1
|
Teixeira P, Galland R, Chevrollier A. Super-resolution microscopies, technological breakthrough to decipher mitochondrial structure and dynamic. Semin Cell Dev Biol 2024; 159-160:38-51. [PMID: 38310707 DOI: 10.1016/j.semcdb.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/06/2024]
Abstract
Mitochondria are complex organelles with an outer membrane enveloping a second inner membrane that creates a vast matrix space partitioned by pockets or cristae that join the peripheral inner membrane with several thin junctions. Several micrometres long, mitochondria are generally close to 300 nm in diameter, with membrane layers separated by a few tens of nanometres. Ultrastructural data from electron microscopy revealed the structure of these mitochondria, while conventional optical microscopy revealed their extraordinary dynamics through fusion, fission, and migration processes but its limited resolution power restricted the possibility to go further. By overcoming the limits of light diffraction, Super-Resolution Microscopy (SRM) now offers the potential to establish the links between the ultrastructure and remodelling of mitochondrial membranes, leading to major advances in our understanding of mitochondria's structure-function. Here we review the contributions of SRM imaging to our understanding of the relationship between mitochondrial structure and function. What are the hopes for these new imaging approaches which are particularly important for mitochondrial pathologies?
Collapse
Affiliation(s)
- Pauline Teixeira
- Univ. Angers, INSERM, CNRS, MITOVASC, Equipe MITOLAB, SFR ICAT, F-49000 Angers, France
| | - Rémi Galland
- Univ. Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR 5297, F-33000 Bordeaux, France
| | - Arnaud Chevrollier
- Univ. Angers, INSERM, CNRS, MITOVASC, Equipe MITOLAB, SFR ICAT, F-49000 Angers, France.
| |
Collapse
|
2
|
A multifunctional peroxidase-based reaction for imaging, sensing and networking of spatial biology. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119428. [PMID: 36610614 DOI: 10.1016/j.bbamcr.2022.119428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023]
Abstract
Peroxidase is a heme-containing enzyme that reduces hydrogen peroxide to water by extracting electron(s) from aromatic compounds via a sequential turnover reaction. This reaction can generate various aromatic radicals in the form of short-lived "spray" molecules. These can be either covalently attached to proximal proteins or polymerized via radical-radical coupling. Recent studies have shown that these peroxidase-generated radicals can be utilized as effective tools for spatial research in biological systems, including imaging studies aimed at the spatial localization of proteins using electron microscopy, spatial proteome mapping, and spatial sensing of metabolites (e.g., heme and hydrogen peroxide). This review may facilitate the wider utilization of these peroxidase-based methods for spatial discovery in cellular biology.
Collapse
|
3
|
Liu L, Yang S, Liu Y, Li X, Hu J, Xiao L, Xu T. DeepContact: High-throughput quantification of membrane contact sites based on electron microscopy imaging. J Cell Biol 2022; 221:213379. [PMID: 35929833 PMCID: PMC9361564 DOI: 10.1083/jcb.202106190] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 03/04/2022] [Accepted: 07/09/2022] [Indexed: 11/22/2022] Open
Abstract
Membrane contact site (MCS)-mediated organelle interactions play essential roles in the cell. Quantitative analysis of MCSs reveals vital clues for cellular responses under various physiological and pathological conditions. However, an efficient tool is lacking. Here, we developed DeepContact, a deep-learning protocol for optimizing organelle segmentation and contact analysis based on label-free EM. DeepContact presents high efficiency and flexibility in interactive visualizations, accommodating new morphologies of organelles and recognizing contacts in versatile width ranges, which enables statistical analysis of various types of MCSs in multiple systems. DeepContact profiled previously unidentified coordinative rearrangements of MCS types in cultured cells with combined nutritional conditions. DeepContact also unveiled a subtle wave of ER-mitochondrial entanglement in Sertoli cells during the seminiferous epithelial cycle, indicating its potential in bridging MCS dynamics to physiological and pathological processes.
