1
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Tan ZY, Cai S, Noble AJ, Chen JK, Shi J, Gan L. Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ. eLife 2023; 12:RP87672. [PMID: 37503920 PMCID: PMC10382156 DOI: 10.7554/elife.87672] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ is otherwise poorly understood. Using cryo-electron tomography (cryo-ET) and 3D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expected in situ. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are found ex vivo (in nuclear lysates), but not in situ. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosome's DNA is partially detached in situ.
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Affiliation(s)
- Zhi Yang Tan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Shujun Cai
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Jon K Chen
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Jian Shi
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Lu Gan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
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2
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Ma OX, Chong WG, Lee JKE, Cai S, Siebert CA, Howe A, Zhang P, Shi J, Surana U, Gan L. Cryo-ET detects bundled triple helices but not ladders in meiotic budding yeast. PLoS One 2022; 17:e0266035. [PMID: 35421110 PMCID: PMC9009673 DOI: 10.1371/journal.pone.0266035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 03/13/2022] [Indexed: 11/19/2022] Open
Abstract
In meiosis, cells undergo two sequential rounds of cell division, termed meiosis I and meiosis II. Textbook models of the meiosis I substage called pachytene show that nuclei have conspicuous 100-nm-wide, ladder-like synaptonemal complexes and ordered chromatin loops. It remains unknown if these cells have any other large, meiosis-related intranuclear structures. Here we present cryo-ET analysis of frozen-hydrated budding yeast cells before, during, and after pachytene. We found no cryo-ET densities that resemble dense ladder-like structures or ordered chromatin loops. Instead, we found large numbers of 12-nm-wide triple-helices that pack into ordered bundles. These structures, herein called meiotic triple helices (MTHs), are present in meiotic cells, but not in interphase cells. MTHs are enriched in the nucleus but not enriched in the cytoplasm. Bundles of MTHs form at the same timeframe as synaptonemal complexes (SCs) in wild-type cells and in mutant cells that are unable to form SCs. These results suggest that in yeast, SCs coexist with previously unreported large, ordered assemblies.
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Affiliation(s)
- Olivia X. Ma
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Wen Guan Chong
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Joy K. E. Lee
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - C. Alistair Siebert
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Andrew Howe
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
| | - Peijun Zhang
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, Oxfordshire, United Kingdom
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Proteos, Singapore
- Bioprocessing Technology Institute, A*STAR, Singapore, Singapore
- Biotransformation Innovation Platform, A*STAR, Singapore, Singapore
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
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3
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Harastani M, Eltsov M, Leforestier A, Jonic S. TomoFlow: Analysis of Continuous Conformational Variability of Macromolecules in Cryogenic Subtomograms based on 3D Dense Optical Flow. J Mol Biol 2021; 434:167381. [PMID: 34848215 DOI: 10.1016/j.jmb.2021.167381] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 01/14/2023]
Abstract
Cryogenic Electron Tomography (cryo-ET) allows structural and dynamics studies of macromolecules in situ. Averaging different copies of imaged macromolecules is commonly used to obtain their structure at higher resolution and discrete classification to analyze their dynamics. Instrumental and data processing developments are progressively equipping cryo-ET studies with the ability to escape the trap of classification into a complete continuous conformational variability analysis. In this work, we propose TomoFlow, a method for analyzing macromolecular continuous conformational variability in cryo-ET subtomograms based on a three-dimensional dense optical flow (OF) approach. The resultant lower-dimensional conformational space allows generating movies of macromolecular motion and obtaining subtomogram averages by grouping conformationally similar subtomograms. The animations and the subtomogram group averages reveal accurate trajectories of macromolecular motion based on a novel mathematical model that makes use of OF properties. This paper describes TomoFlow with tests on simulated datasets generated using different techniques, namely Normal Mode Analysis and Molecular Dynamics Simulation. It also shows an application of TomoFlow on a dataset of nucleosomes in situ, which provided promising results coherent with previous findings using the same dataset but without imposing any prior knowledge on the analysis of the conformational variability. The method is discussed with its potential uses and limitations.
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Affiliation(s)
- Mohamad Harastani
- IMPMC - UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France; Laboratoire de Physique des Solides (LPS), UMR 8502 CNRS, Université Paris-Saclay, Orsay, France. https://twitter.com/moh_harastani
| | - Mikhail Eltsov
- Department of Integrated Structural Biology, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France. https://twitter.com/EltsovMikhail
| | - Amélie Leforestier
- Laboratoire de Physique des Solides (LPS), UMR 8502 CNRS, Université Paris-Saclay, Orsay, France
| | - Slavica Jonic
- IMPMC - UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris, France.
