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Fukata Y, Fukata M, MacGillavry HD, Nair D, Hosy E. Celebrating the Birthday of AMPA Receptor Nanodomains: Illuminating the Nanoscale Organization of Excitatory Synapses with 10 Nanocandles. J Neurosci 2024; 44:e2104232024. [PMID: 38839340 PMCID: PMC11154862 DOI: 10.1523/jneurosci.2104-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 06/07/2024] Open
Abstract
A decade ago, in 2013, and over the course of 4 summer months, three separate observations were reported that each shed light independently on a new molecular organization that fundamentally reshaped our perception of excitatory synaptic transmission (Fukata et al., 2013; MacGillavry et al., 2013; Nair et al., 2013). This discovery unveiled an intricate arrangement of AMPA-type glutamate receptors and their principal scaffolding protein PSD-95, at synapses. This breakthrough was made possible, thanks to advanced super-resolution imaging techniques. It fundamentally changed our understanding of excitatory synaptic architecture and paved the way for a brand-new area of research. In this Progressions article, the primary investigators of the nanoscale organization of synapses have come together to chronicle the tale of their discovery. We recount the initial inquiry that prompted our research, the preceding studies that inspired our work, the technical obstacles that were encountered, and the breakthroughs that were made in the subsequent decade in the realm of nanoscale synaptic transmission. We review the new discoveries made possible by the democratization of super-resolution imaging techniques in the field of excitatory synaptic physiology and architecture, first by the extension to other glutamate receptors and to presynaptic proteins and then by the notion of trans-synaptic organization. After describing the organizational modifications occurring in various pathologies, we discuss briefly the latest technical developments made possible by super-resolution imaging and emerging concepts in synaptic physiology.
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Affiliation(s)
- Yuko Fukata
- Division of Molecular and Cellular Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masaki Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
- Division of Neuropharmacology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Harold D MacGillavry
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Deepak Nair
- Centre for Neuroscience, Indian Institute of Science, Bangalore 560012, Karnataka, India
| | - Eric Hosy
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, CNRS UMR5297, Bordeaux F-33000, France
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2
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Teixeira P, Galland R, Chevrollier A. Super-resolution microscopies, technological breakthrough to decipher mitochondrial structure and dynamic. Semin Cell Dev Biol 2024; 159-160:38-51. [PMID: 38310707 DOI: 10.1016/j.semcdb.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/06/2024]
Abstract
Mitochondria are complex organelles with an outer membrane enveloping a second inner membrane that creates a vast matrix space partitioned by pockets or cristae that join the peripheral inner membrane with several thin junctions. Several micrometres long, mitochondria are generally close to 300 nm in diameter, with membrane layers separated by a few tens of nanometres. Ultrastructural data from electron microscopy revealed the structure of these mitochondria, while conventional optical microscopy revealed their extraordinary dynamics through fusion, fission, and migration processes but its limited resolution power restricted the possibility to go further. By overcoming the limits of light diffraction, Super-Resolution Microscopy (SRM) now offers the potential to establish the links between the ultrastructure and remodelling of mitochondrial membranes, leading to major advances in our understanding of mitochondria's structure-function. Here we review the contributions of SRM imaging to our understanding of the relationship between mitochondrial structure and function. What are the hopes for these new imaging approaches which are particularly important for mitochondrial pathologies?
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Affiliation(s)
- Pauline Teixeira
- Univ. Angers, INSERM, CNRS, MITOVASC, Equipe MITOLAB, SFR ICAT, F-49000 Angers, France
| | - Rémi Galland
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Arnaud Chevrollier
- Univ. Angers, INSERM, CNRS, MITOVASC, Equipe MITOLAB, SFR ICAT, F-49000 Angers, France.
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3
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Rimbault C, Breillat C, Compans B, Toulmé E, Vicente FN, Fernandez-Monreal M, Mascalchi P, Genuer C, Puente-Muñoz V, Gauthereau I, Hosy E, Claverol S, Giannone G, Chamma I, Mackereth CD, Poujol C, Choquet D, Sainlos M. Engineering paralog-specific PSD-95 recombinant binders as minimally interfering multimodal probes for advanced imaging techniques. eLife 2024; 13:e69620. [PMID: 38167295 PMCID: PMC10803022 DOI: 10.7554/elife.69620] [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: 05/04/2021] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Despite the constant advances in fluorescence imaging techniques, monitoring endogenous proteins still constitutes a major challenge in particular when considering dynamics studies or super-resolution imaging. We have recently evolved specific protein-based binders for PSD-95, the main postsynaptic scaffold proteins at excitatory synapses. Since the synthetic recombinant binders recognize epitopes not directly involved in the target protein activity, we consider them here as tools to develop endogenous PSD-95 imaging probes. After confirming their lack of impact on PSD-95 function, we validated their use as intrabody fluorescent probes. We further engineered the probes and demonstrated their usefulness in different super-resolution imaging modalities (STED, PALM, and DNA-PAINT) in both live and fixed neurons. Finally, we exploited the binders to enrich at the synapse genetically encoded calcium reporters. Overall, we demonstrate that these evolved binders constitute a robust and efficient platform to selectively target and monitor endogenous PSD-95 using various fluorescence imaging techniques.
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Affiliation(s)
- Charlotte Rimbault
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Christelle Breillat
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Benjamin Compans
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Estelle Toulmé
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Filipe Nunes Vicente
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Monica Fernandez-Monreal
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4BordeauxFrance
| | - Patrice Mascalchi
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4BordeauxFrance
| | - Camille Genuer
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Virginia Puente-Muñoz
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Isabel Gauthereau
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Eric Hosy
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | | | - Gregory Giannone
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Ingrid Chamma
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | | | - Christel Poujol
- University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4BordeauxFrance
| | - Daniel Choquet
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
| | - Matthieu Sainlos
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297BordeauxFrance
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4
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Basumatary J, Baro N, Joshi P, Mondal PP. Scanning single molecule localization microscopy (scanSMLM) for super-resolution volume imaging. Commun Biol 2023; 6:1050. [PMID: 37848705 PMCID: PMC10582190 DOI: 10.1038/s42003-023-05364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Over the last decade, single-molecule localization microscopy (SMLM) has developed into a set of powerful techniques that have improved spatial resolution over diffraction-limited microscopy and demonstrated the ability to resolve biological features down to a few tens of nanometers. We introduce a single molecule-based scanning SMLM (scanSMLM) system that enables rapid volume imaging. Along with epi-illumination, the system employs a scanning-based 4f detection for volume imaging. The 4f system comprises a combination of an electrically-tunable lens and high NA detection objective lens. By rapidly changing the aperture (or equivalently the focus) of an electrically-tunable lens (ETL) in a 4f detection system, the selectivity of the axial object plane is achieved, for which the image forms in the image/detector plane. So, in principle, one can scan the object volume by just altering the aperture of ETL. Two schemes were adopted to carry out volume imaging: cyclic scan and conventional scan. The cyclic scheme scans the volume in each scan cycle, whereas plane-wise scanning is performed in the conventional scheme. Hence, the cyclic scan ensures uniform dwell time on each frame during data collection, thereby evenly distributing photobleaching throughout the cell volume. With a minimal change in the system hardware (requiring the addition of an ETL lens and related electronics for step-voltage generation) in the existing SMLM system, volume scanning (along the z-axis) can be achieved. To calibrate and derive critical system parameters, we imaged fluorescent beads embedded in a gel-matrix 3D block as a test sample. Subsequently, scanSMLM is employed to visualize the architecture of actin-filaments and the distribution of Meos-Tom20 molecules on the mitochondrial membrane. The technique is further exploited to understand the clustering of Hemagglutinin (HA) protein single molecules in a transfected cell for studying Influenza-A disease progression. The system, for the first time, enabled 3D visualization of HA distribution that revealed HA cluster formation spanning the entire cell volume, post 24 hrs of transfection. Critical biophysical parameters related to HA clusters (density, the number of HA molecules per cluster, axial span, fraction of clustered molecules, and others) are also determined, giving an unprecedented insight into Influenza-A disease progression at the single-molecule level.
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Affiliation(s)
- Jigmi Basumatary
- Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Neptune Baro
- Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Prakash Joshi
- Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Partha Pratim Mondal
- Nanobioimaging Laboratory, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India.
- Centre for Cryogenic Technology, Indian Institute of Science, Bangalore, 560012, India.
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5
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Perera T, Gunasekara H, Hu YS. Single-Molecule Localization Microscopy Using Time-Lapse Imaging of Single-Antibody Labeling. Curr Protoc 2023; 3:e908. [PMID: 37830764 PMCID: PMC10593501 DOI: 10.1002/cpz1.908] [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] [Indexed: 10/14/2023]
Abstract
In single-molecule localization microscopy (SMLM), immunofluorescence (IF) staining affects the quality of the reconstructed superresolution images. However, optimizing IF staining remains challenging because IF staining is a one-step, irreversible process. Sample labeling through reversible binding presents an alternative strategy, but such techniques require significant technological advancements to enhance the dissociation of labels without sacrificing their binding specificity. In this article, we introduce time-lapse imaging of single-antibody labeling. Our versatile technique utilizes commercially available dye-conjugated antibodies. The method controls the antibody concentrations to capture single-antibody labeling of subcellular targets, thereby achieving SMLM through the labeling process. We further demonstrate dual-color single-antibody labeling to enhance the sample labeling density. The new approach allows the evaluation of antibody binding at the single-antibody level and within the cellular environment. This comprehensive guide offers step-by-step instructions for time-lapse imaging of single-antibody labeling experiments and enables the application of the single-antibody labeling technique to a wide range of targets. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Sample preparation for single-antibody labeling Basic Protocol 2: Data acquisition for single-molecule localization microscopy Alternate Protocol: Dual-color single-antibody labeling using OptoSplit II equation Basic Protocol 3: Image analysis.