Collapse
Affiliation(s)
- Liqing Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shuxin Yang
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,School of Computer and Control Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,School of Computer and Control Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Xixia Li
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Junjie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Li Xiao
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China.,Ningbo HuaMei Hospital, University of Chinese Academy of Sciences, Ningbo, China.,School of Computer and Control Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Tao Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China.,School of Biomedical Engineering, Guangzhou Medical University, Guangzhou, Guangdong, China
| |
Collapse
|
4
|
Tian B, Xu X, Xue Y, Ji W, Xu T. Cryogenic superresolution correlative light and electron microscopy on the frontier of subcellular imaging. Biophys Rev 2021; 13:1163-1171. [DOI: 10.1007/s12551-021-00851-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/03/2021] [Indexed: 12/22/2022] Open
|
5
|
Bayguinov PO, Fisher MR, Fitzpatrick JAJ. Assaying three-dimensional cellular architecture using X-ray tomographic and correlated imaging approaches. J Biol Chem 2020; 295:15782-15793. [PMID: 32938716 PMCID: PMC7667966 DOI: 10.1074/jbc.rev120.009633] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Much of our understanding of the spatial organization of and interactions between cellular organelles and macromolecular complexes has been the result of imaging studies utilizing either light- or electron-based microscopic analyses. These classical approaches, while insightful, are nonetheless limited either by restrictions in resolution or by the sheer complexity of generating multidimensional data. Recent advances in the use and application of X-rays to acquire micro- and nanotomographic data sets offer an alternative methodology to visualize cellular architecture at the nanoscale. These new approaches allow for the subcellular analyses of unstained vitrified cells and three-dimensional localization of specific protein targets and have served as an essential tool in bridging light and electron correlative microscopy experiments. Here, we review the theory, instrumentation details, acquisition principles, and applications of both soft X-ray tomography and X-ray microscopy and how the use of these techniques offers a succinct means of analyzing three-dimensional cellular architecture. We discuss some of the recent work that has taken advantage of these approaches and detail how they have become integral in correlative microscopy workflows.
Collapse
Affiliation(s)
- Peter O Bayguinov
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Max R Fisher
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - James A J Fitzpatrick
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA; Departments of Cell Biology and Physiology and Neuroscience, Washington University School of Medicine, Saint Louis, Missouri, USA; Department of Biomedical Engineering, Washington University in Saint Louis, Saint Louis, Missouri, USA.
| |
Collapse
|
6
|
Three-Dimensional Visualization of APEX2-Tagged Erg11 in Saccharomyces cerevisiae Using Focused Ion Beam Scanning Electron Microscopy. mSphere 2020; 5:5/1/e00981-19. [PMID: 32024705 PMCID: PMC7002314 DOI: 10.1128/msphere.00981-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The determination of the exact location of a protein in the cell is essential to the understanding of biological processes. Here, we report for the first time the visualization of a protein of interest in Saccharomyces cerevisiae using focused ion beam scanning electron microscopy (FIB-SEM). As a proof of concept, the integral endoplasmic reticulum (ER) membrane protein Erg11 has been C-terminally tagged with APEX2, which is an engineered peroxidase that catalyzes an electron-dense deposition of 3,3'-diaminobenzidine (DAB), as such marking the location of the fused protein of interest in electron microscopic images. As DAB is unable to cross the yeast cell wall to react with APEX2, cell walls have been partly removed by the formation of spheroplasts. This has resulted in a clear electron-dense ER signal for the Erg11 protein using FIB-SEM. With this study, we have validated the use of the APEX2 tag for visualization of yeast proteins in electron microscopy. Furthermore, we have introduced a methodology that enables precise and three-dimensional (3D) localization studies in yeast, with nanometer resolution and without the need for antibody staining. Because of these properties, the described technique can offer valuable information on the molecular functions of studied proteins.IMPORTANCE With this study, we have validated the use of the APEX2 tag to define the localization of proteins in the model yeast S. cerevisiae As such, FIB-SEM can identify the exact 3D location of a protein of interest in the cell with nanometer-scale resolution. Such detailed imaging could provide essential information on the elucidation of various biological processes. APEX2, which adds electron density to a fused protein of interest upon addition of the substrate DAB, originally was used in mammalian studies. With this study, we expand its use to protein localization studies in one of the most important models in molecular biology.
Collapse
|
7
|
Pre-embedding labeling for subcellular detection of molecules with electron microscopy. Tissue Cell 2019; 57:103-110. [DOI: 10.1016/j.tice.2018.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
8
|
Boey A, Rybakin V, Kalicharan D, Vints K, Gounko NV. Gold-substituted Silver-intensified Peroxidase Immunolabeling for FIB-SEM Imaging. J Histochem Cytochem 2019; 67:351-360. [PMID: 30624131 DOI: 10.1369/0022155418824335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Modern electron microscopy offers a wide variety of tools to investigate the ultrastructural organization of cells and tissues and to accurately pinpoint intracellular localizations of macromolecules of interest. New volumetric electron microscopy techniques and new instrumentation provide unique opportunities for high-throughput analysis of comparatively large volumes of tissue and their complete reconstitution in three-dimensional (3D) electron microscopy. However, due to a variety of technical issues such as the limited penetration of label into the tissue, low antigen preservation, substantial electron density of secondary detection reagents, and many others, the adaptation of immuno-detection techniques for use with such 3D imaging methods as focused ion beam-scanning electron microscopy (FIB-SEM) has been challenging. Here, we describe a sample preparation method for 3D FIB-SEM, which results in an optimal preservation and staining of ultrastructural details at a resolution necessary for tracing immunolabeled neuronal structures and detailed reconstruction of synapses. This technique is applicable to neuronal and non-neuronal cells, tissues, and a wide variety of antigens.
