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Abstract
Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.
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Affiliation(s)
- Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; ,
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; , .,Howard Hughes Medical Institute, Pasadena, California 91125
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52
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Joshi A, Joshi A, Patel H, Ponnoth D, Stagni G. Cutaneous Penetration-Enhancing Effect of Menthol: Calcium Involvement. J Pharm Sci 2017; 106:1923-1932. [PMID: 28400197 DOI: 10.1016/j.xphs.2017.03.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/24/2017] [Accepted: 03/27/2017] [Indexed: 11/27/2022]
Abstract
Menthol is a naturally occurring terpene used as a penetration enhancer in topical and transdermal formulations. Literature shows a growing interest in menthol's interactions with the transient receptor potential melastatin 8. A decrease in extracellular Ca2+ due to the activation of the transient receptor potential melastatin 8 receptor produces inhibition of E-cadherin expression that is responsible for cell-cell adhesion. Because calcium is present in the entire epidermis, the purpose of this study is to evaluate whether the aforementioned properties of menthol are also related to its penetration-enhancing effects. We formulated 16 gels: (i) drug-alone (diphenhydramine or lidocaine), (ii) drug with menthol, (iii) drug, menthol, and calcium channel blocker (CCB; verapamil or diltiazem), and (iv) drug and CCB. In vitro studies showed no effect of the CCB on the release of the drugs either with or without menthol. In vivo experiments were performed for each drug/menthol/CCB combination gel by applying 4 formulations on a shaved rabbit's dorsum on the same day. Dermis concentration profiles were assessed with microdialysis. The gels containing menthol showed higher penetration of drugs than those without whereas the addition of the CCB consistently inhibited the penetration-enhancing effects of menthol. In summary, these findings strongly support the involvement of calcium in the penetration-enhancing effect of menthol.
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Affiliation(s)
- Amit Joshi
- Division of Pharmaceutical Sciences, Arnold and Marie Schwartz College of Pharmacy, Long Island University, Brooklyn, New York 11201
| | - Abhay Joshi
- Division of Pharmaceutical Sciences, Arnold and Marie Schwartz College of Pharmacy, Long Island University, Brooklyn, New York 11201
| | - Hiren Patel
- Division of Pharmaceutical Sciences, Arnold and Marie Schwartz College of Pharmacy, Long Island University, Brooklyn, New York 11201
| | - Dovenia Ponnoth
- Division of Pharmaceutical Sciences, Arnold and Marie Schwartz College of Pharmacy, Long Island University, Brooklyn, New York 11201
| | - Grazia Stagni
- Division of Pharmaceutical Sciences, Arnold and Marie Schwartz College of Pharmacy, Long Island University, Brooklyn, New York 11201.
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53
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Chen J, Wu Y. Understanding the Functional Roles of Multiple Extracellular Domains in Cell Adhesion Molecules with a Coarse-Grained Model. J Mol Biol 2017; 429:1081-1095. [PMID: 28237680 PMCID: PMC5989558 DOI: 10.1016/j.jmb.2017.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/08/2017] [Accepted: 02/13/2017] [Indexed: 01/15/2023]
Abstract
Intercellular contacts in multicellular organisms are maintained by membrane receptors called cell adhesion molecules (CAMs), which are expressed on cell surfaces. One interesting feature of CAMs is that almost all of their extracellular regions contain repeating copies of structural domains. It is not clear why so many extracellular domains need to be evolved through natural selection. We tackled this problem by computational modeling. A generic model of CAMs was constructed based on the domain organization of neuronal CAM, which is engaged in maintaining neuron-neuron adhesion in central nervous system. By placing these models on a cell-cell interface, we developed a Monte-Carlo simulation algorithm that incorporates both molecular factors including conformational changes of CAMs and cellular factor including fluctuations of plasma membranes to approach the physical process of CAM-mediated adhesion. We found that the presence of multiple domains at the extracellular region of a CAM plays a positive role in regulating its trans-interaction with other CAMs from the opposite side of cell surfaces. The trans-interaction can further be facilitated by the intramolecular contacts between different extracellular domains of a CAM. Finally, if more than one CAM is introduced on each side of cell surfaces, the lateral binding (cis-interactions) between these CAMs will positively correlate with their trans-interactions only within a small energetic range, suggesting that cell adhesion is an elaborately designed process in which both trans- and cis-interactions are fine-tuned collectively by natural selection. In short, this study deepens our general understanding of the molecular mechanisms of cell adhesion.
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Affiliation(s)
- Jiawen Chen
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY10461, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY10461, USA.
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54
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Jorgens DM, Inman JL, Wojcik M, Robertson C, Palsdottir H, Tsai WT, Huang H, Bruni-Cardoso A, López CS, Bissell MJ, Xu K, Auer M. Deep nuclear invaginations are linked to cytoskeletal filaments - integrated bioimaging of epithelial cells in 3D culture. J Cell Sci 2017; 130:177-189. [PMID: 27505896 PMCID: PMC5394780 DOI: 10.1242/jcs.190967] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/28/2016] [Indexed: 02/04/2023] Open
Abstract
The importance of context in regulation of gene expression is now an accepted principle; yet the mechanism by which the microenvironment communicates with the nucleus and chromatin in healthy tissues is poorly understood. A functional role for nuclear and cytoskeletal architecture is suggested by the phenotypic differences observed between epithelial and mesenchymal cells. Capitalizing on recent advances in cryogenic techniques, volume electron microscopy and super-resolution light microscopy, we studied human mammary epithelial cells in three-dimensional (3D) cultures forming growth-arrested acini. Intriguingly, we found deep nuclear invaginations and tunnels traversing the nucleus, encasing cytoskeletal actin and/or intermediate filaments, which connect to the outer nuclear envelope. The cytoskeleton is also connected both to other cells through desmosome adhesion complexes and to the extracellular matrix through hemidesmosomes. This finding supports a physical and/or mechanical link from the desmosomes and hemidesmosomes to the nucleus, which had previously been hypothesized but now is visualized for the first time. These unique structures, including the nuclear invaginations and the cytoskeletal connectivity to the cell nucleus, are consistent with a dynamic reciprocity between the nucleus and the outside of epithelial cells and tissues.
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Affiliation(s)
- Danielle M Jorgens
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
- Department of Biomedical Engineering, Oregon Health and Science University, 3181 Sam Jackson Park Road, Portland, OR 97239, USA
| | - Jamie L Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michal Wojcik
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Claire Robertson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hildur Palsdottir
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
| | - Wen-Ting Tsai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
| | - Haina Huang
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Alexandre Bruni-Cardoso
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry Instituto de Quimica, Universidade de Sao Paulo, Sao Paulo, 05508-000, Brazil
| | - Claudia S López
- Department of Biomedical Engineering, Oregon Health and Science University, 3181 Sam Jackson Park Road, Portland, OR 97239, USA
| | - Mina J Bissell
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ke Xu
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Manfred Auer
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS Donner, Berkeley, CA 94720, USA
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55
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Winklbauer R. Cell adhesion strength from cortical tension - an integration of concepts. J Cell Sci 2016; 128:3687-93. [PMID: 26471994 DOI: 10.1242/jcs.174623] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Morphogenetic mechanisms such as cell movement or tissue separation depend on cell attachment and detachment processes, which involve adhesion receptors as well as the cortical cytoskeleton. The interplay between the two components is of stunning complexity. Most strikingly, the binding energy of adhesion molecules is usually too small for substantial cell-cell attachment, pointing to a main deficit in our present understanding of adhesion. In this Opinion article, I integrate recent findings and conceptual advances in the field into a coherent framework for cell adhesion. I argue that active cortical tension is best viewed as an integral part of adhesion, and propose on this basis a non-arbitrary measure of adhesion strength - the tissue surface tension of cell aggregates. This concept of adhesion integrates heterogeneous molecular inputs into a single mechanical property and simplifies the analysis of attachment-detachment processes. It draws attention to the enormous variation of adhesion strengths among tissues, whose origin and function is little understood.
