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Schwartz J, Di ZW, Jiang Y, Manassa J, Pietryga J, Qian Y, Cho MG, Rowell JL, Zheng H, Robinson RD, Gu J, Kirilin A, Rozeveld S, Ercius P, Fessler JA, Xu T, Scott M, Hovden R. Imaging 3D chemistry at 1 nm resolution with fused multi-modal electron tomography. Nat Commun 2024; 15:3555. [PMID: 38670945 PMCID: PMC11053043 DOI: 10.1038/s41467-024-47558-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Measuring the three-dimensional (3D) distribution of chemistry in nanoscale matter is a longstanding challenge for metrological science. The inelastic scattering events required for 3D chemical imaging are too rare, requiring high beam exposure that destroys the specimen before an experiment is completed. Even larger doses are required to achieve high resolution. Thus, chemical mapping in 3D has been unachievable except at lower resolution with the most radiation-hard materials. Here, high-resolution 3D chemical imaging is achieved near or below one-nanometer resolution in an Au-Fe3O4 metamaterial within an organic ligand matrix, Co3O4-Mn3O4 core-shell nanocrystals, and ZnS-Cu0.64S0.36 nanomaterial using fused multi-modal electron tomography. Multi-modal data fusion enables high-resolution chemical tomography often with 99% less dose by linking information encoded within both elastic (HAADF) and inelastic (EDX/EELS) signals. We thus demonstrate that sub-nanometer 3D resolution of chemistry is measurable for a broad class of geometrically and compositionally complex materials.
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Affiliation(s)
- Jonathan Schwartz
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Zichao Wendy Di
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Yi Jiang
- Advanced Photon Source Facility, Argonne National Laboratory, Lemont, IL, USA
| | - Jason Manassa
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jacob Pietryga
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Material Science and Engineering, Northwestern University, Evanston, IL, USA
| | - Yiwen Qian
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, CA, USA
| | - Min Gee Cho
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, CA, USA
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jonathan L Rowell
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Huihuo Zheng
- Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, IL, USA
| | - Richard D Robinson
- Department of Material Science and Engineering, Cornell University, Ithaca, NY, USA
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, USA
| | - Junsi Gu
- Dow Chemical Co., Collegeville, PA, USA
| | | | | | - Peter Ercius
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeffrey A Fessler
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Ting Xu
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, CA, USA
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mary Scott
- Department of Materials Science and Engineering, University of California at Berkeley, Berkeley, CA, USA.
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Robert Hovden
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI, USA.
- Applied Physics Program, University of Michigan, Ann Arbor, MI, USA.
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2
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Umrekar TR, Cohen E, Drobnič T, Gonzalez-Rodriguez N, Beeby M. CryoEM of bacterial secretion systems: A primer for microbiologists. Mol Microbiol 2020; 115:366-382. [PMID: 33140482 DOI: 10.1111/mmi.14637] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
"CryoEM" has come of age, enabling considerable structural insights into many facets of molecular biology. Here, we present a primer for microbiologists to understand the capabilities and limitations of two complementary cryoEM techniques for studying bacterial secretion systems. The first, single particle analysis, determines the structures of purified protein complexes to resolutions sufficient for molecular modeling, while the second, electron cryotomography and subtomogram averaging, tends to determine more modest resolution structures of protein complexes in intact cells. We illustrate these abilities with examples of insights provided into how secretion systems work by cryoEM, with a focus on type III secretion systems.
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Affiliation(s)
| | - Eli Cohen
- Department of Life Sciences, Imperial College London, London, UK
| | - Tina Drobnič
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, UK
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Wagner FR, Watanabe R, Schampers R, Singh D, Persoon H, Schaffer M, Fruhstorfer P, Plitzko J, Villa E. Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. Nat Protoc 2020; 15:2041-2070. [PMID: 32405053 PMCID: PMC8053421 DOI: 10.1038/s41596-020-0320-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/06/2020] [Indexed: 12/31/2022]
Abstract
Recent advances have made cryogenic (cryo) electron microscopy a key technique to achieve near-atomic-resolution structures of biochemically isolated macromolecular complexes. Cryo-electron tomography (cryo-ET) can give unprecedented insight into these complexes in the context of their natural environment. However, the application of cryo-ET is limited to samples that are thinner than most cells, thereby considerably reducing its applicability. Cryo-focused-ion-beam (cryo-FIB) milling has been used to carve (micromachining) out 100-250-nm-thin regions (called lamella) in the intact frozen cells. This procedure opens a window into the cells for high-resolution cryo-ET and structure determination of biomolecules in their native environment. Further combination with fluorescence microscopy allows users to determine cells or regions of interest for the targeted fabrication of lamellae and cryo-ET imaging. Here, we describe how to prepare lamellae using a microscope equipped with both FIB and scanning electron microscopy modalities. Such microscopes (Aquilos Cryo-FIB/Scios/Helios or CrossBeam) are routinely referred to as dual-beam microscopes, and they are equipped with a cryo-stage for all operations in cryogenic conditions. The basic principle of the described methodologies is also applicable for other types of dual-beam microscopes equipped with a cryo-stage. We also briefly describe how to integrate fluorescence microscopy data for targeted milling and critical considerations for cryo-ET data acquisition of the lamellae. Users familiar with cryo-electron microscopy who get basic training in dual-beam microscopy can complete the protocol within 2-3 d, allowing for several pause points during the procedure.
