1
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Froehlich T, Jenner A, Cavarischia-Rega C, Fagbadebo FO, Lurz Y, Frecot DI, Kaiser PD, Nueske S, Scholz AM, Schäffer E, Garcia-Saez AJ, Macek B, Rothbauer U. Nanobodies as novel tools to monitor the mitochondrial fission factor Drp1. Life Sci Alliance 2024; 7:e202402608. [PMID: 38816213 PMCID: PMC11140114 DOI: 10.26508/lsa.202402608] [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: 01/22/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
In cells, mitochondria undergo constant fusion and fission. An essential factor for fission is the mammalian dynamin-related protein 1 (Drp1). Dysregulation of Drp1 is associated with neurodegenerative diseases including Parkinson's, cardiovascular diseases and cancer, making Drp1 a pivotal biomarker for monitoring mitochondrial status and potential pathophysiological conditions. Here, we developed nanobodies (Nbs) as versatile binding molecules for proteomics, advanced microscopy and live cell imaging of Drp1. To specifically enrich endogenous Drp1 with interacting proteins for proteomics, we functionalized high-affinity Nbs into advanced capture matrices. Furthermore, we detected Drp1 by bivalent Nbs combined with site-directed fluorophore labelling in super-resolution STORM microscopy. For real-time imaging of Drp1, we intracellularly expressed fluorescently labelled Nbs, so-called chromobodies (Cbs). To improve the signal-to-noise ratio, we further converted Cbs into a "turnover-accelerated" format. With these imaging probes, we visualized the dynamics of endogenous Drp1 upon compound-induced mitochondrial fission in living cells. Considering the wide range of research applications, the presented Nb toolset will open up new possibilities for advanced functional studies of Drp1 in disease-relevant models.
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Affiliation(s)
- Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Andreas Jenner
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Claudia Cavarischia-Rega
- Quantitative Proteomics, Department of Biology, Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | | | - Yannic Lurz
- Center for Plant Molecular Biology (ZMBP), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Philipp D Kaiser
- https://ror.org/03a1kwz48 NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Stefan Nueske
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University Munich, Munich, Germany
| | - Armin M Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University Munich, Munich, Germany
| | - Erik Schäffer
- Center for Plant Molecular Biology (ZMBP), Eberhard Karls University Tübingen, Tübingen, Germany
| | - Ana J Garcia-Saez
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Boris Macek
- Quantitative Proteomics, Department of Biology, Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
- https://ror.org/03a1kwz48 Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
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2
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Zhang L, Zhou Y, Xie Y, Ying Y, Li Y, Ye S, Wang Z. Adjunctive clozapine with bright light mitigates cognitive deficits by synaptic plasticity and neurogenesis in sub-chronic MK-801 treated mice. Pharmacol Biochem Behav 2024; 243:173821. [PMID: 39002805 DOI: 10.1016/j.pbb.2024.173821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
Schizophrenia impacts about 1 % of the global population, with clozapine (CLZ) being a critical treatment for refractory cases despite its limitations in effectiveness and adverse effects. Therefore, the search for more effective treatments remains urgent. Light treatment (LT) recognized for enhancing cognition and mood, presents a promising complementary approach. This study investigated the effects of CLZ and LT on cognitive impairments in a sub-chronic MK-801 induced schizophrenia mouse model. Results showed that both CLZ and CLZ + LT treatment elevate cognitive performance of sub-chronic MK-801 treated mice in serial behavioral tests over two months. Histological analysis revealed increased dendritic spine density and branching, and synaptic repair in the hippocampus with CLZ and CLZ + LT interventions. Furthermore, both treatments increased brain-derived neurotrophic factor (BDNF) expression in the hippocampus, likely contributing to cognitive amelioration in MK-801 treated mice. Additionally, BrdU labeling revealed that CLZ + LT further enhances neurogenesis in the dentate gyrus (DG) and lateral ventricle (LV) of sub-chronic MK-801 treated mice. These findings may have implications for the development of noninvasive and adjunctive treatment strategies aimed at alleviating cognitive impairments and improving functional outcomes in individuals with schizophrenia.
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Affiliation(s)
- Lizhi Zhang
- Zhejiang Key Laboratory of Pathophysiology, Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Rd, Ningbo, Zhejiang 315211, China; Key Laboratory of Addiction Research of Zhejiang Province, Kang Ning Hospital, Ningbo 315010, China
| | - Yiying Zhou
- Zhejiang Key Laboratory of Pathophysiology, Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Rd, Ningbo, Zhejiang 315211, China; Key Laboratory of Addiction Research of Zhejiang Province, Kang Ning Hospital, Ningbo 315010, China
| | - Yanhong Xie
- Zhejiang Key Laboratory of Pathophysiology, Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Rd, Ningbo, Zhejiang 315211, China; Key Laboratory of Addiction Research of Zhejiang Province, Kang Ning Hospital, Ningbo 315010, China
| | - Yudong Ying
- Zhejiang Key Laboratory of Pathophysiology, Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Rd, Ningbo, Zhejiang 315211, China; Key Laboratory of Addiction Research of Zhejiang Province, Kang Ning Hospital, Ningbo 315010, China
| | - Yan Li
- Zhejiang Key Laboratory of Pathophysiology, Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Rd, Ningbo, Zhejiang 315211, China; Key Laboratory of Addiction Research of Zhejiang Province, Kang Ning Hospital, Ningbo 315010, China
| | - Sen Ye
- Zhejiang Key Laboratory of Pathophysiology, Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Rd, Ningbo, Zhejiang 315211, China; Key Laboratory of Addiction Research of Zhejiang Province, Kang Ning Hospital, Ningbo 315010, China
| | - Zhengchun Wang
- Zhejiang Key Laboratory of Pathophysiology, Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Rd, Ningbo, Zhejiang 315211, China; The Affiliated People's Hospital of Ningbo University, Ningbo 315100, China; Key Laboratory of Addiction Research of Zhejiang Province, Kang Ning Hospital, Ningbo 315010, China.
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3
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Hines AD, Kewin AB, Van De Poll MN, Anggono V, Bademosi AT, van Swinderen B. Synapse-Specific Trapping of SNARE Machinery Proteins in the Anesthetized Drosophila Brain. J Neurosci 2024; 44:e0588232024. [PMID: 38749704 PMCID: PMC11170680 DOI: 10.1523/jneurosci.0588-23.2024] [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: 03/29/2023] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024] Open
Abstract
General anesthetics disrupt brain network dynamics through multiple pathways, in part through postsynaptic potentiation of inhibitory ion channels as well as presynaptic inhibition of neuroexocytosis. Common clinical general anesthetic drugs, such as propofol and isoflurane, have been shown to interact and interfere with core components of the exocytic release machinery to cause impaired neurotransmitter release. Recent studies however suggest that these drugs do not affect all synapse subtypes equally. We investigated the role of the presynaptic release machinery in multiple neurotransmitter systems under isoflurane general anesthesia in the adult female Drosophila brain using live-cell super-resolution microscopy and optogenetic readouts of exocytosis and neural excitability. We activated neurotransmitter-specific mushroom body output neurons and imaged presynaptic function under isoflurane anesthesia. We found that isoflurane impaired synaptic release and presynaptic protein dynamics in excitatory cholinergic synapses. In contrast, isoflurane had little to no effect on inhibitory GABAergic or glutamatergic synapses. These results present a distinct inhibitory mechanism for general anesthesia, whereby neuroexocytosis is selectively impaired at excitatory synapses, while inhibitory synapses remain functional. This suggests a presynaptic inhibitory mechanism that complements the other inhibitory effects of these drugs.