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Affiliation(s)
- Rudolf Winklbauer
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada
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56
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Ellebrecht CT, Bhoj VG, Nace A, Choi EJ, Mao X, Cho MJ, Di Zenzo G, Lanzavecchia A, Seykora JT, Cotsarelis G, Milone MC, Payne AS. Reengineering chimeric antigen receptor T cells for targeted therapy of autoimmune disease. Science 2016; 353:179-84. [PMID: 27365313 PMCID: PMC5343513 DOI: 10.1126/science.aaf6756] [Citation(s) in RCA: 444] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/09/2016] [Indexed: 12/18/2022]
Abstract
Ideally, therapy for autoimmune diseases should eliminate pathogenic autoimmune cells while sparing protective immunity, but feasible strategies for such an approach have been elusive. Here, we show that in the antibody-mediated autoimmune disease pemphigus vulgaris (PV), autoantigen-based chimeric immunoreceptors can direct T cells to kill autoreactive B lymphocytes through the specificity of the B cell receptor (BCR). We engineered human T cells to express a chimeric autoantibody receptor (CAAR), consisting of the PV autoantigen, desmoglein (Dsg) 3, fused to CD137-CD3ζ signaling domains. Dsg3 CAAR-T cells exhibit specific cytotoxicity against cells expressing anti-Dsg3 BCRs in vitro and expand, persist, and specifically eliminate Dsg3-specific B cells in vivo. CAAR-T cells may provide an effective and universal strategy for specific targeting of autoreactive B cells in antibody-mediated autoimmune disease.
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Affiliation(s)
| | - Vijay G Bhoj
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Arben Nace
- Department of Dermatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eun Jung Choi
- Department of Dermatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xuming Mao
- Department of Dermatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Jeffrey Cho
- Department of Dermatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Giovanni Di Zenzo
- Laboratory of Molecular and Cellular Biology, Istituto Dermopatico dell'Immacolata (IDI-IRCCS), 00167 Rome, Italy
| | | | - John T Seykora
- Department of Dermatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George Cotsarelis
- Department of Dermatology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Milone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Aimee S Payne
- Department of Dermatology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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57
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Grahammer F, Wigge C, Schell C, Kretz O, Patrakka J, Schneider S, Klose M, Kind J, Arnold SJ, Habermann A, Bräuniger R, Rinschen MM, Völker L, Bregenzer A, Rubbenstroth D, Boerries M, Kerjaschki D, Miner JH, Walz G, Benzing T, Fornoni A, Frangakis AS, Huber TB. A flexible, multilayered protein scaffold maintains the slit in between glomerular podocytes. JCI Insight 2016; 1:86177. [PMID: 27430022 DOI: 10.1172/jci.insight.86177] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Vertebrate life critically depends on renal filtration and excretion of low molecular weight waste products. This process is controlled by a specialized cell-cell contact between podocyte foot processes: the slit diaphragm (SD). Using a comprehensive set of targeted KO mice of key SD molecules, we provided genetic, functional, and high-resolution ultrastructural data highlighting a concept of a flexible, dynamic, and multilayered architecture of the SD. Our data indicate that the mammalian SD is composed of NEPHRIN and NEPH1 molecules, while NEPH2 and NEPH3 do not participate in podocyte intercellular junction formation. Unexpectedly, homo- and heteromeric NEPHRIN/NEPH1 complexes are rarely observed. Instead, single NEPH1 molecules appear to form the lower part of the junction close to the glomerular basement membrane with a width of 23 nm, while single NEPHRIN molecules form an adjacent junction more apically with a width of 45 nm. In both cases, the molecules are quasiperiodically spaced 7 nm apart. These structural findings, in combination with the flexibility inherent to the repetitive Ig folds of NEPHRIN and NEPH1, indicate that the SD likely represents a highly dynamic cell-cell contact that forms an adjustable, nonclogging barrier within the renal filtration apparatus.
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Affiliation(s)
- Florian Grahammer
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Wigge
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Christoph Schell
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine.,Faculty of Biology, and
| | - Oliver Kretz
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,BIOSS Center for Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany.,Institute of Anatomy, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jaakko Patrakka
- KI/AZ Integrated Cardio-Metabolic Center (ICMC), Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Simon Schneider
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Martin Klose
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium and.,German Cancer Research Center, Heidelberg, Germany
| | - Julia Kind
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian J Arnold
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,BIOSS Center for Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany.,Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anja Habermann
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Ricarda Bräuniger
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Markus M Rinschen
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Linus Völker
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Andreas Bregenzer
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dennis Rubbenstroth
- Institute of Virology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Melanie Boerries
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium and.,German Cancer Research Center, Heidelberg, Germany
| | | | - Jeffrey H Miner
- Renal Division, Washington University, St. Louis, Missouri, USA
| | - Gerd Walz
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Alessia Fornoni
- Division of Nephrology and Katz Family Drug Discovery Center, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Achilleas S Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Tobias B Huber
- Department of Medicine, Division of Nephrology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine.,BIOSS Center for Biological Signalling Studies, Albert-Ludwigs University of Freiburg, Freiburg, Germany.,FRIAS, Freiburg Institute for Advanced Studies and ZBSA, Center for Biological System Analysis, Albert-Ludwigs-University of Freiburg, Germany
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58
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Abstract
Desmosomes are intercellular adhesive junctions that impart strength to vertebrate tissues. Their dense, ordered intercellular attachments are formed by desmogleins (Dsgs) and desmocollins (Dscs), but the nature of trans-cellular interactions between these specialized cadherins is unclear. Here, using solution biophysics and coated-bead aggregation experiments, we demonstrate family-wise heterophilic specificity: All Dsgs form adhesive dimers with all Dscs, with affinities characteristic of each Dsg:Dsc pair. Crystal structures of ectodomains from Dsg2 and Dsg3 and from Dsc1 and Dsc2 show binding through a strand-swap mechanism similar to that of homophilic classical cadherins. However, conserved charged amino acids inhibit Dsg:Dsg and Dsc:Dsc interactions by same-charge repulsion and promote heterophilic Dsg:Dsc interactions through opposite-charge attraction. These findings show that Dsg:Dsc heterodimers represent the fundamental adhesive unit of desmosomes and provide a structural framework for understanding desmosome assembly.
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59
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Al-Afeef A, Cockshott WP, MacLaren I, McVitie S. Electron tomography image reconstruction using data-driven adaptive compressed sensing. SCANNING 2016; 38:251-276. [PMID: 26435074 DOI: 10.1002/sca.21271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
Electron tomography (ET) is an increasingly important technique for the study of the three-dimensional morphologies of nanostructures. ET involves the acquisition of a set of two-dimensional projection images, followed by the reconstruction into a volumetric image by solving an inverse problem. However, due to limitations in the acquisition process, this inverse problem is ill-posed (i.e., a unique solution may not exist). Furthermore, reconstruction usually suffers from missing wedge artifacts (e.g., star, fan, blurring, and elongation artifacts). Recently, compressed sensing (CS) has been applied to ET and showed promising results for reducing missing wedge artifacts. This uses image sparsity as a priori knowledge to improve the accuracy of reconstruction, and can require fewer projections than other reconstruction techniques. The performance of CS relies heavily on the degree of sparsity in the selected transform domain and this depends essentially on the choice of sparsifying transform. We propose a new image reconstruction algorithm for ET that learns the sparsifying transform adaptively using a dictionary-based approach. We demonstrate quantitatively using simulations from complex phantoms that this new approach reconstructs the morphology with higher fidelity than either analytically based CS reconstruction algorithms or traditional weighted back projection from the same dataset. SCANNING 38:251-276, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Ala' Al-Afeef
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
- SUPA School of Physics and Astronomy, University of Glasgow, Glasgow, United Kingdom
| | - W Paul Cockshott
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Ian MacLaren
- SUPA School of Physics and Astronomy, University of Glasgow, Glasgow, United Kingdom
| | - Stephen McVitie
- SUPA School of Physics and Astronomy, University of Glasgow, Glasgow, United Kingdom
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60
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Strale PO, Duchesne L, Peyret G, Montel L, Nguyen T, Png E, Tampé R, Troyanovsky S, Hénon S, Ladoux B, Mège RM. The formation of ordered nanoclusters controls cadherin anchoring to actin and cell-cell contact fluidity. J Cell Biol 2016. [PMID: 26195669 PMCID: PMC4508897 DOI: 10.1083/jcb.201410111] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Visualization of single cadherins within cell membrane at nanometric resolution shows that E-cadherins arrange in ordered clusters and that these clusters control the anchoring of cadherin to actin and cell–cell contact fluidity. Oligomerization of cadherins could provide the stability to ensure tissue cohesion. Cadherins mediate cell–cell adhesion by forming trans-interactions. They form cis-interactions whose role could be essential to stabilize intercellular junctions by shifting cadherin clusters from a fluid to an ordered phase. However, no evidence has been provided so far for cadherin oligomerization in cellulo and for its impact on cell–cell contact stability. Visualizing single cadherins within cell membrane at a nanometric resolution, we show that E-cadherins arrange in ordered clusters, providing the first demonstration of the existence of oligomeric cadherins at cell–cell contacts. Studying the consequences of the disruption of the cis-interface, we show that it is not essential for adherens junction formation. Its disruption, however, increased the mobility of junctional E-cadherin. This destabilization strongly affected E-cadherin anchoring to actin and cell–cell rearrangement during collective cell migration, indicating that the formation of oligomeric clusters controls the anchoring of cadherin to actin and cell–cell contact fluidity.