Collapse
Affiliation(s)
- Adrian Boey
- Institute of Molecular and Cell Biology-Institute of Medical Biology Joint Electron Microscopy Suite, Agency for Science, Technology and Research, Singapore, Singapore
| | - Vasily Rybakin
- Laboratory of Immunobiology, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Dharamdajal Kalicharan
- Institute of Molecular and Cell Biology-Institute of Medical Biology Joint Electron Microscopy Suite, Agency for Science, Technology and Research, Singapore, Singapore
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Natalia V Gounko
- Institute of Molecular and Cell Biology-Institute of Medical Biology Joint Electron Microscopy Suite, Agency for Science, Technology and Research, Singapore, Singapore.,VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium.,Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| |
Collapse
|
9
|
Guo HY, Cui ZJ. Extracellular Histones Activate Plasma Membrane Toll-Like Receptor 9 to Trigger Calcium Oscillations in Rat Pancreatic Acinar Tumor Cell AR4-2J. Cells 2018; 8:E3. [PMID: 30577532 PMCID: PMC6356355 DOI: 10.3390/cells8010003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/11/2018] [Accepted: 12/17/2018] [Indexed: 02/07/2023] Open
Abstract
In acute pancreatitis, histones are released by infiltrating neutrophils, but how histones modulate pancreatic acinar cell function has not been investigated. We have examined histone modulation of rat pancreatic acini and pancreatic acinar tumor cell AR4-2J by calcium imaging. Histones were found to have no effect on calcium in pancreatic acini but blocked calcium oscillations induced by cholecystokinin or acetylcholine. Both mixed (Hx) and individual (H1, H2A, H2B, H3, H4) histones induced calcium oscillations in AR4-2J. RT-PCR and Western blot verified the expression of histone-targeted Toll-like receptor (TLR) 2, 4 and 9. Immunocytochemistry identified TLR2/TLR4 on apical plasma membrane and TLR9 in zymogen granule regions in pancreatic acini. TLR2 was found on neighboring and TLR9 on peripheral plasma membranes, but TLR4 was in the nucleus in AR4-2J clusters. Neither TLR2 agonist zymosan-A nor TLR4 agonist lipopolysaccharide had any effect on calcium, but TLR9 agonist ODN1826 induced calcium oscillations; TLR9 antagonist ODN2088 blocked H4-induced calcium oscillations in AR4-2J, which also disappeared after treatment of AR4-2J with glucocorticoid dexamethasone, with concurrent TLR9 migration from plasma membrane to cell interiors. TLR9 down regulation with siRNA suppressed H4-induced calcium oscillations. These data together suggest that extracellular histones activate plasma membrane TLR9 to trigger calcium oscillations in AR4-2J cells.
Collapse
Affiliation(s)
- Hai Yan Guo
- Institute of Cell Biology, Beijing Normal University, Beijing 100875, China.
| | - Zong Jie Cui
- Institute of Cell Biology, Beijing Normal University, Beijing 100875, China.
| |
Collapse
|
10
|
Publisher Note. Tissue Cell 2018. [DOI: 10.1016/j.tice.2018.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
11
|
Ariotti N, Rae J, Giles N, Martel N, Sierecki E, Gambin Y, Hall TE, Parton RG. Ultrastructural localisation of protein interactions using conditionally stable nanobodies. PLoS Biol 2018; 16:e2005473. [PMID: 29621251 PMCID: PMC5903671 DOI: 10.1371/journal.pbio.2005473] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/17/2018] [Accepted: 03/20/2018] [Indexed: 01/21/2023] Open
Abstract
We describe the development and application of a suite of modular tools for high-resolution detection of proteins and intracellular protein complexes by electron microscopy (EM). Conditionally stable GFP- and mCherry-binding nanobodies (termed csGBP and csChBP, respectively) are characterized using a cell-free expression and analysis system and subsequently fused to an ascorbate peroxidase (APEX) enzyme. Expression of these cassettes alongside fluorescently labelled proteins results in recruitment and stabilisation of APEX, whereas unbound APEX nanobodies are efficiently degraded by the proteasome. This greatly simplifies correlative analyses, enables detection of less-abundant proteins, and eliminates the need to balance expression levels between fluorescently labelled and APEX nanobody proteins. Furthermore, we demonstrate the application of this system to bimolecular complementation ('EM split-fluorescent protein'), for localisation of protein-protein interactions at the ultrastructural level.
Collapse
Affiliation(s)
- Nicholas Ariotti
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - James Rae
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - Nichole Giles
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, The University of New South Wales, Sydney, New South Wales, Australia
| | - Nick Martel
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, The University of New South Wales, Sydney, New South Wales, Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, The University of New South Wales, Sydney, New South Wales, Australia
| | - Thomas E. Hall
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
| | - Robert G. Parton
- The University of Queensland, Institute for Molecular Bioscience, Queensland, Australia
- The University of Queensland, Centre for Microscopy and Microanalysis, Brisbane, Queensland, Australia
| |
Collapse
|