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4
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Kaplan M, Nicolas WJ, Zhao W, Carter SD, Metskas LA, Chreifi G, Ghosal D, Jensen GJ. In Situ Imaging and Structure Determination of Biomolecular Complexes Using Electron Cryo-Tomography. Methods Mol Biol 2021; 2215:83-111. [PMID: 33368000 DOI: 10.1007/978-1-0716-0966-8_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Electron cryo-tomography (cryo-ET) is a technique that allows the investigation of intact macromolecular complexes while they are in their cellular milieu. Over the years, cryo-ET has had a huge impact on our understanding of how large biomolecular complexes look like, how they assemble, disassemble, function, and evolve(d). Recent hardware and software developments and combining cryo-ET with other techniques, e.g., focused ion beam milling (FIB-milling) and cryo-light microscopy, has extended the realm of cryo-ET to include transient molecular complexes embedded deep in thick samples (like eukaryotic cells) and enhanced the resolution of structures obtained by cryo-ET. In this chapter, we will present an outline of how to perform cryo-ET studies on a wide variety of biological samples including prokaryotic and eukaryotic cells and biological plant tissues. This outline will include sample preparation, data collection, and data processing as well as hybrid approaches like FIB-milling, cryosectioning, and cryo-correlated light and electron microscopy (cryo-CLEM).
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - William J Nicolas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Wei Zhao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Stephen D Carter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - Georges Chreifi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Molecular Biology; and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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5
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Ng CT, Ladinsky MS, Gan L. Serial Cryomicrotomy of Saccharomyces cerevisiae for Serial Electron Cryotomography. Bio Protoc 2020; 10:e3831. [PMID: 33659481 DOI: 10.21769/bioprotoc.3831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/18/2020] [Accepted: 09/28/2020] [Indexed: 11/02/2022] Open
Abstract
Electron cryotomography (cryo-ET) is an increasingly popular technique to study cellular structures and macromolecules in situ. Due to poor penetration of electrons through thick biological samples, the vitreously frozen samples for cryo-ET need to be thin. For frozen-hydrated cells, such samples can be produced either by cryomicrotomy or cryo-FIB-milling. As a result, a tomogram of such a sample contains information of a small fraction of the entire cell volume, making it challenging to image rare structures in the cell or to determine the distribution of scattered structures. Here, we describe the tools and workflow that we designed to facilitate serial cryomicrotomy, which makes possible the exploration of a larger volume of individual cells at molecular resolution. We successfully used serial cryomicrotomy to locate and image the Dam1/DASH complex located at microtubule plus ends inside mitotic Saccharomyces cerevisiae cells.
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Affiliation(s)
- Cai Tong Ng
- Centre of BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Mark S Ladinsky
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Lu Gan
- Centre of BioImaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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6
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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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7
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Jun S, Ro HJ, Bharda A, Kim SI, Jeoung D, Jung HS. Advances in Cryo-Correlative Light and Electron Microscopy: Applications for Studying Molecular and Cellular Events. Protein J 2020; 38:609-615. [PMID: 31396855 DOI: 10.1007/s10930-019-09856-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cryo-correlative light and electron microscopy (Cryo-CLEM) is materializing as a widespread approach amalgamating the advantages of both fluorescence light microscopy (FLM) as well as three dimensional (3D) cryo-electron tomography (cryo-ET) to reveal the ultrastructure of significant target molecules with specific cellular functions. Cryo-CLEM allows imaging of cells by means of fluorescence microscopy exhibiting the location of the destined molecule at high temporal and spatial resolution while cryo-ET is employed to analyze the 3D structure at a molecular resolution in close-to-physiological condition. Present review focuses upon the practical strategies for Cryo-CLEM and recent technical developments that will assist the broad implementation of this technique to investigate and answer questions pertaining to various biological events occurring in the cell.
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Affiliation(s)
- Sangmi Jun
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea. .,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea. .,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea.
| | - Hyun-Joo Ro
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Anahita Bharda
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Seung Il Kim
- Drug & Disease Target Team, Korea Basic Science Institute, 162, Yeongudanji-ro, Ochang-eup, Cheongwon-gu, Cheongju-Si, Chungcheongbuk-do, 28119, South Korea.,Convergent Research Center for Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, South Korea.,Bio-Analytical Science, University of Science & Technology, Daejeon, South Korea
| | - Dooil Jeoung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-Si, Gangwon-do, 200-701, South Korea.