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Affiliation(s)
- Felix R Wagner
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Reika Watanabe
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Digvijay Singh
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hans Persoon
- Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Peter Fruhstorfer
- Thermo Fisher Scientific, Eindhoven, the Netherlands
- Eppendorf AG, Hamburg, Germany
| | - Jürgen Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elizabeth Villa
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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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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Hermannsdörfer J, Tinnemann V, Peckys DB, de Jonge N. The Effect of Electron Beam Irradiation in Environmental Scanning Transmission Electron Microscopy of Whole Cells in Liquid. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:656-665. [PMID: 27137077 DOI: 10.1017/s1431927616000763] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Whole cells can be studied in their native liquid environment using electron microscopy, and unique information about the locations and stoichiometry of individual membrane proteins can be obtained from many cells thus taking cell heterogeneity into account. Of key importance for the further development of this microscopy technology is knowledge about the effect of electron beam radiation on the samples under investigation. We used environmental scanning electron microscopy (ESEM) with scanning transmission electron microscopy (STEM) detection to examine the effect of radiation for whole fixed COS7 fibroblasts in liquid. The main observation was the localization of nanoparticle labels attached to epidermal growth factor receptors (EGFRs). It was found that the relative distances between the labels remained mostly unchanged (<1.5%) for electron doses ranging from the undamaged native state at 10 e-/Å2 toward 103 e-/Å2. This dose range was sufficient to determine the EGFR locations with nanometer resolution and to distinguish between monomers and dimers. Various different forms of radiation damage became visible at higher doses, including severe dislocation, and the dissolution of labels.
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Affiliation(s)
| | - Verena Tinnemann
- 1INM - Leibniz Institute for New Materials,66123 Saarbrücken,Germany
| | - Diana B Peckys
- 2Department of Biophysics,Saarland University,66421 Homburg/Saar,Germany
| | - Niels de Jonge
- 1INM - Leibniz Institute for New Materials,66123 Saarbrücken,Germany
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6
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Kishchenko GP, Danev R, Fisher R, He J, Hsieh C, Marko M, Sui H. Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM. J Struct Biol 2015. [PMID: 26210582 DOI: 10.1016/j.jsb.2015.07.009] [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] [Indexed: 01/09/2023]
Abstract
Zernike phase-plate (ZPP) imaging greatly increases contrast in cryo-electron microscopy, however fringe artifacts appear in the images. A computational de-fringing method has been proposed, but it has not been widely employed, perhaps because the importance of de-fringing has not been clearly demonstrated. For testing purposes, we employed Zernike phase-plate imaging in a cryo-electron tomographic study of radial-spoke complexes attached to microtubule doublets. We found that the contrast enhancement by ZPP imaging made nonlinear denoising insensitive to the filtering parameters, such that simple low-frequency band-pass filtering made the same improvement in map quality. We employed sub-tomogram averaging, which compensates for the effect of the "missing wedge" and considerably improves map quality. We found that fringes (caused by the abrupt cut-on of the central hole in the phase plate) can lead to incorrect representation of a structure that is well-known from the literature. The expected structure was restored by amplitude scaling, as proposed in the literature. Our results show that de-fringing is an important part of image-processing for cryo-electron tomography of macromolecular complexes with ZPP imaging.
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Affiliation(s)
- Gregory P Kishchenko
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Radostin Danev
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Rebecca Fisher
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Jie He
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Chyongere Hsieh
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Michael Marko
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Haixin Sui
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States; Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY 12201, United States.
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Ishikawa T. Cryo-electron tomography of motile cilia and flagella. Cilia 2015; 4:3. [PMID: 25646146 PMCID: PMC4313461 DOI: 10.1186/s13630-014-0012-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 12/23/2014] [Indexed: 11/13/2022] Open
Abstract
Cryo-electron tomography has been a valuable tool in the analysis of 3D structures of cilia at molecular and cellular levels. It opened a way to reconstruct 3D conformations of proteins in cilia at 3-nm resolution, revealed networks of a number of component proteins in cilia, and has even allowed the study of component dynamics. In particular, we have identified the locations and conformations of all the regular inner and outer dyneins, as well as various regulators such as radial spokes. Since the mid 2000s, cryo-electron tomography has provided us with new knowledge, concepts, and questions in the area of cilia research. Now, after nearly 10 years of application of this technique, we are turning a corner and are at the stage to discuss the next steps. We expect further development of this technique for specimen preparation, data acquisition, and analysis. While combining this tool with other methodologies has already made cryo-electron tomography more biologically significant, we need to continue this cooperation using recently developed biotechnology and cell biology approaches. In this review, we will provide an up-to-date overview of the biological insights obtained by cryo-electron tomography and will discuss future possibilities of this technique in the context of cilia research.