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Affiliation(s)
- Adam D Hines
- Queensland Brain Institute, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Amber B Kewin
- Queensland Brain Institute, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Matthew N Van De Poll
- Queensland Brain Institute, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Victor Anggono
- Queensland Brain Institute, The University of Queensland, St Lucia 4072, Queensland, Australia
- Clem Jones Centre for Ageing and Dementia Research, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Adekunle T Bademosi
- Queensland Brain Institute, The University of Queensland, St Lucia 4072, Queensland, Australia
- Clem Jones Centre for Ageing and Dementia Research, The University of Queensland, St Lucia 4072, Queensland, Australia
| | - Bruno van Swinderen
- Queensland Brain Institute, The University of Queensland, St Lucia 4072, Queensland, Australia
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4
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Markusson S, Raasakka A, Schröder M, Sograte-Idrissi S, Rahimi AM, Asadpour O, Körner H, Lodygin D, Eichel-Vogel MA, Chowdhury R, Sutinen A, Muruganandam G, Iyer M, Cooper MH, Weigel MK, Ambiel N, Werner HB, Zuchero JB, Opazo F, Kursula P. Nanobodies against the myelin enzyme CNPase as tools for structural and functional studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595513. [PMID: 38826303 PMCID: PMC11142274 DOI: 10.1101/2024.05.25.595513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) is an abundant constituent of central nervous system non-compact myelin, frequently used as a marker antigen for myelinating cells. The catalytic activity of CNPase, the 3'-hydrolysis of 2',3'-cyclic nucleotides, is well characterised in vitro, but the in vivo function of CNPase remains unclear. CNPase interacts with the actin cytoskeleton to counteract the developmental closure of cytoplasmic channels that travel through compact myelin; its enzymatic activity may be involved in adenosine metabolism and RNA degradation. We developed a set of high-affinity nanobodies recognizing the phosphodiesterase domain of CNPase, and the crystal structures of each complex show that the five nanobodies have distinct epitopes. One of the nanobodies bound deep into the CNPase active site and acted as an inhibitor. Moreover, the nanobodies were characterised in imaging applications and as intrabodies, expressed in mammalian cells, such as primary oligodendrocytes. Fluorescently labelled nanobodies functioned in imaging of teased nerve fibers and whole brain tissue sections, as well as super-resolution microscopy. These anti-CNPase nanobodies provide new tools for structural and functional biology of myelination, including high-resolution imaging of nerve tissue.
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Affiliation(s)
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Neurosurgery Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Marcel Schröder
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Shama Sograte-Idrissi
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany
| | - Amir Mohammad Rahimi
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany
| | - Ommolbanin Asadpour
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany
| | - Henrike Körner
- Department for Neuroimmunology and Multiple Sclerosis Research, University of Göttingen Medical Center, 37075 Göttingen, Germany
| | - Dmitri Lodygin
- Department for Neuroimmunology and Multiple Sclerosis Research, University of Göttingen Medical Center, 37075 Göttingen, Germany
| | - Maria A. Eichel-Vogel
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, D-37075 Göttingen, Germany
| | - Risha Chowdhury
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Aleksi Sutinen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Gopinath Muruganandam
- VIB-VUB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Department of Bioengineering Sciences, Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium
| | - Manasi Iyer
- Neurosurgery Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Madeline H. Cooper
- Neurosurgery Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Maya K. Weigel
- Neurosurgery Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas Ambiel
- Neurosurgery Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Hauke B. Werner
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, D-37075 Göttingen, Germany
| | - J. Bradley Zuchero
- Neurosurgery Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Felipe Opazo
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
- NanoTag Biotechnologies GmbH, 37079 Göttingen, Germany
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
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5
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Valdes PA, Yu CC(J, Aronson J, Ghosh D, Zhao Y, An B, Bernstock JD, Bhere D, Felicella MM, Viapiano MS, Shah K, Chiocca EA, Boyden ES. Improved immunostaining of nanostructures and cells in human brain specimens through expansion-mediated protein decrowding. Sci Transl Med 2024; 16:eabo0049. [PMID: 38295184 PMCID: PMC10911838 DOI: 10.1126/scitranslmed.abo0049] [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: 01/06/2022] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
Proteins are densely packed in cells and tissues, where they form complex nanostructures. Expansion microscopy (ExM) variants have been used to separate proteins from each other in preserved biospecimens, improving antibody access to epitopes. Here, we present an ExM variant, decrowding expansion pathology (dExPath), that can expand proteins away from each other in human brain pathology specimens, including formalin-fixed paraffin-embedded (FFPE) clinical specimens. Immunostaining of dExPath-expanded specimens reveals, with nanoscale precision, previously unobserved cellular structures, as well as more continuous patterns of staining. This enhanced molecular staining results in observation of previously invisible disease marker-positive cell populations in human glioma specimens, with potential implications for tumor aggressiveness. dExPath results in improved fluorescence signals even as it eliminates lipofuscin-associated autofluorescence. Thus, this form of expansion-mediated protein decrowding may, through improved epitope access for antibodies, render immunohistochemistry more powerful in clinical science and, perhaps, diagnosis.
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Affiliation(s)
- Pablo A. Valdes
- Department of Neurosurgery, University of Texas Medical Branch, Galveston, TX, 77555
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
| | - Chih-Chieh (Jay) Yu
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Engineering, MIT, MA, USA, 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- RIKEN Center for Brain Science, Saitama, Japan, 351-0198
| | - Jenna Aronson
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- RIKEN Center for Brain Science, Saitama, Japan, 351-0198
| | - Debarati Ghosh
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA, 02139
| | - Yongxin Zhao
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA, 15213
| | - Bobae An
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
| | - Joshua D. Bernstock
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Koch Institute, MIT, Cambridge, MA, USA, 02139
| | - Deepak Bhere
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Department of Pathology, Microbiology and Immunology, School of Medicine Columbia, University of South Carolina, Columbia, SC, USA, 29209
- Center for Stem Cell and Translational Immunotherapy, Harvard Medical School/Brigham and Women’s Hospital, Boston, MA, USA, 02115
| | - Michelle M. Felicella
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA, 77555
| | - Mariano S. Viapiano
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY, USA, 13210
| | - Khalid Shah
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
- Center for Stem Cell and Translational Immunotherapy, Harvard Medical School/Brigham and Women’s Hospital, Boston, MA, USA, 02115
| | - E. Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA, 02115
| | - Edward S. Boyden
- Media Arts and Sciences, MIT, Cambridge, MA, USA, 02115
- Department of Biological Engineering, MIT, MA, USA, 02139
- McGovern Institute for Brain Research, MIT, Cambridge, MA, USA, 02139
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA, 02139
- Koch Institute, MIT, Cambridge, MA, USA, 02139
- MIT Center for Neurobiological Engineering and K. Lisa Yang Center for Bionics, MIT, Cambridge, MA, USA, 02139
- Howard Hughes Medical Institute, Cambridge, MA, USA, 02139
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6
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Jeong S, Koh D, Gwak E, Srambickal CV, Seo D, Widengren J, Lee JC. Pushing the Resolution Limit of Stimulated Emission Depletion Optical Nanoscopy. Int J Mol Sci 2023; 25:26. [PMID: 38203197 PMCID: PMC10779414 DOI: 10.3390/ijms25010026] [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: 09/15/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Optical nanoscopy, also known as super-resolution optical microscopy, has provided scientists with the means to surpass the diffraction limit of light microscopy and attain new insights into nanoscopic structures and processes that were previously inaccessible. In recent decades, numerous studies have endeavored to enhance super-resolution microscopy in terms of its spatial (lateral) resolution, axial resolution, and temporal resolution. In this review, we discuss recent efforts to push the resolution limit of stimulated emission depletion (STED) optical nanoscopy across multiple dimensions, including lateral resolution, axial resolution, temporal resolution, and labeling precision. We introduce promising techniques and methodologies building on the STED concept that have emerged in the field, such as MINSTED, isotropic STED, and event-triggered STED, and evaluate their respective strengths and limitations. Moreover, we discuss trade-off relationships that exist in far-field optical microscopy and how they come about in STED optical nanoscopy. By examining the latest developments addressing these aspects, we aim to provide an updated overview of the current state of STED nanoscopy and its potential for future research.
