1
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Cada AK, Mizuno N. Molecular cartography within axons. Curr Opin Cell Biol 2024; 88:102358. [PMID: 38608424 DOI: 10.1016/j.ceb.2024.102358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
Recent advances in imaging methods begin to further illuminate the inner workings of neurons. Views of the axonal landscape through the lens of in situ cryo-electron tomography (cryo-ET) provide a high-resolution atlas of the macromolecular organization in near-native conditions, leading to our growing understanding of the vital roles of compositional and structural organization in maintaining neuronal homeostasis. In this review, we discuss the latest observations concerning the fundamental components found within neuronal compartments, with special emphasis on the axon, branch points, and growth cone. We describe the similarity and difference in organization of organelles and molecules in varying compartments. Finally, we highlight outstanding questions on the dynamics and localization of various components along the axon that may be answered using orthogonal approaches.
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Affiliation(s)
- A King Cada
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA
| | - Naoko Mizuno
- Laboratory of Structural Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA; National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA.
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2
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Cruz-León S, Majtner T, Hoffmann PC, Kreysing JP, Kehl S, Tuijtel MW, Schaefer SL, Geißler K, Beck M, Turoňová B, Hummer G. High-confidence 3D template matching for cryo-electron tomography. Nat Commun 2024; 15:3992. [PMID: 38734767 PMCID: PMC11088655 DOI: 10.1038/s41467-024-47839-8] [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: 10/31/2023] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures of macromolecules. However, their applicability remains limited in terms of both the abundance and size of the molecular targets. Here we show that the performance of TM is greatly improved by using template-specific search parameter optimization and by including higher-resolution information. We establish a TM pipeline with systematically tuned parameters for the automated, objective and comprehensive identification of structures with confidence 10 to 100-fold above the noise level. We demonstrate high-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, fatty acid synthases, lipid membranes and microtubules, and individual subunits inside crowded eukaryotic cells. We provide software tools for the generic implementation of our method that is broadly applicable towards realizing visual proteomics.
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Affiliation(s)
- Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Tomáš Majtner
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Patrick C Hoffmann
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Sebastian Kehl
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85748, Garching, Germany
| | - Maarten W Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Stefan L Schaefer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Katharina Geißler
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biochemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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3
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Ko J, Hyung S, Cheong S, Chung Y, Li Jeon N. Revealing the clinical potential of high-resolution organoids. Adv Drug Deliv Rev 2024; 207:115202. [PMID: 38336091 DOI: 10.1016/j.addr.2024.115202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/01/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
The symbiotic interplay of organoid technology and advanced imaging strategies yields innovative breakthroughs in research and clinical applications. Organoids, intricate three-dimensional cell cultures derived from pluripotent or adult stem/progenitor cells, have emerged as potent tools for in vitro modeling, reflecting in vivo organs and advancing our grasp of tissue physiology and disease. Concurrently, advanced imaging technologies such as confocal, light-sheet, and two-photon microscopy ignite fresh explorations, uncovering rich organoid information. Combined with advanced imaging technologies and the power of artificial intelligence, organoids provide new insights that bridge experimental models and real-world clinical scenarios. This review explores exemplary research that embodies this technological synergy and how organoids reshape personalized medicine and therapeutics.
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Affiliation(s)
- Jihoon Ko
- Department of BioNano Technology, Gachon University, Gyeonggi 13120, Republic of Korea
| | - Sujin Hyung
- Precision Medicine Research Institute, Samsung Medical Center, Seoul 08826, Republic of Korea; Division of Hematology-Oncology, Department of Medicine, Sungkyunkwan University, Samsung Medical Center, Seoul 08826, Republic of Korea
| | - Sunghun Cheong
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yoojin Chung
- Division of Computer Engineering, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea
| | - Noo Li Jeon
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Department of Mechanical Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Institute of Advanced Machines and Design, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Qureator, Inc., San Diego, CA, USA.