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Affiliation(s)
- Takashi Ishikawa
- Group of Electron Microscopy of Complex Cellular System, Laboratory of Biomolecular Research, Paul Scherrer Institute, OFLG/010, 5232 Villigen PSI, Switzerland
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8
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Palmer CM, Löwe J. A cylindrical specimen holder for electron cryo-tomography. Ultramicroscopy 2014; 137:20-9. [PMID: 24275523 PMCID: PMC4054515 DOI: 10.1016/j.ultramic.2013.10.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/25/2013] [Accepted: 10/28/2013] [Indexed: 01/20/2023]
Abstract
The use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. This leads to the "missing wedge" problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. Cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. Such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but never for frozen-hydrated specimens. Here, we demonstrate the use of thin-walled carbon tubes as specimen holders, allowing the preparation of cylindrical frozen-hydrated samples of ribosomes, liposomes and whole bacterial cells. Images acquired from these cylinders have equal quality at all viewing angles, and the accessible tilt range is restricted only by the physical limits of the microscope. Tomographic reconstructions of these specimens demonstrate that the effects of the missing wedge are substantially reduced, and could be completely eliminated if a full tilt range was used. The overall quality of these tomograms is still lower than that obtained by existing methods, but improvements are likely in future.
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Affiliation(s)
- Colin M Palmer
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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9
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Abstract
The field of mechanobiology has witnessed an explosive growth over the past several years as interest has greatly increased in understanding how mechanical forces are transduced by cells and how cells migrate, adhere and generate traction. Actin, a highly abundant and anomalously conserved protein, plays a large role in forming the dynamic cytoskeleton that is so essential for cell form, motility and mechanosensitivity. While the actin filament (F-actin) has been viewed as dynamic in terms of polymerization and depolymerization, new results suggest that F-actin itself may function as a highly dynamic tension sensor. This property may help explain the unusual conservation of actin's sequence, as well as shed further light on actin's essential role in structures from sarcomeres to stress fibers.
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Affiliation(s)
- Vitold E Galkin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908-0733, USA
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10
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Fisch C, Dupuis-Williams P. [The rebirth of the ultrastructure of cilia and flagella]. Biol Aujourdhui 2012; 205:245-67. [PMID: 22251859 DOI: 10.1051/jbio/2011023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Indexed: 11/14/2022]
Abstract
The sensory and motility functions of eukaryotic cilia and flagella are essential for cell survival in protozoans and for cell differentiation and homoeostasis in metazoans. Ciliary biology has benefited early on from the input of electron microscopy. Over the last decade, the visualization of cellular structures has greatly progressed, thus it becomes timely to review the ultrastructure of cilia and flagella. Briefly touching upon the typical features of a 9+2 axoneme, we dwell extensively on the transition zone, the singlet zone, the ciliary necklace, cap and crown. The relation of the singlet zone to sensory and/or motile function, the link of the ciliary cap to microtubule dynamics and to ciliary beat, the involvement of the ciliary crown in ovocyte and mucosal propulsion, and the role of the transition zone/the ciliary necklace in axonemal stabilization, autotomy and as a diffusion barrier will all be discussed.
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Affiliation(s)
- Cathy Fisch
- ATIGE Centriole et Pathologies Associées, INSERM/UEVE U829, 91000 Évry, France.
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11
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Abstract
Eukaryotic cilia and flagella perform motility and sensory functions which are essential for cell survival in protozoans, and to organism development and homoeostasis in metazoans. Their ultrastructure has been studied from the early beginnings of electron microscopy, and these studies continue to contribute to much of our understanding about ciliary biology. In the light of the progress made in the visualization of cellular structures over the last decade, we revisit the ultrastructure of cilia and flagella. We briefly describe the typical features of a 9+2 axoneme before focusing extensively on the transition zone, the ciliary necklace, the singlet zone, the ciliary cap and the ciliary crown. We discuss how the singlet zone is linked to sensory and/or motile function, the contribution of the ciliary crown to ovocyte and mucosal propulsion, and the relationship between the ciliary cap and microtubule growth and shortening, and its relation to ciliary beat. We further examine the involvement of the transition zone/the ciliary necklace in axonemal stabilization, autotomy and as a diffusion barrier.
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13
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Cryo-electron tomography elucidates the molecular architecture of Treponema pallidum, the syphilis spirochete. J Bacteriol 2009; 191:7566-80. [PMID: 19820083 DOI: 10.1128/jb.01031-09] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cryo-electron tomography (CET) was used to examine the native cellular organization of Treponema pallidum, the syphilis spirochete. T. pallidum cells appeared to form flat waves, did not contain an outer coat and, except for bulges over the basal bodies and widening in the vicinity of flagellar filaments, displayed a uniform periplasmic space. Although the outer membrane (OM) generally was smooth in contour, OM extrusions and blebs frequently were observed, highlighting the structure's fluidity and lack of attachment to underlying periplasmic constituents. Cytoplasmic filaments converged from their attachment points opposite the basal bodies to form arrays that ran roughly parallel to the flagellar filaments along the inner surface of the cytoplasmic membrane (CM). Motile treponemes stably attached to rabbit epithelial cells predominantly via their tips. CET revealed that T. pallidum cell ends have a complex morphology and assume at least four distinct morphotypes. Images of dividing treponemes and organisms shedding cell envelope-derived blebs provided evidence for the spirochete's complex membrane biology. In the regions without flagellar filaments, peptidoglycan (PG) was visualized as a thin layer that divided the periplasmic space into zones of higher and lower electron densities adjacent to the CM and OM, respectively. Flagellar filaments were observed overlying the PG layer, while image modeling placed the PG-basal body contact site in the vicinity of the stator-P-collar junction. Bioinformatics and homology modeling indicated that the MotB proteins of T. pallidum, Treponema denticola, and Borrelia burgdorferi have membrane topologies and PG binding sites highly similar to those of their well-characterized Escherichia coli and Helicobacter pylori orthologs. Collectively, our results help to clarify fundamental differences in cell envelope ultrastructure between spirochetes and gram-negative bacteria. They also confirm that PG stabilizes the flagellar motor and enable us to propose that in most spirochetes motility results from rotation of the flagellar filaments against the PG.