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8
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Ng CT, Gan L. Investigating eukaryotic cells with cryo-ET. Mol Biol Cell 2020; 31:87-100. [PMID: 31935172 PMCID: PMC6960407 DOI: 10.1091/mbc.e18-05-0329] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 01/06/2023] Open
Abstract
The interior of eukaryotic cells is mysterious. How do the large communities of macromolecular machines interact with each other? How do the structures and positions of these nanoscopic entities respond to new stimuli? Questions like these can now be answered with the help of a method called electron cryotomography (cryo-ET). Cryo-ET will ultimately reveal the inner workings of a cell at the protein, secondary structure, and perhaps even side-chain levels. Combined with genetic or pharmacological perturbation, cryo-ET will allow us to answer previously unimaginable questions, such as how structure, biochemistry, and forces are related in situ. Because it bridges structural biology and cell biology, cryo-ET is indispensable for structural cell biology-the study of the 3-D macromolecular structure of cells. Here we discuss some of the key ideas, strategies, auxiliary techniques, and innovations that an aspiring structural cell biologist will consider when planning to ask bold questions.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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9
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Abstract
Cell division in many eukaryotes is driven by a ring containing actin and myosin. While much is known about the main proteins involved, the precise arrangement of actin filaments within the contractile machinery, and how force is transmitted to the membrane, remains unclear. Here we use cryosectioning and cryofocused ion beam milling to gain access to cryopreserved actomyosin rings in Schizosaccharomyces pombe for direct 3D imaging by electron cryotomography. Our results show that straight, overlapping actin filaments, running nearly parallel to each other and to the membrane, form a loose bundle of ∼150 nm in diameter that "saddles" the inward-bending membrane at the leading edge of the division septum. The filaments do not make direct contact with the membrane. Our analysis of the actin filaments reveals the variability in filament number, nearest-neighbor distances between filaments within the bundle, their distance from the membrane, and angular distribution with respect to the membrane.
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10
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Wolf SG, Mutsafi Y, Dadosh T, Ilani T, Lansky Z, Horowitz B, Rubin S, Elbaum M, Fass D. 3D visualization of mitochondrial solid-phase calcium stores in whole cells. eLife 2017; 6:29929. [PMID: 29106371 PMCID: PMC5703638 DOI: 10.7554/elife.29929] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
The entry of calcium into mitochondria is central to metabolism, inter-organelle communication, and cell life/death decisions. Long-sought transporters involved in mitochondrial calcium influx and efflux have recently been identified. To obtain a unified picture of mitochondrial calcium utilization, a parallel advance in understanding the forms and quantities of mitochondrial calcium stores is needed. We present here the direct 3D visualization of mitochondrial calcium in intact mammalian cells using cryo-scanning transmission electron tomography (CSTET). Amorphous solid granules containing calcium and phosphorus were pervasive in the mitochondrial matrices of a variety of mammalian cell types. Analysis based on quantitative electron scattering revealed that these repositories are equivalent to molar concentrations of dissolved ions. These results demonstrate conclusively that calcium buffering in the mitochondrial matrix in live cells occurs by phase separation, and that solid-phase stores provide a major ion reservoir that can be mobilized for bioenergetics and signaling.
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Affiliation(s)
- Sharon Grayer Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Mutsafi
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tali Dadosh
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Ilani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zipora Lansky
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ben Horowitz
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Rubin
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Elbaum
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel
| | - Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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11
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Briegel A, Jensen G. Progress and Potential of Electron Cryotomography as Illustrated by Its Application to Bacterial Chemoreceptor Arrays. Annu Rev Biophys 2017; 46:1-21. [PMID: 28301773 DOI: 10.1146/annurev-biophys-070816-033555] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Electron cryotomography (ECT) can produce three-dimensional images of biological samples such as intact cells in a near-native, frozen-hydrated state to macromolecular resolution (∼4 nm). Because one of its first and most common applications has been to bacterial chemoreceptor arrays, ECT's contributions to this field illustrate well its past, present, and future. While X-ray crystallography and nuclear magnetic resonance spectroscopy have revealed the structures of nearly all the individual components of chemoreceptor arrays, ECT has revealed the mesoscale information about how the components are arranged within cells. Receptors assemble into a universally conserved 12-nm hexagonal lattice linked by CheA/CheW rings. Membrane-bound arrays are single layered; cytoplasmic arrays are double layered. Images of in vitro reconstitutions have led to a model of how arrays assemble, and images of native arrays in different states have shown that the conformational changes associated with signal transduction are subtle, constraining models of activation and system cooperativity. Phase plates, better detectors, and more stable stages promise even higher resolution and broader application in the near future.
