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Zaklit J, Cabrera A, Shaw A, Aoun R, Vernier PT, Leblanc N, Craviso GL. 5 ns electric pulses induce Ca 2+-dependent exocytotic release of catecholamine from adrenal chromaffin cells. Bioelectrochemistry 2021; 140:107830. [PMID: 33965669 DOI: 10.1016/j.bioelechem.2021.107830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022]
Abstract
Previously we reported that adrenal chromaffin cells exposed to a 5 ns, 5 MV/m pulse release the catecholamines norepinephrine (NE) and epinephrine (EPI) in a Ca2+-dependent manner. Here we determined that NE and EPI release increased with pulse number (one versus five and ten pulses at 1 Hz), established that release occurs by exocytosis, and characterized the exocytotic response in real-time. Evidence of an exocytotic mechanism was the appearance of dopamine-β-hydroxylase on the plasma membrane, and the demonstration by total internal reflection fluorescence microscopy studies that a train of five or ten pulses at 1 Hz triggered the release of the fluorescent dye acridine orange from secretory granules. Release events were Ca2+-dependent, longer-lived relative to those evoked by nicotinic receptor stimulation, and occurred with a delay of several seconds despite an immediate rise in Ca2+. In complementary studies, cells labeled with the plasma membrane fluorescent dye FM 1-43 and exposed to a train of ten pulses at 1 Hz underwent Ca2+-dependent increases in FM 1-43 fluorescence indicative of granule fusion with the plasma membrane due to exocytosis. These results demonstrate the effectiveness of ultrashort electric pulses for stimulating catecholamine release, signifying their promise as a novel electrostimulation modality for neurosecretion.
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11
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Guha A, McGuire ML, Leriche G, Yang J, Mayer M. A single-liposome assay that enables temperature-dependent measurement of proton permeability of extremophile-inspired lipid membranes. Biochim Biophys Acta Biomembr 2021; 1863:183567. [PMID: 33476579 DOI: 10.1016/j.bbamem.2021.183567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Affiliation(s)
- Anirvan Guha
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Melissa L McGuire
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
| | - Geoffray Leriche
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, United States of America
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland.
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12
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Abstract
In eukaryotic cells, the genomic DNA is packaged into chromatin, the basic unit of which is the nucleosome. Studying the mechanism of chromatin formation under physiological conditions is inherently difficult due to the limitations of research approaches. Here we describe how to prepare a biochemical system called yeast nucleoplasmic extracts (YNPE). YNPE is derived from yeast nuclei, and the in vitro system can mimic the physiological conditions of the yeast nucleus in vivo. In YNPE, the dynamic process of chromatin assembly has been observed in real time at the single-molecule level by total internal reflection fluorescence microscopy. YNPE provides a novel tool to investigate many aspects of chromatin assembly under physiological conditions and is competent for single-molecule approaches.
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13
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Johnson A, Gnyliukh N, Kaufmann WA, Narasimhan M, Vert G, Bednarek SY, Friml J. Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis. J Cell Sci 2020; 133:jcs248062. [PMID: 32616560 DOI: 10.1242/jcs.248062] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/22/2020] [Indexed: 12/29/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and intercellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how CME functions in planta To facilitate the direct quantitative study of plant CME, we review current routinely used methods and present refined, standardized quantitative imaging protocols that allow the detailed characterization of CME at multiple scales in plant tissues. These protocols include: (1) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultrastructure of clathrin-coated vesicles; (2) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (3) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (4) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Alexander Johnson
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Nataliia Gnyliukh
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Walter A Kaufmann
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | | | - Grégory Vert
- Plant Science Research Laboratory (LRSV), UMR5546 CNRS/Université Toulouse 3, 24 chemin de Borde Rouge, 31320 Auzeville Tolosane, France
| | | | - Jiří Friml
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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14
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Senju Y, Suetsugu S. Spatiotemporal Analysis of Caveolae Dynamics Using Total Internal Reflection Fluorescence Microscopy. Methods Mol Biol 2020; 2169:63-70. [PMID: 32548819 DOI: 10.1007/978-1-0716-0732-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Total internal reflection fluorescence microscopy enables to analyze the localizations and dynamics of cellular events that occur at or near the plasma membrane. Total internal reflection fluorescence microscopy exclusively illuminates molecules in the close vicinity of the glass surface, thereby reducing background fluorescence and enabling observation of the plasma membrane in the glass-attached cells with a high signal-to-noise ratio. Here, we describe the application of total internal reflection fluorescence microscopy to analyze the dynamics of caveolae, which play essential physiological functions, including membrane tension buffering, endocytosis, and signaling at the plasma membrane.