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Affiliation(s)
- Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Hirushi Gunasekara
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Ying S. Hu
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
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6
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Zhu M, Zhang L, Jin L, Chen Y, Yang H, Ji B, Xu Y. Deep learning-enabled fast DNA-PAINT imaging in cells. BIOPHYSICS REPORTS 2023; 9:177-187. [PMID: 38516619 PMCID: PMC10951475 DOI: 10.52601/bpr.2023.230014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/07/2023] [Indexed: 03/23/2024] Open
Abstract
DNA-based point accumulation in nanoscale topography (DNA-PAINT) is a well-established technique for single-molecule localization microscopy (SMLM), enabling resolution of up to a few nanometers. Traditionally, DNA-PAINT involves the utilization of tens of thousands of single-molecule fluorescent images to generate a single super-resolution image. This process can be time-consuming, which makes it unfeasible for many researchers. Here, we propose a simplified DNA-PAINT labeling method and a deep learning-enabled fast DNA-PAINT imaging strategy for subcellular structures, such as microtubules. By employing our method, super-resolution reconstruction can be achieved with only one-tenth of the raw data previously needed, along with the option of acquiring the widefield image. As a result, DNA-PAINT imaging is significantly accelerated, making it more accessible to a wider range of biological researchers.
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Affiliation(s)
- Min Zhu
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
| | - Luhao Zhang
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
- Binjiang Institute of Zhejiang University, Hangzhou 310053, China
| | - Luhong Jin
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
| | - Yunyue Chen
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
| | - Haixu Yang
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
| | - Baohua Ji
- Department of Engineering Mechanics, Biomechanics and Biomaterials Laboratory, Zhejiang University, Hangzhou 310027, China
| | - Yingke Xu
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, State Key Laboratory of Extreme Photonics and Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for Clinical Evaluation and Translational Research, Zhejiang University, Hangzhou 310027, China
- Binjiang Institute of Zhejiang University, Hangzhou 310053, China
- Department of Endocrinology, Children’s Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Children’s Health, Hangzhou 310051, China
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7
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Tholen MME, Tas RP, Wang Y, Albertazzi L. Beyond DNA: new probes for PAINT super-resolution microscopy. Chem Commun (Camb) 2023; 59:8332-8342. [PMID: 37306078 PMCID: PMC10318573 DOI: 10.1039/d3cc00757j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/26/2023] [Indexed: 06/13/2023]
Abstract
In the last decade, point accumulation for imaging in nanoscale topography (PAINT) has emerged as a versatile tool for single-molecule localization microscopy (SMLM). Currently, DNA-PAINT is the most widely used, in which a transient stochastically binding DNA docking-imaging pair is used to reconstruct specific characteristics of biological or synthetic materials on a single-molecule level. Slowly, the need for PAINT probes that are not dependent on DNA has emerged. These probes can be based on (i) endogenous interactions, (ii) engineered binders, (iii) fusion proteins, or (iv) synthetic molecules and provide complementary applications for SMLM. Therefore, researchers have been expanding the PAINT toolbox with new probes. In this review, we provide an overview of the currently existing probes that go beyond DNA and their applications and challenges.
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Affiliation(s)
- Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Roderick P Tas
- Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing Soft Matter, Eindhoven University of Technology, Eindhoven, 5612 AP, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
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8
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Gunasekara H, Perera T, Anderson J, Saed B, Ramseier N, Keshta N, Hu YS. Superresolution Imaging with Single-Antibody Labeling. Bioconjug Chem 2023; 34:825-833. [PMID: 37145839 PMCID: PMC10859171 DOI: 10.1021/acs.bioconjchem.3c00178] [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] [Indexed: 05/06/2023]
Abstract
We present a versatile single-molecule localization microscopy technique utilizing time-lapse imaging of single-antibody labeling. By performing single-molecule imaging in the subminute time scale and tuning the antibody concentration to create sparse single-molecule binding, we captured antibody labeling of subcellular targets to generate superresolution images. Single-antibody labeling enabled dual-target superresolution imaging using dye-conjugated monoclonal and polyclonal antibodies. We further demonstrate a dual-color strategy to increase the sample labeling density. Single-antibody labeling paves a new way to evaluate antibody binding for superresolution imaging in the native cellular environment.
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Affiliation(s)
| | - Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences
| | - Jesse Anderson
- Department of Chemical Engineering, College of Engineering
| | - Badeia Saed
- Department of Chemistry, College of Liberal Arts and Sciences
| | - Neal Ramseier
- Department of Chemistry, College of Liberal Arts and Sciences
| | - Neama Keshta
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Ying S. Hu
- Department of Chemistry, College of Liberal Arts and Sciences
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9
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Nunes Vicente F, Chen T, Rossier O, Giannone G. Novel imaging methods and force probes for molecular mechanobiology of cytoskeleton and adhesion. Trends Cell Biol 2023; 33:204-220. [PMID: 36055943 DOI: 10.1016/j.tcb.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 12/01/2022]
Abstract
Detection and conversion of mechanical forces into biochemical signals is known as mechanotransduction. From cells to tissues, mechanotransduction regulates migration, proliferation, and differentiation in processes such as immune responses, development, and cancer progression. Mechanosensitive structures such as integrin adhesions, the actin cortex, ion channels, caveolae, and the nucleus sense and transmit forces. In vitro approaches showed that mechanosensing is based on force-dependent protein deformations and reorganizations. However, the mechanisms in cells remained unclear since cell imaging techniques lacked molecular resolution. Thanks to recent developments in super-resolution microscopy (SRM) and molecular force sensors, it is possible to obtain molecular insight of mechanosensing in live cells. We discuss how understanding of molecular mechanotransduction was revolutionized by these innovative approaches, focusing on integrin adhesions, actin structures, and the plasma membrane.
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Affiliation(s)
- Filipe Nunes Vicente
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Tianchi Chen
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France
| | - Olivier Rossier
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France
| | - Grégory Giannone
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
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10
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Youn Y, Lau GW, Lee Y, Maity BK, Gouaux E, Chung HJ, Selvin PR. Quantitative DNA-PAINT imaging of AMPA receptors in live neurons. CELL REPORTS METHODS 2023; 3:100408. [PMID: 36936077 PMCID: PMC10014303 DOI: 10.1016/j.crmeth.2023.100408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/25/2022] [Accepted: 01/25/2023] [Indexed: 02/18/2023]
Abstract
DNA-point accumulation for imaging at nanoscale topography (DNA-PAINT) can image fixed biological specimens with nanometer resolution and absolute stoichiometry. In living systems, however, the usage of DNA-PAINT has been limited due to high salt concentration in the buffer required for specific binding of the imager to the docker attached to the target. Here, we used multiple binding motifs of the docker, from 2 to 16, to accelerate the binding speed of the imager under physiological buffer conditions without compromising spatial resolution and maintaining the basal level homeostasis during the measurement. We imaged endogenous α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) in cultured neurons-critical proteins involved in nerve communication-by DNA-PAINT in 3-dimensions using a monovalent single-chain variable fragment (scFv) to the GluA1 subunit of AMPAR. We found a heterogeneous distribution of synaptic AMPARs: ≈60% are immobile, primarily in nanodomains, defined as AMPARs that are within 0.3 μm of the Homer1 protein in the postsynaptic density; the other ∼40% of AMPARs have restricted mobility and trajectory.
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Affiliation(s)
- Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gloria W. Lau
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yongjae Lee
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Barun Kumar Maity
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
- Howard Hughes Medical Institute, Portland, OR, USA
| | - Hee Jung Chung
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paul R. Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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11
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Arizono M, Idziak A, Quici F, Nägerl UV. Getting sharper: the brain under the spotlight of super-resolution microscopy. Trends Cell Biol 2023; 33:148-161. [PMID: 35906123 DOI: 10.1016/j.tcb.2022.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/18/2022] [Accepted: 06/20/2022] [Indexed: 01/25/2023]
Abstract
Brain cells such as neurons and astrocytes exhibit an extremely elaborate morphology, and their functional specializations like synapses and glial processes often fall below the resolution limit of conventional light microscopy. This is a huge obstacle for neurobiologists because the nanoarchitecture critically shapes fundamental functions like synaptic transmission and Ca2+ signaling. Super-resolution microscopy can overcome this problem, offering the chance to visualize the structural and molecular organization of brain cells in a living and dynamic tissue context, unlike traditional methods like electron microscopy or atomic force microscopy. This review covers the basic principles of the main super-resolution microscopy techniques in use today and explains how their specific strengths can illuminate the nanoscale mechanisms that govern brain physiology.
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Affiliation(s)
- Misa Arizono
- Interdisciplinary Institute for Neuroscience, University of Bordeaux and CNRS, Bordeaux, France; Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Agata Idziak
- Interdisciplinary Institute for Neuroscience, University of Bordeaux and CNRS, Bordeaux, France
| | - Federica Quici
- Interdisciplinary Institute for Neuroscience, University of Bordeaux and CNRS, Bordeaux, France
| | - U Valentin Nägerl
- Interdisciplinary Institute for Neuroscience, University of Bordeaux and CNRS, Bordeaux, France.