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Affiliation(s)
- Sejoo Jeong
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Dongbin Koh
- School of Undergraduate Studies, DGIST, Daegu 42988, Republic of Korea
| | - Eunha Gwak
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Chinmaya V. Srambickal
- Exp. Biomol. Physics, Dept. Applied Physics, KTH—Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Daeha Seo
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Jerker Widengren
- Exp. Biomol. Physics, Dept. Applied Physics, KTH—Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Jong-Chan Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
- New Biology Research Center, DGIST, Daegu 42988, Republic of Korea
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7
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de Jong-Bolm D, Sadeghi M, Bogaciu CA, Bao G, Klaehn G, Hoff M, Mittelmeier L, Basmanav FB, Opazo F, Noé F, Rizzoli SO. Protein nanobarcodes enable single-step multiplexed fluorescence imaging. PLoS Biol 2023; 21:e3002427. [PMID: 38079451 PMCID: PMC10735187 DOI: 10.1371/journal.pbio.3002427] [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: 08/30/2022] [Revised: 12/21/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Multiplexed cellular imaging typically relies on the sequential application of detection probes, as antibodies or DNA barcodes, which is complex and time-consuming. To address this, we developed here protein nanobarcodes, composed of combinations of epitopes recognized by specific sets of nanobodies. The nanobarcodes are read in a single imaging step, relying on nanobodies conjugated to distinct fluorophores, which enables a precise analysis of large numbers of protein combinations. Fluorescence images from nanobarcodes were used as input images for a deep neural network, which was able to identify proteins with high precision. We thus present an efficient and straightforward protein identification method, which is applicable to relatively complex biological assays. We demonstrate this by a multicell competition assay, in which we successfully used our nanobarcoded proteins together with neurexin and neuroligin isoforms, thereby testing the preferred binding combinations of multiple isoforms, in parallel.
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Affiliation(s)
- Daniëlle de Jong-Bolm
- Department of Neuro- and Sensory physiology, University of Göttingen Medical Center, Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
| | - Mohsen Sadeghi
- Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
| | - Cristian A. Bogaciu
- Department of Neuro- and Sensory physiology, University of Göttingen Medical Center, Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
| | - Guobin Bao
- Institute of Pharmacology and Toxicology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Gabriele Klaehn
- Department of Neuro- and Sensory physiology, University of Göttingen Medical Center, Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
| | - Merle Hoff
- Department of Neuro- and Sensory physiology, University of Göttingen Medical Center, Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
| | - Lucas Mittelmeier
- Department of Neuro- and Sensory physiology, University of Göttingen Medical Center, Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
| | - F. Buket Basmanav
- Department of Neuro- and Sensory physiology, University of Göttingen Medical Center, Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
- Campus Laboratory for Advanced Imaging, Microscopy and Spectroscopy, University of Göttingen, Göttingen, Germany
| | - Felipe Opazo
- Department of Neuro- and Sensory physiology, University of Göttingen Medical Center, Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, Göttingen, Germany
- NanoTag Biotechnologies GmbH, Göttingen, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany
- Department of Physics, Free University of Technology, Berlin, Germany
- Department of Chemistry, Rice University, Houston, Texas, United States of America
- Microsoft Research AI4Science, Berlin, Germany
| | - Silvio O. Rizzoli
- Department of Neuro- and Sensory physiology, University of Göttingen Medical Center, Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Göttingen, Germany
- NanoTag Biotechnologies GmbH, Göttingen, Germany
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8
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Frecot DI, Froehlich T, Rothbauer U. 30 years of nanobodies - an ongoing success story of small binders in biological research. J Cell Sci 2023; 136:jcs261395. [PMID: 37937477 DOI: 10.1242/jcs.261395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A milestone in the field of recombinant binding molecules was achieved 30 years ago with the discovery of single-domain antibodies from which antigen-binding variable domains, better known as nanobodies (Nbs), can be derived. Being only one tenth the size of conventional antibodies, Nbs feature high affinity and specificity, while being highly stable and soluble. In addition, they display accessibility to cryptic sites, low off-target accumulation and deep tissue penetration. Efficient selection methods, such as (semi-)synthetic/naïve or immunized cDNA libraries and display technologies, have facilitated the isolation of Nbs against diverse targets, and their single-gene format enables easy functionalization and high-yield production. This Review highlights recent advances in Nb applications in various areas of biological research, including structural biology, proteomics and high-resolution and in vivo imaging. In addition, we provide insights into intracellular applications of Nbs, such as live-cell imaging, biosensors and targeted protein degradation.
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Affiliation(s)
- Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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9
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Queiroz Zetune Villa Real K, Mougios N, Rehm R, Sograte-Idrissi S, Albert L, Rahimi AM, Maidorn M, Hentze J, Martínez-Carranza M, Hosseini H, Saal KA, Oleksiievets N, Prigge M, Tsukanov R, Stenmark P, Fornasiero EF, Opazo F. A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging And Low Linkage-Error in Super-Resolution Microscopy. SMALL METHODS 2023; 7:e2300218. [PMID: 37421204 DOI: 10.1002/smtd.202300218] [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: 02/21/2023] [Revised: 06/09/2023] [Indexed: 07/10/2023]
Abstract
Imaging of living synapses has relied for over two decades on the overexpression of synaptic proteins fused to fluorescent reporters. This strategy alters the stoichiometry of synaptic components and ultimately affects synapse physiology. To overcome these limitations, here a nanobody is presented that binds the calcium sensor synaptotagmin-1 (NbSyt1). This nanobody functions as an intrabody (iNbSyt1) in living neurons and is minimally invasive, leaving synaptic transmission almost unaffected, as suggested by the crystal structure of the NbSyt1 bound to Synaptotagmin-1 and by the physiological data. Its single-domain nature enables the generation of protein-based fluorescent reporters, as showcased here by measuring spatially localized presynaptic Ca2+ with a NbSyt1- jGCaMP8 chimera. Moreover, the small size of NbSyt1 makes it ideal for various super-resolution imaging methods. Overall, NbSyt1 is a versatile binder that will enable imaging in cellular and molecular neuroscience with unprecedented precision across multiple spatiotemporal scales.