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15
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Abstract
Introduction Amyloid-β oligomers (AβOs) are assumed to impair the ability of learning and memory by suppressing the induction of synaptic plasticity, such as long-term potentiation (LTP) in the early stage of Alzheimer's disease. However, the direct molecular mechanism of how AβOs affect excitatory synaptic plasticity remains to be elucidated. Methods In order to study the effects of AβOs on LTP-associated changes of AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid)-type glutamate receptor (AMPAR) movement, we performed live-cell imaging of fluorescently labeled AMPAR subunit GluA1 or GluA2 with total internal reflection fluorescence microscopy. Results Incubation of cultured hippocampal neurons with AβOs for 1–2 days inhibited the increase in GluA1 number and GluA1 exocytosis frequency in both postsynaptic and extrasynaptic membranes during LTP. In contrast, AβOs did not inhibit the increase in GluA2 number or exocytosis frequency. Discussion These results suggest that AβOs primarily inhibit the increase in the number of GluA1 homomers and suppress hippocampal LTP expression.
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Affiliation(s)
- Hiromitsu Tanaka
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Daiki Sakaguchi
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoo Hirano
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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Mularski A, Marie-Anaïs F, Mazzolini J, Niedergang F. Observing Frustrated Phagocytosis and Phagosome Formation and Closure Using Total Internal Reflection Fluorescence Microscopy (TIRFM). Methods Mol Biol 2018; 1784:165-75. [PMID: 29761398 DOI: 10.1007/978-1-4939-7837-3_16] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Complementary methods to observe frustrated phagocytosis and phagosome closure using total internal reflection fluorescence microscopy (TIRFM) are described here. Frustrated phagocytosis occurs when phagocytic cells are exposed to an opsonized surface and spread as if trying to engulf it, allowing for the observation of phagocytic spreading and the biochemical events that directly precede it. Phagosome formation and closure is an inherently three-dimensional process though, and cannot be studied in the "frustrated" situation. Here we describe a method to visualize with unprecedented high-resolution phagosome formation and closure in three dimensions. It allows for observation of the base of the phagocytic cup, the extending pseudopods, as well as the precise site of phagosome scission.
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17
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Mataragka S, Taylor CW. All three IP 3 receptor subtypes generate Ca 2+ puffs, the universal building blocks of IP 3-evoked Ca 2+ signals. J Cell Sci 2018; 131:jcs.220848. [PMID: 30097556 PMCID: PMC6127726 DOI: 10.1242/jcs.220848] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/27/2018] [Indexed: 12/19/2022] Open
Abstract
All three subtypes of inositol 1,4,5-trisphosphate receptor (IP3R) are intracellular Ca2+ channels that are co-regulated by IP3 and Ca2+. This allows IP3Rs to evoke regenerative Ca2+ signals, the smallest of which are Ca2+ puffs that reflect the coordinated opening of a few clustered IP3Rs. We use total internal reflection microscopy (TIRF) microscopy to record Ca2+ signals in HEK cells expressing all three IP3R subtypes or a single native subtype. Ca2+ puffs are less frequent in cells expressing one IP3R subtype, commensurate with them expressing fewer IP3Rs than wild-type cells. However, all three IP3R subtypes generate broadly similar Ca2+ puffs with similar numbers of IP3Rs contributing to each. This suggests that IP3R clusters may be assembled by conserved mechanisms that generate similarly sized clusters across different IP3R expression levels. The Ca2+ puffs evoked by IP3R2 had slower kinetics and more prolonged durations, which may be due to IP3 binding with greater affinity to IP3R2. We conclude that Ca2+ puffs are the building blocks for the Ca2+ signals evoked by all IP3Rs. Summary: All IP3 receptor subtypes can generate Ca2+ puffs, suggesting that these coordinated openings of clustered IP3Rs are the building blocks of all IP3-evoked Ca2+ signals.