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Affiliation(s)
- Ariane Briegel
- Department of Biology, Leiden University, 2333 Leiden, Netherlands
| | - Grant 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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12
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Briegel A, Ladinsky MS, Oikonomou C, Jones CW, Harris MJ, Fowler DJ, Chang YW, Thompson LK, Armitage JP, Jensen GJ. Structure of bacterial cytoplasmic chemoreceptor arrays and implications for chemotactic signaling. eLife 2014; 3:e02151. [PMID: 24668172 PMCID: PMC3964821 DOI: 10.7554/elife.02151] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Most motile bacteria sense and respond to their environment through a transmembrane chemoreceptor array whose structure and function have been well-studied, but many species also contain an additional cluster of chemoreceptors in their cytoplasm. Although the cytoplasmic cluster is essential for normal chemotaxis in some organisms, its structure and function remain unknown. Here we use electron cryotomography to image the cytoplasmic chemoreceptor cluster in Rhodobacter sphaeroides and Vibrio cholerae. We show that just like transmembrane arrays, cytoplasmic clusters contain trimers-of-receptor-dimers organized in 12-nm hexagonal arrays. In contrast to transmembrane arrays, however, cytoplasmic clusters comprise two CheA/CheW baseplates sandwiching two opposed receptor arrays. We further show that cytoplasmic fragments of normally transmembrane E. coli chemoreceptors form similar sandwiched structures in the presence of molecular crowding agents. Together these results suggest that the 12-nm hexagonal architecture is fundamentally important and that sandwiching and crowding can replace the stabilizing effect of the membrane. DOI:http://dx.doi.org/10.7554/eLife.02151.001 Many bacteria swim through water by rotating tiny hair-like structures called flagella. In E. coli, if all the flagella on the surface of a bacterium rotate in a counterclockwise fashion, then it will swim in a particular direction, but if the flagella all rotate in an clockwise fashion, then the bacterium will stop swimming and start to tumble. Bacteria use a combination of swimming and tumbling in order to move towards or away from certain chemicals. For example, a bacterium is able to move towards a source of nutrients because it is constantly evaluating its environment and will swim forward for longer periods of time when it recognizes the concentration of the nutrient is increasing. And if it senses that the nutrient concentration is decreasing, it will tumble in an effort to move in a different direction. Many bacteria, such as E. coli, rely on proteins in their cell membrane called chemoreceptors to sense specific chemicals and then send signals that tell the flagella how to rotate. These transmembrane receptors and their role in chemotaxis—that is, movement towards or away from specific chemicals in the environment—have been widely studied. However, other bacteria also have chemoreceptors in the cytoplasm inside the bacterial cell, and much less is known about these. Now, Briegel et al. have examined the cytoplasmic chemoreceptors of two unrelated bacteria, R. sphaeroides and V. cholera, and found that the cytoplasmic chemoreceptors arrange themselves in hexagonal arrays, similar to the way that transmembrane chemoreceptors are arranged. However, the cytoplasmic chemoreceptors arrange themselves in a two-layer sandwich-like structure, whereas the transmembrane chemoreceptors are arranged in just one layer. The next step is to understand how chemical binding causes these arrays to send their signals to the motor. A complete understanding of this signaling system may ultimately allow scientists to re-engineer it to draw bacteria to targets of medical or environmental interest, such as cancer cells or contaminated soils. DOI:http://dx.doi.org/10.7554/eLife.02151.002
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Affiliation(s)
- Ariane Briegel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
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13
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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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14
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Pilhofer M, Aistleitner K, Ladinsky MS, König L, Horn M, Jensen GJ. Architecture and host interface of environmental chlamydiae revealed by electron cryotomography. Environ Microbiol 2013; 16:417-29. [PMID: 24118768 PMCID: PMC4949044 DOI: 10.1111/1462-2920.12299] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 09/26/2013] [Indexed: 01/14/2023]
Abstract
Chlamydiae comprise important pathogenic and symbiotic bacteria that alternate between morphologically and physiologically different life stages during their developmental cycle. Using electron cryotomography, we characterize the ultrastructure of the developmental stages of three environmental chlamydiae: Parachlamydia acanthamoebae, Protochlamydia amoebophila and Simkania negevensis. We show that chemical fixation and dehydration alter the cell shape of Parachlamydia and that the crescent body is not a developmental stage, but an artefact of conventional electron microscopy. We further reveal type III secretion systems of environmental chlamydiae at macromolecular resolution and find support for a chlamydial needle-tip protein. Imaging bacteria inside their host cells by cryotomography for the first time, we observe marked differences in inclusion morphology and development as well as host organelle recruitment between the three chlamydial organisms, with Simkania inclusions being tightly enveloped by the host endoplasmic reticulum. The study demonstrates the power of electron cryotomography to reveal structural details of bacteria-host interactions that are not accessible using traditional methods.