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Affiliation(s)
- Karine Queiroz Zetune Villa Real
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Nikolaos Mougios
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Ronja Rehm
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Shama Sograte-Idrissi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - László Albert
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Amir Mohammad Rahimi
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Manuel Maidorn
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Jannik Hentze
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Markel Martínez-Carranza
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Stockholm, SE-10691, Sweden
| | - Hassan Hosseini
- Research Group Neuromodulatory Networks, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
| | - Kim-Ann Saal
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Nazar Oleksiievets
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Matthias Prigge
- Research Group Neuromodulatory Networks, Leibniz Institute for Neurobiology, 39118, Magdeburg, Germany
- Center for Behavioral Brain Sciences, 39118, Magdeburg, Germany
| | - Roman Tsukanov
- III. Institute of Physics - Biophysics, Georg August University, 37077, Göttingen, Germany
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Stockholm, SE-10691, Sweden
| | - Eugenio F Fornasiero
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
| | - Felipe Opazo
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, 37075, Göttingen, Germany
- NanoTag Biotechnologies GmbH, 37079, Göttingen, Germany
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10
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Kilisch M, Gere-Becker M, Wüstefeld L, Bonnas C, Crauel A, Mechmershausen M, Martens H, Götzke H, Opazo F, Frey S. Simple and Highly Efficient Detection of PSD95 Using a Nanobody and Its Recombinant Heavy-Chain Antibody Derivatives. Int J Mol Sci 2023; 24:ijms24087294. [PMID: 37108454 PMCID: PMC10138605 DOI: 10.3390/ijms24087294] [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: 03/16/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The post-synaptic density protein 95 (PSD95) is a crucial scaffolding protein participating in the organization and regulation of synapses. PSD95 interacts with numerous molecules, including neurotransmitter receptors and ion channels. The functional dysregulation of PSD95 as well as its abundance and localization has been implicated with several neurological disorders, making it an attractive target for developing strategies able to monitor PSD95 accurately for diagnostics and therapeutics. This study characterizes a novel camelid single-domain antibody (nanobody) that binds strongly and with high specificity to rat, mouse, and human PSD95. This nanobody allows for more precise detection and quantification of PSD95 in various biological samples. We expect that the flexibility and unique performance of this thoroughly characterized affinity tool will help to further understand the role of PSD95 in normal and diseased neuronal synapses.
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Affiliation(s)
- Markus Kilisch
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Maja Gere-Becker
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Liane Wüstefeld
- Synaptic Systems GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Christel Bonnas
- Synaptic Systems GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Alexander Crauel
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Maja Mechmershausen
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Henrik Martens
- Synaptic Systems GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Hansjörg Götzke
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
| | - Felipe Opazo
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
- Institute of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), University of Göttingen Medical Center, 37075 Göttingen, Germany
| | - Steffen Frey
- NanoTag Biotechnologies GmbH, Rudolf-Wissell-Straβe 28a, 37079 Göttingen, Germany
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11
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Saal KA, Shaib AH, Mougios N, Crzan D, Opazo F, Rizzoli SO. Heat denaturation enables multicolor X10-STED microscopy. Sci Rep 2023; 13:5366. [PMID: 37005431 PMCID: PMC10067834 DOI: 10.1038/s41598-023-32524-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/29/2023] [Indexed: 04/04/2023] Open
Abstract
Expansion microscopy (ExM) improves imaging quality by physically enlarging the biological specimens. In principle, combining a large expansion factor with optical super-resolution should provide extremely high imaging precision. However, large expansion factors imply that the expanded specimens are dim and are therefore poorly suited for optical super-resolution. To solve this problem, we present a protocol that ensures the expansion of the samples up to 10-fold, in a single expansion step, through high-temperature homogenization (X10ht). The resulting gels exhibit a higher fluorescence intensity than gels homogenized using enzymatic digestion (based on proteinase K). This enables the sample analysis by multicolor stimulated emission depletion (STED) microscopy, for a final resolution of 6-8 nm in neuronal cell cultures or isolated vesicles. X10ht also enables the expansion of 100-200 µm thick brain samples, up to 6-fold. The better epitope preservation also enables the use of nanobodies as labeling probes and the implementation of post-expansion signal amplification. We conclude that X10ht is a promising tool for nanoscale resolution in biological samples.
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Affiliation(s)
- Kim Ann Saal
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Ali H Shaib
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Nikolaos Mougios
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Sieboldt-Str. 3a, 37075, Göttingen, Germany
| | - Dagmar Crzan
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
- NanoTag Biotechnologies GmbH, Rudolf Wissell Str. 28a, 37079, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Sieboldt-Str. 3a, 37075, Göttingen, Germany
| | - Silvio O Rizzoli
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Sieboldt-Str. 3a, 37075, Göttingen, Germany.
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12
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Affiliation(s)
- Sven Truckenbrodt
- Convergent Research, E11 Bio. 1600 Harbor Bay Parkway, Alameda, California94502, United States
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13
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Lycas MD, Ejdrup AL, Sørensen AT, Haahr NO, Jørgensen SH, Guthrie DA, Støier JF, Werner C, Newman AH, Sauer M, Herborg F, Gether U. Nanoscopic dopamine transporter distribution and conformation are inversely regulated by excitatory drive and D2 autoreceptor activity. Cell Rep 2022; 40:111431. [PMID: 36170827 PMCID: PMC9617621 DOI: 10.1016/j.celrep.2022.111431] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/22/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
The nanoscopic organization and regulation of individual molecular components in presynaptic varicosities of neurons releasing modulatory volume neurotransmitters like dopamine (DA) remain largely elusive. Here we show, by application of several super-resolution microscopy techniques to cultured neurons and mouse striatal slices, that the DA transporter (DAT), a key protein in varicosities of dopaminergic neurons, exists in the membrane in dynamic equilibrium between an inward-facing nanodomain-localized and outward-facing unclustered configuration. The balance between these configurations is inversely regulated by excitatory drive and DA D2 autoreceptor activation in a manner dependent on Ca2+ influx via N-type voltage-gated Ca2+ channels. The DAT nanodomains contain tens of transporters molecules and overlap with nanodomains of PIP2 (phosphatidylinositol-4,5-bisphosphate) but show little overlap with D2 autoreceptor, syntaxin-1, and clathrin nanodomains. The data reveal a mechanism for rapid alterations of nanoscopic DAT distribution and show a striking link of this to the conformational state of the transporter.
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Affiliation(s)
- Matthew D Lycas
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Aske L Ejdrup
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Andreas T Sørensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Nicolai O Haahr
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Søren H Jørgensen
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Daryl A Guthrie
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jonatan F Støier
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Christian Werner
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Freja Herborg
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark
| | - Ulrik Gether
- Molecular Neuropharmacology and Genetics Laboratory, Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Maersk Tower 7.5, 2200 Copenhagen, Denmark.
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14
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Neurotransmitter uptake of synaptic vesicles studied by X-ray diffraction. EUROPEAN BIOPHYSICS JOURNAL 2022; 51:465-482. [PMID: 35904588 PMCID: PMC9463337 DOI: 10.1007/s00249-022-01609-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Abstract
The size, polydispersity, and electron density profile of synaptic vesicles (SVs) can be studied by small-angle X-ray scattering (SAXS), i.e. by X-ray diffraction from purified SV suspensions in solution. Here we show that size and shape transformations, as they appear in the functional context of these important synaptic organelles, can also be monitored by SAXS. In particular, we have investigated the active uptake of neurotransmitters, and find a mean vesicle radius increase of about 12% after the uptake of glutamate, which indicates an unusually large extensibility of the vesicle surface, likely to be accompanied by conformational changes of membrane proteins and rearrangements of the bilayer. Changes in the electron density profile (EDP) give first indications for such a rearrangement. Details of the protein structure are screened, however, by SVs polydispersity. To overcome the limitations of large ensemble averages and heterogeneous structures, we therefore propose serial X-ray diffraction by single free electron laser pulses. Using simulated data for realistic parameters, we show that this is in principle feasible, and that even spatial distances between vesicle proteins could be assessed by this approach.