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12
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mGluR5 is transiently confined in perisynaptic nanodomains to shape synaptic function. Nat Commun 2023; 14:244. [PMID: 36646691 PMCID: PMC9842668 DOI: 10.1038/s41467-022-35680-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 12/19/2022] [Indexed: 01/18/2023] Open
Abstract
The unique perisynaptic distribution of postsynaptic metabotropic glutamate receptors (mGluRs) at excitatory synapses is predicted to directly shape synaptic function, but mechanistic insight into how this distribution is regulated and impacts synaptic signaling is lacking. We used live-cell and super-resolution imaging approaches, and developed molecular tools to resolve and acutely manipulate the dynamic nanoscale distribution of mGluR5. Here we show that mGluR5 is dynamically organized in perisynaptic nanodomains that localize close to, but not in the synapse. The C-terminal domain of mGluR5 critically controlled perisynaptic confinement and prevented synaptic entry. We developed an inducible interaction system to overcome synaptic exclusion of mGluR5 and investigate the impact on synaptic function. We found that mGluR5 recruitment to the synapse acutely increased synaptic calcium responses. Altogether, we propose that transient confinement of mGluR5 in perisynaptic nanodomains allows flexible modulation of synaptic function.
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13
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Pramanik SK, Sreedharan S, Tiwari R, Dutta S, Kandoth N, Barman S, Aderinto SO, Chattopadhyay S, Das A, Thomas JA. Nanoparticles for super-resolution microscopy: intracellular delivery and molecular targeting. Chem Soc Rev 2022; 51:9882-9916. [PMID: 36420611 DOI: 10.1039/d1cs00605c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Following an overview of the approaches and techniques used to acheive super-resolution microscopy, this review presents the advantages supplied by nanoparticle based probes for these applications. The various clases of nanoparticles that have been developed toward these goals are then critically described and these discussions are illustrated with a variety of examples from the recent literature.
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Affiliation(s)
- Sumit Kumar Pramanik
- CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India.
| | - Sreejesh Sreedharan
- Human Science Research Centre, University of Derby, Kedleston road, DE22 1GB, UK
| | - Rajeshwari Tiwari
- CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar, Gujarat 364002, India.
| | - Sourav Dutta
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Noufal Kandoth
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Surajit Barman
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Stephen O Aderinto
- Department of Chemistry, University of Sheffield, Western Bank, Sheffield, S3 7HF, UK.
| | - Samit Chattopadhyay
- Department of Biological Sciences, BITS-Pilani, K K Birla Goa Campus, NH 17B, Zuarinagar, Goa 403726, India.
| | - Amitava Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research, Kolkata, West Bengal, India.
| | - Jim A Thomas
- Department of Chemistry, University of Sheffield, Western Bank, Sheffield, S3 7HF, UK.
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14
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Glogger M, Wang D, Kompa J, Balakrishnan A, Hiblot J, Barth HD, Johnsson K, Heilemann M. Synergizing Exchangeable Fluorophore Labels for Multitarget STED Microscopy. ACS NANO 2022; 16:17991-17997. [PMID: 36223885 PMCID: PMC9706782 DOI: 10.1021/acsnano.2c07212] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Investigating the interplay of cellular proteins with optical microscopy requires multitarget labeling. Spectral multiplexing using high-affinity or covalent labels is limited in the number of fluorophores that can be discriminated in a single imaging experiment. Advanced microscopy methods such as STED microscopy additionally demand balanced excitation, depletion, and emission wavelengths for all fluorophores, further reducing multiplexing capabilities. Noncovalent, weak-affinity labels bypass this "spectral barrier" through label exchange and sequential imaging of different targets. Here, we combine exchangeable HaloTag ligands, weak-affinity DNA hybridization, and hydrophophic and protein-peptide interactions to increase labeling flexibility and demonstrate six-target STED microscopy in single cells. We further show that exchangeable labels reduce photobleaching as well as facilitate long acquisition times and multicolor live-cell and high-fidelity 3D STED microscopy. The synergy of different types of exchangeable labels increases the multiplexing capabilities in fluorescence microscopy, and by that, the information content of microscopy images.
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Affiliation(s)
- Marius Glogger
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Dongni Wang
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Julian Kompa
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Ashwin Balakrishnan
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Hans-Dieter Barth
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Mike Heilemann
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue Str. 7, 60438 Frankfurt, Germany
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15
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ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ. Nat Methods 2022; 19:1403-1410. [PMID: 36280724 PMCID: PMC9838136 DOI: 10.1038/s41592-022-01653-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 09/16/2022] [Indexed: 01/18/2023]
Abstract
RNA labeling in situ has enormous potential to visualize transcripts and quantify their levels in single cells, but it remains challenging to produce high levels of signal while also enabling multiplexed detection of multiple RNA species simultaneously. Here, we describe clampFISH 2.0, a method that uses an inverted padlock design to efficiently detect many RNA species and exponentially amplify their signals at once, while also reducing the time and cost compared with the prior clampFISH method. We leverage the increased throughput afforded by multiplexed signal amplification and sequential detection to detect 10 different RNA species in more than 1 million cells. We also show that clampFISH 2.0 works in tissue sections. We expect that the advantages offered by clampFISH 2.0 will enable many applications in spatial transcriptomics.
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16
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Ko J, Wilkovitsch M, Oh J, Kohler RH, Bolli E, Pittet MJ, Vinegoni C, Sykes DB, Mikula H, Weissleder R, Carlson JCT. Spatiotemporal multiplexed immunofluorescence imaging of living cells and tissues with bioorthogonal cycling of fluorescent probes. Nat Biotechnol 2022; 40:1654-1662. [PMID: 35654978 PMCID: PMC9669087 DOI: 10.1038/s41587-022-01339-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/28/2022] [Indexed: 02/07/2023]
Abstract
Cells in complex organisms undergo frequent functional changes, but few methods allow comprehensive longitudinal profiling of living cells. Here we introduce scission-accelerated fluorophore exchange (SAFE), a method for multiplexed temporospatial imaging of living cells with immunofluorescence. SAFE uses a rapid bioorthogonal click chemistry to remove immunofluorescent signals from the surface of labeled cells, cycling the nanomolar-concentration reagents in seconds and enabling multiple rounds of staining of the same samples. It is non-toxic and functional in both dispersed cells and intact living tissues. We demonstrate multiparameter (n ≥ 14), non-disruptive imaging of murine peripheral blood mononuclear and bone marrow cells to profile cellular differentiation. We also show longitudinal multiplexed imaging of bone marrow progenitor cells as they develop into neutrophils over 6 days and real-time multiplexed cycling of living mouse hepatic tissues. We anticipate that SAFE will find broad utility for investigating physiologic dynamics in living systems.
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Affiliation(s)
- Jina Ko
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Juhyun Oh
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Rainer H Kohler
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Evangelia Bolli
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Mikael J Pittet
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Zurich, Switzerland
- AGORA Cancer Center, Lausanne, Switzerland
| | - Claudio Vinegoni
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannes Mikula
- Institute of Applied Synthetic Chemistry, TU Wien, Vienna, Austria
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Jonathan C T Carlson
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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17
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Hu B, Sajid M, Lv R, Liu L, Sun C. A review of spatial profiling technologies for characterizing the tumor microenvironment in immuno-oncology. Front Immunol 2022; 13:996721. [PMID: 36389765 PMCID: PMC9659855 DOI: 10.3389/fimmu.2022.996721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/17/2022] [Indexed: 08/13/2023] Open
Abstract
Interpreting the mechanisms and principles that govern gene activity and how these genes work according to -their cellular distribution in organisms has profound implications for cancer research. The latest technological advancements, such as imaging-based approaches and next-generation single-cell sequencing technologies, have established a platform for spatial transcriptomics to systematically quantify the expression of all or most genes in the entire tumor microenvironment and explore an array of disease milieus, particularly in tumors. Spatial profiling technologies permit the study of transcriptional activity at the spatial or single-cell level. This multidimensional classification of the transcriptomic and proteomic signatures of tumors, especially the associated immune and stromal cells, facilitates evaluation of tumor heterogeneity, details of the evolutionary trajectory of each tumor, and multifaceted interactions between each tumor cell and its microenvironment. Therefore, spatial profiling technologies may provide abundant and high-resolution information required for the description of clinical-related features in immuno-oncology. From this perspective, the present review will highlight the importance of spatial transcriptomic and spatial proteomics analysis along with the joint use of other sequencing technologies and their implications in cancers and immune-oncology. In the near future, advances in spatial profiling technologies will undoubtedly expand our understanding of tumor biology and highlight possible precision therapeutic targets for cancer patients.
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Affiliation(s)
- Bian Hu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Muhammad Sajid
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rong Lv
- Blood Transfusion Laboratory, Anhui Blood Center, Hefei, China
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cheng Sun
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
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18
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Abstract
Fluorescence microscopy is a highly effective tool for interrogating biological structure and function, particularly when imaging across multiple spatiotemporal scales. Here we survey recent innovations and applications in the relatively understudied area of multiscale fluorescence imaging of living samples. We discuss fundamental challenges in live multiscale imaging and describe successful examples that highlight the power of this approach. We attempt to synthesize general strategies from these test cases, aiming to help accelerate progress in this exciting area.