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Affiliation(s)
- Pierre-Olivier Strale
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, 75205 Paris, France Mechanobiology Institute, University of Singapore, Singapore 117411, Singapore
| | - Laurence Duchesne
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, 75205 Paris, France Institut de Génétique et Développement de Rennes, Centre National de la Recherche Scientifique, Université de Rennes 1, 35042 Rennes, France
| | - Grégoire Peyret
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, 75205 Paris, France
| | - Lorraine Montel
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique, Université Paris Diderot, 75205 Paris, France
| | - Thao Nguyen
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, 75205 Paris, France
| | - Evelyn Png
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, 75205 Paris, France Ocular Surface Research Group, Singapore Eye Research Institute, Singapore 169856, Singapore
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, D-60438 Frankfurt, Germany
| | | | - Sylvie Hénon
- Laboratoire Matière et Systèmes Complexes, Centre National de la Recherche Scientifique, Université Paris Diderot, 75205 Paris, France
| | - Benoit Ladoux
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, 75205 Paris, France Mechanobiology Institute, University of Singapore, Singapore 117411, Singapore
| | - René-Marc Mège
- Institut Jacques Monod, Centre National de la Recherche Scientifique, Université Paris Diderot, 75205 Paris, France
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61
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Irobalieva RN, Martins B, Medalia O. Cellular structural biology as revealed by cryo-electron tomography. J Cell Sci 2016; 129:469-76. [DOI: 10.1242/jcs.171967] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
ABSTRACT
Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.
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Affiliation(s)
- Rossitza N. Irobalieva
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Bruno Martins
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel
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62
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In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology. J Mol Biol 2016; 428:332-343. [DOI: 10.1016/j.jmb.2015.09.030] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 11/24/2022]
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63
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Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells. Viruses 2015; 7:6316-45. [PMID: 26633469 PMCID: PMC4690864 DOI: 10.3390/v7122940] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/16/2015] [Accepted: 11/16/2015] [Indexed: 02/06/2023] Open
Abstract
As obligate intracellular parasites, viruses need to hijack their cellular hosts and reprogram their machineries in order to replicate their genomes and produce new virions. For the direct visualization of the different steps of a viral life cycle (attachment, entry, replication, assembly and egress) electron microscopy (EM) methods are extremely helpful. While conventional EM has given important information about virus-host cell interactions, the development of three-dimensional EM (3D-EM) approaches provides unprecedented insights into how viruses remodel the intracellular architecture of the host cell. During the last years several 3D-EM methods have been developed. Here we will provide a description of the main approaches and examples of innovative applications.
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64
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Visualization of adherent cell monolayers by cryo-electron microscopy: A snapshot of endothelial adherens junctions. J Struct Biol 2015; 192:470-477. [DOI: 10.1016/j.jsb.2015.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 01/05/2023]
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65
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Vielmuth F, Waschke J, Spindler V. Loss of Desmoglein Binding Is Not Sufficient for Keratinocyte Dissociation in Pemphigus. J Invest Dermatol 2015; 135:3068-3077. [DOI: 10.1038/jid.2015.324] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/06/2015] [Accepted: 07/20/2015] [Indexed: 11/10/2022]
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66
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Cryo-planing of frozen-hydrated samples using cryo triple ion gun milling (CryoTIGM™). J Struct Biol 2015; 192:569-579. [PMID: 26549007 DOI: 10.1016/j.jsb.2015.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 11/23/2022]
Abstract
Cryo-SEM is a high throughput technique for imaging biological ultrastructure in its most pristine state, i.e. without chemical fixation, embedding, or drying. Freeze fracture is routinely used to prepare internal surfaces for cryo-SEM imaging. However, the propagation of the fracture plane is highly dependent on sample properties, and the resulting surface frequently shows substantial topography, which can complicate image analysis and interpretation. We have developed a broad ion beam milling technique, called cryogenic triple ion gun milling (CryoTIGM™ ['krī-ə-,tīm]), for cryo-planing frozen-hydrated biological specimens. Comparing sample preparation by CryoTIGM™ and freeze fracture in three model systems, Baker's yeast, mouse liver tissue, and whole sea urchin embryos, we find that CryoTIGM™ yields very large (∼700,000 μm(2)) and smooth sections that present ultrastructural details at similar or better quality than freeze-fractured samples. A particular strength of CryoTIGM™ is the ability to section samples with hard-soft contrast such as brittle calcite (CaCO3) spicules in the sea urchin embryo.
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67
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Song X, Tang Y, Lei C, Cao M, Shen Y, Yang Y. In situ visualizing T-Tubule/SR junction reveals the ultra-structures of calcium storage and release machinery. Int J Biol Macromol 2015; 82:7-12. [PMID: 26454109 DOI: 10.1016/j.ijbiomac.2015.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
In skeletal muscle, Ca(2+) release from sarcoplasmic reticulum (SR) following the action potential relies on the delicate architecture of the T-Tubule/SR junction. The T-Tubule/SR junction comprises two membrane systems: the integral proteins DHPR and RyR1 and the Ca(2+)-buffering apparatus within the SR lumen. The arrangement and interactions of the components have remained elusive due to technological limitations. Here, we determined whether electron tomography is effective fort the in situ determination of the relationships between RyR1 and DHPR, the SR membrane and other involved structures. First, we visually confirmed that RyR1 and DHPR are close neighbors that are mutually staggered with each other and directly interact with one of RyR1 subunits. Second, the Ca(2+) storage network within the SR lumen is directly correlated with RyR1. These results suggest that the excitation of the T-Tubule may induce Ca(2+) release through a direct interaction among DHPR, RyR1 and the Ca(2+) buffering apparatus. These results indicate that electron tomography has potential as an efficient method for the in situ characterization of the complex architecture and arrangement of two integral-integral-membrane proteins in the context of the surrounding phospholipid-bilayer and proteins.
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Affiliation(s)
- XiaoWei Song
- Department of Biophysics, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Ying Tang
- Department of Biophysics, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - ChangHai Lei
- Department of Biophysics, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - Mi Cao
- Department of Biophysics, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - YaFeng Shen
- Department of Biophysics, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
| | - YongJi Yang
- Department of Biophysics, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China.