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Affiliation(s)
- Stefania Mataragka
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Colin W Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
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18
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Hu X, Fan J, Duan B, Zhang H, He Y, Duan P, Li X. Single-molecule catalytic hairpin assembly for rapid and direct quantification of circulating miRNA biomarkers. Anal Chim Acta 2018; 1042:109-15. [PMID: 30428976 DOI: 10.1016/j.aca.2018.08.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/14/2018] [Accepted: 08/21/2018] [Indexed: 11/24/2022]
Abstract
The emergence of circulating miRNAs as potential biomarkers for cancer necessitates reliable approaches to detect miRNAs with high sensitivity and specificity. We disclose a highly sensitive method for rapid and direct quantification of circulating miRNA in serum by combining dynamic DNA circuit and single-molecule fluorescence detection. The product of DNA circuits based amplification is detected by total internal reflection fluorescence microscopy (TIRFM). The single-molecule counting allows the quantification of miRNA targets. Owing to the high sensitivity for fluorophore labeled nucleic acids of TIRFM, the products generated by 15 min amplification are sufficient for quantification. Meanwhile, the fast detection also addresses the problem of leakage because non-target triggered DNA circuits is relatively slow. There miRNA biomarkers miR-141, miR-21, miR-16 were detected with remarkable sensitivity as detection limits of 0.017, 0.012, 0.006 fM, respectively. This approach was applied for the direct quantification of the circulating miRNAs in human serum. The results of 29 health samples, 18 prostate cancer samples, 23 breast cancer samples imply that miR-141 and miR-21 are up-regulated in the prostate cancer samples and the breast cancer samples, respectively, and as reference miR-16 shows no difference in health and patient samples.
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19
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Sum CH, Shortall SM, Nicastro JA, Slavcev R. Specific Systems for Imaging. Exp Suppl 2018; 110:69-97. [PMID: 30536227 DOI: 10.1007/978-3-319-78259-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Microscopy allows for the characterization of small objects invisible to the naked eye, a technique that, since its conception, has played a key role in the development across nearly every field of science and technology. Given the nanometer size of the materials explored in the field of nanotechnology, the contributions of modern microscopes that can visualize these materials are indispensable, and the ever-improving technology is paramount to the future success of the field. This chapter will focus on four fundamental areas of microscopy used in the field of nanotechnology including fluorescence microscopy (Sect. 3.1), particle tracking and photoactivated localization microscopy (Sect. 3.2), quantum dots and fluorescence resonance energy transfer (Sect. 3.3), and cellular MRI and PET labeling (Sect. 3.4). The functionality, as well as the current and recommended usage of each given imaging system, will be discussed.
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20
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Abstract
RNA-induced silencing complex (RISC) is a small RNA-protein complex that mediates silencing of complementary target RNAs. Biochemistry has been successfully used to characterize the molecular mechanism of RISC assembly and function for nearly two decades. However, further dissection of intermediate states during the reactions has been warranted to fill in the gaps in our understanding of RNA silencing mechanisms. Single-molecule analysis with total internal reflection fluorescence (TIRF) microscopy is a powerful imaging-based approach to interrogate complex formation and dynamics at the individual molecule level with high sensitivity. Combining this technique with our recently established in vitro reconstitution system of fly Ago2-RISC, we have developed a single-molecule observation system for RISC assembly. In this chapter, we summarize the detailed protocol for single-molecule analysis of chaperone-assisted assembly of fly Ago2-RISC as well as its target cleavage reaction.
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Affiliation(s)
- Hiroshi M Sasaki
- Intsitute for Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, CLSB, Boston, MA, 02115, USA
| | - Hisashi Tadakuma
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan
| | - Yukihide Tomari
- Intsitute for Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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21
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Subramanyam S, Kinz-Thompson CD, Gonzalez RL Jr, Spies M. Observation and Analysis of RAD51 Nucleation Dynamics at Single-Monomer Resolution. Methods Enzymol 2018; 600:201-32. [PMID: 29458759 DOI: 10.1016/bs.mie.2017.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Human RAD51 promotes accurate DNA repair by homologous recombination and is involved in protection and repair of damaged DNA replication forks. The active species of RAD51 and related recombinases in all organisms is a nucleoprotein filament assembled on single-stranded DNA (ssDNA). The formation of a nucleoprotein filament competent for the recombination reaction, or for DNA replication support, is a delicate and strictly regulated process, which occurs through filament nucleation followed by filament extension. The rates of these two phases of filament formation define the capacity of RAD51 to compete with the ssDNA-binding protein RPA, as well as the lengths of the resulting filament segments. Single-molecule approaches can provide a wealth of quantitative information on the kinetics of RAD51 nucleoprotein filament assembly, internal dynamics, and disassembly. In this chapter, we describe how to set up a single-molecule total internal reflection fluorescence microscopy experiment to monitor the initial steps of RAD51 nucleoprotein filament formation in real-time and at single-monomer resolution. This approach is based on the unique, stretched-ssDNA conformation within the recombinase nucleoprotein filament and follows the efficiency of Förster resonance energy transfer (EFRET) between two DNA-conjugated fluorophores. We will discuss the practical aspects of the experimental setup, extraction of the FRET trajectories, and how to analyze and interpret the data to obtain information on RAD51 nucleation kinetics, the mechanism of nucleation, and the oligomeric species involved in filament formation.