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Affiliation(s)
- Yicong Wu
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Hari Shroff
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
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19
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Monitoring cell membrane recycling dynamics of proteins using whole-cell fluorescence recovery after photobleaching of pH-sensitive genetic tags. Nat Protoc 2022; 17:3056-3079. [PMID: 36064755 DOI: 10.1038/s41596-022-00732-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 06/07/2022] [Indexed: 11/08/2022]
Abstract
Population behavior of signaling molecules on the cell surface is key to their adaptive function. Live imaging of proteins tagged with fluorescent molecules has been an essential tool in understanding this behavior. Typically, genetic or chemical tags are used to target molecules present throughout the cell, whereas antibody-based tags label the externally exposed molecular domains only. Both approaches could potentially overlook the intricate process of in-out membrane recycling in which target molecules appear or disappear on the cell surface. This limitation is overcome by using a pH-sensitive fluorescent tag, such as Super-Ecliptic pHluorin (SEP), because its emission depends on whether it resides inside or outside the cell. Here we focus on the main glial glutamate transporter GLT1 and describe a genetic design that equips GLT1 molecules with SEP without interfering with the transporter's main function. Expressing GLT1-SEP in astroglia in cultures or in hippocampal slices enables monitoring of the real-time dynamics of the cell-surface and cytosolic fractions of the transporter in living cells. Whole-cell fluorescence recovery after photobleaching and quantitative image-kinetic analysis of the resulting time-lapse images enables assessment of the rate of GLT1-SEP recycling on the cell surface, a fundamental trafficking parameter unattainable previously. The present protocol takes 15-20 d to set up cell preparations, and 2-3 d to carry out live cell experiments and data analyses. The protocol can be adapted to study different membrane molecules of interest, particularly those proteins whose lifetime on the cell surface is critical to their adaptive function.
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20
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S A, Joshi P, Mondal PP. Detection of fortunate molecules induce particle resolution shift (PAR-shift) toward single-molecule limit in SMLM: A technique for resolving molecular clusters in cellular system. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:093704. [PMID: 36182464 DOI: 10.1063/5.0101009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
Molecules capable of emitting a large number of photons (also known as fortunate molecules) are crucial for achieving a resolution close to single molecule limit (the actual size of a single molecule). We propose a long-exposure single molecule localization microscopy (leSMLM) technique that enables detection of fortunate molecules, which is based on the fact that detecting a relatively small subset of molecules with large photon emission increases its localization precision (∼r0/N). Fortunate molecules have the ability to emit a large burst of photons over a prolonged time (> average blinking lifetime). So, a long exposure time allows the time window necessary to detect these elite molecules. The technique involves the detection of fortunate molecules to generate enough statistics for a quality reconstruction of the target protein distribution in a cellular system. Studies show a significant PArticle Resolution Shift (PAR-shift) of about 6 and 11 nm toward single-molecule-limit (far from diffraction-limit) for an exposure time window of 60 and 90 ms, respectively. In addition, a significant decrease in the fraction of fortunate molecules (single molecules with small localization precision) is observed. Specifically, 8.33% and 3.43% molecules are found to emit in 30-60 ms and >60 ms, respectively, when compared to single molecule localization microscopy (SMLM). The long exposure has enabled better visualization of the Dendra2HA molecular cluster, resolving sub-clusters within a large cluster. Thus, the proposed technique leSMLM facilitates a better study of cluster formation in fixed samples. Overall, leSMLM technique offers a spatial resolution improvement of ~ 10 nm compared to traditional SMLM at the cost of marginally poor temporal resolution.
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Affiliation(s)
- Aravinth S
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India
| | - Prakash Joshi
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India
| | - Partha Pratim Mondal
- Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore 560012, India
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21
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Getz AM, Ducros M, Breillat C, Lampin-Saint-Amaux A, Daburon S, François U, Nowacka A, Fernández-Monreal M, Hosy E, Lanore F, Zieger HL, Sainlos M, Humeau Y, Choquet D. High-resolution imaging and manipulation of endogenous AMPA receptor surface mobility during synaptic plasticity and learning. SCIENCE ADVANCES 2022; 8:eabm5298. [PMID: 35895810 PMCID: PMC9328687 DOI: 10.1126/sciadv.abm5298] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/10/2022] [Indexed: 05/18/2023]
Abstract
Regulation of synaptic neurotransmitter receptor content is a fundamental mechanism for tuning synaptic efficacy during experience-dependent plasticity and behavioral adaptation. However, experimental approaches to track and modify receptor movements in integrated experimental systems are limited. Exploiting AMPA-type glutamate receptors (AMPARs) as a model, we generated a knock-in mouse expressing the biotin acceptor peptide (AP) tag on the GluA2 extracellular N-terminal. Cell-specific introduction of biotin ligase allows the use of monovalent or tetravalent avidin variants to respectively monitor or manipulate the surface mobility of endogenous AMPAR containing biotinylated AP-GluA2 in neuronal subsets. AMPAR immobilization precluded the expression of long-term potentiation and formation of contextual fear memory, allowing target-specific control of the expression of synaptic plasticity and animal behavior. The AP tag knock-in model offers unprecedented access to resolve and control the spatiotemporal dynamics of endogenous receptors, and opens new avenues to study the molecular mechanisms of synaptic plasticity and learning.
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Affiliation(s)
- Angela M. Getz
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Mathieu Ducros
- Université de Bordeaux, CNRS, INSERM, Bordeaux Imaging Center (BIC), UAR 3420, US 4, F-33000 Bordeaux, France
| | - Christelle Breillat
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Aurélie Lampin-Saint-Amaux
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Sophie Daburon
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Urielle François
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Agata Nowacka
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Mónica Fernández-Monreal
- Université de Bordeaux, CNRS, INSERM, Bordeaux Imaging Center (BIC), UAR 3420, US 4, F-33000 Bordeaux, France
| | - Eric Hosy
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Frédéric Lanore
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Hanna L. Zieger
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Matthieu Sainlos
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Yann Humeau
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
| | - Daniel Choquet
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience (IINS), UMR 5297, F-33000 Bordeaux, France
- Université de Bordeaux, CNRS, INSERM, Bordeaux Imaging Center (BIC), UAR 3420, US 4, F-33000 Bordeaux, France
- Corresponding author.
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22
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Measuring Molecular Diffusion in Dynamic Subcellular Nanostructures by Fast Raster Image Correlation Spectroscopy and 3D Orbital Tracking. Int J Mol Sci 2022; 23:ijms23147623. [PMID: 35886970 PMCID: PMC9323805 DOI: 10.3390/ijms23147623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 06/21/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Here we provide demonstration that fast fluorescence fluctuation spectroscopy is a fast and robust approach to extract information on the dynamics of molecules enclosed within subcellular nanostructures (e.g., organelles or vesicles) which are also moving in the complex cellular environment. In more detail, Raster Image Correlation Spectroscopy (RICS) performed at fast timescales (i.e., microseconds) reveals the fast motion of fluorescently labeled molecules within two exemplary dynamic subcellular nanostructures of biomedical interest, the lysosome and the insulin secretory granule (ISG). The measurement of molecular diffusion is then used to extract information on the average properties of subcellular nanostructures, such as macromolecular crowding or molecular aggregation. Concerning the lysosome, fast RICS on a fluorescent tracer allowed us to quantitatively assess the increase in organelle viscosity in the pathological condition of Krabbe disease. In the case of ISGs, fast RICS on two ISG-specific secreting peptides unveiled their differential aggregation propensity depending on intragranular concentration. Finally, a combination of fast RICS and feedback-based 3D orbital tracking was used to subtract the slow movement of subcellular nanostructures from the fast diffusion of molecules contained within them and independently validate the results. Results presented here not only demonstrate the acquired ability to address the dynamic behavior of molecules in moving, nanoscopic reference systems, but prove the relevance of this approach to advance our knowledge on cell function at the subcellular scale.
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23
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Nienhaus K, Nienhaus GU. Genetically encodable fluorescent protein markers in advanced optical imaging. Methods Appl Fluoresc 2022; 10. [PMID: 35767981 DOI: 10.1088/2050-6120/ac7d3f] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Optical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
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24
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Lim JS, Kim HJ, Park I, Woo S, Kim JH, Park JW. Force Mapping Reveals the Spatial Distribution of Individual Proteins in a Neuron. NANO LETTERS 2022; 22:3865-3871. [PMID: 35549313 DOI: 10.1021/acs.nanolett.1c04395] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Conventional methods for studying the spatial distribution and expression level of proteins within neurons have primarily relied on immunolabeling and/or signal amplification. Here, we present an atomic force microscopy (AFM)-based nanoscale force mapping method, where Anti-LIMK1-tethered AFM probes were used to visualize individual LIMK1 proteins in cultured neurons directly through force measurements. We observed that the number density of LIMK1 decreased in neuronal somas after the cells were depolarized. We also elucidated the spatial distribution of LIMK1 in single spine areas and found that the protein predominantly locates at heads of spines rather than dendritic shafts. The study demonstrates that our method enables unveiling of the abundance and spatial distribution of a protein of interest in neurons without signal amplification or labeling. We expected that this approach should facilitate the studies of protein expression phenomena in depth in a wide range of biological systems.
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Affiliation(s)
- Ji-Seon Lim
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Hyun Jin Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Ikbum Park
- Analysis and Assessment Research Center, Research Institute of Industrial Science and Technology, 67 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Sungwook Woo
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joung-Hun Kim
- Department of Life Sciences, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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25
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Bodzęta A, Berger F, MacGillavry HD. Subsynaptic mobility of presynaptic mGluR types is differentially regulated by intra- and extracellular interactions. Mol Biol Cell 2022; 33:ar66. [PMID: 35511883 PMCID: PMC9635276 DOI: 10.1091/mbc.e21-10-0484] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Presynaptic metabotropic glutamate receptors (mGluRs) are essential for the control of synaptic transmission. However, how the subsynaptic dynamics of these receptors is controlled and contributes to synaptic signaling remain poorly understood quantitatively. Particularly, since the affinity of individual mGluR subtypes for glutamate differs considerably, the activation of mGluR subtypes critically depends on their precise subsynaptic distribution. Here, using superresolution microscopy and single-molecule tracking, we unravel novel molecular mechanisms that control the nanoscale distribution and mobility of presynaptic mGluRs in hippocampal neurons. We demonstrate that the high-affinity group II receptor mGluR2 localizes diffusely along the axon, and is highly mobile, while the low-affinity group III receptor mGluR7 is stably anchored at the active zone. We demonstrate that intracellular interactions modulate surface diffusion of mGluR2, while immobilization of mGluR7 at the active zone relies on its extracellular domain. Receptor activation or increases in synaptic activity do not alter the surface mobility of presynaptic mGluRs. Finally, computational modeling of presynaptic mGluR activity revealed that this particular nanoscale arrangement directly impacts their ability to modulate neurotransmitter release. Altogether, this study demonstrates that distinct mechanisms control surface mobility of presynaptic mGluRs to contribute differentially to glutamatergic synaptic transmission.