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15
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JONIĆ S, SORZANO C, BOISSET N. Comparison of single-particle analysis and electron tomography approaches: an overview. J Microsc 2008; 232:562-79. [DOI: 10.1111/j.1365-2818.2008.02119.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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The flat-ribbon configuration of the periplasmic flagella of Borrelia burgdorferi and its relationship to motility and morphology. J Bacteriol 2008; 191:600-7. [PMID: 19011030 DOI: 10.1128/jb.01288-08] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Electron cryotomography was used to analyze the structure of the Lyme disease spirochete, Borrelia burgdorferi. This methodology offers a new means for studying the native architecture of bacteria by eliminating the chemical fixing, dehydration, and staining steps of conventional electron microscopy. Using electron cryotomography, we noted that membrane blebs formed at the ends of the cells. These blebs may be precursors to vesicles that are released from cells grown in vivo and in vitro. We found that the periplasmic space of B. burgdorferi was quite narrow (16.0 nm) compared to those of Escherichia coli and Pseudomonas aeruginosa. However, in the vicinity of the periplasmic flagella, this space was considerably wider (42.3 nm). In contrast to previous results, the periplasmic flagella did not form a bundle but rather formed a tight-fitting ribbon that wraps around the protoplasmic cell cylinder in a right-handed sense. We show how the ribbon configuration of the assembled periplasmic flagella is more advantageous than a bundle for both swimming and forming the flat-wave morphology. Previous results indicate that B. burgdorferi motility is dependent on the rotation of the periplasmic flagella in generating backward-moving waves along the length of the cell. This swimming requires that the rotation of the flagella exerts force on the cell cylinder. Accordingly, a ribbon is more beneficial than a bundle, as this configuration allows each periplasmic flagellum to have direct contact with the cell cylinder in order to exert that force, and it minimizes interference between the rotating filaments.
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Lupetti P, Lanzavecchia S, Mercati D, Cantele F, Dallai R, Mencarelli C. Three-dimensional reconstruction of axonemal outer dynein arms in situ by electron tomography. ACTA ACUST UNITED AC 2008; 62:69-83. [PMID: 16106450 DOI: 10.1002/cm.20084] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present here for the first time a 3D reconstruction of in situ axonemal outer dynein arms. This reconstruction has been obtained by electron tomography applied to a series of tilted images collected from metal replicas of rapidly frozen, cryofractured, and metal-replicated sperm axonemes of the cecidomid dipteran Monarthropalpus flavus. This peculiar axonemal model consists of several microtubular laminae that proved to be particularly suitable for this type of analysis. These laminae are sufficiently planar to allow the visualization of many dynein molecules within the same fracture face, allowing us to recover a significant number of equivalent objects and to improve the signal-to-noise ratio of the reconstruction by applying advanced averaging protocols. The 3D model we obtained showed the following interesting structural features: First, each dynein arm has two head domains that are almost parallel and are obliquely oriented with respect to the longitudinal axis of microtubules. The two heads are therefore positioned at different distances from the surface of the A-tubule. Second, each head domain consists of a series of globular subdomains that are positioned on the same plane. Third, a stalk domain originates as a conical region from the proximal head and ends with a small globular domain that contacts the B-tubule. Fourth, the stem region comprises several globular subdomains and presents two distinct points of anchorage to the surface of the A-tubule. Finally, and most importantly, contrary to what has been observed in isolated dynein molecules adsorbed to flat surfaces, the stalk and the stem domains are not in the same plane as the head.
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Affiliation(s)
- Pietro Lupetti
- Laboratory of Cryotechniques for Electron Microscopy, Dipartimento di Biologia Evolutiva, Università di Siena, I-53100 Siena, Italy
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Izard J, Hsieh CE, Limberger RJ, Mannella CA, Marko M. Native cellular architecture of Treponema denticola revealed by cryo-electron tomography. J Struct Biol 2008; 163:10-7. [PMID: 18468917 DOI: 10.1016/j.jsb.2008.03.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 03/20/2008] [Accepted: 03/21/2008] [Indexed: 11/26/2022]
Abstract
Using cryo-electron tomography, we are developing a refined description of native cellular structures in the pathogenic spirochete Treponema denticola. Tightly organized bundles of periplasmic flagella were readily observed in intact plunge-frozen cells. The periplasmic space was measured in both wild-type and aflagellate strains, and found to widen by less than the diameter of flagella when the latter are present. This suggests that a structural change occurs in the peptidoglycan layer to accommodate the presence of the flagella. In dividing cells, the flagellar filaments were found to bridge the cytoplasmic cylinder constriction site. Cytoplasmic filaments, adjacent to the inner membrane, run parallel to the tightly organized flagellar filaments. The cytoplasmic filaments may be anchored by a narrow plate-like structure. The tapering of the cell ends was conserved between cells, with a patella-shaped structure observed in the periplasm at the tip of each cytoplasmic cylinder. Several incompletely characterized structures have been observed in the periplasm between dividing cells, including a cable-like structure linking two cytoplasmic cylinders and complex foil-shaped structures.
