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Zheng T, Cai S. Recent technical advances in cellular cryo-electron tomography. Int J Biochem Cell Biol 2024; 175:106648. [PMID: 39181502 DOI: 10.1016/j.biocel.2024.106648] [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: 05/01/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Understanding the in situ structure, organization, and interactions of macromolecules is essential for elucidating their functions and mechanisms of action. Cellular cryo-electron tomography (cryo-ET) is a cutting-edge technique that reveals in situ molecular-resolution architectures of macromolecules in their lifelike states. It also provides insights into the three-dimensional distribution of macromolecules and their spatial relationships with various subcellular structures. Thus, cellular cryo-ET bridges the gap between structural biology and cell biology. With rapid advancements, this technique achieved substantial improvements in throughput, automation, and resolution. This review presents the fundamental principles and methodologies of cellular cryo-ET, highlighting recent developments in sample preparation, data collection, and image processing. We also discuss emerging trends and potential future directions. As cellular cryo-ET continues to develop, it is set to play an increasingly vital role in structural cell biology.
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Affiliation(s)
- Tianyu Zheng
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shujun Cai
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China.
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2
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Papantoniou C, Laugks U, Betzin J, Capitanio C, Ferrero JJ, Sánchez-Prieto J, Schoch S, Brose N, Baumeister W, Cooper BH, Imig C, Lučić V. Munc13- and SNAP25-dependent molecular bridges play a key role in synaptic vesicle priming. SCIENCE ADVANCES 2023; 9:eadf6222. [PMID: 37343100 DOI: 10.1126/sciadv.adf6222] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/17/2023] [Indexed: 06/23/2023]
Abstract
Synaptic vesicle tethering, priming, and neurotransmitter release require a coordinated action of multiple protein complexes. While physiological experiments, interaction data, and structural studies of purified systems were essential for our understanding of the function of the individual complexes involved, they cannot resolve how the actions of individual complexes integrate. We used cryo-electron tomography to simultaneously image multiple presynaptic protein complexes and lipids at molecular resolution in their native composition, conformation, and environment. Our detailed morphological characterization suggests that sequential synaptic vesicle states precede neurotransmitter release, where Munc13-comprising bridges localize vesicles <10 nanometers and soluble N-ethylmaleimide-sensitive factor attachment protein 25-comprising bridges <5 nanometers from the plasma membrane, the latter constituting a molecularly primed state. Munc13 activation supports the transition to the primed state via vesicle bridges to plasma membrane (tethers), while protein kinase C promotes the same transition by reducing vesicle interlinking. These findings exemplify a cellular function performed by an extended assembly comprising multiple molecularly diverse complexes.
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Affiliation(s)
- Christos Papantoniou
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ulrike Laugks
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Julia Betzin
- Department of Neuropathology, University Hospital of Bonn, 53127 Bonn, Germany
| | - Cristina Capitanio
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - José Javier Ferrero
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense, and Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, 28040 Madrid, Spain
| | - José Sánchez-Prieto
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense, and Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, 28040 Madrid, Spain
| | - Susanne Schoch
- Department of Neuropathology, University Hospital of Bonn, 53127 Bonn, Germany
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute of Multidisciplinary Sciences, City Campus, 37075 Göttingen, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Benjamin H Cooper
- Department of Molecular Neurobiology, Max Planck Institute of Multidisciplinary Sciences, City Campus, 37075 Göttingen, Germany
| | - Cordelia Imig
- Department of Molecular Neurobiology, Max Planck Institute of Multidisciplinary Sciences, City Campus, 37075 Göttingen, Germany
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Vladan Lučić
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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3
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Radecke J, Seeger R, Kádková A, Laugks U, Khosrozadeh A, Goldie KN, Lučić V, Sørensen JB, Zuber B. Morphofunctional changes at the active zone during synaptic vesicle exocytosis. EMBO Rep 2023; 24:e55719. [PMID: 36876590 PMCID: PMC10157379 DOI: 10.15252/embr.202255719] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/30/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023] Open
Abstract
Synaptic vesicle (SV) fusion with the plasma membrane (PM) proceeds through intermediate steps that remain poorly resolved. The effect of persistent high or low exocytosis activity on intermediate steps remains unknown. Using spray-mixing plunge-freezing cryo-electron tomography we observe events following synaptic stimulation at nanometer resolution in near-native samples. Our data suggest that during the stage that immediately follows stimulation, termed early fusion, PM and SV membrane curvature changes to establish a point contact. The next stage-late fusion-shows fusion pore opening and SV collapse. During early fusion, proximal tethered SVs form additional tethers with the PM and increase the inter-SV connector number. In the late-fusion stage, PM-proximal SVs lose their interconnections, allowing them to move toward the PM. Two SNAP-25 mutations, one arresting and one disinhibiting spontaneous release, cause connector loss. The disinhibiting mutation causes loss of membrane-proximal multiple-tethered SVs. Overall, tether formation and connector dissolution are triggered by stimulation and respond to spontaneous fusion rate manipulation. These morphological observations likely correspond to SV transition from one functional pool to another.