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15
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A Reliable Approach for Revealing Molecular Targets in Secondary Ion Mass Spectrometry. Int J Mol Sci 2022; 23:ijms23094615. [PMID: 35563005 PMCID: PMC9103194 DOI: 10.3390/ijms23094615] [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: 03/03/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/10/2022] Open
Abstract
Nano secondary ion mass spectrometry (nanoSIMS) imaging is a rapidly growing field in biological sciences, which enables investigators to describe the chemical composition of cells and tissues with high resolution. One of the major challenges of nanoSIMS is to identify specific molecules or organelles, as these are not immediately recognizable in nanoSIMS and need to be revealed by SIMS-compatible probes. Few laboratories have generated such probes, and none are commercially available. To address this, we performed a systematic study of probes initially developed for electron microscopy. Relying on nanoscale SIMS, we found that antibodies coupled to 6 nm gold particles are surprisingly efficient in terms of labeling specificity while offering a reliable detection threshold. These tools enabled accurate visualization and sample analysis and were easily employed in correlating SIMS with other imaging approaches, such as fluorescence microscopy. We conclude that antibodies conjugated to moderately sized gold particles are promising tools for SIMS imaging.
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16
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Saul P, Yang S, Mamone S, Opazo F, Meyer A, Rizzoli SO, Glöggler S. Exotic nuclear spin behavior in dendritic macromolecules. Phys Chem Chem Phys 2021; 23:26349-26355. [PMID: 34792046 DOI: 10.1039/d1cp04483d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dendrimers are a class of branched, highly symmetric macromolecules that have been shown to be useful for a vast number of different applications. Potential uses as fluorescence sensors, in catalysis and perhaps most importantly in medical applications as drug delivery systems or cytotoxica have been proposed. Herein we report on an exotic behaviour of the nuclear spins in a dendritic macromolecule in the presence of different paramagnetic ions. We show that the stability of the long lived nuclear singlet state, is affected by the presence of Cu(II), whereas other ions did not have any influence at all. This effect could not be observed in the case of a simple tripeptide, in which the nuclear singlet stability was influenced by all investigated paramagnetic ions, a potentially useful effect in the development of Cu(II) selective probes. By adding a fluorescent marker to our molecule we could show that the nuclear singlet multimer (NUSIMER) is taken up by living cells. Furthermore we were able to show that nuclear singlet state NMR can be used to investigate the NUSIMER in the presence of living cells, showing that an application in in vivo NMR can be feasible.
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Affiliation(s)
- Philip Saul
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration, Von-Siebold-Straße 3A, 37075 Göttingen, Germany
| | - Shengjun Yang
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration, Von-Siebold-Straße 3A, 37075 Göttingen, Germany
| | - Salvatore Mamone
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration, Von-Siebold-Straße 3A, 37075 Göttingen, Germany
| | - Felipe Opazo
- Center for Biostructural Imaging of Neurodegeneration, Von-Siebold-Straße 3A, 37075 Göttingen, Germany.,Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Andreas Meyer
- Research Group Electron Paramagnetic Resonance, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Stefan Glöggler
- Research Group for NMR Signal Enhancement, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. .,Center for Biostructural Imaging of Neurodegeneration, Von-Siebold-Straße 3A, 37075 Göttingen, Germany
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17
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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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18
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Gold-Conjugated Nanobodies for Targeted Imaging Using High-Resolution Secondary Ion Mass Spectrometry. NANOMATERIALS 2021; 11:nano11071797. [PMID: 34361183 PMCID: PMC8308316 DOI: 10.3390/nano11071797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/20/2022]
Abstract
Nanoscale imaging with the ability to identify cellular organelles and protein complexes has been a highly challenging subject in the secondary ion mass spectrometry (SIMS) of biological samples. This is because only a few isotopic tags can be used successfully to target specific proteins or organelles. To address this, we generated gold nanoprobes, in which gold nanoparticles are conjugated to nanobodies. The nanoprobes were well suited for specific molecular imaging using NanoSIMS at subcellular resolution. They were demonstrated to be highly selective to different proteins of interest and sufficiently sensitive for SIMS detection. The nanoprobes offer the possibility of correlating the investigation of cellular isotopic turnover to the positions of specific proteins and organelles, thereby enabling an understanding of functional and structural relations that are currently obscure.
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19
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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: 62] [Impact Index Per Article: 20.7] [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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20
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Zhong X, Yu Y, Wang C, Zhu Q, Wu J, Ke W, Ji D, Niu C, Yang X, Wei Y. Hippocampal proteomic analysis reveals the disturbance of synaptogenesis and neurotransmission induced by developmental exposure to organophosphate flame retardant triphenyl phosphate. JOURNAL OF HAZARDOUS MATERIALS 2021; 404:124111. [PMID: 33189059 DOI: 10.1016/j.jhazmat.2020.124111] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/14/2020] [Accepted: 09/20/2020] [Indexed: 06/11/2023]
Abstract
With the spread of organophosphorus flame retardants (OPFRs), the environmental and health risks they induce are attracting attention. Triphenyl phosphate (TPHP) is a popular alternative to brominated flame retardant and halogenated OPFRs. Neurodevelopmental toxicity is TPHP's primary adverse effect, whereas the biomarkers and the modes of action have yet to be elucidated. In the present study, 0.5, 5, and 50 mg/kg of TPHP were orally administered to mice from postnatal day 10 (P10) to P70. The behavioral tests showed a compromised learning and memory capability. Proteomic analysis of the hippocampus exposed to 0.5 or 50 mg/kg of TPHP identified 531 differentially expressed proteins that were mainly involved in axon guidance, synaptic function, neurotransmitter transport, exocytosis, and energy metabolism. Immunoblot and immunofluorescence analysis showed that exposure to TPHP reduced the protein levels of TUBB3 and SYP in the synapses of hippocampal neurons. TPHP exposure also downregulated the gene expression of neurotransmitter receptors including Grins, Htr1α, and Adra1α in a dose-dependent fashion. Moreover, the calcium-dependent synaptic exocytosis governed by synaptic vesicle proteins STX1A and SYT1 was inhibited in the TPHP-treated hippocampus. Our results reveal that TPHP exposure causes abnormal learning and memory behaviors by disturbing synaptogenesis and neurotransmission.
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Affiliation(s)
- Xiali Zhong
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yuejin Yu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Can Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Qicheng Zhu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingwei Wu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Weijian Ke
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Di Ji
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Congying Niu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xifei Yang
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Medical Key Subject of Health Toxicology, Shenzhen Center for Disease Control and Prevention, Shenzhen 518172, China
| | - Yanhong Wei
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
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21
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Schneider F, Sych T, Eggeling C, Sezgin E. Influence of nanobody binding on fluorescence emission, mobility, and organization of GFP-tagged proteins. iScience 2021; 24:101891. [PMID: 33364580 PMCID: PMC7753935 DOI: 10.1016/j.isci.2020.101891] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/02/2020] [Accepted: 12/01/2020] [Indexed: 12/22/2022] Open
Abstract
Advanced fluorescence microscopy studies require specific and monovalent molecular labeling with bright and photostable fluorophores. This necessity led to the widespread use of fluorescently labeled nanobodies against commonly employed fluorescent proteins (FPs). However, very little is known how these nanobodies influence their target molecules. Here, we tested commercially available nanobodies and observed clear changes of the fluorescence properties, mobility and organization of green fluorescent protein (GFP) tagged proteins after labeling with the anti-GFP nanobody. Intriguingly, we did not observe any co-diffusion of fluorescently labeled nanobodies with the GFP-labeled proteins. Our results suggest significant binding of the nanobodies to a non-emissive, likely oligomerized, form of the FPs, promoting disassembly into monomeric form after binding. Our findings have significant implications on the application of nanobodies and GFP labeling for studying dynamic and quantitative protein organization in the plasma membrane of living cells using advanced imaging techniques.