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22
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Abstract
In eukaryotic cells, the smallest subunit of chromatin is the nucleosome, which consists of a segment of DNA wound on histone protein cores. Despite many years of effort, the process of nucleosome assembly and disassembly is still not very clear. Here, we present a convenient method to investigate the process of nucleosome assembly at the single molecule level. We invented a novel system derived from the yeast nucleoplasmic extracts (YNPE), and demonstrated that the YNPE supports the nucleosome assembly under physiological condition. By combining the total internal reflection fluorescence microscopy with microfluidic flow-cell technique, the dynamic process of nucleosome assembly in YNPE was visualized at single-molecule level. Our system provides a novel in vitro single-molecule tool to investigate the dynamics of nucleosome assembly under physiological conditions.
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Affiliation(s)
- Xiuqiang Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ershuang Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu V Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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23
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Itofusa R, Tojima T, Kamiguchi H. Visualization of Clathrin-Mediated Endocytosis During Semaphorin-Guided Axonal Growth. Methods Mol Biol 2017; 1493:287-298. [PMID: 27787859 DOI: 10.1007/978-1-4939-6448-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Semaphorin3A (Sema3A) guides axonal growth during neuronal network development. Accumulating evidence indicates that Sema3A-induced growth cone collapse and repulsion involve endocytic membrane trafficking in the growth cone. It is now possible to visualize endocytic processes in living cells using total internal reflection fluorescence microscopy (TIRFM), a powerful tool for imaging dynamic subcellular events at the plasma membrane. In this chapter, we describe a method for TIRFM observation and analysis of clathrin-mediated endocytosis in growth cones of chicken dorsal root ganglion neurons that receive an extracellular concentration gradient of Sema3A in a culture medium.
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Affiliation(s)
- Rurika Itofusa
- Laboratory for Neuronal Growth Mechanisms, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takuro Tojima
- Laboratory for Neuronal Growth Mechanisms, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Hiroyuki Kamiguchi
- Laboratory for Neuronal Growth Mechanisms, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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Abstract
Homologous recombination is an important pathway involved in the repair of double-stranded DNA breaks. Genetic studies form the foundation of our knowledge on homologous recombination. Significant progress has also been made toward understanding the biochemical and biophysical properties of the proteins, complexes, and reaction intermediates involved in this essential DNA repair pathway. However, heterogeneous or transient recombination intermediates remain extremely difficult to assess through traditional ensemble methods, leaving an incomplete mechanistic picture of many steps that take place during homologous recombination. To help overcome some of these limitations, we have established DNA curtain methodologies as an experimental platform for studying homologous DNA recombination in real-time at the single-molecule level. Here, we present a detailed overview describing the preparation and use of single-stranded DNA curtains in applications related to the study of homologous DNA recombination with emphasis on recent work related to the study of the eukaryotic recombinase Rad51.
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25
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Chang HF, Bzeih H, Chitirala P, Ravichandran K, Sleiman M, Krause E, Hahn U, Pattu V, Rettig J. Preparing the lethal hit: interplay between exo- and endocytic pathways in cytotoxic T lymphocytes. Cell Mol Life Sci 2016; 74:399-408. [PMID: 27585956 PMCID: PMC5241346 DOI: 10.1007/s00018-016-2350-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/08/2016] [Accepted: 08/29/2016] [Indexed: 12/11/2022]
Abstract
Cytotoxic T lymphocytes patrol our body in search for infected cells which they kill through the release of cytotoxic substances contained in cytotoxic granules. The fusion of cytotoxic granules occurs at a specially formed contact site, the immunological synapse, and is tightly controlled to ensure specificity. In this review, we discuss the contribution of two intracellular compartments, endosomes and cytotoxic granules, to the formation, function and disassembly of the immunological synapse. We highlight a recently proposed sequential process of fusion events at the IS upon target cell recognition. First, recycling endosomes fuse with the plasma membrane to deliver cargo required for the docking of cytotoxic granules. Second, cytotoxic granules arrive and fuse upon docking in a SNARE-dependent manner. Following fusion, membrane components of the cytotoxic granule are retrieved through endocytosis to ensure the fast, efficient serial killing of target cells that is characteristic of cytotoxic T lymphocytes.