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Affiliation(s)
- Julika Radecke
- Institute of AnatomyUniversity of BernBernSwitzerland
- Department of Neuroscience, University of CopenhagenCopenhagenDenmark
- Diamond Light Source LtdDidcotUK
- Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland
| | - Raphaela Seeger
- Institute of AnatomyUniversity of BernBernSwitzerland
- Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland
| | - Anna Kádková
- Department of Neuroscience, University of CopenhagenCopenhagenDenmark
| | - Ulrike Laugks
- Max‐Planck‐Institute of BiochemistryMartinsriedGermany
| | - Amin Khosrozadeh
- Institute of AnatomyUniversity of BernBernSwitzerland
- Graduate School for Cellular and Biomedical SciencesUniversity of BernBernSwitzerland
| | | | - Vladan Lučić
- Max‐Planck‐Institute of BiochemistryMartinsriedGermany
| | - Jakob B Sørensen
- Department of Neuroscience, University of CopenhagenCopenhagenDenmark
| | - Benoît Zuber
- Institute of AnatomyUniversity of BernBernSwitzerland
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4
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Kim HHS, Uddin MR, Xu M, Chang YW. Computational Methods Toward Unbiased Pattern Mining and Structure Determination in Cryo-Electron Tomography Data. J Mol Biol 2023; 435:168068. [PMID: 37003470 PMCID: PMC10164694 DOI: 10.1016/j.jmb.2023.168068] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/19/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Cryo-electron tomography can uniquely probe the native cellular environment for macromolecular structures. Tomograms feature complex data with densities of diverse, densely crowded macromolecular complexes, low signal-to-noise, and artifacts such as the missing wedge effect. Post-processing of this data generally involves isolating regions or particles of interest from tomograms, organizing them into related groups, and rendering final structures through subtomogram averaging. Template-matching and reference-based structure determination are popular analysis methods but are vulnerable to biases and can often require significant user input. Most importantly, these approaches cannot identify novel complexes that reside within the imaged cellular environment. To reliably extract and resolve structures of interest, efficient and unbiased approaches are therefore of great value. This review highlights notable computational software and discusses how they contribute to making automated structural pattern discovery a possibility. Perspectives emphasizing the importance of features for user-friendliness and accessibility are also presented.