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Affiliation(s)
- Anna Bodzęta
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, The Netherlands
| | - Florian Berger
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, The Netherlands
| | - Harold D MacGillavry
- Division of Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH, The Netherlands
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26
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Baranovic J, Braunbeck S, Zaki N, Minniberger S, Chebli M, Plested AJR. The action of Con-ikot-ikot toxin on single AMPA-type glutamate receptors. J Gen Physiol 2022; 154:213109. [PMID: 35377397 PMCID: PMC9195068 DOI: 10.1085/jgp.202112912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 01/21/2022] [Accepted: 03/10/2022] [Indexed: 01/28/2023] Open
Abstract
Conotoxins are a large group of naturally occurring toxic peptides produced by the predatory sea snails of the genus Conus. Many of these toxins target ion channels, often with high specificity and affinity. As such, they have proven to be invaluable for basic research, as well as acting as leads for therapeutic strategies. Con-ikot-ikot is the only conotoxin so far identified that targets AMPA-type glutamate receptors, the main mediators of excitatory neurotransmission in the vertebrate brain. Here, we describe how the toxin modifies the activity of AMPA receptors at the single-channel level. The toxin binds to the AMPA receptor with EC50 of 5 nM, and once bound takes minutes to wash out. As shown previously, it effectively blocks desensitization of AMPA receptors; however, compared to other desensitization blockers, it is a poor stabilizer of the open channel because toxin-bound AMPA receptors undergo frequent brief closures. We propose that this is a direct consequence of the toxin's unique binding mode to the ligand-binding domains (LBDs). Unlike other blockers of desensitization, which stabilize individual dimers within an AMPA receptor tetramer, the toxin immobilizes all four LBDs of the tetramer. This result further emphasizes that quaternary reorganization of independent LBD dimers is essential for the full activity of AMPA receptors.
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Affiliation(s)
- Jelena Baranovic
- Leibniz Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,NeuroCure, Charité Universitätsmedizin, Berlin, Germany.,Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany.,University of Edinburgh, School of Biological Sciences, Edinburgh, UK
| | - Sebastian Braunbeck
- Leibniz Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,NeuroCure, Charité Universitätsmedizin, Berlin, Germany.,Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Nikolai Zaki
- Leibniz Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,NeuroCure, Charité Universitätsmedizin, Berlin, Germany.,Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Sonja Minniberger
- Leibniz Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,NeuroCure, Charité Universitätsmedizin, Berlin, Germany.,Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany
| | - Miriam Chebli
- Leibniz Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,NeuroCure, Charité Universitätsmedizin, Berlin, Germany
| | - Andrew J R Plested
- Leibniz Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,NeuroCure, Charité Universitätsmedizin, Berlin, Germany.,Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany
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27
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Adhikari S, Orrit M. Progress and perspectives in single-molecule optical spectroscopy. J Chem Phys 2022; 156:160903. [PMID: 35489995 DOI: 10.1063/5.0087003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We review some of the progress of single-molecule optical experiments in the past 20 years and propose some perspectives for the coming years. We particularly focus on methodological advances in fluorescence, super-resolution, photothermal contrast, and interferometric scattering and briefly discuss a few of the applications. These advances have enabled the exploration of new emitters and quantum optics; the chemistry and biology of complex heterogeneous systems, nanoparticles, and plasmonics; and the detection and study of non-fluorescing and non-absorbing nano-objects. We conclude by proposing some ideas for future experiments. The field will move toward more and better signals of a broader variety of objects and toward a sharper view of the surprising complexity of the nanoscale world of single (bio-)molecules, nanoparticles, and their nano-environments.
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Affiliation(s)
- Subhasis Adhikari
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2333 CA Leiden, The Netherlands
| | - Michel Orrit
- Huygens-Kamerlingh Onnes Laboratory, Leiden University, P.O. Box 9504, 2333 CA Leiden, The Netherlands
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28
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Lagardère M, Drouet A, Sainlos M, Thoumine O. High-Resolution Fluorescence Imaging Combined With Computer Simulations to Quantitate Surface Dynamics and Nanoscale Organization of Neuroligin-1 at Synapses. Front Synaptic Neurosci 2022; 14:835427. [PMID: 35546899 PMCID: PMC9083120 DOI: 10.3389/fnsyn.2022.835427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
Neuroligins (NLGNs) form a family of cell adhesion molecules implicated in synapse development, but the mechanisms that retain these proteins at synapses are still incompletely understood. Recent studies indicate that surface-associated NLGN1 is diffusionally trapped at synapses, where it interacts with quasi-static scaffolding elements of the post-synaptic density. Whereas single molecule tracking reveals rapid diffusion and transient immobilization of NLGN1 at synapses within seconds, fluorescence recovery after photobleaching experiments indicate instead a long-term turnover of NLGN1 at synapse, in the hour time range. To gain insight into the mechanisms supporting NLGN1 anchorage at post-synapses and try to reconcile those experimental paradigms, we quantitatively analyzed here live-cell and super-resolution imaging experiments performed on NLGN1 using a newly released simulator of membrane protein dynamics for fluorescence microscopy, FluoSim. Based on a small set of parameters including diffusion coefficients, binding constants, and photophysical rates, the framework describes fairly well the dynamic behavior of extra-synaptic and synaptic NLGN1 over both short and long time ranges, and provides an estimate of NLGN1 copy numbers in post-synaptic densities at steady-state (around 50 dimers). One striking result is that the residence time of NLGN1 at synapses is much longer than what can be expected from extracellular interactions with pre-synaptic neurexins only, suggesting that NLGN1 is stabilized at synapses through multivalent interactions with intracellular post-synaptic scaffolding proteins.
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29
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Nandi S, Caicedo K, Cognet L. When Super-Resolution Localization Microscopy Meets Carbon Nanotubes. NANOMATERIALS 2022; 12:nano12091433. [PMID: 35564142 PMCID: PMC9105540 DOI: 10.3390/nano12091433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 12/16/2022]
Abstract
We recently assisted in a revolution in the realm of fluorescence microscopy triggered by the advent of super-resolution techniques that surpass the classic diffraction limit barrier. By providing optical images with nanometer resolution in the far field, super-resolution microscopy (SRM) is currently accelerating our understanding of the molecular organization of bio-specimens, bridging the gap between cellular observations and molecular structural knowledge, which was previously only accessible using electron microscopy. SRM mainly finds its roots in progress made in the control and manipulation of the optical properties of (single) fluorescent molecules. The flourishing development of novel fluorescent nanostructures has recently opened the possibility of associating super-resolution imaging strategies with nanomaterials’ design and applications. In this review article, we discuss some of the recent developments in the field of super-resolution imaging explicitly based on the use of nanomaterials. As an archetypal class of fluorescent nanomaterial, we mainly focus on single-walled carbon nanotubes (SWCNTs), which are photoluminescent emitters at near-infrared (NIR) wavelengths bearing great interest for biological imaging and for information optical transmission. Whether for fundamental applications in nanomaterial science or in biology, we show how super-resolution techniques can be applied to create nanoscale images “in”, “of” and “with” SWCNTs.
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Affiliation(s)
- Somen Nandi
- Laboratoire Photonique Numérique et Nanosciences, Université de Bordeaux, UMR 5298, 33400 Talence, France; (S.N.); (K.C.)
- Institut d’Optique and CNRS, LP2N UMR 5298, 33400 Talence, France
| | - Karen Caicedo
- Laboratoire Photonique Numérique et Nanosciences, Université de Bordeaux, UMR 5298, 33400 Talence, France; (S.N.); (K.C.)
- Institut d’Optique and CNRS, LP2N UMR 5298, 33400 Talence, France
| | - Laurent Cognet
- Laboratoire Photonique Numérique et Nanosciences, Université de Bordeaux, UMR 5298, 33400 Talence, France; (S.N.); (K.C.)
- Institut d’Optique and CNRS, LP2N UMR 5298, 33400 Talence, France
- Correspondence:
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30
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Chater TE, Goda Y. The Shaping of AMPA Receptor Surface Distribution by Neuronal Activity. Front Synaptic Neurosci 2022; 14:833782. [PMID: 35387308 PMCID: PMC8979068 DOI: 10.3389/fnsyn.2022.833782] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/25/2022] [Indexed: 12/29/2022] Open
Abstract
Neurotransmission is critically dependent on the number, position, and composition of receptor proteins on the postsynaptic neuron. Of these, α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs) are responsible for the majority of postsynaptic depolarization at excitatory mammalian synapses following glutamate release. AMPARs are continually trafficked to and from the cell surface, and once at the surface, AMPARs laterally diffuse in and out of synaptic domains. Moreover, the subcellular distribution of AMPARs is shaped by patterns of activity, as classically demonstrated by the synaptic insertion or removal of AMPARs following the induction of long-term potentiation (LTP) and long-term depression (LTD), respectively. Crucially, there are many subtleties in the regulation of AMPARs, and exactly how local and global synaptic activity drives the trafficking and retention of synaptic AMPARs of different subtypes continues to attract attention. Here we will review how activity can have differential effects on AMPAR distribution and trafficking along with its subunit composition and phosphorylation state, and we highlight some of the controversies and remaining questions. As the AMPAR field is extensive, to say the least, this review will focus primarily on cellular and molecular studies in the hippocampus. We apologise to authors whose work could not be cited directly owing to space limitations.