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Affiliation(s)
- Hsin-Fang Chang
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421, Homburg, Germany
| | - Hawraa Bzeih
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421, Homburg, Germany
| | - Praneeth Chitirala
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421, Homburg, Germany
| | - Keerthana Ravichandran
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421, Homburg, Germany
| | - Marwa Sleiman
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421, Homburg, Germany
| | - Elmar Krause
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421, Homburg, Germany
| | - Ulrike Hahn
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421, Homburg, Germany
| | - Varsha Pattu
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421, Homburg, Germany
| | - Jens Rettig
- Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421, Homburg, Germany.
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26
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Wei L, Ye Z, Luo W, Chen B, Xiao L. Redistribution of fluorescent molecules at the solid/liquid interface with total internal reflection illumination. Talanta 2016; 155:229-34. [PMID: 27216678 DOI: 10.1016/j.talanta.2016.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 04/06/2016] [Accepted: 04/09/2016] [Indexed: 10/21/2022]
Abstract
Many intriguing physical and chemical processes commonly take place at the solid/liquid interface. Total internal reflection illumination, together with single molecule spectroscopy, provides a robust platform for the selective exploration of kinetic processes close the interface. With these techniques, it was observed that the distribution of Rhodamine B molecules close to a solid/liquid interface could be regulated in a photo-induced route. The laser-induced repulsion force at this interface is enough to compromise the Brownian diffusion of single molecules in a range of several hundred nanometers normal to the solid/liquid interface. This observation is fundamentally and practically interesting because moderate laser intensity is enough to initiate this repulsion effect. Therefore, it might display extensive applications in the development of photo-modulation technique with high throughput capability.
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Affiliation(s)
- Lin Wei
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, PR China
| | - Zhongju Ye
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, PR China
| | - Wenjuan Luo
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, PR China
| | - Bo Chen
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, PR China
| | - Lehui Xiao
- Dynamic Optical Microscopic Imaging Laboratory, Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, Key Laboratory of Phytochemical R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, Hunan 410081, PR China.
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27
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Blumenthal D, Edidin M, Gheber LA. Trafficking of MHC molecules to the cell surface creates dynamic protein patches. J Cell Sci 2016; 129:3342-50. [PMID: 27466380 DOI: 10.1242/jcs.187112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 07/21/2016] [Indexed: 11/20/2022] Open
Abstract
Major histocompatibility complex class I (MHC-I) molecules signal infection or transformation by engaging receptors on T lymphocytes. The spatial organization of MHC-I on the plasma membranes is important for this engagement. We and others have shown that MHC-I molecules, like other membrane proteins, are not uniformly distributed, but occur in patches in the plasma membrane. Here, we describe the temporal details of MHC-I patch formation and combine them with the spatial details, which we have described earlier, to yield a comprehensive quantitative description of patch formation. MHC-I is delivered to the plasma membrane in clathrin-coated vesicles, arriving at a rate of ∼2.5×10(-3) μm(-1) min(-1) (or about two arrivals per minute over the whole cell). The vesicles dock and fuse at non-random, apparently targeted, locations on the membrane and the newly delivered MHC-I molecules form patches that are a few hundred nanometers in diameter. The patches are maintained at steady state by a dynamic equilibrium between the rate of delivery and the rate of hindered diffusion of MHC-I molecules out of the patches (caused by components of the actin cytoskeleton).
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Affiliation(s)
- Daniel Blumenthal
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer-Sheva, 8410501 Israel
| | - Michael Edidin
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Levi A Gheber
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer-Sheva, 8410501 Israel
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Tang Q, Pollard LW, Lord M. Measurements of Myosin-II Motor Activity During Cytokinesis in Fission Yeast. Methods Mol Biol 2016; 1369:137-50. [PMID: 26519311 DOI: 10.1007/978-1-4939-3145-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Fission yeast myosin-II (Myo2p) represents the critical actin-based motor protein that drives actomyosin ring assembly and constriction during cytokinesis. We detail three different methods to measure Myo2p motor function. Actin-activated ATPases provide a readout of actomyosin ATPase motor activity in a bulk assay; actin filament motility assays reveal the speed and efficiency of myosin-driven actin filament gliding (when motors are anchored); myosin-bead motility assays reveal the speed and efficiency of myosin ensembles traveling along actin filaments (when actin is anchored). Collectively, these methods allow us to combine the standard in vivo approaches common to fission yeast with in vitro biochemical methods to learn more about the mechanistic action of myosin-II during cytokinesis.