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Affiliation(s)
- Hannah Hyun-Sook Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. https://twitter.com/hannahinthelab
| | - Mostofa Rafid Uddin
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA. https://twitter.com/duran_rafid
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Jung JH, Chen X, Reese TS. Cryo-EM tomography and automatic segmentation delineate modular structures in the postsynaptic density. Front Synaptic Neurosci 2023; 15:1123564. [PMID: 37091879 PMCID: PMC10117989 DOI: 10.3389/fnsyn.2023.1123564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/02/2023] [Indexed: 04/08/2023] Open
Abstract
Postsynaptic densities (PSDs) are large protein complexes associated with the postsynaptic membrane of excitatory synapses important for synaptic function including plasticity. Conventional electron microscopy (EM) typically depicts PSDs as compact disk-like structures of hundreds of nanometers in size. Biochemically isolated PSDs were also similar in dimension revealing a predominance of proteins with the ability to polymerize into an extensive scaffold; several EM studies noted their irregular contours with often small granular structures (<30 nm) and holes. Super-resolution light microscopy studies observed clusters of PSD elements and their activity-induced lateral movement. Furthermore, our recent EM study on PSD fractions after sonication observed PSD fragments (40–90 nm in size) separate from intact PSDs; however, such structures within PSDs remained unidentified. Here we examined isolated PSDs by cryo-EM tomography with our new approach of automatic segmentation that enables delineation of substructures and their quantitative analysis. The delineated substructures broadly varied in size, falling behind 30 nm or exceeding 100 nm and showed that a considerable portion of the substructures (>38%) in isolated PSDs was in the same size range as those fragments. Furthermore, substructures spanning the entire thickness of the PSD were found, large enough to contain both membrane-associated and cytoplasmic proteins of the PSD; interestingly, they were similar to nanodomains in frequency. The structures detected here appear to constitute the isolated PSD as modules of various compositions, and this modular nature may facilitate remodeling of the PSD for proper synaptic function and plasticity.
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Computational methods for ultrastructural analysis of synaptic complexes. Curr Opin Neurobiol 2022; 76:102611. [PMID: 35952541 DOI: 10.1016/j.conb.2022.102611] [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: 02/28/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/21/2022]
Abstract
Electron microscopy (EM) provided fundamental insights about the ultrastructure of neuronal synapses. The large amount of information present in the contemporary EM datasets precludes a thorough assessment by visual inspection alone, thus requiring computational methods for the analysis of the data. Here, I review image processing software methods ranging from membrane tracing in large volume datasets to high resolution structures of synaptic complexes. Particular attention is payed to molecular level analysis provided by recent cryo-electron microscopy and tomography methods.
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Sazzed S, Scheible P, He J, Wriggers W. Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms. Biomolecules 2022; 12:1022. [PMID: 35892332 PMCID: PMC9394354 DOI: 10.3390/biom12081022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/13/2022] [Accepted: 07/17/2022] [Indexed: 11/30/2022] Open
Abstract
Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between-or specific shape on-individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D maps of subcellular components. Assuming that the tomogram can be rotated such that the filaments are oriented in a mean direction, the proposed framework first identifies local seed points for candidate filament segments, which are then grown from the seeds using a dynamic programming algorithm. We validate various algorithmic variations of our framework on simulated tomograms that closely mimic the noise and appearance of experimental maps. As we know the ground truth in the simulated tomograms, the statistical analysis consisting of precision, recall, and F1 scores allows us to optimize the performance of this new approach. We find that a bipyramidal accumulation scheme for path density is superior to straight-line accumulation. In addition, the multiplication of forward and backward path densities provides for an efficient filter that lifts the filament density above the noise level. Resulting from our tests is a robust method that can be expected to perform well (F1 scores 0.86-0.95) under experimental noise conditions.
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Affiliation(s)
- Salim Sazzed
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA; (S.S.); (P.S.)
| | - Peter Scheible
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA; (S.S.); (P.S.)
| | - Jing He
- Department of Computer Science, Old Dominion University, Norfolk, VA 23529, USA; (S.S.); (P.S.)
| | - Willy Wriggers
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA 23529, USA
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8
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Schneider J, Jasnin M. Capturing actin assemblies in cells using in situ cryo-electron tomography. Eur J Cell Biol 2022; 101:151224. [PMID: 35500467 DOI: 10.1016/j.ejcb.2022.151224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Actin contributes to an exceptionally wide range of cellular processes through the assembly and disassembly of highly dynamic and ordered structures. Visualizing these structures in cells can help us understand how the molecular players of the actin machinery work together to produce force-generating systems. In recent years, cryo-electron tomography (cryo-ET) has become the method of choice for structural analysis of the cell interior at the molecular scale. Here we review advances in cryo-ET workflows that have enabled this transformation, especially the automation of sample preparation procedures, data collection, and processing. We discuss new structural analyses of dynamic actin assemblies in cryo-preserved cells, which have provided mechanistic insights into actin assembly and function at the nanoscale. Finally, we highlight the latest visual proteomics studies of actin filaments and their interactors reaching sub-nanometer resolutions in cells.