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68
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Cryo-focused-ion-beam applications in structural biology. Arch Biochem Biophys 2015; 581:122-30. [DOI: 10.1016/j.abb.2015.02.009] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 01/30/2023]
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69
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Abstract
Desmosomes represent adhesive, spot-like intercellular junctions that in association with intermediate filaments mechanically link neighboring cells and stabilize tissue architecture. In addition to this structural function, desmosomes also act as signaling platforms involved in the regulation of cell proliferation, differentiation, migration, morphogenesis, and apoptosis. Thus, deregulation of desmosomal proteins has to be considered to contribute to tumorigenesis. Proteolytic fragmentation and downregulation of desmosomal cadherins and plaque proteins by transcriptional or epigenetic mechanisms were observed in different cancer entities suggesting a tumor-suppressive role. However, discrepant data in the literature indicate that context-dependent differences based on alternative intracellular, signal transduction lead to altered outcome. Here, modulation of Wnt/β-catenin signaling by plakoglobin or desmoplakin and of epidermal growth factor receptor signaling appears to be of special relevance. This review summarizes current evidence on how desmosomal proteins participate in carcinogenesis, and depicts the molecular mechanisms involved.
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Affiliation(s)
- Otmar Huber
- a Institute of Biochemistry II, Jena University Hospital, Friedrich-Schiller-University Jena , Nonnenplan 2-4, 07743 Jena , Germany.,b Center for Sepsis Control and Care, Jena University Hospital , Erlanger Allee 101, 07747 Jena , Germany
| | - Iver Petersen
- c Institute of Pathology, Jena University Hospital, Friedrich-Schiller-University Jena , Ziegelmühlenweg 1, 07743 Jena , Germany
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Kant S, Holthöfer B, Magin TM, Krusche CA, Leube RE. Desmoglein 2-Dependent Arrhythmogenic Cardiomyopathy Is Caused by a Loss of Adhesive Function. ACTA ACUST UNITED AC 2015; 8:553-63. [PMID: 26085008 DOI: 10.1161/circgenetics.114.000974] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/09/2015] [Indexed: 01/01/2023]
Abstract
BACKGROUND The desmosomal cadherin desmoglein 2 (Dsg2) localizes to the intercalated disc coupling adjacent cardiomyocytes. Desmoglein 2 gene (DSG2) mutations cause arrhythmogenic cardiomyopathy (AC) in human and transgenic mice. AC is characterized by arrhythmia, cardiodilation, cardiomyocyte necrosis with replacement fibrosis, interstitial fibrosis, and intercalated disc dissociation. The genetic DSG2 constellations encountered are compatible with loss of adhesion and altered signaling. To further elucidate pathomechanisms, we examined whether heart-specific Dsg2 depletion triggers cardiomyopathy. METHODS AND RESULTS Because DSG2 knockouts die during early embryogenesis, mice were prepared with cardiomyocyte-specific DSG2 ablation. Healthy transgenic animals were born with a functional heart presenting intercalated discs with incorporated desmosomal proteins. Dsg2 protein expression was reduced below 3% in the heart. All animals developed AC during postnatal growth with pronounced chamber dilation, calcifying cardiomyocyte necrosis, aseptic inflammation, interstitial and focal replacement fibrosis, and conduction defects with altered connexin 43 distribution. Electron microscopy revealed absence of desmosome-like structures and regional loss of intercalated disc adhesion. Mice carrying 2 mutant DSG2 alleles coding for Dsg2 lacking part of the adhesive EC1-EC2 domains present an indistinguishable phenotype, which is similar to that observed in human AC patients. CONCLUSIONS The observations show that the presence of Dsg2 is not essential for late heart morphogenesis and for cardiac contractility to support postnatal life. On increasing mechanical demands, heart function is severely compromised as evidenced by the onset of cardiomyopathy with pronounced morphological alterations. We propose that loss of Dsg2 compromises adhesion, and that this is a major pathogenic mechanism in DSG2-related and probably other desmosome-related ACs.
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Affiliation(s)
- Sebastian Kant
- From the Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany (S.K., B.H., C.A.K., R.E.L.); and Institute of Biology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany (T.M.M.)
| | - Bastian Holthöfer
- From the Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany (S.K., B.H., C.A.K., R.E.L.); and Institute of Biology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany (T.M.M.)
| | - Thomas M Magin
- From the Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany (S.K., B.H., C.A.K., R.E.L.); and Institute of Biology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany (T.M.M.)
| | - Claudia A Krusche
- From the Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany (S.K., B.H., C.A.K., R.E.L.); and Institute of Biology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany (T.M.M.)
| | - Rudolf E Leube
- From the Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany (S.K., B.H., C.A.K., R.E.L.); and Institute of Biology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany (T.M.M.).
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71
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Tariq H, Bella J, Jowitt TA, Holmes DF, Rouhi M, Nie Z, Baldock C, Garrod D, Tabernero L. Cadherin flexibility provides a key difference between desmosomes and adherens junctions. Proc Natl Acad Sci U S A 2015; 112:5395-400. [PMID: 25855637 PMCID: PMC4418904 DOI: 10.1073/pnas.1420508112] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Desmosomes and adherens junctions are intercellular adhesive structures essential for the development and integrity of vertebrate tissue, including the epidermis and heart. Their cell adhesion molecules are cadherins: type 1 cadherins in adherens junctions and desmosomal cadherins in desmosomes. A fundamental difference is that desmosomes have a highly ordered structure in their extracellular region and exhibit calcium-independent hyperadhesion, whereas adherens junctions appear to lack such ordered arrays, and their adhesion is always calcium-dependent. We present here the structure of the entire ectodomain of desmosomal cadherin desmoglein 2 (Dsg2), using a combination of small-angle X-ray scattering, electron microscopy, and solution-based biophysical techniques. This structure reveals that the ectodomain of Dsg2 is flexible even in the calcium-bound state and, on average, is shorter than the type 1 cadherin crystal structures. The Dsg2 structure has an excellent fit with the electron tomography reconstructions of human desmosomes. This fit suggests an arrangement in which desmosomal cadherins form trans interactions but are too far apart to interact in cis, in agreement with previously reported observations. Cadherin flexibility may be key to explaining the plasticity of desmosomes that maintain tissue integrity in their hyperadhesive form, but can adopt a weaker, calcium-dependent adhesion during wound healing and early development.
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Affiliation(s)
- Humera Tariq
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Jordi Bella
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Thomas A Jowitt
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - David F Holmes
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Mansour Rouhi
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Zhuxiang Nie
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Clair Baldock
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - David Garrod
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Lydia Tabernero
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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72
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Gunkel M, Schöneberg J, Alkhaldi W, Irsen S, Noé F, Kaupp UB, Al-Amoudi A. Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure 2015; 23:628-38. [PMID: 25728926 DOI: 10.1016/j.str.2015.01.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/16/2015] [Accepted: 01/22/2015] [Indexed: 12/23/2022]
Abstract
The visual pigment rhodopsin belongs to the family of G protein-coupled receptors that can form higher oligomers. It is controversial whether rhodopsin forms oligomers and whether oligomers are functionally relevant. Here, we study rhodopsin organization in cryosections of dark-adapted mouse rod photoreceptors by cryoelectron tomography. We identify four hierarchical levels of organization. Rhodopsin forms dimers; at least ten dimers form a row. Rows form pairs (tracks) that are aligned parallel to the disk incisures. Particle-based simulation shows that the combination of tracks with fast precomplex formation, i.e. rapid association and dissociation between inactive rhodopsin and the G protein transducin, leads to kinetic trapping: rhodopsin first activates transducin from its own track, whereas recruitment of transducin from other tracks proceeds more slowly. The trap mechanism could produce uniform single-photon responses independent of rhodopsin lifetime. In general, tracks might provide a platform that coordinates the spatiotemporal interaction of signaling molecules.
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Affiliation(s)
- Monika Gunkel
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Johannes Schöneberg
- Computational Molecular Biology Group, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - Weaam Alkhaldi
- German Center of Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Stephan Irsen
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Frank Noé
- Computational Molecular Biology Group, Freie Universität Berlin, Arnimallee 6, 14195 Berlin, Germany
| | - U Benjamin Kaupp
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
| | - Ashraf Al-Amoudi
- German Center of Neurodegenerative Diseases, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany.