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31
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Nieves DJ, Pandzic E, Gunasinghe SD, Goyette J, Owen DM, Justin Gooding J, Gaus K. The T cell receptor displays lateral signal propagation involving non-engaged receptors. NANOSCALE 2022; 14:3513-3526. [PMID: 35171177 DOI: 10.1039/d1nr05855j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
T cells are highly sensitive to low levels of antigen, but how this sensitivity is achieved is currently unknown. Here, we imaged proximal TCR-CD3 signal propagation with single molecule localization microscopy (SMLM) in T cells activated with nanoscale clusters of TCR stimuli. We observed the formation of large TCR-CD3 clusters that exceeded the area of the ligand clusters, and required multivalent interactions facilitated by TCR-CD3 phosphorylation for assembly. Within these clustered TCR-CD3 domains, TCR-CD3 signaling spread laterally for ∼500 nm, far beyond the activating site, via non-engaged receptors. Local receptor density determined the functional cooperativity between engaged and non-engaged receptors, but lateral signal propagation was not influenced by the genetic deletion of ZAP70. Taken together, our data demonstrates that clustered ligands induced the clustering of non-ligated TCR-CD3 into domains that cooperatively facilitate lateral signal propagation.
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Affiliation(s)
- Daniel J Nieves
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
- Institute of Immunology and Immunotherapy, School of Mathematics, and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.
| | - Elvis Pandzic
- Katharina Gaus Light Microscopy Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Sachith D Gunasinghe
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, School of Mathematics, and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.
| | - J Justin Gooding
- School of Chemistry and Australian Centre for NanoMedicine, University of New South Wales, Sydney, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, Australia
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32
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Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
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Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
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33
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Dudok B, Soltesz I. Imaging the endocannabinoid signaling system. J Neurosci Methods 2022; 367:109451. [PMID: 34921843 PMCID: PMC8734437 DOI: 10.1016/j.jneumeth.2021.109451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/18/2021] [Accepted: 12/13/2021] [Indexed: 02/03/2023]
Abstract
The endocannabinoid (eCB) system is one of the most widespread neuromodulatory systems in the mammalian brain, with a multifaceted role in functions ranging from development to synaptic plasticity. Endocannabinoids are synthesized on demand from membrane lipid precursors, and act primarily on a single G-protein coupled receptor type, CB1, to carry out diverse functions. Despite the importance of the eCB system both in healthy brain function and in disease, critically important details of eCB signaling remained unknown. How eCBs are released from the membrane, how these lipid molecules are transported between cells, and how the distribution of their receptors is controlled, remained elusive. Recent advances in optical microscopy methods and biosensor engineering may open up new avenues for studying eCB signaling. We summarize applications of superresolution microscopy using single molecule localization to reveal distinct patterns of nanoscale CB1 distribution in neuronal axons and axon terminals. We review single particle tracking studies using quantum dots that allowed visualizing CB1 trajectories. We highlight the recent development of fluorescent eCB biosensors, that revealed spatiotemporally specific eCB release in live cells and live animals. Finally, we discuss future directions where method development may help to advance a precise understanding of eCB signaling.
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Affiliation(s)
- Barna Dudok
- Department of Neurosurgery, Stanford University, Stanford, CA, USA.
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
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34
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Abstract
Molecular assembly in a complex cellular environment is vital for understanding underlying biological mechanisms. Biophysical parameters (such as single-molecule cluster density, cluster-area, pairwise distance, and number of molecules per cluster) related to molecular clusters directly associate with the physiological state (healthy/diseased) of a cell. Using super-resolution imaging along with powerful clustering methods (K-means, Gaussian mixture, and point clustering), we estimated these critical biophysical parameters associated with dense and sparse molecular clusters. We investigated Hemaglutinin (HA) molecules in an Influenza type A disease model. Subsequently, clustering parameters were estimated for transfected NIH3T3 cells. Investigations on test sample (randomly generated clusters) and NIH3T3 cells (expressing Dendra2-Hemaglutinin (Dendra2-HA) photoactivable molecules) show a significant disparity among the existing clustering techniques. It is observed that a single method is inadequate for estimating all relevant biophysical parameters accurately. Thus, a multimodel approach is necessary in order to characterize molecular clusters and determine critical parameters. The proposed study involving optical system development, photoactivable sample synthesis, and advanced clustering methods may facilitate a better understanding of single molecular clusters. Potential applications are in the emerging field of cell biology, biophysics, and fluorescence imaging.
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35
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Gagliano G, Nelson T, Saliba N, Vargas-Hernández S, Gustavsson AK. Light Sheet Illumination for 3D Single-Molecule Super-Resolution Imaging of Neuronal Synapses. Front Synaptic Neurosci 2021; 13:761530. [PMID: 34899261 PMCID: PMC8651567 DOI: 10.3389/fnsyn.2021.761530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 01/02/2023] Open
Abstract
The function of the neuronal synapse depends on the dynamics and interactions of individual molecules at the nanoscale. With the development of single-molecule super-resolution microscopy over the last decades, researchers now have a powerful and versatile imaging tool for mapping the molecular mechanisms behind the biological function. However, imaging of thicker samples, such as mammalian cells and tissue, in all three dimensions is still challenging due to increased fluorescence background and imaging volumes. The combination of single-molecule imaging with light sheet illumination is an emerging approach that allows for imaging of biological samples with reduced fluorescence background, photobleaching, and photodamage. In this review, we first present a brief overview of light sheet illumination and previous super-resolution techniques used for imaging of neurons and synapses. We then provide an in-depth technical review of the fundamental concepts and the current state of the art in the fields of three-dimensional single-molecule tracking and super-resolution imaging with light sheet illumination. We review how light sheet illumination can improve single-molecule tracking and super-resolution imaging in individual neurons and synapses, and we discuss emerging perspectives and new innovations that have the potential to enable and improve single-molecule imaging in brain tissue.
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Affiliation(s)
- Gabriella Gagliano
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Tyler Nelson
- Department of Chemistry, Rice University, Houston, TX, United States
- Applied Physics Program, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
| | - Nahima Saliba
- Department of Chemistry, Rice University, Houston, TX, United States
| | - Sofía Vargas-Hernández
- Department of Chemistry, Rice University, Houston, TX, United States
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
| | - Anna-Karin Gustavsson
- Department of Chemistry, Rice University, Houston, TX, United States
- Smalley-Curl Institute, Rice University, Houston, TX, United States
- Institute of Biosciences & Bioengineering, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
- Laboratory for Nanophotonics, Rice University, Houston, TX, United States
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Single-molecule imaging of glycan-lectin interactions on cells with Glyco-PAINT. Nat Chem Biol 2021; 17:1281-1288. [PMID: 34764473 DOI: 10.1038/s41589-021-00896-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 09/10/2021] [Indexed: 11/08/2022]
Abstract
Most lectins bind carbohydrate ligands with relatively low affinity, making the identification of optimal ligands challenging. Here we introduce a point accumulation in nanoscale topography (PAINT) super-resolution microscopy method to capture weak glycan-lectin interactions at the single-molecule level in living cells (Glyco-PAINT). Glyco-PAINT exploits weak and reversible sugar binding to directly achieve single-molecule detection and quantification in cells and is used to establish the relative kon and koff rates of a synthesized library of carbohydrate-based probes, as well as the diffusion coefficient of the receptor-sugar complex. Uptake of ligands correlates with their binding affinity and residence time to establish structure-function relations for various synthetic glycans. We reveal how sugar multivalency and presentation geometry can be optimized for binding and internalization. Overall, Glyco-PAINT represents a powerful approach to study weak glycan-lectin interactions on the surface of living cells, one that can be potentially extended to a variety of lectin-sugar interactions.
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37
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Rahm JV, Malkusch S, Endesfelder U, Dietz MS, Heilemann M. Diffusion State Transitions in Single-Particle Trajectories of MET Receptor Tyrosine Kinase Measured in Live Cells. FRONTIERS IN COMPUTER SCIENCE 2021. [DOI: 10.3389/fcomp.2021.757653] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single-particle tracking enables the analysis of the dynamics of biomolecules in living cells with nanometer spatial and millisecond temporal resolution. This technique reports on the mobility of membrane proteins and is sensitive to the molecular state of a biomolecule and to interactions with other biomolecules. Trajectories describe the mobility of single particles over time and provide information such as the diffusion coefficient and diffusion state. Changes in particle dynamics within single trajectories lead to segmentation, which allows to extract information on transitions of functional states of a biomolecule. Here, mean-squared displacement analysis is developed to classify trajectory segments into immobile, confined diffusing, and freely diffusing states, and to extract the occurrence of transitions between these modes. We applied this analysis to single-particle tracking data of the membrane receptor MET in live cells and analyzed state transitions in single trajectories of the un-activated receptor and the receptor bound to the ligand internalin B. We found that internalin B-bound MET shows an enhancement of transitions from freely and confined diffusing states into the immobile state as compared to un-activated MET. Confined diffusion acts as an intermediate state between immobile and free, as this state is most likely to change the diffusion state in the following segment. This analysis can be readily applied to single-particle tracking data of other membrane receptors and intracellular proteins under various conditions and contribute to the understanding of molecular states and signaling pathways.