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Affiliation(s)
- Jonathan Schneider
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marion Jasnin
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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9
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Zuber B, Lučić V. Neurons as a model system for cryo-electron tomography. J Struct Biol X 2022; 6:100067. [PMID: 35310407 PMCID: PMC8924422 DOI: 10.1016/j.yjsbx.2022.100067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Cryo-ET imaging of neurons is a versatile system for cell biology in situ. Structural and spatial localization analysis yields new insights into synaptic transmission. The synapse provides a rich environment for the development of image processing tools.
Cryo-electron tomography (Cryo-ET) provides unique opportunities to image cellular components at high resolution in their native state and environment. While many different cell types were investigated by cryo-ET, here we review application to neurons. We show that neurons are a versatile system that can be used to investigate general cellular components such as the cytoskeleton and membrane-bound organelles, in addition to neuron-specific processes such as synaptic transmission. Furthermore, the synapse provides a rich environment for the development of cryo-ET image processing tools suitable to elucidate the functional and spatial organization of compositionally and morphologically heterogeneous macromolecular complexes involved in biochemical signaling cascades, within their native, crowded cellular environments.
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10
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Pöge M, Mahamid J, Imanishi SS, Plitzko JM, Palczewski K, Baumeister W. Determinants shaping the nanoscale architecture of the mouse rod outer segment. eLife 2021; 10:e72817. [PMID: 34931611 PMCID: PMC8758146 DOI: 10.7554/elife.72817] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022] Open
Abstract
The unique membrane organization of the rod outer segment (ROS), the specialized sensory cilium of rod photoreceptor cells, provides the foundation for phototransduction, the initial step in vision. ROS architecture is characterized by a stack of identically shaped and tightly packed membrane disks loaded with the visual receptor rhodopsin. A wide range of genetic aberrations have been reported to compromise ROS ultrastructure, impairing photoreceptor viability and function. Yet, the structural basis giving rise to the remarkably precise arrangement of ROS membrane stacks and the molecular mechanisms underlying genetically inherited diseases remain elusive. Here, cryo-electron tomography (cryo-ET) performed on native ROS at molecular resolution provides insights into key structural determinants of ROS membrane architecture. Our data confirm the existence of two previously observed molecular connectors/spacers which likely contribute to the nanometer-scale precise stacking of the ROS disks. We further provide evidence that the extreme radius of curvature at the disk rims is enforced by a continuous supramolecular assembly composed of peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) oligomers. We suggest that together these molecular assemblies constitute the structural basis of the highly specialized ROS functional architecture. Our Cryo-ET data provide novel quantitative and structural information on the molecular architecture in ROS and substantiate previous results on proposed mechanisms underlying pathologies of certain PRPH2 mutations leading to blindness.
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Affiliation(s)
- Matthias Pöge
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
| | - Julia Mahamid
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
| | - Sanae S Imanishi
- Eugene and Marilyn Glick Eye Institute and the Department of Ophthalmology, Indiana University School of MedicineyIndianapolisUnited States
| | - Jürgen M Plitzko
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, Center for Translational Vision Research, Department of Physiology & Biophysics, Department of Chemistry, Department of Molecular Biology and BiochemistryIrvineUnited States
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
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11
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Radulović S, Sunkara S, Maurer C, Leitinger G. Digging Deeper: Advancements in Visualization of Inhibitory Synapses in Neurodegenerative Disorders. Int J Mol Sci 2021; 22:12470. [PMID: 34830352 PMCID: PMC8623765 DOI: 10.3390/ijms222212470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/02/2022] Open
Abstract
Recent research has provided strong evidence that neurodegeneration may develop from an imbalance between synaptic structural components in the brain. Lately, inhibitory synapses communicating via the neurotransmitters GABA or glycine have come to the center of attention. Increasing evidence suggests that imbalance in the structural composition of inhibitory synapses affect deeply the ability of neurons to communicate effectively over synaptic connections. Progressive failure of synaptic plasticity and memory are thus hallmarks of neurodegenerative diseases. In order to prove that structural changes at synapses contribute to neurodegeneration, we need to visualize single-molecule interactions at synaptic sites in an exact spatial and time frame. This visualization has been restricted in terms of spatial and temporal resolution. New developments in electron microscopy and super-resolution microscopy have improved spatial and time resolution tremendously, opening up numerous possibilities. Here we critically review current and recently developed methods for high-resolution visualization of inhibitory synapses in the context of neurodegenerative diseases. We present advantages, strengths, weaknesses, and current limitations for selected methods in research, as well as present a future perspective. A range of new options has become available that will soon help understand the involvement of inhibitory synapses in neurodegenerative disorders.