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Affiliation(s)
- Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
- Jena Center of Soft Matters, Friedrich-Schiller-University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
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22
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Carvalhais LG, Martinho VC, Ferreiro E, Pinheiro PS. Unraveling the Nanoscopic Organization and Function of Central Mammalian Presynapses With Super-Resolution Microscopy. Front Neurosci 2021; 14:578409. [PMID: 33584169 PMCID: PMC7874199 DOI: 10.3389/fnins.2020.578409] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 12/22/2022] Open
Abstract
The complex, nanoscopic scale of neuronal function, taking place at dendritic spines, axon terminals, and other minuscule structures, cannot be adequately resolved using standard, diffraction-limited imaging techniques. The last couple of decades saw a rapid evolution of imaging methods that overcome the diffraction limit imposed by Abbe's principle. These techniques, including structured illumination microscopy (SIM), stimulated emission depletion (STED), photo-activated localization microscopy (PALM), and stochastic optical reconstruction microscopy (STORM), among others, have revolutionized our understanding of synapse biology. By exploiting the stochastic nature of fluorophore light/dark states or non-linearities in the interaction of fluorophores with light, by using modified illumination strategies that limit the excitation area, these methods can achieve spatial resolutions down to just a few tens of nm or less. Here, we review how these advanced imaging techniques have contributed to unprecedented insight into the nanoscopic organization and function of mammalian neuronal presynapses, revealing new organizational principles or lending support to existing views, while raising many important new questions. We further discuss recent technical refinements and newly developed tools that will continue to expand our ability to delve deeper into how synaptic function is orchestrated at the nanoscopic level.
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Affiliation(s)
- Lia G Carvalhais
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Vera C Martinho
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Elisabete Ferreiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Paulo S Pinheiro
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Center for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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23
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Nanobodies as Versatile Tool for Multiscale Imaging Modalities. Biomolecules 2020; 10:biom10121695. [PMID: 33353213 PMCID: PMC7767244 DOI: 10.3390/biom10121695] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
Molecular imaging is constantly growing in different areas of preclinical biomedical research. Several imaging methods have been developed and are continuously updated for both in vivo and in vitro applications, in order to increase the information about the structure, localization and function of molecules involved in physiology and disease. Along with these progresses, there is a continuous need for improving labeling strategies. In the last decades, the single domain antigen-binding fragments nanobodies (Nbs) emerged as important molecular imaging probes. Indeed, their small size (~15 kDa), high stability, affinity and modularity represent desirable features for imaging applications, providing higher tissue penetration, rapid targeting, increased spatial resolution and fast clearance. Accordingly, several Nb-based probes have been generated and applied to a variety of imaging modalities, ranging from in vivo and in vitro preclinical imaging to super-resolution microscopy. In this review, we will provide an overview of the state-of-the-art regarding the use of Nbs in several imaging modalities, underlining their extreme versatility and their enormous potential in targeting molecules and cells of interest in both preclinical and clinical studies.
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24
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Trimmer JS. Recombinant Antibodies in Basic Neuroscience Research. CURRENT PROTOCOLS IN NEUROSCIENCE 2020; 94:e106. [PMID: 33151027 PMCID: PMC7665837 DOI: 10.1002/cpns.106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Basic neuroscience research employs antibodies as key reagents to label, capture, and modulate the function of proteins of interest. Antibodies are immunoglobulin proteins. Recombinant antibodies are immunoglobulin proteins whose nucleic acid coding regions, or fragments thereof, have been cloned into expression plasmids that allow for unlimited production. Recombinant antibodies offer many advantages over conventional antibodies including their unambiguous identification and digital archiving via DNA sequencing, reliable expression, ease and reliable distribution as DNA sequences and as plasmids, and the opportunity for numerous forms of engineering to enhance their utility. Recombinant antibodies exist in many different forms, each of which offers potential advantages and disadvantages for neuroscience research applications. I provide an overview of recombinant antibodies and their development. Examples of their emerging use as valuable reagents in basic neuroscience research are also discussed. Many of these examples employ recombinant antibodies in innovative experimental approaches that cannot be pursued with conventional antibodies. © 2020 Wiley Periodicals LLC.
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Affiliation(s)
- James S Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, California
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25
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de Beer MA, Giepmans BNG. Nanobody-Based Probes for Subcellular Protein Identification and Visualization. Front Cell Neurosci 2020; 14:573278. [PMID: 33240044 PMCID: PMC7667270 DOI: 10.3389/fncel.2020.573278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.
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Affiliation(s)
- Marit A de Beer
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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26
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Quantitative Synaptic Biology: A Perspective on Techniques, Numbers and Expectations. Int J Mol Sci 2020; 21:ijms21197298. [PMID: 33023247 PMCID: PMC7582872 DOI: 10.3390/ijms21197298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/31/2022] Open
Abstract
Synapses play a central role for the processing of information in the brain and have been analyzed in countless biochemical, electrophysiological, imaging, and computational studies. The functionality and plasticity of synapses are nevertheless still difficult to predict, and conflicting hypotheses have been proposed for many synaptic processes. In this review, we argue that the cause of these problems is a lack of understanding of the spatiotemporal dynamics of key synaptic components. Fortunately, a number of emerging imaging approaches, going beyond super-resolution, should be able to provide required protein positions in space at different points in time. Mathematical models can then integrate the resulting information to allow the prediction of the spatiotemporal dynamics. We argue that these models, to deal with the complexity of synaptic processes, need to be designed in a sufficiently abstract way. Taken together, we suggest that a well-designed combination of imaging and modelling approaches will result in a far more complete understanding of synaptic function than currently possible.
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27
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Reshetniak S, Ußling J, Perego E, Rammner B, Schikorski T, Fornasiero EF, Truckenbrodt S, Köster S, Rizzoli SO. A comparative analysis of the mobility of 45 proteins in the synaptic bouton. EMBO J 2020; 39:e104596. [PMID: 32627850 PMCID: PMC7429486 DOI: 10.15252/embj.2020104596] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 02/01/2023] Open
Abstract
Many proteins involved in synaptic transmission are well known, and their features, as their abundance or spatial distribution, have been analyzed in systematic studies. This has not been the case, however, for their mobility. To solve this, we analyzed the motion of 45 GFP-tagged synaptic proteins expressed in cultured hippocampal neurons, using fluorescence recovery after photobleaching, particle tracking, and modeling. We compared synaptic vesicle proteins, endo- and exocytosis cofactors, cytoskeleton components, and trafficking proteins. We found that movement was influenced by the protein association with synaptic vesicles, especially for membrane proteins. Surprisingly, protein mobility also correlated significantly with parameters as the protein lifetimes, or the nucleotide composition of their mRNAs. We then analyzed protein movement thoroughly, taking into account the spatial characteristics of the system. This resulted in a first visualization of overall protein motion in the synapse, which should enable future modeling studies of synaptic physiology.