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Affiliation(s)
- Jacques Izard
- Department of Molecular Genetics, The Forsyth Institute, 140 Fenway, Boston, MA 02135, USA.
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19
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McEwen BF, Renken C, Marko M, Mannella C. Chapter 6 Principles and Practice in Electron Tomography. Methods Cell Biol 2008; 89:129-68. [DOI: 10.1016/s0091-679x(08)00606-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Dong Y, VandenBeldt KJ, Meng X, Khodjakov A, McEwen BF. The outer plate in vertebrate kinetochores is a flexible network with multiple microtubule interactions. Nat Cell Biol 2007; 9:516-22. [PMID: 17435749 PMCID: PMC2895818 DOI: 10.1038/ncb1576] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 03/28/2007] [Indexed: 11/09/2022]
Abstract
Intricate interactions between kinetochores and microtubules are essential for the proper distribution of chromosomes during mitosis. A crucial long-standing question is how vertebrate kinetochores generate chromosome motion while maintaining attachments to the dynamic plus ends of the multiple kinetochore MTs (kMTs) in a kinetochore fibre. Here, we demonstrate that individual kMTs in PtK(1) cells are attached to the kinetochore outer plate by several fibres that either embed the microtubule plus-end tips in a radial mesh, or extend out from the outer plate to bind microtubule walls. The extended fibres also interact with the walls of nearby microtubules that are not part of the kinetochore fibre. These structural data, in combination with other recent reports, support a network model of kMT attachment wherein the fibrous network in the unbound outer plate, including the Hec1-Ndc80 complex, dissociates and rearranges to form kMT attachments.
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Affiliation(s)
- Yimin Dong
- Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY 12201, USA
| | | | - Xing Meng
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Alexey Khodjakov
- Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY 12201, USA
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Bruce F. McEwen
- Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY 12201, USA
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
- Correspondence should be addressed to B.F.M ()
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21
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Marko M, Hsieh CE. Three-dimensional cryotransmission electron microscopy of cells and organelles. Methods Mol Biol 2007; 369:407-29. [PMID: 17656762 DOI: 10.1007/978-1-59745-294-6_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cryoelectron microscopy of frozen-hydrated specimens is currently the only available technique for determining the "native" three-dimensional ultrastructure of individual examples of organelles and cells. Two techniques are available, stereo pair imaging and electron tomography, the latter providing full three-dimensional information about the specimen. A resolution of 4 to 10 nm can currently be obtained with cryotomography. We describe specimen preparation by means of plunge-freezing, which is straightforward and rapid compared with conventional EM techniques. We detail the considerations and preparation needed for successful cryotomography. Frozen-hydrated specimens are very radiation-sensitive and have low contrast because they lack heavy metal stains. The total electron dose that can be applied without damage to the specimen at a given resolution must be estimated, and this dose is fractionated among the images in the tilt series. The desired resolution determines the number and magnification of the images in the tilt series, as well as the objective lens defocus used for phase contrast imaging. The combination of the desired resolution and the maximum number of images into which a given dose can be fractionated sets an upper limit on specimen thickness. Because of these constraints, careful choice of imaging conditions, use of a sensitive CCD camera system, and microscope automation, are important requirements for conducting cryoelectron tomography.
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Affiliation(s)
- Michael Marko
- Resource for Visualization of Biological Complexity, Wadsworth Center, Empire State Plaza, Albany, New York, USA
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22
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McEwen BF, Dong Y, VandenBeldt KJ. Using Electron Microscopy to Understand Functional Mechanisms of Chromosome Alignment on the Mitotic Spindle. Methods Cell Biol 2007; 79:259-93. [PMID: 17327161 DOI: 10.1016/s0091-679x(06)79011-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Bruce F McEwen
- Wadsworth Center, New York State Department of Health, Albany, New York 12201, USA
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23
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Affiliation(s)
- Paul Mooney
- Gatan, Inc., Pleasanton, California 94588, USA
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24
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Izard J. Cytoskeletal cytoplasmic filament ribbon of Treponema: a member of an intermediate-like filament protein family. J Mol Microbiol Biotechnol 2006; 11:159-66. [PMID: 16983193 DOI: 10.1159/000094052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Development of genetic systems for many bacterial genera, including Treponema, now allow the study of structures that are specific to certain pathogens. The cytoplasmic filament ribbon of treponemes that is involved in the cell division cycle has a unique organization. Cytoplasmic bridging proteins connect the filaments, maintaining the distance between them and providing the overall ribbon-like structure. The filaments are anchored by proteins associated with the inner membrane. Each filament is composed of a unique monomer, the cytoplasmic filament protein A (CfpA), with coiled-coils secondary structures. CfpA is part of a growing family of proteins that we propose to call bacterial intermediate-like filaments (BILF).