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29
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Bain FE, Wu CG, Spies M. Single-molecule sorting of DNA helicases. Methods 2016; 108:14-23. [PMID: 27223403 DOI: 10.1016/j.ymeth.2016.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 11/22/2022] Open
Abstract
DNA helicases participate in virtually all aspects of cellular DNA metabolism by using ATP-fueled directional translocation along the DNA molecule to unwind DNA duplexes, dismantle nucleoprotein complexes, and remove non-canonical DNA structures. Post-translational modifications and helicase interacting partners are often viewed as determining factors in controlling the switch between bona fide helicase activity and other functions of the enzyme that do not involve duplex separation. The bottleneck in developing a mechanistic understanding of human helicases and their control by post-translational modifications is obtaining sufficient quantities of the modified helicase for traditional structure-functional analyses and biochemical reconstitutions. This limitation can be overcome by single-molecule analysis, where several hundred surface-tethered molecules are sufficient to obtain a complete kinetic and thermodynamic description of the helicase-mediated substrate binding and rearrangement. Synthetic oligonucleotides site-specifically labeled with Cy3 and Cy5 fluorophores can be used to create a variety of DNA substrates that can be used to characterize DNA binding, as well as helicase translocation and duplex unwinding activities. This chapter describes "single-molecule sorting", a robust experimental approach to simultaneously quantify, and distinguish the activities of helicases carrying their native post-translational modifications. Using this technique, a DNA helicase of interest can be produced and biotinylated in human cells to enable surface-tethering for the single-molecule studies by total internal reflection fluorescence microscopy. The pool of helicases extracted from the cells is expected to contain a mixture of post-translationally modified and unmodified enzymes, and the contributions from either population can be monitored separately, but in the same experiment providing a direct route to evaluating the effect of a given modification.
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Qi Z, Greene EC. Visualizing recombination intermediates with single-stranded DNA curtains. Methods 2016; 105:62-74. [PMID: 27038747 DOI: 10.1016/j.ymeth.2016.03.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/08/2016] [Accepted: 03/29/2016] [Indexed: 01/23/2023] Open
Abstract
Homologous recombination (HR) is a critical cellular process for repairing double-stranded DNA breaks (DSBs) - a toxic type of DNA lesion that can result in chromosomal rearrangements and cancer. During the early stages of HR, members from the Rad51/RecA family of recombinases assemble into long filaments on the single-stranded DNA overhangs that are present at processed DSBs. These nucleoprotein filaments are referred to as presynaptic complexes, and these presynaptic complexes must align and pair homologous DNA sequences during HR. Traditional ensemble methods cannot easily access the transient and often heterogeneous intermediates that are typical of DNA recombination reactions, and as a consequence, there remain many open questions with respect to the molecular details of this pathway. Novel single-molecule approaches that are capable of directly visualizing reaction intermediates in solution and in real time offer the potential for new insights into the mechanism of homologous DNA recombination. Here we highlight recently developed single stranded DNA curtain methods for studying the properties of individual Rad51 presynaptic complexes and other related recombination intermediates at the single-molecule level.
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31
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Boehm EM, Subramanyam S, Ghoneim M, Washington MT, Spies M. Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy. Methods Enzymol 2016; 581:105-45. [PMID: 27793278 DOI: 10.1016/bs.mie.2016.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Large, dynamic macromolecular complexes play essential roles in many cellular processes. Knowing how the components of these complexes associate with one another and undergo structural rearrangements is critical to understanding how they function. Single-molecule total internal reflection fluorescence (TIRF) microscopy is a powerful approach for addressing these fundamental issues. In this article, we first discuss single-molecule TIRF microscopes and strategies to immobilize and fluorescently label macromolecules. We then review the use of single-molecule TIRF microscopy to study the formation of binary macromolecular complexes using one-color imaging and inhibitors. We conclude with a discussion of the use of TIRF microscopy to examine the formation of higher-order (i.e., ternary) complexes using multicolor setups. The focus throughout this article is on experimental design, controls, data acquisition, and data analysis. We hope that single-molecule TIRF microscopy, which has largely been the province of specialists, will soon become as common in the tool box of biophysicists and biochemists as structural approaches have become today.
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Abstract
Trafficking studies of plasma membrane-localized intracellular estrogen receptors have mainly relied on biochemical and histological techniques to locate the receptor before and after estradiol stimulation. More often than not these experiments were performed using postmortem, lysed, or fixed tissue samples, whose tissue or cellular structure is typically severely altered or at times completely lost, making the definitive localization of estrogen receptors difficult to ascertain. To overcome this limitation we began using total internal reflection fluorescence microscopy (TIRFM) to study the trafficking of plasma membrane estrogen receptors. This real-time imaging approach, described in this chapter, permits observation of live, intact cells while allowing visualization of the steps (in time and spatial distribution) involved in receptor activation by estradiol and movements on and near the membrane. TIRFM yields high-contrast real-time images of fluorescently labeled E6BSA molecules on and just below the cell surface and is ideal for studying estrogen receptor trafficking in living cells.