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73
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Friedman LG, Benson DL, Huntley GW. Cadherin-based transsynaptic networks in establishing and modifying neural connectivity. Curr Top Dev Biol 2015; 112:415-65. [PMID: 25733148 DOI: 10.1016/bs.ctdb.2014.11.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is tacitly understood that cell adhesion molecules (CAMs) are critically important for the development of cells, circuits, and synapses in the brain. What is less clear is what CAMs continue to contribute to brain structure and function after the early period of development. Here, we focus on the cadherin family of CAMs to first briefly recap their multidimensional roles in neural development and then to highlight emerging data showing that with maturity, cadherins become largely dispensible for maintaining neuronal and synaptic structure, instead displaying new and narrower roles at mature synapses where they critically regulate dynamic aspects of synaptic signaling, structural plasticity, and cognitive function. At mature synapses, cadherins are an integral component of multiprotein networks, modifying synaptic signaling, morphology, and plasticity through collaborative interactions with other CAM family members as well as a variety of neurotransmitter receptors, scaffolding proteins, and other effector molecules. Such recognition of the ever-evolving functions of synaptic cadherins may yield insight into the pathophysiology of brain disorders in which cadherins have been implicated and that manifest at different times of life.
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Affiliation(s)
- Lauren G Friedman
- Fishberg Department of Neuroscience, Friedman Brain Institute and the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Deanna L Benson
- Fishberg Department of Neuroscience, Friedman Brain Institute and the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - George W Huntley
- Fishberg Department of Neuroscience, Friedman Brain Institute and the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA.
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74
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Saibil HR, Grünewald K, Stuart DI. A national facility for biological cryo-electron microscopy. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:127-35. [PMID: 25615867 PMCID: PMC4304693 DOI: 10.1107/s1399004714025280] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 11/18/2014] [Indexed: 11/16/2022]
Abstract
Three-dimensional electron microscopy is an enormously powerful tool for structural biologists. It is now able to provide an understanding of the molecular machinery of cells, disease processes and the actions of pathogenic organisms from atomic detail through to the cellular context. However, cutting-edge research in this field requires very substantial resources for equipment, infrastructure and expertise. Here, a brief overview is provided of the plans for a UK national three-dimensional electron-microscopy facility for integrated structural biology to enable internationally leading research on the machinery of life. State-of-the-art equipment operated with expert support will be provided, optimized for both atomic-level single-particle analysis of purified macromolecules and complexes and for tomography of cell sections. The access to and organization of the facility will be modelled on the highly successful macromolecular crystallography (MX) synchrotron beamlines, and will be embedded at the Diamond Light Source, facilitating the development of user-friendly workflows providing near-real-time experimental feedback.
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Affiliation(s)
- Helen R. Saibil
- Crystallography, Institute for Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - David I. Stuart
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
- Diamond Light Source, Didcot OX11 0DE, England
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75
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Abstract
Desmosomes are intercellular junctions that provide strong adhesion or hyper-adhesion in tissues. Here, we discuss the molecular and structural basis of this with particular reference to the desmosomal cadherins (DCs), their isoforms and evolution. We also assess the role of DCs as regulators of epithelial differentiation. New data on the role of desmosomes in development and human disease, especially wound healing and pemphigus, are briefly discussed, and the importance of regulation of the adhesiveness of desmosomes in tissue dynamics is considered.
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Affiliation(s)
- Mohamed Berika
- Department of Anatomy, Faculty of Medicine, Mansoura University , Mansoura City , Egypt
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76
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Miyaguchi K. Direct imaging electron microscopy (EM) methods in modern structural biology: overview and comparison with X-ray crystallography and single-particle cryo-EM reconstruction in the studies of large macromolecules. Biol Cell 2014; 106:323-45. [PMID: 25040059 DOI: 10.1111/boc.201300081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 07/01/2014] [Indexed: 11/28/2022]
Abstract
Determining the structure of macromolecules is important for understanding their function. The fine structure of large macromolecules is currently studied primarily by X-ray crystallography and single-particle cryo-electron microscopy (EM) reconstruction. Before the development of these techniques, macromolecular structure was often examined by negative-staining, rotary-shadowing and freeze-etching EM, which are categorised here as 'direct imaging EM methods'. In this review, the results are summarised by each of the above techniques and compared with respect to four macromolecules: the ryanodine receptor, cadherin, rhodopsin and the ribosome-translocon complex (RTC). The results of structural analysis of the ryanodine receptor and cadherin are consistent between each technique. The results obtained for rhodopsin vary to some extent within each technique and between the different techniques. Finally, the results for RTC are inconsistent between direct imaging EM and other analytical techniques, especially with respect to the space within RTC, the reasons for which are discussed. Then, the role of direct imaging EM methods in modern structural biology is discussed. Direct imaging methods should support and verify the results obtained by other analytical methods capable of solving three-dimensional molecular architecture, and they should still be used as a primary tool for studying macromolecule structure in vivo.
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Affiliation(s)
- Katsuyuki Miyaguchi
- Shinsapporokeiaikai Hospital, 5-5-35 Ooyachihigashi, Atsubetsuku, Sapporo, 004-0041, Japan
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77
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Kitajima Y. 150(th) anniversary series: Desmosomes and autoimmune disease, perspective of dynamic desmosome remodeling and its impairments in pemphigus. ACTA ACUST UNITED AC 2014; 21:269-80. [PMID: 25078507 DOI: 10.3109/15419061.2014.943397] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Desmosomes are the most important intercellular adhering junctions that adhere two adjacent keratinocytes directly with desmosomal cadherins, that is, desmogleins (Dsgs) and desmocollins, forming an epidermal sheet. Recently, two cell-cell adhesion states of desmosomes, that is, "stable hyper-adhesion" and "dynamic weak-adhesion" conditions have been recognized. They are mutually reversible through cell signaling events involving protein kinase C (PKC), Src and epidermal growth factor receptor (EGFR) during Ca(2+)-switching and wound healing. This remodeling is impaired in pemphigus vulgaris (PV, an autoimmune blistering disease), caused by anti-Dsg3 antibodies. The antibody binding to Dsg3 activates PKC, Src and EGFR, linked to generation of dynamic weak-adhesion desmosomes, followed by p38MAPK-mediated endocytosis of Dsg3, resulting in the specific depletion of Dsg3 from desmosomes and acantholysis. A variety of pemphigus outside-in signaling may explain different clinical (non-inflammatory, inflammatory, and necrolytic) types of pemphigus. Pemphigus could be referred to a "desmosome-remodeling disease involving pemphigus IgG-activated outside-in signaling events".
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Affiliation(s)
- Yasuo Kitajima
- Department of Dermatology, Kizawa Memorial Hospital, Professor Emeritus Gifu University School of Medicine , Minokamo City, Gifu Prefecture , Japan
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78
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Abstract
Since electron microscopy (EM) first appeared in the 1930s, it has held centre stage as the primary tool for the exploration of biological structure. Yet, with the recent developments of light microscopy techniques that overcome the limitations imposed by the diffraction boundary, the question arises as to whether the importance of EM in on the wane. This Commentary describes some of the pioneering studies that have shaped our understanding of cell structure. These include the development of cryo-EM techniques that have given researchers the ability to capture images of native structures and at the molecular level. It also describes how a number of recent developments significantly increase the ability of EM to visualise biological systems across a range of length scales, and in 3D, ensuring that EM will remain at the forefront of biology research for the foreseeable future.
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Affiliation(s)
- Graham Knott
- BioEM Facility, Centre Interdisciplinaire de Microscopie Electronique, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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79
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Liu B, Yu H, Verbridge SS, Sun L, Wang G. Dictionary-learning-based reconstruction method for electron tomography. SCANNING 2014. [PMID: 25104167 DOI: 10.1002/sca.21127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Electron tomography usually suffers from so-called “missing wedge” artifacts caused by limited tilt angle range. An equally sloped tomography (EST) acquisition scheme (which should be called the linogram sampling scheme) was recently applied to achieve 2.4-angstrom resolution. On the other hand, a compressive sensing inspired reconstruction algorithm, known as adaptive dictionary based statistical iterative reconstruction (ADSIR), has been reported for X-ray computed tomography. In this paper, we evaluate the EST, ADSIR, and an ordered-subset simultaneous algebraic reconstruction technique (OS-SART), and compare the ES and equally angled (EA) data acquisition modes. Our results show that OS-SART is comparable to EST, and the ADSIR outperforms EST and OS-SART. Furthermore, the equally sloped projection data acquisition mode has no advantage over the conventional equally angled mode in this context.