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Affiliation(s)
- Sofiia Reshetniak
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
- International Max Planck Research School for Molecular BiologyGöttingenGermany
| | - Jan‐Eike Ußling
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
| | - Eleonora Perego
- Institute for X‐Ray PhysicsUniversity of GöttingenGöttingenGermany
| | - Burkhard Rammner
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
| | - Thomas Schikorski
- Department of NeuroscienceUniversidad Central del CaribeBayamonPRUSA
| | - Eugenio F Fornasiero
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
| | - Sven Truckenbrodt
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
- International Max Planck Research School for Molecular BiologyGöttingenGermany
| | - Sarah Köster
- Institute for X‐Ray PhysicsUniversity of GöttingenGöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGöttingenGermany
| | - Silvio O Rizzoli
- Institute for Neuro‐ and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) CenterUniversity Medical Center GöttingenGöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGöttingenGermany
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28
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Nosov G, Kahms M, Klingauf J. The Decade of Super-Resolution Microscopy of the Presynapse. Front Synaptic Neurosci 2020; 12:32. [PMID: 32848695 PMCID: PMC7433402 DOI: 10.3389/fnsyn.2020.00032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 07/21/2020] [Indexed: 01/05/2023] Open
Abstract
The presynaptic compartment of the chemical synapse is a small, yet extremely complex structure. Considering its size, most methods of optical microscopy are not able to resolve its nanoarchitecture and dynamics. Thus, its ultrastructure could only be studied by electron microscopy. In the last decade, new methods of optical superresolution microscopy have emerged allowing the study of cellular structures and processes at the nanometer scale. While this is a welcome addition to the experimental arsenal, it has necessitated careful analysis and interpretation to ensure the data obtained remains artifact-free. In this article we review the application of nanoscopic techniques to the study of the synapse and the progress made over the last decade with a particular focus on the presynapse. We find to our surprise that progress has been limited, calling for imaging techniques and probes that allow dense labeling, multiplexing, longer imaging times, higher temporal resolution, while at least maintaining the spatial resolution achieved thus far.
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Affiliation(s)
- Georgii Nosov
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany.,CIM-IMPRS Graduate Program in Münster, Münster, Germany
| | - Martin Kahms
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
| | - Jurgen Klingauf
- Institute of Medical Physics and Biophysics, University of Münster, Münster, Germany
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29
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Carrington G, Tomlinson D, Peckham M. Exploiting nanobodies and Affimers for superresolution imaging in light microscopy. Mol Biol Cell 2020; 30:2737-2740. [PMID: 31609674 PMCID: PMC6789155 DOI: 10.1091/mbc.e18-11-0694] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antibodies have long been the main approach used for localizing proteins of interest by light microscopy. In the past 5 yr or so, and with the advent of superresolution microscopy, the diversity of tools for imaging has rapidly expanded. One main area of expansion has been in the area of nanobodies, small single-chain antibodies from camelids or sharks. The other has been the use of artificial scaffold proteins, including Affimers. The small size of nanobodies and Affimers compared with the traditional antibody provides several advantages for superresolution imaging.
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Affiliation(s)
- Glenn Carrington
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Darren Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Michelle Peckham
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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30
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Gerdes C, Waal N, Offner T, Fornasiero EF, Wender N, Verbarg H, Manzini I, Trenkwalder C, Mollenhauer B, Strohäker T, Zweckstetter M, Becker S, Rizzoli SO, Basmanav FB, Opazo F. A nanobody-based fluorescent reporter reveals human α-synuclein in the cell cytosol. Nat Commun 2020; 11:2729. [PMID: 32483166 PMCID: PMC7264335 DOI: 10.1038/s41467-020-16575-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Aggregation and spreading of α-Synuclein (αSyn) are hallmarks of several neurodegenerative diseases, thus monitoring human αSyn (hαSyn) in animal models or cell cultures is vital for the field. However, the detection of native hαSyn in such systems is challenging. We show that the nanobody NbSyn87, previously-described to bind hαSyn, also shows cross-reactivity for the proteasomal subunit Rpn10. As such, when the NbSyn87 is expressed in the absence of hαSyn, it is continuously degraded by the proteasome, while it is stabilized when it binds to hαSyn. Here, we exploit this feature to design a new Fluorescent Reporter for hαSyn (FluoReSyn) by fusing NbSyn87 to fluorescent proteins, which results in fluorescence signal fluctuations depending on the presence and amounts of intracellular hαSyn. We characterize this biosensor in cells and tissues to finally reveal the presence of transmittable αSyn in human cerebrospinal fluid, demonstrating the potential of FluoReSyn for clinical research and diagnostics.
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Affiliation(s)
- Christoph Gerdes
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Natalia Waal
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Thomas Offner
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus-Liebig University Giessen, 35390, Giessen, Germany
- Institute of Neurophysiology and Cellular Biophysics, University of Göttingen, Göttingen, Germany
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Nora Wender
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Hannes Verbarg
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
| | - Ivan Manzini
- Institute of Animal Physiology, Department of Animal Physiology and Molecular Biomedicine, Justus-Liebig University Giessen, 35390, Giessen, Germany
- Institute of Neurophysiology and Cellular Biophysics, University of Göttingen, Göttingen, Germany
| | - Claudia Trenkwalder
- Department of Neurosurgery, University Medical Center Göttingen, D-37075, Göttingen, Germany
- Paracelsus-Elena-Klinik, Klinikstraße 16, 34128, Kassel, Germany
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Klinikstraße 16, 34128, Kassel, Germany
- Department of Neurology, University Medical Center Göttingen, D-37075, Göttingen, Germany
| | - Timo Strohäker
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Göttingen, Germany
| | - Fitnat Buket Basmanav
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany
- Campus Laboratory for Advanced Imaging, Microscopy and Spectroscopy, University of Göttingen, D-37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, D-37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, D-37073, Göttingen, Germany.
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31
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Dong JX, Lee Y, Kirmiz M, Palacio S, Dumitras C, Moreno CM, Sando R, Santana LF, Südhof TC, Gong B, Murray KD, Trimmer JS. A toolbox of nanobodies developed and validated for use as intrabodies and nanoscale immunolabels in mammalian brain neurons. eLife 2019; 8:48750. [PMID: 31566565 PMCID: PMC6785268 DOI: 10.7554/elife.48750] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/18/2019] [Indexed: 12/30/2022] Open
Abstract
Nanobodies (nAbs) are small, minimal antibodies that have distinct attributes that make them uniquely suited for certain biomedical research, diagnostic and therapeutic applications. Prominent uses include as intracellular antibodies or intrabodies to bind and deliver cargo to specific proteins and/or subcellular sites within cells, and as nanoscale immunolabels for enhanced tissue penetration and improved spatial imaging resolution. Here, we report the generation and validation of nAbs against a set of proteins prominently expressed at specific subcellular sites in mammalian brain neurons. We describe a novel hierarchical validation pipeline to systematically evaluate nAbs isolated by phage display for effective and specific use as intrabodies and immunolabels in mammalian cells including brain neurons. These nAbs form part of a robust toolbox for targeting proteins with distinct and highly spatially-restricted subcellular localization in mammalian brain neurons, allowing for visualization and/or modulation of structure and function at those sites.
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Affiliation(s)
- Jie-Xian Dong
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Yongam Lee
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Michael Kirmiz
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Stephanie Palacio
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Camelia Dumitras
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Claudia M Moreno
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States.,Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Richard Sando
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford School of Medicine, Stanford, United States
| | - L Fernando Santana
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford School of Medicine, Stanford, United States
| | - Belvin Gong
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - Karl D Murray
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States
| | - James S Trimmer
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, United States.,Department of Physiology and Membrane Biology, University of California, Davis, Davis, United States
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32
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The ALFA-tag is a highly versatile tool for nanobody-based bioscience applications. Nat Commun 2019; 10:4403. [PMID: 31562305 PMCID: PMC6764986 DOI: 10.1038/s41467-019-12301-7] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 08/28/2019] [Indexed: 11/08/2022] Open
Abstract
Specialized epitope tags are widely used for detecting, manipulating or purifying proteins, but often their versatility is limited. Here, we introduce the ALFA-tag, a rationally designed epitope tag that serves a remarkably broad spectrum of applications in life sciences while outperforming established tags like the HA-, FLAG®- or myc-tag. The ALFA-tag forms a small and stable α-helix that is functional irrespective of its position on the target protein in prokaryotic and eukaryotic hosts. We characterize a nanobody (NbALFA) binding ALFA-tagged proteins from native or fixed specimen with low picomolar affinity. It is ideally suited for super-resolution microscopy, immunoprecipitations and Western blotting, and also allows in vivo detection of proteins. We show the crystal structure of the complex that enabled us to design a nanobody mutant (NbALFAPE) that permits efficient one-step purifications of native ALFA-tagged proteins, complexes and even entire living cells using peptide elution under physiological conditions. Epitope tags are widely used in various applications, but often lack versatility. Here, the authors introduce a small, alpha helical tag, which is recognized by a high affinity nanobody and can be used in a range of different applications, from protein purification to super-resolution imaging and in vivo detection of proteins.