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4
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Ching C, Maufront J, di Cicco A, Lévy D, Dezi M. C ool-contacts: Cryo-Electron Microscopy of Membrane Contact Sites and Their Components. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2024; 7:25152564241231364. [PMID: 38410695 PMCID: PMC10895918 DOI: 10.1177/25152564241231364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024]
Abstract
Electron microscopy has played a pivotal role in elucidating the ultrastructure of membrane contact sites between cellular organelles. The advent of cryo-electron microscopy has ushered in the ability to determine atomic models of constituent proteins or protein complexes within sites of membrane contact through single particle analysis. Furthermore, it enables the visualization of the three-dimensional architecture of membrane contact sites, encompassing numerous copies of proteins, whether in vitro reconstituted or directly observed in situ using cryo-electron tomography. Nevertheless, there exists a scarcity of cryo-electron microscopy studies focused on the site of membrane contact and their constitutive proteins. This review provides an overview of the contributions made by cryo-electron microscopy to our understanding of membrane contact sites, outlines the associated limitations, and explores prospects in this field.
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Affiliation(s)
- Cyan Ching
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Julien Maufront
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Aurélie di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
| | - Manuela Dezi
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physique des Cellules et Cancer, Paris, France
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5
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Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling Difficult Cryo-ET Samples: A Study with Primary Neurons from Drosophila melanogaster. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2127-2148. [PMID: 37966978 PMCID: PMC11168236 DOI: 10.1093/micmic/ozad125] [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: 07/17/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons having been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
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Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA
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6
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Weber N, Hinks B, Jensen J, Lidahl T, Mendonça L. Sample Preparation for In Situ Cryotomography of Mammalian Cells. J Vis Exp 2023:10.3791/65697. [PMID: 38163272 PMCID: PMC10921979 DOI: 10.3791/65697] [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] [Indexed: 01/03/2024] Open
Abstract
In situ cellular cryotomography is a powerful technique for studying complex objects in their native frozen-hydrated cellular context, making it highly relevant to cellular biology and virology. The potential of combining cryotomography with other microscopy modalities makes it a perfect technique for integrative and correlative imaging. However, sample preparation for in situ cellular tomography is not straightforward, as cells do not readily attach and stretch over the electron microscopy grid. Additionally, the grids themselves are fragile and can break if handled too forcefully, resulting in the loss of imageable areas. The geometry of tissue culture dishes can also pose a challenge when manipulating the grids with tweezers. Here, we describe the tips and tricks to overcome these (and other) challenges and prepare good-quality samples for in situ cellular cryotomography and correlative imaging of adherent mammalian cells. With continued advances in cryomicroscopy technology, this technique holds enormous promise for advancing our understanding of complex biological systems.
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Affiliation(s)
- Noah Weber
- College of Liberal Arts, University of Minnesota; Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota
| | - Brennan Hinks
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota; College of Biological Sciences, University of Minnesota
| | - Jacob Jensen
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota
| | - Thomas Lidahl
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota; College of Biological Sciences, University of Minnesota
| | - Luiza Mendonça
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota;
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7
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Smith G, Sweeney ST, O’Kane CJ, Prokop A. How neurons maintain their axons long-term: an integrated view of axon biology and pathology. Front Neurosci 2023; 17:1236815. [PMID: 37564364 PMCID: PMC10410161 DOI: 10.3389/fnins.2023.1236815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
Axons are processes of neurons, up to a metre long, that form the essential biological cables wiring nervous systems. They must survive, often far away from their cell bodies and up to a century in humans. This requires self-sufficient cell biology including structural proteins, organelles, and membrane trafficking, metabolic, signalling, translational, chaperone, and degradation machinery-all maintaining the homeostasis of energy, lipids, proteins, and signalling networks including reactive oxygen species and calcium. Axon maintenance also involves specialised cytoskeleton including the cortical actin-spectrin corset, and bundles of microtubules that provide the highways for motor-driven transport of components and organelles for virtually all the above-mentioned processes. Here, we aim to provide a conceptual overview of key aspects of axon biology and physiology, and the homeostatic networks they form. This homeostasis can be derailed, causing axonopathies through processes of ageing, trauma, poisoning, inflammation or genetic mutations. To illustrate which malfunctions of organelles or cell biological processes can lead to axonopathies, we focus on axonopathy-linked subcellular defects caused by genetic mutations. Based on these descriptions and backed up by our comprehensive data mining of genes linked to neural disorders, we describe the 'dependency cycle of local axon homeostasis' as an integrative model to explain why very different causes can trigger very similar axonopathies, providing new ideas that can drive the quest for strategies able to battle these devastating diseases.