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80
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Abstract
Hyper-adhesion is a unique, strongly adhesive form of desmosomal adhesion that functions to maintain tissue integrity. In this short review, we define hyper-adhesion, summarise the evidence for it in culture and in vivo, discuss its role in development, wound healing, and skin disease, and speculate about its molecular and cellular basis.
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Affiliation(s)
- David Garrod
- Faculty of Life Sciences, University of Manchester , Manchester , UK
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81
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Cho MJ, Lo ASY, Mao X, Nagler AR, Ellebrecht CT, Mukherjee EM, Hammers CM, Choi EJ, Sharma PM, Uduman M, Li H, Rux AH, Farber SA, Rubin CB, Kleinstein SH, Sachais BS, Posner MR, Cavacini LA, Payne AS. Shared VH1-46 gene usage by pemphigus vulgaris autoantibodies indicates common humoral immune responses among patients. Nat Commun 2014; 5:4167. [PMID: 24942562 PMCID: PMC4120239 DOI: 10.1038/ncomms5167] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/20/2014] [Indexed: 12/13/2022] Open
Abstract
Pemphigus vulgaris (PV) is a potentially fatal blistering disease caused by autoantibodies (autoAbs) against desmoglein 3 (Dsg3). Here, we clone anti-Dsg3 antibodies (Abs) from four PV patients and identify pathogenic VH1-46 autoAbs from all four patients. Unexpectedly, VH1-46 autoAbs had relatively few replacement mutations. We reverted antibody somatic mutations to their germline sequences to determine the requirement of mutations for autoreactivity. Three of five VH1-46 germline-reverted Abs maintain Dsg3 binding, compared with zero of five non-VH1-46 germline-reverted Abs. Site-directed mutagenesis of VH1-46 Abs demonstrates that acidic amino-acid residues introduced by somatic mutation or heavy chain VDJ recombination are necessary and sufficient for Dsg3 binding. Our data suggest that VH1-46 autoantibody gene usage is commonly found in PV because VH1-46 Abs require few to no mutations to acquire Dsg3 autoreactivity, which may favour their early selection. Common VH gene usage indicates common humoral immune responses, even among unrelated patients.
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Affiliation(s)
- Michael Jeffrey Cho
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Agnes S Y Lo
- Division of Hematology-Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
| | - Xuming Mao
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Arielle R Nagler
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Christoph T Ellebrecht
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Eric M Mukherjee
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Christoph M Hammers
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Eun-Jung Choi
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Preety M Sharma
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Mohamed Uduman
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06511, USA
| | - Hong Li
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ann H Rux
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Sara A Farber
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Courtney B Rubin
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06511, USA
| | - Bruce S Sachais
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Marshall R Posner
- The Tisch Cancer Institute, Mount Sinai Medical Center, New York, New York 10029, USA
| | - Lisa A Cavacini
- The Tisch Cancer Institute, Mount Sinai Medical Center, New York, New York 10029, USA
| | - Aimee S Payne
- Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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82
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Sotomayor M, Gaudet R, Corey DP. Sorting out a promiscuous superfamily: towards cadherin connectomics. Trends Cell Biol 2014; 24:524-36. [PMID: 24794279 DOI: 10.1016/j.tcb.2014.03.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/23/2014] [Accepted: 03/25/2014] [Indexed: 12/21/2022]
Abstract
Members of the cadherin superfamily of proteins are involved in diverse biological processes such as morphogenesis, sound transduction, and neuronal connectivity. Key to cadherin function is their extracellular domain containing cadherin repeats, which can mediate interactions involved in adhesion and cell signaling. Recent cellular, biochemical, and structural studies have revealed that physical interaction among cadherins is more complex than originally thought. Here we review work on new cadherin complexes and discuss how the classification of the mammalian family can be used to search for additional cadherin-interacting partners. We also highlight some of the challenges in cadherin research; namely, the characterization of a cadherin connectome in biochemical and structural terms, as well as the elucidation of molecular mechanisms underlying the functional diversity of nonclassical cadherins in vivo.
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Affiliation(s)
- Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus OH 43210, USA.
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - David P Corey
- Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA.
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83
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Özkan E, Chia PH, Wang RR, Goriatcheva N, Borek D, Otwinowski Z, Walz T, Shen K, Garcia KC. Extracellular architecture of the SYG-1/SYG-2 adhesion complex instructs synaptogenesis. Cell 2014; 156:482-94. [PMID: 24485456 PMCID: PMC3962013 DOI: 10.1016/j.cell.2014.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 09/04/2013] [Accepted: 01/06/2014] [Indexed: 01/29/2023]
Abstract
SYG-1 and SYG-2 are multipurpose cell adhesion molecules (CAMs) that have evolved across all major animal taxa to participate in diverse physiological functions, ranging from synapse formation to formation of the kidney filtration barrier. In the crystal structures of several SYG-1 and SYG-2 orthologs and their complexes, we find that SYG-1 orthologs homodimerize through a common, bispecific interface that similarly mediates an unusual orthogonal docking geometry in the heterophilic SYG-1/SYG-2 complex. C. elegans SYG-1's specification of proper synapse formation in vivo closely correlates with the heterophilic complex affinity, which appears to be tuned for optimal function. Furthermore, replacement of the interacting domains of SYG-1 and SYG-2 with those from CAM complexes that assume alternative docking geometries or the introduction of segmental flexibility compromised synaptic function. These results suggest that SYG extracellular complexes do not simply act as "molecular velcro" and that their distinct structural features are important in instructing synaptogenesis. PAPERFLICK:
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Affiliation(s)
- Engin Özkan
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Poh Hui Chia
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Ruiqi Rachel Wang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Natalia Goriatcheva
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dominika Borek
- Departments of Biochemistry and Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Zbyszek Otwinowski
- Departments of Biochemistry and Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kang Shen
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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84
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KIZILYAPRAK C, DARASPE J, HUMBEL B. Focused ion beam scanning electron microscopy in biology. J Microsc 2014; 254:109-14. [DOI: 10.1111/jmi.12127] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/12/2014] [Indexed: 12/27/2022]
Affiliation(s)
- C. KIZILYAPRAK
- Electron Microscopy Facility; University of Lausanne; Biophore 1015 Lausanne Switzerland
| | - J. DARASPE
- Electron Microscopy Facility; University of Lausanne; Biophore 1015 Lausanne Switzerland
| | - B.M. HUMBEL
- Electron Microscopy Facility; University of Lausanne; Biophore 1015 Lausanne Switzerland
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85
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Abstract
To truly understand bioenergetic processes such as ATP synthesis, membrane-bound substrate transport or flagellar rotation, systems need to be analysed in a cellular context. Cryo-ET (cryo-electron tomography) is an essential part of this process, as it is currently the only technique which can directly determine the spatial organization of proteins at the level of both the cell and the individual protein complexes. The need to assess bioenergetic processes at a cellular level is becoming more and more apparent with the increasing interest in mitochondrial diseases. In recent years, cryo-ET has contributed significantly to our understanding of the molecular organization of mitochondria and chloroplasts. The present mini-review first describes the technique of cryo-ET and then discusses its role in membrane bioenergetics specifically in chloroplasts and mitochondrial research.