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25
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Abstract
Sectioning vitrified cells and tissues for cryo-electron microscopy is more challenging than room-temperature sectioning of plastic-embedded samples. As the sample must be kept very cold (<-130 degrees C) and because there is no liquid upon which the sections can float as they are cut, transferring the sections from the knife edge to a grid is one of the more difficult steps in the process. We employed a micromanipulator to hold and control the cryo-sections as they come off the knife. This allows slower cutting speeds than are typically used in vitreous cryo-sectioning and contributes to better control during cutting, which facilitates repeatable placement of a ribbon of sections onto a grid. The ribbon is kept under tension during the entire cutting process, which may decrease folding and/or compression, features that are inherent to vitreous sections. Furthermore, the added control afforded by this technique makes it easier for multiple ribbons to be placed on a single grid, thereby increasing the number of sections that can be examined and imaged during a microscopy session. It even allows for serial cryo-electron microscopy. As such, this approach is an advance in the cryo-microtomy of vitreous sections.
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Affiliation(s)
- Mark S Ladinsky
- Boulder Laboratory for Three Dimensional Electron Microscopy of Cells, Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.
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26
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Abstract
Electron microscope tomography produces three-dimensional reconstructions and has been used to image organelles both isolated and in situ, providing new insight into their structure and function. It is analogous to the various tomographies used in medical imaging. Compared with light microscopy, electron tomography offers an improvement in resolution of 30- to 80-fold and currently ranges from 3 to 8 nm, thus filling the gap between high-resolution structure determinations of isolated macromolecules and larger-scale studies on cells and tissues by light microscopy. Here, we provide an introduction to electron tomography and applications of the method in characterizing organelle architecture that also show its power for suggesting functional significance. Further improvements in labeling modalities, imaging tools, specimen preparation, and reconstruction algorithms promise to increase the quality and breadth of reconstructions by electron tomography and eventually to allow the mapping of the cellular proteomes onto detailed three-dimensional models of cellular structure.
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Affiliation(s)
- Terrence G Frey
- Department of Biology, San Diego State University, San Diego, California 92182-4614, USA.
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27
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Jiang M, Ji Q, McEwen BF. Automated extraction of fine features of kinetochore microtubules and plus-ends from electron tomography volume. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2006; 15:2035-48. [PMID: 16830922 DOI: 10.1109/tip.2006.877054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Kinetochore microtubules (KMTs) and the associated plus-ends have been areas of intense investigation in both cell biology and molecular medicine. Though electron tomography opens up new possibilities in understanding their function by imaging their high-resolution structures, the interpretation of the acquired data remains an obstacle because of the complex and cluttered cellular environment. As a result, practical segmentation of the electron tomography data has been dominated by manual operation, which is time consuming and subjective. In this paper, we propose a model-based automated approach to extracting KMTs and the associated plus-ends with a coarse-to-fine scale scheme consisting of volume preprocessing, microtubule segmentation and plus-end tracing. In volume preprocessing, we first apply an anisotropic invariant wavelet transform and a tube-enhancing filter to enhance the microtubules at coarse level for localization. This is followed with a surface-enhancing filter to accentuate the fine microtubule boundary features. The microtubule body is then segmented using a modified active shape model method. Starting from the segmented microtubule body, the plus-ends are extracted with a probabilistic tracing method improved with rectangular window based feature detection and the integration of multiple cues. Experimental results demonstrate that our automated method produces results comparable to manual segmentation but using only a fraction of the manual segmentation time.
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Affiliation(s)
- Ming Jiang
- Department of Electrical, Computer and System Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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28
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Chiu W, Baker ML, Almo SC. Structural biology of cellular machines. Trends Cell Biol 2006; 16:144-50. [PMID: 16459078 DOI: 10.1016/j.tcb.2006.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2005] [Revised: 12/06/2005] [Accepted: 01/19/2006] [Indexed: 01/29/2023]
Abstract
Multi-component macromolecular machines contribute to all essential biological processes, from cell motility and signal transduction to information storage and processing. Structural analysis of assemblies at atomic resolution is emerging as the field of structural cell biology. Several recent studies, including those focused on the ribosome, the acrosomal bundle and bacterial flagella, have demonstrated the ability of a hybrid approach that combines imaging, crystallography and computational tools to generate testable atomic models of fundamental biological machines. A complete understanding of cellular and systems biology will require the detailed structural understanding of hundreds of biological machines. The realization of this goal demands a concerted effort to develop and apply new strategies for the systematic identification, isolation, structural characterization and mechanistic analysis of multi-component assemblies at all resolution ranges. The establishment of a database describing the structural and dynamic properties of protein assemblies will provide novel opportunities to define the molecular and atomic mechanisms controlling overall cell physiology.
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Affiliation(s)
- Wah Chiu
- National Center for Macromolecular Imaging and Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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29
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Dallai R, Lupetti P, Mencarelli C. Unusual Axonemes of Hexapod Spermatozoa. INTERNATIONAL REVIEW OF CYTOLOGY 2006; 254:45-99. [PMID: 17147997 DOI: 10.1016/s0074-7696(06)54002-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hexapod spermatozoa exhibit a great variation in their axoneme structure. The 9+2 pattern organization is present in a few basal taxa and in some derived groups. In most hexapods, a crown of nine accessory microtubules surrounds the 9+2 array, giving rise to the so-called 9+9+2 pattern. This general organization, however, displays a number of modifications in several taxa. In this review, the main variations concerning the number and localization of the accessory tubules, microtubular doublets, central microtubules, dynein arms, and axonemal length are summarized. We discuss the phylogenetic significance of all this structural information as well as the current hypotheses relating the sperm size and sperm polymorphism with reproductive success of some hexapod species. Also described are the biochemical data and the motility patterns which are currently known on some peculiar aberrant axonemes, in light of the contribution these models may give to the comprehension of the general functioning of the conventional 9+2 axoneme. Finally, we summarize methodological developments for the study of axoneme ultrastructure and the new opportunities for the molecular analysis of hexapod axonemes.