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Affiliation(s)
- Gaynor Smith
- Cardiff University, School of Medicine, College of Biomedical and Life Sciences, Cardiff, United Kingdom
| | - Sean T. Sweeney
- Department of Biology, University of York and York Biomedical Research Institute, York, United Kingdom
| | - Cahir J. O’Kane
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Andreas Prokop
- Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biology, The University of Manchester, Manchester, United Kingdom
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8
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Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling difficult cryo-ET samples: A study with primary neurons from Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548468. [PMID: 37502991 PMCID: PMC10369871 DOI: 10.1101/2023.07.10.548468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
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Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI, 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53715, USA
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9
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Ganeva I, Lim K, Boulanger J, Hoffmann PC, Muriel O, Borgeaud AC, Hagen WJH, Savage DB, Kukulski W. The architecture of Cidec-mediated interfaces between lipid droplets. Cell Rep 2023; 42:112107. [PMID: 36800289 PMCID: PMC9989828 DOI: 10.1016/j.celrep.2023.112107] [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: 08/09/2021] [Revised: 10/14/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Lipid droplets (LDs) are intracellular organelles responsible for storing surplus energy as neutral lipids. Their size and number vary enormously. In white adipocytes, LDs can reach 100 μm in diameter, occupying >90% of the cell. Cidec, which is strictly required for the formation of large LDs, is concentrated at interfaces between adjacent LDs and facilitates directional flux of neutral lipids from the smaller to the larger LD. The mechanism of lipid transfer is unclear, in part because the architecture of interfaces between LDs remains elusive. Here we visualize interfaces between LDs by electron cryo-tomography and analyze the kinetics of lipid transfer by quantitative live fluorescence microscopy. We show that transfer occurs through closely apposed monolayers, is slowed down by increasing the distance between the monolayers, and follows exponential kinetics. Our data corroborate the notion that Cidec facilitates pressure-driven transfer of neutral lipids through two "leaky" monolayers between LDs.
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Affiliation(s)
- Iva Ganeva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Koini Lim
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Jerome Boulanger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Patrick C Hoffmann
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Olivia Muriel
- Electron Microscopy Facility, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland; Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Alicia C Borgeaud
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - David B Savage
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Wanda Kukulski
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
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10
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Yperman K, Kuijpers M. Neuronal endoplasmic reticulum architecture and roles in axonal physiology. Mol Cell Neurosci 2023; 125:103822. [PMID: 36781033 DOI: 10.1016/j.mcn.2023.103822] [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: 11/17/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
The endoplasmic reticulum (ER) is the largest membrane compartment within eukaryotic cells and is emerging as a key coordinator of many cellular processes. The ER can modulate local calcium fluxes and communicate with other organelles like the plasma membrane. The importance of ER in neuronal processes such as neurite growth, axon repair and neurotransmission has recently gained much attention. In this review, we highlight the importance of the ER tubular network in axonal homeostasis and discuss how the generation and maintenance of the thin tubular ER network in axons and synapses, requires a cooperative effort of ER-shaping proteins, cytoskeleton and autophagy processes.
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Affiliation(s)
- Klaas Yperman
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Marijn Kuijpers
- Department of Molecular Neurobiology, Donders Institute for Brain, Cognition and Behaviour and Faculty of Science, Radboud University, 6525 AJ Nijmegen, the Netherlands.
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11
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Tsuji C, Dodding MP. Lumenal components of cytoplasmic microtubules. Biochem Soc Trans 2022; 50:1953-1962. [PMID: 36524962 DOI: 10.1042/bst20220851] [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: 10/10/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 07/30/2023]
Abstract
The lumen of cytoplasmic microtubules is a poorly explored expanse of intracellular space. Although typically represented in textbooks as a hollow tube, studies over several decades have shown that the microtubule lumen is occupied by a range of morphologically diverse components. These are predominantly globular particles of varying sizes which appear to exist either in isolation, bind to the microtubule wall, or form discontinuous columns that extend through the lumenal space. Actin filaments with morphologies distinct from the canonical cytoplasmic forms have also now been found within the microtubule lumen. In this review, we examine the historic literature that observed these lumenal components in tissues from diverse species and integrate it with recent cryo-electron tomography studies that have begun to identify lumenal proteins. We consider their cell and tissue distribution, possible mechanisms of incorporation, and potential functions. It is likely that continuing work in this area will open a new frontier in cytoskeletal biology.