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Affiliation(s)
- Snježana Radulović
- Gottfried Schatz Research Center, Division of Cell Biology, Histology and Embryology, Medical University of Graz, 8010 Graz, Austria; (S.R.); (S.S.)
| | - Sowmya Sunkara
- Gottfried Schatz Research Center, Division of Cell Biology, Histology and Embryology, Medical University of Graz, 8010 Graz, Austria; (S.R.); (S.S.)
| | - Christa Maurer
- Gottfried Schatz Research Center, Division of Macroscopic and Clinical Anatomy, Medical University of Graz, 8010 Graz, Austria;
| | - Gerd Leitinger
- Gottfried Schatz Research Center, Division of Cell Biology, Histology and Embryology, Medical University of Graz, 8010 Graz, Austria; (S.R.); (S.S.)
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12
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Martinez-Sanchez A, Laugks U, Kochovski Z, Papantoniou C, Zinzula L, Baumeister W, Lučić V. Trans-synaptic assemblies link synaptic vesicles and neuroreceptors. SCIENCE ADVANCES 2021; 7:7/10/eabe6204. [PMID: 33674312 PMCID: PMC7935360 DOI: 10.1126/sciadv.abe6204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Synaptic transmission is characterized by fast, tightly coupled processes and complex signaling pathways that require a precise protein organization, such as the previously reported nanodomain colocalization of pre- and postsynaptic proteins. Here, we used cryo-electron tomography to visualize synaptic complexes together with their native environment comprising interacting proteins and lipids on a 2- to 4-nm scale. Using template-free detection and classification, we showed that tripartite trans-synaptic assemblies (subcolumns) link synaptic vesicles to postsynaptic receptors and established that a particular displacement between directly interacting complexes characterizes subcolumns. Furthermore, we obtained de novo average structures of ionotropic glutamate receptors in their physiological composition, embedded in plasma membrane. These data support the hypothesis that synaptic function is carried by precisely organized trans-synaptic units. It provides a framework for further exploration of synaptic and other large molecular assemblies that link different cells or cellular regions and may require weak or transient interactions to exert their function.
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Affiliation(s)
- Antonio Martinez-Sanchez
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Department of Computer Sciences, Faculty of Sciences, University of Oviedo, Federico Garcia Lorca 18, 33007, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, University of Oviedo, Avenida Hospital Universitario s/n, 33011 Oviedo, Spain
- Institute of Neuropathology, University Medical Center Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Ulrike Laugks
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Zdravko Kochovski
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christos Papantoniou
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Luca Zinzula
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Vladan Lučić
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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13
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Hylton RK, Seader VH, Swulius MT. Cryo-Electron Tomography and Automatic Segmentation of Cultured Hippocampal Neurons. Methods Mol Biol 2021; 2215:25-48. [PMID: 33367998 DOI: 10.1007/978-1-0716-0966-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cryo-electron tomography is fast becoming a preferred method for studying intracellular environments at the molecular scale. Increases in data collection throughput means that large numbers of tomograms can be generated at rates too fast for humans to easily explore quantitatively. Currently, there is a large effort to make data collection and segmentation tools more automated. Here, we describe a workflow for preparing cultured neurons on electron microscopy grids, batch tomographic data collection, reconstruction and automatic segmentation using freely and commercially available software.