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Affiliation(s)
- Romano Dallai
- Department of Evolutionary Biology, University of Siena, Via A Moro 2, I-53100 Siena, Italy
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30
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Abstract
Electron tomography (ET) is uniquely suited to obtain three-dimensional reconstructions of pleomorphic structures, such as cells, organelles or supramolecular assemblies. Although the principles of ET have been known for decades, its use has gathered momentum only in recent years, thanks to technological advances and its combination with improved specimen preparation techniques. The rapid freezing/freeze-substitution preparation is applicable to whole cells and tissues, and it is the method of choice for ET investigations of cellular ultrastructure. The frozen-hydrated preparation provides the best possible structural preservation and allows the imaging of molecules, complexes, and supramolecular assemblies in their native state and their natural environment. Devoid of staining and chemical fixation artifacts, cryo-ET provides a faithful representation of both the surface and internal structure of molecules. In combination with advanced computational methods, such as molecular identification based on pattern recognition techniques, cryo-ET is currently the most promising approach to comprehensively map macromolecular architecture inside cellular tomograms.
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Affiliation(s)
- Vladan Lucić
- Department of Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried, Germany.
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31
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McIntosh R, Nicastro D, Mastronarde D. New views of cells in 3D: an introduction to electron tomography. Trends Cell Biol 2005; 15:43-51. [PMID: 15653077 DOI: 10.1016/j.tcb.2004.11.009] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The most important goal of structural cell biology is to elucidate the mechanisms of the processes of life. The structure of a membrane system or fibrous array, the changes in such structures over time or the localizations of enzymes relative to organelle boundaries can often illuminate associated cellular functions. To be of maximal value, structural studies should provide isotropic, 3D information about well-preserved samples at the highest possible resolution. Electron tomography can provide such information about many kinds of cells and organelles.
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Affiliation(s)
- Richard McIntosh
- Laboratory for 3D Electron Microscopy of Cells, Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA.
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32
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Marsh BJ. Lessons from tomographic studies of the mammalian Golgi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1744:273-92. [PMID: 15896857 DOI: 10.1016/j.bbamcr.2005.04.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Revised: 04/11/2005] [Accepted: 04/11/2005] [Indexed: 11/22/2022]
Abstract
Basic structure studies of the biosynthetic machinery of the cell by electron microscopy (EM) have underpinned much of our fundamental knowledge in the areas of molecular cell biology and membrane traffic. Driven by our collective desire to understand how changes in the complex and dynamic structure of this enigmatic organelle relate to its pivotal roles in the cell, the comparatively high-resolution glimpses of the Golgi and other compartments of the secretory pathway offered to us through EM have helped to inspire the development and application of some of our most informative, complimentary (molecular, biochemical and genetic) approaches. Even so, no one has yet even come close to relating the basic molecular mechanisms of transport, through and from the Golgi, to its ultrastructure, to everybody's satisfaction. Over the past decade, EM tomography has afforded new insights into structure-function relationships of the Golgi and provoked a re-evaluation of older paradigms. By providing a set of tools for structurally dissecting cells at high-resolution in three-dimensions (3D), EM tomography has emerged as a method for studying molecular cell biology in situ. As we move rapidly toward the establishment of molecular atlases of organelles through advances in proteomics and genomics, tomographic studies of the Golgi offer the tantalizing possibility that one day, we will be able to map the spatio-temporal coordinates of Golgi-related proteins and lipids accurately in the context of 4D cellular space.
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Affiliation(s)
- Brad J Marsh
- Institute for Molecular Bioscience, Centre for Microscopy and Microanalysis, and School of Molecular and Microbial Sciences, The University of Queensland, St. Lucia QLD 4072, Australia.
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33
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Marco S, Boudier T, Messaoudi C, Rigaud JL. Electron tomography of biological samples. BIOCHEMISTRY (MOSCOW) 2005; 69:1219-25. [PMID: 15627375 DOI: 10.1007/s10541-005-0067-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron tomography allows computing three-dimensional (3D) reconstructions of objects from their projections recorded at several angles. Combined with transmission electron microscopy, electron tomography has contributed greatly to the understanding of subcellular structures and organelles. Performed on frozen-hydrated samples, electron tomography has yielded useful information about complex biological structures. Combined with energy filtered transmission electron microscopy (EFTEM) it can be used to analyze the spatial distribution of chemical elements in biological or material sciences samples. In the present review, we present an overview of the requirements, applications, and perspectives of electron tomography in structural biology.
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Affiliation(s)
- S Marco
- Institut Curie, Section Recherche, UMR-CNRS 168 et LRC-CEA 34V 11, 75005 Paris, France.