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86
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Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau VV, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS. Correlative light- and electron microscopy with chemical tags. J Struct Biol 2014; 186:205-13. [PMID: 24698954 DOI: 10.1016/j.jsb.2014.03.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
Correlative microscopy incorporates the specificity of fluorescent protein labeling into high-resolution electron micrographs. Several approaches exist for correlative microscopy, most of which have used the green fluorescent protein (GFP) as the label for light microscopy. Here we use chemical tagging and synthetic fluorophores instead, in order to achieve protein-specific labeling, and to perform multicolor imaging. We show that synthetic fluorophores preserve their post-embedding fluorescence in the presence of uranyl acetate. Post-embedding fluorescence is of such quality that the specimen can be prepared with identical protocols for scanning electron microscopy (SEM) and transmission electron microscopy (TEM); this is particularly valuable when singular or otherwise difficult samples are examined. We show that synthetic fluorophores give bright, well-resolved signals in super-resolution light microscopy, enabling us to superimpose light microscopic images with a precision of up to 25 nm in the x-y plane on electron micrographs. To exemplify the preservation quality of our new method we visualize the molecular arrangement of cadherins in adherens junctions of mouse epithelial cells.
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Affiliation(s)
- Mario Perkovic
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Michael Kunz
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Ulrike Endesfelder
- Goethe University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue Str. 13, 60438 Frankfurt am Main, Germany
| | - Stefanie Bunse
- Max-Planck-Institute for Brain Research, Max-von-Laue Str. 4, 60438 Frankfurt am Main, Germany
| | - Christoph Wigge
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Zhou Yu
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Victor-Valentin Hodirnau
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Margot P Scheffer
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Anja Seybert
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany
| | - Sebastian Malkusch
- Goethe University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue Str. 13, 60438 Frankfurt am Main, Germany
| | - Erin M Schuman
- Max-Planck-Institute for Brain Research, Max-von-Laue Str. 4, 60438 Frankfurt am Main, Germany
| | - Mike Heilemann
- Goethe University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue Str. 13, 60438 Frankfurt am Main, Germany
| | - Achilleas S Frangakis
- Goethe University Frankfurt, Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Max-von-Laue Str. 15, 60438 Frankfurt am Main, Germany.
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87
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Harapin J, Eibauer M, Medalia O. Structural analysis of supramolecular assemblies by cryo-electron tomography. Structure 2014; 21:1522-30. [PMID: 24010711 DOI: 10.1016/j.str.2013.08.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 11/29/2022]
Abstract
Structural analysis of macromolecular assemblies in their physiological environment is a challenging task that is instrumental in answering fundamental questions in cellular and molecular structural biology. The continuous development of computational and analytical tools for cryo-electron tomography (cryo-ET) enables the study of these assemblies at a resolution of a few nanometers. Through the implementation of thinning procedures, cryo-ET can now be applied to the reconstruction of macromolecular structures located inside thick regions of vitrified cells and tissues, thus becoming a central tool for structural determinations in various biological disciplines. Here, we focus on the successful in situ applications of cryo-ET to reveal structures of macromolecular complexes within eukaryotic cells.
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Affiliation(s)
- Jan Harapin
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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88
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Lowndes M, Rakshit S, Shafraz O, Borghi N, Harmon RM, Green KJ, Sivasankar S, Nelson WJ. Different roles of cadherins in the assembly and structural integrity of the desmosome complex. J Cell Sci 2014; 127:2339-50. [PMID: 24610950 DOI: 10.1242/jcs.146316] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Adhesion between cells is established by the formation of specialized intercellular junctional complexes, such as desmosomes. Desmosomes contain isoforms of two members of the cadherin superfamily of cell adhesion proteins, desmocollins (Dsc) and desmogleins (Dsg), but their combinatorial roles in desmosome assembly are not understood. To uncouple desmosome assembly from other cell-cell adhesion complexes, we used micro-patterned substrates of Dsc2aFc and/or Dsg2Fc and collagen IV; we show that Dsc2aFc, but not Dsg2Fc, was necessary and sufficient to recruit desmosome-specific desmoplakin into desmosome puncta and produce strong adhesive binding. Single-molecule force spectroscopy showed that monomeric Dsc2a, but not Dsg2, formed Ca(2+)-dependent homophilic bonds, and that Dsg2 formed Ca(2+)-independent heterophilic bonds with Dsc2a. A W2A mutation in Dsc2a inhibited Ca(2+)-dependent homophilic binding, similar to classical cadherins, and Dsc2aW2A, but not Dsg2W2A, was excluded from desmosomes in MDCK cells. These results indicate that Dsc2a, but not Dsg2, is required for desmosome assembly through homophilic Ca(2+)- and W2-dependent binding, and that Dsg2 might be involved later in regulating a switch to Ca(2+)-independent adhesion in mature desmosomes.
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Affiliation(s)
- Molly Lowndes
- Cancer Biology Program, Stanford University, Stanford, CA 94305, USA
| | - Sabyasachi Rakshit
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA Ames Laboratory, United States Department of Energy, Ames, IA 50011, USA
| | - Omer Shafraz
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA Ames Laboratory, United States Department of Energy, Ames, IA 50011, USA
| | - Nicolas Borghi
- Institut Jacques Monod, Unité Mixte de Recherche 7592, Centre National de la Recherche Scientifique, and Université Paris-Diderot, 75013 Paris, France
| | - Robert M Harmon
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kathleen J Green
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sanjeevi Sivasankar
- Department of Physics and Astronomy, Iowa State University, Ames, IA 50011, USA Ames Laboratory, United States Department of Energy, Ames, IA 50011, USA
| | - W James Nelson
- Cancer Biology Program, Stanford University, Stanford, CA 94305, USA Department of Biology, Stanford University, Stanford, CA 94305, USA Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
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89
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Hirabayashi A, Fukunaga Y, Miyazawa A. Structural analysis of the PSD-95 cluster by electron tomography and CEMOVIS: a proposal for the application of the genetically encoded metallothionein tag. Microscopy (Oxf) 2014; 63:227-34. [DOI: 10.1093/jmicro/dfu006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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90
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Waschke J, Spindler V. Desmosomes and Extradesmosomal Adhesive Signaling Contacts in Pemphigus. Med Res Rev 2014; 34:1127-45. [DOI: 10.1002/med.21310] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jens Waschke
- Institute of Anatomy and Cell Biology, Department I; Ludwig-Maximilians-Universität (LMU) Munich; Pettenkoferstrasse 11 D-80336 Munich Germany
| | - Volker Spindler
- Institute of Anatomy and Cell Biology, Department I; Ludwig-Maximilians-Universität (LMU) Munich; Pettenkoferstrasse 11 D-80336 Munich Germany
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91
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Abstract
High-pressure freeze fixation is the method of choice to arrest instantly all dynamic and physiological processes inside cells, tissues, and small organisms. Embedded in vitreous ice, such samples can be further processed by freeze substitution or directly analyzed in their fully hydrated state by cryo-electron microscopy of vitreous sections (CEMOVIS) to explore cellular ultrastructure as close as possible to the native state. Here, we describe the procedure of self-pressurized rapid freezing as fast, easy-to-use, and low-cost freeze fixation method, avoiding the usage of a high-pressure freezing (HPF) apparatus. Cells or small organisms are placed in capillary metal tubes, which are tightly closed and plunged directly into liquid ethane cooled by liquid nitrogen. In parts of the tube, crystalline ice is formed and builds up pressure sufficient for the liquid-glass transition of the remaining specimen. The quality of samples is equivalent to preparations by conventional HPF apparatus, allowing for high-resolution cryo-EM applications or for freeze substitution and plastic embedding.
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Affiliation(s)
- Markus Grabenbauer
- Institute for Anatomy and Cell Biology Germany, University of Heidelberg, Heidelberg, Germany
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92
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Baum MM, Gunawardana M, Webster P. Experimental approaches to investigating the vaginal biofilm microbiome. Methods Mol Biol 2014; 1147:85-103. [PMID: 24664828 PMCID: PMC8801157 DOI: 10.1007/978-1-4939-0467-9_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Unraveling the complex ecology of the vaginal biofilm microbiome relies on a number of complementary techniques. Here, we describe the experimental approaches for studying vaginal microbial biofilm samples with a focus on specimen preparation for subsequent analysis. The techniques include fluorescence microscopy, fluorescence in situ hybridization, and scanning and transmission electron microscopy. Isolation of microbial DNA and RNA from these samples is covered along with a brief discussion of chemical analysis methods.