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Affiliation(s)
- Ryan K Hylton
- Department of Biochemistry and Molecular Biology, The Penn State College of Medicine, Hershey, PA, USA
| | - Victoria H Seader
- Department of Biochemistry and Molecular Biology, The Penn State College of Medicine, Hershey, PA, USA
| | - Matthew T Swulius
- Department of Biochemistry and Molecular Biology, The Penn State College of Medicine, Hershey, PA, USA.
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14
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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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15
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Reliable estimation of membrane curvature for cryo-electron tomography. PLoS Comput Biol 2020; 16:e1007962. [PMID: 32776920 PMCID: PMC7444595 DOI: 10.1371/journal.pcbi.1007962] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 08/20/2020] [Accepted: 05/18/2020] [Indexed: 01/01/2023] Open
Abstract
Curvature is a fundamental morphological descriptor of cellular membranes. Cryo-electron tomography (cryo-ET) is particularly well-suited to visualize and analyze membrane morphology in a close-to-native state and molecular resolution. However, current curvature estimation methods cannot be applied directly to membrane segmentations in cryo-ET, as these methods cannot cope with some of the artifacts introduced during image acquisition and membrane segmentation, such as quantization noise and open borders. Here, we developed and implemented a Python package for membrane curvature estimation from tomogram segmentations, which we named PyCurv. From a membrane segmentation, a signed surface (triangle mesh) is first extracted. The triangle mesh is then represented by a graph, which facilitates finding neighboring triangles and the calculation of geodesic distances necessary for local curvature estimation. PyCurv estimates curvature based on tensor voting. Beside curvatures, this algorithm also provides robust estimations of surface normals and principal directions. We tested PyCurv and three well-established methods on benchmark surfaces and biological data. This revealed the superior performance of PyCurv not only for cryo-ET, but also for data generated by other techniques such as light microscopy and magnetic resonance imaging. Altogether, PyCurv is a versatile open-source software to reliably estimate curvature of membranes and other surfaces in a wide variety of applications. Membrane curvature plays a central role in many cellular processes like cell division, organelle shaping and membrane contact sites. While cryo-electron tomography (cryo-ET) allows the visualization of cellular membranes in 3D at molecular resolution and close-to-native conditions, there is a lack of computational methods to quantify membrane curvature from cryo-ET data. Therefore, we developed a computational procedure for membrane curvature estimation from tomogram segmentations and implemented it in a software package called PyCurv. PyCurv converts a membrane segmentation, i.e. a set of voxels, into a surface, i.e. a mesh of triangles. PyCurv uses the local geometrical information to reliably estimate the local surface orientation, the principal (maximum and minimum) curvatures and their directions. PyCurv outperforms well-established curvature estimation methods, and it can also be applied to data generated by other imaging techniques.
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Cryo-Electron microscopy for the study of self-assembled poly(ionic liquid) nanoparticles and protein supramolecular structures. Colloid Polym Sci 2020. [DOI: 10.1007/s00396-020-04657-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
AbstractCryo-electron microscopy (cryo-EM) is a powerful structure determination technique that is well-suited to the study of protein and polymer self-assembly in solution. In contrast to conventional transmission electron microscopy (TEM) sample preparation, which often times involves drying and staining, the frozen-hydrated sample preparation allows the specimens to be kept and imaged in a state closest to their native one. Here, we give a short overview of the basic principles of Cryo-EM and review our results on applying it to the study of different protein and polymer self-assembled nanostructures. More specifically, we show how we have applied cryo-electron tomography (cryo-ET) to visualize the internal morphology of self-assembled poly(ionic liquid) nanoparticles and cryo-EM single particle analysis (SPA) to determine the three-dimensional (3D) structures of artificial protein microtubules.