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Affiliation(s)
- Chisato Tsuji
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, U.K
| | - Mark P Dodding
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, U.K
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12
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Lickfett S, Menacho C, Zink A, Telugu NS, Beller M, Diecke S, Cambridge S, Prigione A. High-content analysis of neuronal morphology in human iPSC-derived neurons. STAR Protoc 2022; 3:101567. [PMID: 35990743 PMCID: PMC9386098 DOI: 10.1016/j.xpro.2022.101567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We present a high-content analysis (HCA) protocol for monitoring the outgrowth capacity of human neurons derived from induced pluripotent stem cells (iPSCs). We describe steps to perform HCA imaging, followed by quantifying the morphology of dendrites and axons within a high-throughput system to evaluate neurons obtained through various differentiation approaches. This protocol can be used to screen for modulators of neuronal morphogenesis or neurotoxicity. The approach can be applied to patient-derived iPSCs to identify patient-specific defects and possible therapeutic strategies. For complete details on the use and execution of this protocol, please refer to Zink et al. (2020) and Inak et al. (2021). The protocol can be used in combination with Zink et al. (2022). High-content analysis of human iPSC-derived neurons Automated microscopy to quantify neuronal morphology Quantification of axonal and dendritic outgrowths Data analysis based on open-source software CellProfiler
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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Affiliation(s)
- Selene Lickfett
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; Department of Anatomy II, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Carmen Menacho
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Annika Zink
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Narasimha Swamy Telugu
- Max Delbrück Center for Molecular Medicine (MDC) and Berlin Institute of Health (BIH), 13125 Berlin, Germany
| | - Mathias Beller
- Institute for Mathematical Modeling of Biological Systems, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Sebastian Diecke
- Max Delbrück Center for Molecular Medicine (MDC) and Berlin Institute of Health (BIH), 13125 Berlin, Germany
| | - Sidney Cambridge
- Department of Anatomy II, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany; Dr. Senckenbergische Anatomie, Goethe-Universität Frankfurt, 60590 Frankfurt am Main, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany.
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The Mechanical Microenvironment Regulates Axon Diameters Visualized by Cryo-Electron Tomography. Cells 2022; 11:cells11162533. [PMID: 36010609 PMCID: PMC9406316 DOI: 10.3390/cells11162533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/07/2022] [Accepted: 08/10/2022] [Indexed: 12/21/2022] Open
Abstract
Axonal varicosities or swellings are enlarged structures along axon shafts and profoundly affect action potential propagation and synaptic transmission. These structures, which are defined by morphology, are highly heterogeneous and often investigated concerning their roles in neuropathology, but why they are present in the normal brain remains unknown. Combining confocal microscopy and cryo-electron tomography (Cryo-ET) with in vivo and in vitro systems, we report that non-uniform mechanical interactions with the microenvironment can lead to 10-fold diameter differences within an axon of the central nervous system (CNS). In the brains of adult Thy1-YFP transgenic mice, individual axons in the cortex displayed significantly higher diameter variation than those in the corpus callosum. When being cultured on lacey carbon film-coated electron microscopy (EM) grids, CNS axons formed varicosities exclusively in holes and without microtubule (MT) breakage, and they contained mitochondria, multivesicular bodies (MVBs), and/or vesicles, similar to the axonal varicosities induced by mild fluid puffing. Moreover, enlarged axon branch points often contain MT free ends leading to the minor branch. When the axons were fasciculated by mimicking in vivo axonal bundles, their varicosity levels reduced. Taken together, our results have revealed the extrinsic regulation of the three-dimensional ultrastructures of central axons by the mechanical microenvironment under physiological conditions.