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Affiliation(s)
- Marc M Baum
- Department of Chemistry, Oak Crest Institute of Science, 2275 E Foothill Boulevard, Pasadena, CA, 91107, USA,
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93
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A new tool based on two micromanipulators facilitates the handling of ultrathin cryosection ribbons. J Struct Biol 2014; 185:125-8. [DOI: 10.1016/j.jsb.2013.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 11/13/2013] [Accepted: 11/16/2013] [Indexed: 01/03/2023]
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94
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Abstract
Electron tomography (ET) is an emerging electron microscopy (EM) technique for three-dimensional (3D) visualization of molecular arrangements and ultrastructural architectures in organelles, cells, and tissues at 2-10 nm resolution. The 3D tomogram is reconstructed from a series of 2D EM images taken from a single specimen at different projecting orientations. The specimen for ET must be specially prepared to meet the ET imaging requirements, i.e., ultrastructural preservation, specimen thickness, tolerance of electron dose and vacuum, and image contrast. In this chapter, the strategies of specimen preparation of organelles, cells, and tissues and the corresponding EM imaging requirements for ET will be described in detail. In addition, the general procedures tomographic reconstruction and tomogram interpretation will be described.
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Affiliation(s)
- Wanzhong He
- National Institute of Biological Sciences, Beijing, China
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95
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Abstract
More than 30 years ago two groups independently reported the vitrification of pure water, which was until then regarded as impossible without a cryoprotectant [1, 2]. This opened the opportunity to cryo-electron microscopy (cryo-EM) to observe biological samples at nanometer scale, close to their native state. However, poor electron penetration through biological samples sets the limit for sample thickness to less than the average size of the mammalian cell. In order to image bulky specimens at the cell or tissue level in transmission electron microscopy (TEM), a sample has to be either thinned by focused ion beam or mechanically sectioned. The latter technique, Cryo-Electron Microscopy of Vitreous Section (CEMOVIS), employs cryo-ultramicrotomy to produce sections with thicknesses of 40-100 μm of vitreous biological material suitable for cryo-EM. CEMOVIS consists of trimming and sectioning a sample with a diamond knife, placing and attaching the section onto an electron microscopy grid, transferring the grid to the cryo-electron microscope and imaging. All steps must be carried on below devitrification temperature to obtain successful results. In this chapter we provide a step-by-step guide to produce and image vitreous sections of a biological sample.
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Affiliation(s)
- Petr Chlanda
- National Institute of Health, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
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96
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CRIS-a novel cAMP-binding protein controlling spermiogenesis and the development of flagellar bending. PLoS Genet 2013; 9:e1003960. [PMID: 24339785 PMCID: PMC3854790 DOI: 10.1371/journal.pgen.1003960] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/30/2013] [Indexed: 12/17/2022] Open
Abstract
The second messengers cAMP and cGMP activate their target proteins by binding to a conserved cyclic nucleotide-binding domain (CNBD). Here, we identify and characterize an entirely novel CNBD-containing protein called CRIS (cyclic nucleotide receptor involved in sperm function) that is unrelated to any of the other members of this protein family. CRIS is exclusively expressed in sperm precursor cells. Cris-deficient male mice are either infertile due to a lack of sperm resulting from spermatogenic arrest, or subfertile due to impaired sperm motility. The motility defect is caused by altered Ca(2+) regulation of flagellar beat asymmetry, leading to a beating pattern that is reminiscent of sperm hyperactivation. Our results suggest that CRIS interacts during spermiogenesis with Ca(2+)-regulated proteins that--in mature sperm--are involved in flagellar bending.
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97
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Lučič V, Rigort A, Baumeister W. Cryo-electron tomography: the challenge of doing structural biology in situ. ACTA ACUST UNITED AC 2013; 202:407-19. [PMID: 23918936 PMCID: PMC3734081 DOI: 10.1083/jcb.201304193] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Electron microscopy played a key role in establishing cell biology as a discipline, by producing fundamental insights into cellular organization and ultrastructure. Many seminal discoveries were made possible by the development of new sample preparation methods and imaging modalities. Recent technical advances include sample vitrification that faithfully preserves molecular structures, three-dimensional imaging by electron tomography, and improved image-processing methods. These new techniques have enabled the extraction of high fidelity structural information and are beginning to reveal the macromolecular organization of unperturbed cellular environments.
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Affiliation(s)
- Vladan Lučič
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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98
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Abstract
Desmosomes anchor intermediate filaments at sites of cell contact established by the interaction of cadherins extending from opposing cells. The incorporation of cadherins, catenin adaptors, and cytoskeletal elements resembles the closely related adherens junction. However, the recruitment of intermediate filaments distinguishes desmosomes and imparts a unique function. By linking the load-bearing intermediate filaments of neighboring cells, desmosomes create mechanically contiguous cell sheets and, in so doing, confer structural integrity to the tissues they populate. This trait and a well-established role in human disease have long captured the attention of cell biologists, as evidenced by a publication record dating back to the mid-1860s. Likewise, emerging data implicating the desmosome in signaling events pertinent to organismal development, carcinogenesis, and genetic disorders will secure a prominent role for desmosomes in future biological and biomedical investigations.
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Affiliation(s)
- Robert M Harmon
- Department of Pathology, Northwestern University Feinberg, School of Medicine , Chicago, IL , USA
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99
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Cryo FIB-SEM: Volume imaging of cellular ultrastructure in native frozen specimens. J Struct Biol 2013; 184:355-60. [DOI: 10.1016/j.jsb.2013.09.024] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 08/22/2013] [Accepted: 09/27/2013] [Indexed: 11/21/2022]
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100
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Truong Quang BA, Mani M, Markova O, Lecuit T, Lenne PF. Principles of E-cadherin supramolecular organization in vivo. Curr Biol 2013; 23:2197-2207. [PMID: 24184100 DOI: 10.1016/j.cub.2013.09.015] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/29/2013] [Accepted: 09/05/2013] [Indexed: 12/16/2022]
Abstract
BACKGROUND E-cadherin plays a pivotal role in tissue morphogenesis by forming clusters that support intercellular adhesion and transmit tension. What controls E-cadherin mesoscopic organization in clusters is unclear. RESULTS We use 3D superresolution quantitative microscopy in Drosophila embryos to characterize the size distribution of E-cadherin nanometric clusters. The cluster size follows power-law distributions over three orders of magnitude with exponential decay at large cluster sizes. By exploring the predictions of a general theoretical framework including cluster fusion and fission events and recycling of E-cadherin, we identify two distinct active mechanisms setting the cluster-size distribution. Dynamin-dependent endocytosis targets large clusters only, thereby imposing a cutoff size. Moreover, interactions between E-cadherin clusters and actin filaments control the fission in a size-dependent manner. CONCLUSIONS E-cadherin clustering depends on key cortical regulators, which provide tunable and local control over E-cadherin organization. Our data provide the foundation for a quantitative understanding of how E-cadherin distribution affects adhesion and might regulate force transmission in vivo.
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Affiliation(s)
- Binh-An Truong Quang
- Developmental Biology Institute of Marseilles, UMR 7288 CNRS, Aix-Marseille Université, 13288 Marseille Cedex 9, France
| | - Madhav Mani
- Kavli Institute of Theoretical Physics, Santa Barbara, CA 93101, USA; University of California, Department of Physics, Santa Barbara, CA 93101, USA
| | - Olga Markova
- Developmental Biology Institute of Marseilles, UMR 7288 CNRS, Aix-Marseille Université, 13288 Marseille Cedex 9, France
| | - Thomas Lecuit
- Developmental Biology Institute of Marseilles, UMR 7288 CNRS, Aix-Marseille Université, 13288 Marseille Cedex 9, France
| | - Pierre-François Lenne
- Developmental Biology Institute of Marseilles, UMR 7288 CNRS, Aix-Marseille Université, 13288 Marseille Cedex 9, France.
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