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Affiliation(s)
- Kassandra Kisler
- Department of Physiology and Biophysics, and the Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, 1501 San Pablo St., ZNI 323, Los Angeles, CA, 90033, USA
| | - Reymundo Dominguez
- Department of Physiology and Biophysics, Keck Schoolof Medicine of the University of Southern California, Los Angeles, CA, USA.
- The Zilkha Neurogenetic Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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Islam MS, Kabir AMR, Inoue D, Sada K, Kakugo A. Enhanced dynamic instability of microtubules in a ROS free inert environment. Biophys Chem 2015; 211:1-8. [PMID: 26774598 DOI: 10.1016/j.bpc.2015.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/19/2015] [Accepted: 11/22/2015] [Indexed: 11/28/2022]
Abstract
Reactive oxygen species (ROS), one of the regulators in various biological processes, have recently been suspected to modulate microtubule (MT) dynamics in cells. However due to complicated cellular environment and unavailability of any in vitro investigation, no detail is understood yet. Here, by performing simple in vitro investigations, we have unveiled the effect of ROS on MT dynamics. By studying dynamic instability of MTs in a ROS free environment and comparing with that in the presence of ROS, we disclosed that MTs showed enhanced dynamics in the ROS free environment. All the parameters that define dynamic instability of MTs e.g., growth and shrinkage rates, rescue and catastrophe frequencies were significantly affected by the presence of ROS. This work clearly reveals the role of ROS in modulating MT dynamics in vitro, and would be a great help in understanding the role of ROS in regulation of MT dynamics in cells.
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Affiliation(s)
- Md Sirajul Islam
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan
| | | | - Daisuke Inoue
- Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Kazuki Sada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan; Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Akira Kakugo
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-0810, Japan; Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.
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34
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Abstract
Using total internal reflection fluorescence microscopy of droplet interface bilayers containing the potassium-sensitive fluorophore APG-4, we imaged the ionic flux through individual electropores. We are able to monitor up to 30 individual pores in parallel and show voltage dependent responses in fluorescence that corresponds to the measured ionic current. These experiments help quantify the scope and current limitations of optical single channel recordings of potassium flux. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.
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35
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Abstract
Recent advances in direct imaging have given us a new appreciation of the spatial and temporal dynamics of membrane trafficking processes, and have allowed us to ask questions that were difficult to address with traditional methods. A relevant example of this is protein sorting in the endosome, which serves as the primary sorting station for proteins internalized from the cell surface. In this chapter, we discuss fluorescence imaging protocols to directly visualize and quantitate the recycling of G protein-coupled receptors (GPCRs)-a highly physiologically relevant family of signaling receptors-in real time in living cells. The protocols allow direct visualization and quantitation of both GPCR exit from the endosome and GPCR delivery to the cell surface. The methods may be extended to study the endolysosomal sorting of many proteins that undergoes endocytic cycling, and may be adapted to other organelles and systems where proteins are sorted.
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Affiliation(s)
- Shanna L Bowman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Amanda L Soohoo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
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36
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Abstract
Processive cytoskeletal motors from the myosin, kinesin, and dynein families walk on actin filaments and microtubules to drive cellular transport and organization in eukaryotic cells. These remarkable molecular machines are able to take hundreds of successive steps at speeds of up to several microns per second, allowing them to effectively move vesicles and organelles throughout the cytoplasm. Here, we focus on single-molecule fluorescence techniques and discuss their wide-ranging applications to the field of cytoskeletal motor research. We cover both traditional fluorescence and sub-diffraction imaging of motors, providing examples of how fluorescence data can be used to measure biophysical parameters of motors such as coordination, stepping mechanism, gating, and processivity. We also outline some remaining challenges in the field and suggest future directions.
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Affiliation(s)
- Vladislav Belyy
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - Ahmet Yildiz
- Department of Physics, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA.