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14
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Abstract
The three-dimensional organization of biomolecules important for the functioning of all living systems can be determined by cryo-electron tomography imaging under native biological contexts. Cryo-electron tomography is continually expanding and evolving, and the development of new methods that use the latest technology for sample thinning is enabling the visualization of ever larger and more complex biological systems, allowing imaging across scales. Quantitative cryo-electron tomography possesses the capability of visualizing the impact of molecular and environmental perturbations in subcellular structure and function to understand fundamental biological processes. This review provides an overview of current hardware and software developments that allow quantitative cryo-electron tomography studies and their limitations and how overcoming them may allow us to unleash the full power of cryo-electron tomography.
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Affiliation(s)
- Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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15
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van den Dries K, Fransen J, Cambi A. Fluorescence CLEM in biology: historic developments and current super-resolution applications. FEBS Lett 2022; 596:2486-2496. [PMID: 35674424 DOI: 10.1002/1873-3468.14421] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022]
Abstract
Correlative light and electron microscopy (CLEM) is a powerful imaging approach that allows the direct correlation of information obtained on a light and an electron microscope. There is a growing interest in the application of CLEM in biology, mainly attributable to technical advances in field of fluorescence microscopy in the past two decades. In this review, we summarize the important developments in CLEM for biological applications, focusing on the combination of fluorescence microscopy and electron microscopy. We first provide a brief overview of the early days of fluorescence CLEM usage starting with the initial rise in the late 1970s and the subsequent optimization of CLEM workflows during the following two decades. Next, we describe how the engineering of fluorescent proteins and the development of super-resolution fluorescence microscopy have significantly renewed the interest in CLEM resulting in the present application of fluorescence CLEM in many different areas of cellular and molecular biology. Lastly, we present the promises and challenges for the future of fluorescence CLEM discussing novel workflows, probe development and quantification possibilities.
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Affiliation(s)
- Koen van den Dries
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Jack Fransen
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands.,Microscopic Imaging Center, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
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16
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Zamponi E, Meehl JB, Voeltz GK. The ER ladder is a unique morphological feature of developing mammalian axons. Dev Cell 2022; 57:1369-1382.e6. [PMID: 35609616 DOI: 10.1016/j.devcel.2022.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022]
Abstract
The endoplasmic reticulum (ER) confronts a challenge to accommodate long, smooth ER tubules into the structural complexity of the axonal compartment. Here, we describe a morphological feature for the axonal ER network in developing neurons we termed the ER ladder. Axonal ER ladders are composed of rungs that wrap tightly around the microtubule bundle and dynamic rails, which slide across microtubules. We found that the ER-shaping protein Reticulon 2 determines the architecture and dynamics of the axonal ER ladder by modulating its interaction with microtubules. Moreover, we show that ER ladder depletion impairs the trafficking of associated vesicular axonal cargoes. Finally, we demonstrate that stromal interaction molecule 1 (Stim1) localizes to ER rungs and translocates to ER-plasma membrane contact sites upon depletion of luminal Ca2+. Our findings uncover fundamental insights into the structural and functional organization of the axonal ER network in developing mammalian neurons.
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Affiliation(s)
- Emiliano Zamponi
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Boulder, CO 80309, USA
| | - Janet B Meehl
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Boulder, CO 80309, USA
| | - Gia K Voeltz
- Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Boulder, CO 80309, USA.
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17
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Foster HE, Ventura Santos C, Carter AP. A cryo-ET survey of microtubules and intracellular compartments in mammalian axons. J Cell Biol 2022; 221:e202103154. [PMID: 34878519 PMCID: PMC7612188 DOI: 10.1083/jcb.202103154] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/28/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022] Open
Abstract
The neuronal axon is packed with cytoskeletal filaments, membranes, and organelles, many of which move between the cell body and axon tip. Here, we used cryo-electron tomography to survey the internal components of mammalian sensory axons. We determined the polarity of the axonal microtubules (MTs) by combining subtomogram classification and visual inspection, finding MT plus and minus ends are structurally similar. Subtomogram averaging of globular densities in the MT lumen suggests they have a defined structure, which is surprising given they likely contain the disordered protein MAP6. We found the endoplasmic reticulum in axons is tethered to MTs through multiple short linkers. We surveyed membrane-bound cargos and describe unexpected internal features such as granules and broken membranes. In addition, we detected proteinaceous compartments, including numerous virus-like capsid particles. Our observations outline novel features of axonal cargos and MTs, providing a platform for identification of their constituents.
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18
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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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