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Perfilov MM, Gavrikov AS, Lukyanov KA, Mishin AS. Transient Fluorescence Labeling: Low Affinity-High Benefits. Int J Mol Sci 2021; 22:11799. [PMID: 34769228 PMCID: PMC8583718 DOI: 10.3390/ijms222111799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
Fluorescent labeling is an established method for visualizing cellular structures and dynamics. The fundamental diffraction limit in image resolution was recently bypassed with the development of super-resolution microscopy. Notably, both localization microscopy and stimulated emission depletion (STED) microscopy impose tight restrictions on the physico-chemical properties of labels. One of them-the requirement for high photostability-can be satisfied by transiently interacting labels: a constant supply of transient labels from a medium replenishes the loss in the signal caused by photobleaching. Moreover, exchangeable tags are less likely to hinder the intrinsic dynamics and cellular functions of labeled molecules. Low-affinity labels may be used both for fixed and living cells in a range of nanoscopy modalities. Nevertheless, the design of optimal labeling and imaging protocols with these novel tags remains tricky. In this review, we highlight the pros and cons of a wide variety of transiently interacting labels. We further discuss the state of the art and future perspectives of low-affinity labeling methods.
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Affiliation(s)
| | | | | | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.P.); (A.S.G.); (K.A.L.)
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39
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Abstract
Fluorescence imaging techniques play a pivotal role in our understanding of the nervous system. The emergence of various super-resolution microscopy methods and specialized fluorescent probes enables direct insight into neuronal structure and protein arrangements in cellular subcompartments with so far unmatched resolution. Super-resolving visualization techniques in neurons unveil a novel understanding of cytoskeletal composition, distribution, motility, and signaling of membrane proteins, subsynaptic structure and function, and neuron-glia interaction. Well-defined molecular targets in autoimmune and neurodegenerative disease models provide excellent starting points for in-depth investigation of disease pathophysiology using novel and innovative imaging methodology. Application of super-resolution microscopy in human brain samples and for testing clinical biomarkers is still in its infancy but opens new opportunities for translational research in neurology and neuroscience. In this review, we describe how super-resolving microscopy has improved our understanding of neuronal and brain function and dysfunction in the last two decades.
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Affiliation(s)
- Christian Werner
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Christian Geis
- Section Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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40
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Liouta K, Chabbert J, Benquet S, Tessier B, Studer V, Sainlos M, De Wit J, Thoumine O, Chamma I. Role of regulatory C-terminal motifs in synaptic confinement of LRRTM2. Biol Cell 2021; 113:492-506. [PMID: 34498765 DOI: 10.1111/boc.202100026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/25/2022]
Abstract
Leucine Rich Repeat Transmembrane proteins (LRRTMs) are neuronal cell adhesion molecules involved in synapse development and plasticity. LRRTM2 is the most synaptogenic isoform of the family, and its expression is strongly restricted to excitatory synapses in mature neurons. However, the mechanisms by which LRRTM2 is trafficked and stabilized at synapses remain unknown. Here, we examine the role of LRRTM2 intracellular domain on its membrane expression and stabilization at excitatory synapses, using a knock-down strategy combined to single molecule tracking and super-resolution dSTORM microscopy. We show that LRRTM2 operates an important shift in mobility after synaptogenesis in hippocampal neurons. Knock-down of LRRTM2 during synapse formation reduced excitatory synapse density in mature neurons. Deletion of LRRTM2 C-terminal domain abolished the compartmentalization of LRRTM2 in dendrites and disrupted its synaptic enrichment. Furtheremore, we show that LRRTM2 diffusion is increased in the absence of its intracellular domain, and that the protein is more dispersed at synapses. Surprisingly, LRRTM2 confinement at synapses was strongly dependent on a YxxC motif in the C-terminal domain, but was independent of the PDZ-like binding motif ECEV. Finally, the nanoscale organization of LRRTM2 at excitatory synapses depended on its C-terminal domain, with involvement of both the PDZ-binding and YxxC motifs. Altogether, these results demonstrate that LRRTM2 trafficking and enrichment at excitatory synapses are dependent on its intracellular domain.
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Affiliation(s)
- Konstantina Liouta
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Julia Chabbert
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Sebastien Benquet
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Béatrice Tessier
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Vincent Studer
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Matthieu Sainlos
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Joris De Wit
- VIB Center for Brain & Disease Research, Leuven, Belgium.,KU Leuven, Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Olivier Thoumine
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
| | - Ingrid Chamma
- Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, Bordeaux, France.,Interdisciplinary Institute for Neuroscience, University of Bordeaux, Bordeaux, France
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41
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Xiang L, Chen K, Xu K. Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy. ACS NANO 2021; 15:12483-12496. [PMID: 34304562 PMCID: PMC8789943 DOI: 10.1021/acsnano.1c04708] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The rise of single-molecule localization microscopy (SMLM) and related super-resolution methods over the past 15 years has revolutionized how we study biological and materials systems. In this Perspective, we reflect on the underlying philosophy of how diffraction-unlimited pictures containing rich spatial and functional information may gradually emerge through the local accumulation of single-molecule measurements. Starting with the basic concepts, we analyze the uniqueness of and opportunities in building up the final picture one molecule at a time. After brief introductions to the more established multicolor and three-dimensional measurements, we highlight emerging efforts to extend SMLM to new dimensions and functionalities as fluorescence polarization, emission spectra, and molecular motions, and discuss rising opportunities and future directions. With single molecules as our quanta, the bottom-up accumulation approach provides a powerful conduit for multidimensional microscopy at the nanoscale.
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42
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Zieger HL, Choquet D. Nanoscale synapse organization and dysfunction in neurodevelopmental disorders. Neurobiol Dis 2021; 158:105453. [PMID: 34314857 DOI: 10.1016/j.nbd.2021.105453] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/18/2021] [Accepted: 07/21/2021] [Indexed: 12/20/2022] Open
Abstract
Neurodevelopmental disorders such as those linked to intellectual disabilities or autism spectrum disorder are thought to originate in part from genetic defects in synaptic proteins. Single gene mutations linked to synapse dysfunction can broadly be separated in three categories: disorders of transcriptional regulation, disorders of synaptic signaling and disorders of synaptic scaffolding and structures. The recent developments in super-resolution imaging technologies and their application to synapses have unraveled a complex nanoscale organization of synaptic components. On the one hand, part of receptors, adhesion proteins, ion channels, scaffold elements and the pre-synaptic release machinery are partitioned in subsynaptic nanodomains, and the respective organization of these nanodomains has tremendous impact on synaptic function. For example, pre-synaptic neurotransmitter release sites are partly aligned with nanometer precision to postsynaptic receptor clusters. On the other hand, a large fraction of synaptic components is extremely dynamic and constantly exchanges between synaptic domains and extrasynaptic or intracellular compartments. It is largely the combination of the exquisitely precise nanoscale synaptic organization of synaptic components and their high dynamic that allows the rapid and profound regulation of synaptic function during synaptic plasticity processes that underlie adaptability of brain function, learning and memory. It is very tempting to speculate that genetic defects that lead to neurodevelopmental disorders and target synaptic scaffolds and structures mediate their deleterious impact on brain function through perturbing synapse nanoscale dynamic organization. We discuss here how applying super-resolution imaging methods in models of neurodevelopmental disorders could help in addressing this question.
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Affiliation(s)
- Hanna L Zieger
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Daniel Choquet
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France; Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, F-33000 Bordeaux, France.
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43
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Bullerjahn JT, Hummer G. Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments. J Chem Phys 2021; 154:234105. [PMID: 34241279 DOI: 10.1063/5.0038174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single-molecule localization microscopy allows practitioners to locate and track labeled molecules in biological systems. When extracting diffusion coefficients from the resulting trajectories, it is common practice to perform a linear fit on mean-squared-displacement curves. However, this strategy is suboptimal and prone to errors. Recently, it was shown that the increments between the observed positions provide a good estimate for the diffusion coefficient, and their statistics are well-suited for likelihood-based analysis methods. Here, we revisit the problem of extracting diffusion coefficients from single-particle tracking experiments subject to static noise and dynamic motion blur using the principle of maximum likelihood. Taking advantage of an efficient real-space formulation, we extend the model to mixtures of subpopulations differing in their diffusion coefficients, which we estimate with the help of the expectation-maximization algorithm. This formulation naturally leads to a probabilistic assignment of trajectories to subpopulations. We employ the theory to analyze experimental tracking data that cannot be explained with a single diffusion coefficient. We test how well a dataset conforms to the assumptions of a diffusion model and determine the optimal number of subpopulations with the help of a quality factor of known analytical distribution. To facilitate use by practitioners, we provide a fast open-source implementation of the theory for the efficient analysis of multiple trajectories in arbitrary dimensions simultaneously.
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Affiliation(s)
- Jakob Tómas Bullerjahn
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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44
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Klatt O, Repetto D, Brockhaus J, Reissner C, El Khallouqi A, Rohlmann A, Heine M, Missler M. Endogenous β-neurexins on axons and within synapses show regulated dynamic behavior. Cell Rep 2021; 35:109266. [PMID: 34133920 DOI: 10.1016/j.celrep.2021.109266] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/21/2020] [Accepted: 05/26/2021] [Indexed: 11/25/2022] Open
Abstract
Neurexins are key organizer molecules that regulate synaptic function and are implicated in autism and schizophrenia. β-neurexins interact with numerous cell adhesion and receptor molecules, but their neuronal localization remains elusive. Using single-molecule tracking and high-resolution microscopy to detect neurexin1β and neurexin3β in primary hippocampal neurons from knockin mice, we demonstrate that endogenous β-neurexins are present in fewer than half of excitatory and inhibitory synapses. Moreover, we observe a large extrasynaptic pool of β-neurexins on axons and show that axonal β-neurexins diffuse with higher surface mobility than those transiently confined within synapses. Stimulation of neuronal activity further increases the mobility of synaptic and axonal β-neurexins, whereas inhibition causes the opposite. Blocking ectodomain cleavage by metalloproteases also reduces β-neurexin mobility and enhances glutamate release. These findings suggest that the surface mobility of endogenous β-neurexins inside and outside of synapses is dynamically regulated and linked to neuronal activity.