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33
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Reshetniak S, Rizzoli SO. Interrogating Synaptic Architecture: Approaches for Labeling Organelles and Cytoskeleton Components. Front Synaptic Neurosci 2019; 11:23. [PMID: 31507402 PMCID: PMC6716447 DOI: 10.3389/fnsyn.2019.00023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/02/2019] [Indexed: 01/06/2023] Open
Abstract
Synaptic transmission has been studied for decades, as a fundamental step in brain function. The structure of the synapse, and its changes during activity, turned out to be key aspects not only in the transfer of information between neurons, but also in cognitive processes such as learning and memory. The overall synaptic morphology has traditionally been studied by electron microscopy, which enables the visualization of synaptic structure in great detail. The changes in the organization of easily identified structures, such as the presynaptic active zone, or the postsynaptic density, are optimally studied via electron microscopy. However, few reliable methods are available for labeling individual organelles or protein complexes in electron microscopy. For such targets one typically relies either on combination of electron and fluorescence microscopy, or on super-resolution fluorescence microscopy. This review focuses on approaches and techniques used to specifically reveal synaptic organelles and protein complexes, such as cytoskeletal assemblies. We place the strongest emphasis on methods detecting the targets of interest by affinity binding, and we discuss the advantages and limitations of each method.
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Affiliation(s)
- Sofiia Reshetniak
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany
- International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Silvio O. Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, Göttingen, Germany
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Mann FA, Lv Z, Großhans J, Opazo F, Kruss S. Nanobody‐Conjugated Nanotubes for Targeted Near‐Infrared In Vivo Imaging and Sensing. Angew Chem Int Ed Engl 2019; 58:11469-11473. [DOI: 10.1002/anie.201904167] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/03/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Florian A. Mann
- Institute of Physical ChemistryGeorg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Germany
| | - Zhiyi Lv
- Institut Für EntwicklungsbiochemieUMG/Georg-August Universität Göttingen Justus-von-Liebig Weg 11 37077 Göttingen Germany
| | - Jörg Großhans
- Institut Für EntwicklungsbiochemieUMG/Georg-August Universität Göttingen Justus-von-Liebig Weg 11 37077 Göttingen Germany
| | - Felipe Opazo
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Strasse 3a 37075 Göttingen Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) Humboldtallee 23 37073 Göttingen Germany
- NanoTag Biotechnologies GmbH Rudolf-Wissell-Straße 28a 37079 Göttingen Germany
| | - Sebastian Kruss
- Institute of Physical ChemistryGeorg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) Humboldtallee 23 37073 Göttingen Germany
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Mann FA, Lv Z, Großhans J, Opazo F, Kruss S. Nanoröhren‐Nanobody‐Konjugate als zielgerichtete Sonden und Marker für die In‐vivo‐Nahinfrarot‐Bildgebung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Florian A. Mann
- Institut für Physikalische ChemieGeorg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Deutschland
| | - Zhiyi Lv
- Institut Für EntwicklungsbiochemieUMG/Georg-August Universität Göttingen Justus-von-Liebig Weg 11 37077 Göttingen Deutschland
| | - Jörg Großhans
- Institut Für EntwicklungsbiochemieUMG/Georg-August Universität Göttingen Justus-von-Liebig Weg 11 37077 Göttingen Deutschland
| | - Felipe Opazo
- Center for Biostructural Imaging of Neurodegeneration Von-Siebold-Strasse 3a 37075 Göttingen Deutschland
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) Humboldtallee 23 37073 Göttingen Deutschland
- NanoTag Biotechnologies GmbH Rudolf-Wissell-Straße 28a 37079 Göttingen Deutschland
| | - Sebastian Kruss
- Institut für Physikalische ChemieGeorg-August Universität Göttingen Tammannstraße 6 37077 Göttingen Deutschland
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB) Humboldtallee 23 37073 Göttingen Deutschland
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Richter KN, Patzelt C, Phan NTN, Rizzoli SO. Antibody-driven capture of synaptic vesicle proteins on the plasma membrane enables the analysis of their interactions with other synaptic proteins. Sci Rep 2019; 9:9231. [PMID: 31239503 PMCID: PMC6592915 DOI: 10.1038/s41598-019-45729-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 06/13/2019] [Indexed: 01/07/2023] Open
Abstract
Many organelles from the secretory pathway fuse to the plasma membrane, to exocytose different cargoes. Their proteins are then retrieved from the plasma membrane by endocytosis, and the organelles are re-formed. It is generally unclear whether the organelle proteins colocalize when they are on the plasma membrane, or whether they disperse. To address this, we generated here a new approach, which we tested on synaptic vesicles, organelles that are known to exo- and endocytose frequently. We tagged the synaptotagmin molecules of newly exocytosed vesicles using clusters of primary and secondary antibodies targeted against the luminal domains of these molecules. The antibody clusters are too large for endocytosis, and thus sequestered the synaptotagmin molecules on the plasma membrane. Immunostainings for other synaptic molecules then revealed whether they colocalized with the sequestered synaptotagmin molecules. We suggest that such assays may be in the future extended to other cell types and other organelles.
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Affiliation(s)
- Katharina N Richter
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
| | - Christina Patzelt
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Nhu T N Phan
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
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Padmanabhan P, Bademosi AT, Kasula R, Lauwers E, Verstreken P, Meunier FA. Need for speed: Super-resolving the dynamic nanoclustering of syntaxin-1 at exocytic fusion sites. Neuropharmacology 2019; 169:107554. [PMID: 30826343 DOI: 10.1016/j.neuropharm.2019.02.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 01/08/2023]
Abstract
Communication between cells relies on regulated exocytosis, a multi-step process that involves the docking, priming and fusion of vesicles with the plasma membrane, culminating in the release of neurotransmitters and hormones. Key proteins and lipids involved in exocytosis are subjected to Brownian movement and constantly switch between distinct motion states which are governed by short-lived molecular interactions. Critical biochemical reactions between exocytic proteins that occur in the confinement of nanodomains underpin the precise sequence of priming steps which leads to the fusion of vesicles. The advent of super-resolution microscopy techniques has provided the means to visualize individual molecules on the plasma membrane with high spatiotemporal resolution in live cells. These techniques are revealing a highly dynamic nature of the nanoscale organization of the exocytic machinery. In this review, we focus on soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) syntaxin-1, which mediates vesicular fusion. Syntaxin-1 is highly mobile at the plasma membrane, and its inherent speed allows fast assembly and disassembly of syntaxin-1 nanoclusters which are associated with exocytosis. We reflect on recent studies which have revealed the mechanisms regulating syntaxin-1 nanoclustering on the plasma membrane and draw inferences on the effect of synaptic activity, phosphoinositides, N-ethylmaleimide-sensitive factor (NSF), α-soluble NSF attachment protein (α-SNAP) and SNARE complex assembly on the dynamic nanoscale organization of syntaxin-1. This article is part of the special issue entitled 'Mobility and trafficking of neuronal membrane proteins'.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Adekunle T Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Ravikiran Kasula
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia
| | - Elsa Lauwers
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences and Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Queensland, Australia.
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