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37
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Christenson W, Yermolenko I, Plochberger B, Camacho-Alanis F, Ros A, Ugarova TP, Ros R. Combined single cell AFM manipulation and TIRFM for probing the molecular stability of multilayer fibrinogen matrices. Ultramicroscopy 2013; 136:211-5. [PMID: 24239757 DOI: 10.1016/j.ultramic.2013.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/06/2013] [Accepted: 10/09/2013] [Indexed: 10/26/2022]
Abstract
Adsorption of fibrinogen on various surfaces produces a nanoscale multilayer matrix, which strongly reduces the adhesion of platelets and leukocytes with implications for hemostasis and blood compatibility of biomaterials. The nonadhesive properties of fibrinogen matrices are based on their extensibility, ensuing the inability to transduce strong mechanical forces via cellular integrins and resulting in weak intracellular signaling. In addition, reduced cell adhesion may arise from the weaker associations between fibrinogen molecules in the superficial layers of the matrix. Such reduced stability would allow integrins to pull fibrinogen molecules out of the matrix with comparable or smaller forces than required to break integrin-fibrinogen bonds. To examine this possibility, we developed a method based on the combination of total internal reflection fluorescence microscopy, single cell manipulation with an atomic force microscope and microcontact printing to study the transfer of fibrinogen molecules out of a matrix onto cells. We calculated the average fluorescence intensities per pixel for wild-type HEK 293 (HEK WT) and HEK 293 cells expressing leukocyte integrin Mac-1 (HEK Mac-1) before and after contact with multilayered matrices of fluorescently labeled fibrinogen. For contact times of 500 s, HEK Mac-1 cells show a median increase of 57% of the fluorescence intensity compared to 6% for HEK WT cells. The results suggest that the integrin Mac-1-fibrinogen interactions are stronger than the intermolecular fibrinogen interactions in the superficial layer of the matrix. The low mechanical stability of the multilayer fibrinogen surface may contribute to the reduced cell adhesive properties of fibrinogen-coated substrates. We anticipate that the described method can be applied to various cell types to examine their integrin-mediated adhesion to the extracellular matrices with a variable protein composition.
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Affiliation(s)
- W Christenson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA; Center for Biological Physics, Arizona State University, Tempe, AZ 85287, USA
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Thomasson MS, Macnaughtan MA. Microscopy basics and the study of actin-actin-binding protein interactions. Anal Biochem 2013; 443:156-65. [PMID: 24044992 DOI: 10.1016/j.ab.2013.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022]
Abstract
Actin is a multifunctional eukaryotic protein with a globular monomer form that polymerizes into a thin, linear microfilament in cells. Through interactions with various actin-binding proteins (ABPs), actin plays an active role in many cellular processes, such as cell motility and structure. Microscopy techniques are powerful tools for determining the role and mechanism of actin-ABP interactions in these processes. In this article, we describe the basic concepts of fluorescent speckle microscopy, total internal reflection fluorescence microscopy, atomic force microscopy, and cryoelectron microscopy and review recent studies that utilize these techniques to visualize the binding of actin with ABPs.
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Affiliation(s)
- Maggie S Thomasson
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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Liu J, Hlady V. Chemical pattern on silica surface prepared by UV irradiation of 3-mercaptopropyltriethoxy silane layer: surface characterization and fibrinogen adsorption. Colloids Surf B Biointerfaces 1996; 8:26-37. [PMID: 25132726 PMCID: PMC4131241 DOI: 10.1016/s0927-7765(96)01298-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A flat silica surface modified with 3-mercaptopropyltriethoxy silane (MTS) was patterned using UV irradiation and a custom-designed mask. The irradiated surface was characterized by X-ray photoelectron spectroscopy (XPS), scanning force microscopy (SFM) and water contact angle measurements. The XPS S2p spectra indicated that the UV treatment resulted in the oxidation of MTS sulfur. The optimal UV irradiation dose for patterning, estimated from the XPS S2p binding energy shifts and water contact angles of irradiated surfaces, was 4.8 J cm-2 at 270 nm. The surface patterns were visualized by total internal reflection fluorescence microscopy, while exposing the pattern to a solution of acridine orange, by water vapor condensation, and by SFM lateral force imaging in dilute electrolyte solution. The adhesion SFM measurements revealed the adhesion force only on the areas which were not UV-irradiated. The adsorption of fluorescein-labeled fibrinogen (FITC-Fgn) from dilute buffer solution also produced visual information on the pattern. The kinetics of FITC-Fgn adsorption onto the oxidized and unoxidized MTS-silica surfaces from dilute protein solution proceeded with identical initial adsorption rates. The steady-state FITC-Fgn adsorption was twice as large on the unoxidized MTS-silica than on the oxidized MTS-silica surface.
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Affiliation(s)
- Jie Liu
- Department of Materials Science and Engineering, University of Utah, Salt Lake City, UT84112, USA
| | - Vladimir Hlady
- Department of Materials Science and Engineering, University of Utah, Salt Lake City, UT84112, USA ; Department of Bioengineering, University of Utah, Salt Lake City, UT84112, USA
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