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Affiliation(s)
- Oliver Klatt
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany; Functional Neurobiology Group, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Daniele Repetto
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany
| | - Johannes Brockhaus
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany
| | - Carsten Reissner
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany
| | - Abderazzaq El Khallouqi
- Functional Neurobiology Group, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg University, 55128 Mainz, Germany
| | - Astrid Rohlmann
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany
| | - Martin Heine
- Functional Neurobiology Group, Institute for Developmental Biology and Neurobiology, Johannes Gutenberg University, 55128 Mainz, Germany.
| | - Markus Missler
- Institute of Anatomy and Molecular Neurobiology, Westfälische Wilhelms-University, 48149 Münster, Germany.
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45
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Compans B, Camus C, Kallergi E, Sposini S, Martineau M, Butler C, Kechkar A, Klaassen RV, Retailleau N, Sejnowski TJ, Smit AB, Sibarita JB, Bartol TM, Perrais D, Nikoletopoulou V, Choquet D, Hosy E. NMDAR-dependent long-term depression is associated with increased short term plasticity through autophagy mediated loss of PSD-95. Nat Commun 2021; 12:2849. [PMID: 33990590 PMCID: PMC8121912 DOI: 10.1038/s41467-021-23133-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/07/2021] [Indexed: 01/27/2023] Open
Abstract
Long-term depression (LTD) of synaptic strength can take multiple forms and contribute to circuit remodeling, memory encoding or erasure. The generic term LTD encompasses various induction pathways, including activation of NMDA, mGlu or P2X receptors. However, the associated specific molecular mechanisms and effects on synaptic physiology are still unclear. We here compare how NMDAR- or P2XR-dependent LTD affect synaptic nanoscale organization and function in rodents. While both LTDs are associated with a loss and reorganization of synaptic AMPARs, only NMDAR-dependent LTD induction triggers a profound reorganization of PSD-95. This modification, which requires the autophagy machinery to remove the T19-phosphorylated form of PSD-95 from synapses, leads to an increase in AMPAR surface mobility. We demonstrate that these post-synaptic changes that occur specifically during NMDAR-dependent LTD result in an increased short-term plasticity improving neuronal responsiveness of depressed synapses. Our results establish that P2XR- and NMDAR-mediated LTD are associated to functionally distinct forms of LTD.
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Affiliation(s)
- Benjamin Compans
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
| | - Come Camus
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
| | - Emmanouela Kallergi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Silvia Sposini
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
| | - Magalie Martineau
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
| | - Corey Butler
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
| | - Adel Kechkar
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
| | - Remco V Klaassen
- Department Molecular and Cellular Neurobiology, Amsterdam, HV, The Netherlands
| | - Natacha Retailleau
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
| | - Terrence J Sejnowski
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - August B Smit
- Department Molecular and Cellular Neurobiology, Amsterdam, HV, The Netherlands
| | - Jean-Baptiste Sibarita
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
| | - Thomas M Bartol
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - David Perrais
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
| | | | - Daniel Choquet
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France
- Univ. Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, Bordeaux, France
| | - Eric Hosy
- Interdisciplinary Institute for Neuroscience, CNRS, Univ. Bordeaux, IINS, UMR 5297, Bordeaux, France.
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46
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Wolf P, Gavins G, Beck‐Sickinger AG, Seitz O. Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags. Chembiochem 2021; 22:1717-1732. [PMID: 33428317 PMCID: PMC8248378 DOI: 10.1002/cbic.202000797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.
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Affiliation(s)
- Philipp Wolf
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Georgina Gavins
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| | - Annette G. Beck‐Sickinger
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Oliver Seitz
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
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47
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Filius M, Kim SH, Severins I, Joo C. High-Resolution Single-Molecule FRET via DNA eXchange (FRET X). NANO LETTERS 2021; 21:3295-3301. [PMID: 33739111 PMCID: PMC8050827 DOI: 10.1021/acs.nanolett.1c00725] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/10/2021] [Indexed: 05/20/2023]
Abstract
Single-molecule FRET is a versatile tool to study nucleic acids and proteins at the nanometer scale. However, currently, only a couple of FRET pairs can be reliably measured on a single object, which makes it difficult to apply single-molecule FRET for structural analysis of biomolecules. Here, we present an approach that allows for the determination of multiple distances between FRET pairs in a single object. We use programmable, transient binding between short DNA strands to resolve the FRET efficiency of multiple fluorophore pairs. By allowing only a single FRET pair to be formed at a time, we can determine the pair distance with subnanometer precision. The distance between other pairs are determined by sequentially exchanging DNA strands. We name this multiplexing approach FRET X for FRET via DNA eXchange. Our FRET X technology will be a tool for the high-resolution analysis of biomolecules and nanostructures.
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48
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Choquet D, Sainlos M, Sibarita JB. Advanced imaging and labelling methods to decipher brain cell organization and function. Nat Rev Neurosci 2021; 22:237-255. [PMID: 33712727 DOI: 10.1038/s41583-021-00441-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2021] [Indexed: 01/31/2023]
Abstract
The brain is arguably the most complex organ. The branched and extended morphology of nerve cells, their subcellular complexity, the multiplicity of brain cell types as well as their intricate connectivity and the scattering properties of brain tissue present formidable challenges to the understanding of brain function. Neuroscientists have often been at the forefront of technological and methodological developments to overcome these hurdles to visualize, quantify and modify cell and network properties. Over the last few decades, the development of advanced imaging methods has revolutionized our approach to explore the brain. Super-resolution microscopy and tissue imaging approaches have recently exploded. These instrumentation-based innovations have occurred in parallel with the development of new molecular approaches to label protein targets, to evolve new biosensors and to target them to appropriate cell types or subcellular compartments. We review the latest developments for labelling and functionalizing proteins with small localization and functionalized reporters. We present how these molecular tools are combined with the development of a wide variety of imaging methods that break either the diffraction barrier or the tissue penetration depth limits. We put these developments in perspective to emphasize how they will enable step changes in our understanding of the brain.
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Affiliation(s)
- Daniel Choquet
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France. .,University of Bordeaux, CNRS, INSERM, Bordeaux Imaging Center, BIC, UMS 3420, US 4, Bordeaux, France.
| | - Matthieu Sainlos
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
| | - Jean-Baptiste Sibarita
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, Bordeaux, France.
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49
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Harper CB, Smillie KJ. Current molecular approaches to investigate pre-synaptic dysfunction. J Neurochem 2021; 157:107-129. [PMID: 33544872 DOI: 10.1111/jnc.15316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022]
Abstract
Over the course of the last few decades it has become clear that many neurodevelopmental and neurodegenerative disorders have a synaptic defect, which contributes to pathogenicity. A rise in new techniques, and in particular '-omics'-based methods providing large datasets, has led to an increase in potential proteins and pathways implicated in synaptic function and related disorders. Additionally, advancements in imaging techniques have led to the recent discovery of alternative modes of synaptic vesicle recycling. This has resulted in a lack of clarity over the precise role of different pathways in maintaining synaptic function and whether these new pathways are dysfunctional in neurodevelopmental and neurodegenerative disorders. A greater understanding of the molecular detail of pre-synaptic function in health and disease is key to targeting new proteins and pathways for novel treatments and the variety of new techniques currently available provides an ideal opportunity to investigate these functions. This review focuses on techniques to interrogate pre-synaptic function, concentrating mainly on synaptic vesicle recycling. It further examines techniques to determine the underlying molecular mechanism of pre-synaptic dysfunction and discusses methods to identify molecular targets, along with protein-protein interactions and cellular localization. In combination, these techniques will provide an expanding and more complete picture of pre-synaptic function. With the application of recent technological advances, we are able to resolve events with higher spatial and temporal resolution, leading research towards a greater understanding of dysfunction at the presynapse and the role it plays in pathogenicity.
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Affiliation(s)
- Callista B Harper
- Centre for Discovery Brain Sciences, University of Edinburgh, Scotland, UK
| | - Karen J Smillie
- Centre for Discovery Brain Sciences, University of Edinburgh, Scotland, UK
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50
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Okabe S. Recent advances in computational methods for measurement of dendritic spines imaged by light microscopy. Microscopy (Oxf) 2021; 69:196-213. [PMID: 32244257 DOI: 10.1093/jmicro/dfaa016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/04/2020] [Accepted: 03/23/2020] [Indexed: 12/13/2022] Open
Abstract
Dendritic spines are small protrusions that receive most of the excitatory inputs to the pyramidal neurons in the neocortex and the hippocampus. Excitatory neural circuits in the neocortex and hippocampus are important for experience-dependent changes in brain functions, including postnatal sensory refinement and memory formation. Several lines of evidence indicate that synaptic efficacy is correlated with spine size and structure. Hence, precise and accurate measurement of spine morphology is important for evaluation of neural circuit function and plasticity. Recent advances in light microscopy and image analysis techniques have opened the way toward a full description of spine nanostructure. In addition, large datasets of spine nanostructure can be effectively analyzed using machine learning techniques and other mathematical approaches, and recent advances in super-resolution imaging allow researchers to analyze spine structure at an unprecedented level of precision. This review summarizes computational methods that can effectively identify, segment and quantitate dendritic spines in either 2D or 3D imaging. Nanoscale analysis of spine structure and dynamics, combined with new mathematical approaches, will facilitate our understanding of spine functions in physiological and pathological conditions.
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Affiliation(s)
- Shigeo Okabe
- Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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