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Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms. Nat Methods 2020; 17:209-216. [PMID: 31907446 DOI: 10.1038/s41592-019-0675-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/11/2019] [Indexed: 01/12/2023]
Abstract
With faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography provides an accurate representation of molecular architecture of cells. However, detection and precise localization of macromolecular complexes within cellular environments is aggravated by the presence of many molecular species and molecular crowding. We developed a template-free image processing procedure for accurate tracing of complex networks of densities in cryo-electron tomograms, a comprehensive and automated detection of heterogeneous membrane-bound complexes and an unsupervised classification (PySeg). Applications to intact cells and isolated endoplasmic reticulum (ER) allowed us to detect and classify small protein complexes. This classification provided sufficiently homogeneous particle sets and initial references to allow subsequent de novo subtomogram averaging. Spatial distribution analysis showed that ER complexes have different localization patterns forming nanodomains. Therefore, this procedure allows a comprehensive detection and structural analysis of complexes in situ.
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Collado J, Kalemanov M, Campelo F, Bourgoint C, Thomas F, Loewith R, Martínez-Sánchez A, Baumeister W, Stefan CJ, Fernández-Busnadiego R. Tricalbin-Mediated Contact Sites Control ER Curvature to Maintain Plasma Membrane Integrity. Dev Cell 2019; 51:476-487.e7. [PMID: 31743662 PMCID: PMC6863395 DOI: 10.1016/j.devcel.2019.10.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 09/23/2019] [Accepted: 10/16/2019] [Indexed: 12/23/2022]
Abstract
Membrane contact sites (MCS) between the endoplasmic reticulum (ER) and the plasma membrane (PM) play fundamental roles in all eukaryotic cells. ER-PM MCS are particularly abundant in Saccharomyces cerevisiae, where approximately half of the PM surface is covered by cortical ER (cER). Several proteins, including Ist2, Scs2/22, and Tcb1/2/3 are implicated in cER formation, but the specific roles of these molecules are poorly understood. Here, we use cryo-electron tomography to show that ER-PM tethers are key determinants of cER morphology. Notably, Tcb proteins (tricalbins) form peaks of extreme curvature on the cER membrane facing the PM. Combined modeling and functional assays suggest that Tcb-mediated cER peaks facilitate the transport of lipids between the cER and the PM, which is necessary to maintain PM integrity under heat stress. ER peaks were also present at other MCS, implying that membrane curvature enforcement may be a widespread mechanism to regulate MCS function.
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Affiliation(s)
- Javier Collado
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Institute of Neuropathology, University Medical Center Göttingen, Göttingen 37099, Germany; Graduate School of Quantitative Biosciences Munich, Munich 81337, Germany
| | - Maria Kalemanov
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Graduate School of Quantitative Biosciences Munich, Munich 81337, Germany
| | - Felix Campelo
- ICFO, Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels 08860, Spain
| | - Clélia Bourgoint
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Ffion Thomas
- MRC Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland; Swiss National Centre for Competence in Research, Program Chemical Biology, Geneva 1211, Switzerland
| | - Antonio Martínez-Sánchez
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Christopher J Stefan
- MRC Laboratory for Molecular Cell Biology, University College London, London, WC1E 6BT, UK
| | - Rubén Fernández-Busnadiego
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Institute of Neuropathology, University Medical Center Göttingen, Göttingen 37099, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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Zuber B, Lučić V. Molecular architecture of the presynaptic terminal. Curr Opin Struct Biol 2019; 54:129-138. [PMID: 30925443 DOI: 10.1016/j.sbi.2019.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/11/2019] [Accepted: 01/26/2019] [Indexed: 10/27/2022]
Abstract
Neurotransmitter release at the presynaptic terminal is one of the fundamental processes in neuronal communication. It is a complex process comprising signaling pathways that exert a precise spatio-temporal coordination to prepare and bring synaptic vesicles to exocytosis. While many molecular components involved have been identified, their direct observation at different stages of the neurotransmitter release is lacking. Three-dimensional imaging by electron tomography provided remarkable views of the synaptic vesicles and the cytomatrix. Imaging fully hydrated, vitrified samples allowed a direct visualization, precise localization and a quantitative characterization of pleomorphic synaptic vesicle-bound complexes in situ, as well as the elucidation of their function in the neurotransmitter release.