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34
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Lanzavecchia S, Cantele F, Bellon PL, Zampighi L, Kreman M, Wright E, Zampighi GA. Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers. J Struct Biol 2005; 149:87-98. [PMID: 15629660 DOI: 10.1016/j.jsb.2004.09.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Revised: 08/31/2004] [Indexed: 11/18/2022]
Abstract
We have used conical tomography to study the structure of integral proteins in their phospholipid bilayer environments. Complete conical series were collected from replicas of the water channel aquaporin-0 (AQP0), a 6.6 nm side tetramer with a molecular weight of approximately 120 kDa that was purified and reconstituted in liposomes. The replicas were tilted at 38 degrees , 50 degrees or 55 degrees and rotated by 2.5 degrees , 4 degrees , or 5 degrees increments until completing 360 degrees turns. The elliptical paths of between 6 and 12 freeze-fracture particles aligned the images to a common coordinate system. Using the weighted back projection algorithm, small volumes of the replicas were independently reconstructed to reconstitute the field. Using the Fourier Shell Correlation computed from reconstructions of even and odd projections of the series, we estimated a resolution of 2-3 nm, a value that was close to the thickness of the replica (approximately 1.5 nm). The 3D reconstructions exhibited isotropic resolution along the x-y plane, which simplified the analysis of particles oriented randomly in the membrane plane. In contrast to reconstructions from single particles imaged using random conical tilt [J. Mol. Biol. 325 (2003) 210], the reconstructions using conical tomography allowed the size and shape of individual particles representing the AQP0 channel to be identified without averaging or imposing symmetry. In conclusion, the reconstruction of freeze-fracture replicas with electron tomography has provided a novel experimental approach for the study of integral proteins inserted in phospholipid bilayers.
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Affiliation(s)
- S Lanzavecchia
- Dipartimento di Chimica Strutturale, Università di Milano, Italy.
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35
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Electron tomography of biological samples. BIOCHEMISTRY (MOSCOW) 2004. [DOI: 10.1007/pl00021757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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36
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Abstract
Emerging methods in cryo-electron microscopy allow determination of the three-dimensional architectures of objects ranging in size from small proteins to large eukaryotic cells, spanning a size range of more than 12 orders of magnitude. Advances in determining structures by "single particle" microscopy and by "electron tomography" provide exciting opportunities to describe the structures of subcellular assemblies that are either too large or too heterogeneous to be investigated by conventional crystallographic methods. Here, we review selected aspects of progress in structure determination by cryo-electron microscopy at molecular resolution, with a particular emphasis on topics at the interface of single particle and tomographic approaches. The rapid pace of development in this field suggests that comprehensive descriptions of the structures of whole cells and organelles in terms of the spatial arrangements of their molecular components may soon become routine.
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Affiliation(s)
- Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA.
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37
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Izard J, McEwen BF, Barnard RM, Portuese T, Samsonoff WA, Limberger RJ. Tomographic reconstruction of treponemal cytoplasmic filaments reveals novel bridging and anchoring components. Mol Microbiol 2003; 51:609-18. [PMID: 14731266 DOI: 10.1046/j.1365-2958.2003.03864.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An understanding of the involvement of bacterial cytoplasmic filaments in cell division requires the elucidation of the structural organization of those filamentous structures. Treponemal cytoplasmic filaments are composed of one protein, CfpA, and have been demonstrated to be involved in cell division. In this study, we used electron tomography to show that the filaments are part of a complex with a novel molecular organization that includes at least two distinct features decorating the filaments. One set of components appears to anchor the filaments to the cytoplasmic membrane. The other set of components appears to bridge the cytoplasmic filaments on the cytoplasmic side, and to be involved in the interfilament spacing within the cell. The filaments occupy between 3 and 18% of the inner surface of the cytoplasmic membrane. These results reveal a novel filamentous molecular organization of independent filaments linked by bridges and continuously anchored to the membrane.
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Affiliation(s)
- Jacques Izard
- New York State Department of Health, Wadsworth Center, David Axelrod Institute for Public Health, PO Box 22002, Albany, New York 12201-2002, USA.
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38
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Hsieh CE, Marko M, Frank J, Mannella CA. Electron tomographic analysis of frozen-hydrated tissue sections. J Struct Biol 2002; 138:63-73. [PMID: 12160702 DOI: 10.1016/s1047-8477(02)00034-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Electron tomography of frozen-hydrated tissue sections enables analysis of the 3-D structure of cell organelles in situ and in a near-native state. In this study, 160-200-nm-thick sections were cut from high-pressure frozen rat liver, and improved methods were used for handling and mounting the sections. Automated data collection facilitated tilt-series recording at low electron dose (approximately 4000 e(-)/nm(2) at 400 keV). Higher doses (up to 10,000 e(-)/nm(2)) were found to increase contrast and smooth out surface defects, but caused section distortion and movement, with likely loss of high-resolution information. Tomographic reconstruction showed that knife marks were 10-40 nm deep and located on the "knife face" of the section, while crevices were 20-50 nm deep and found on the "block face." The interior of the section was normally free of defects, except for compression, and contained useful structural information. For example, the topology of mitochondrial membranes in tissue was found to be very similar to that in frozen-hydrated whole mounts of isolated mitochondria. In rare cases, a 15-nm banding pattern perpendicular to the cutting direction was observed in the interior of the section, most evident in the uniformly dense, protein-rich material of the mitochondrial matrix.
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Affiliation(s)
- Chyong-Ere Hsieh
- Resource for Visualization of Biological Complexity, Wadsworth Center, Empire State Plaza, Albany, NY 12201, USA
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