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Affiliation(s)
- Benoît Zuber
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
| | - Vladan Lučić
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
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Schrod N, Vanhecke D, Laugks U, Stein V, Fukuda Y, Schaffer M, Baumeister W, Lucic V. Pleomorphic linkers as ubiquitous structural organizers of vesicles in axons. PLoS One 2018; 13:e0197886. [PMID: 29864134 PMCID: PMC5986143 DOI: 10.1371/journal.pone.0197886] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/10/2018] [Indexed: 11/30/2022] Open
Abstract
Many cellular processes depend on a precise structural organization of molecular components. Here, we established that neurons grown in culture provide a suitable system for in situ structural investigations of cellular structures by cryo-electron tomography, a method that allows high resolution, three-dimensional imaging of fully hydrated, vitrified cellular samples. A higher level of detail of cellular components present in our images allowed us to quantitatively characterize presynaptic and cytoskeletal organization, as well as structures involved in axonal transport and endocytosis. In this way we provide a structural framework into which information from other methods need to fit. Importantly, we show that short pleomorphic linkers (tethers and connectors) extensively interconnect different types of spherical vesicles and other lipid membranes in neurons imaged in a close-to-native state. These linkers likely serve to organize and precisely position vesicles involved in endocytosis, axonal transport and synaptic release. Hence, structural interactions via short linkers may serve as ubiquitous vesicle organizers in neuronal cells.
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Affiliation(s)
- Nikolas Schrod
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Dimitri Vanhecke
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Ulrike Laugks
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Valentin Stein
- Institute of Physiology II, University of Bonn, Bonn, Germany
| | - Yoshiyuki Fukuda
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Miroslava Schaffer
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
| | - Vladan Lucic
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Germany
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Vargas KJ, Schrod N, Davis T, Fernandez-Busnadiego R, Taguchi YV, Laugks U, Lucic V, Chandra SS. Synucleins Have Multiple Effects on Presynaptic Architecture. Cell Rep 2017; 18:161-173. [PMID: 28052246 DOI: 10.1016/j.celrep.2016.12.023] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/21/2016] [Accepted: 12/07/2016] [Indexed: 02/01/2023] Open
Abstract
Synucleins (α, β, γ-synuclein) are a family of abundant presynaptic proteins. α-Synuclein is causally linked to the pathogenesis of Parkinson's disease (PD). In an effort to define their physiological and pathological function or functions, we investigated the effects of deleting synucleins and overexpressing α-synuclein PD mutations, in mice, on synapse architecture using electron microscopy (EM) and cryoelectron tomography (cryo-ET). We show that synucleins are regulators of presynapse size and synaptic vesicle (SV) pool organization. Using cryo-ET, we observed that deletion of synucleins increases SV tethering to the active zone but decreases the inter-linking of SVs by short connectors. These ultrastructural changes were correlated with discrete protein phosphorylation changes in αβγ-synuclein-/- neurons. We also determined that α-synuclein PD mutants (PARK1/hA30P and PARK4/hα-syn) primarily affected presynaptic cytomatrix proximal to the active zone, congruent with previous findings that these PD mutations decrease neurotransmission. Collectively, our results suggest that synucleins are important orchestrators of presynaptic terminal topography.
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Affiliation(s)
- Karina J Vargas
- Department of Neurology, Yale University, New Haven, CT 06536, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University, New Haven, CT 06536, USA
| | - Nikolas Schrod
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Taylor Davis
- Department of Neurology, Yale University, New Haven, CT 06536, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University, New Haven, CT 06536, USA
| | - Ruben Fernandez-Busnadiego
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University, New Haven, CT 06536, USA; Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06510, USA; Howard Hughes Medical Institute, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Yumiko V Taguchi
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University, New Haven, CT 06536, USA; Department of Cell Biology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Ulrike Laugks
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Vladan Lucic
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Sreeganga S Chandra
- Department of Neurology, Yale University, New Haven, CT 06536, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University, New Haven, CT 06536, USA; Department of Neuroscience, Yale University, New Haven, CT 06519, USA.
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