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Affiliation(s)
- Martin Pilhofer
- Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA; Howard Hughes Medical Institute, Pasadena, CA, 91125, USA
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Donohoe BS, Ciesielski PN, Vinzant TB. Preservation and preparation of lignocellulosic biomass samples for multi-scale microscopy analysis. Methods Mol Biol 2012; 908:31-47. [PMID: 22843387 DOI: 10.1007/978-1-61779-956-3_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Biomass exhibits structural and chemical complexity over multiple size scales, presenting many challenges to the effective characterization of these materials. The macroscopic nature of plants requires that some form of size reduction, such as dissection and microtomy, be performed to prepare samples and reveal features of interest for any microscopic and nanoscopic analyses. These size reduction techniques, particularly sectioning and microtomy, are complicated by the inherent porosity of plant tissue that often necessitates fixation and embedding in a supporting matrix to preserve structural integrity. The chemical structure of plant cell walls is vastly different from that of the membrane bound organelles and protein macromolecular complexes within the cytosol, which are the focus of many traditional transmission electron microscopy (TEM) investigations in structural biology; thus, staining procedures developed for the latter are not optimized for biomass. While the moisture content of biomass is dramatically reduced compared to the living plant tissue, the residual water is still problematic for microscopic techniques conducted under vacuum such as scanning electron microscopy (SEM). This requires that samples must be carefully dehydrated or that the instrument must be operated in an environmental mode to accommodate the presence of water. In this chapter we highlight tools and techniques that have been successfully used to address these challenges and present procedural details regarding the preparation of biomass samples that enable effective and accurate multi-scale microscopic analysis.
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Affiliation(s)
- Bryon S Donohoe
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, USA.
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Pilhofer M, Ladinsky MS, McDowall AW, Petroni G, Jensen GJ. Microtubules in bacteria: Ancient tubulins build a five-protofilament homolog of the eukaryotic cytoskeleton. PLoS Biol 2011; 9:e1001213. [PMID: 22162949 PMCID: PMC3232192 DOI: 10.1371/journal.pbio.1001213] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 10/25/2011] [Indexed: 01/21/2023] Open
Abstract
Microtubules play crucial roles in cytokinesis, transport, and motility, and are therefore superb targets for anti-cancer drugs. All tubulins evolved from a common ancestor they share with the distantly related bacterial cell division protein FtsZ, but while eukaryotic tubulins evolved into highly conserved microtubule-forming heterodimers, bacterial FtsZ presumably continued to function as single homopolymeric protofilaments as it does today. Microtubules have not previously been found in bacteria, and we lack insight into their evolution from the tubulin/FtsZ ancestor. Using electron cryomicroscopy, here we show that the tubulin homologs BtubA and BtubB form microtubules in bacteria and suggest these be referred to as "bacterial microtubules" (bMTs). bMTs share important features with their eukaryotic counterparts, such as straight protofilaments and similar protofilament interactions. bMTs are composed of only five protofilaments, however, instead of the 13 typical in eukaryotes. These and other results suggest that rather than being derived from modern eukaryotic tubulin, BtubA and BtubB arose from early tubulin intermediates that formed small microtubules. Since we show that bacterial microtubules can be produced in abundance in vitro without chaperones, they should be useful tools for tubulin research and drug screening.
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Affiliation(s)
- Martin Pilhofer
- California Institute of Technology, Pasadena, California, United States of America
- Howard Hughes Medical Institute, Division of Biology, Pasadena, California, United States of America
- * E-mail: (GJJ); (MP)
| | - Mark S. Ladinsky
- California Institute of Technology, Pasadena, California, United States of America
| | - Alasdair W. McDowall
- California Institute of Technology, Pasadena, California, United States of America
| | - Giulio Petroni
- Dipartimento di Biologia, University of Pisa, Pisa, Italy
| | - Grant J. Jensen
- California Institute of Technology, Pasadena, California, United States of America
- Howard Hughes Medical Institute, Division of Biology, Pasadena, California, United States of America
- * E-mail: (GJJ); (MP)
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Abstract
The electron microscope has contributed deep insights into biological structure since its invention nearly 80 years ago. Advances in instrumentation and methodology in recent decades have now enabled electron tomography to become the highest resolution three-dimensional (3D) imaging technique available for unique objects such as cells. Cells can be imaged either plastic-embedded or frozen-hydrated. Then the series of projection images are aligned and back-projected to generate a 3D reconstruction or 'tomogram'. Here, we review how electron tomography has begun to reveal the molecular organization of cells and how the existing and upcoming technologies promise even greater insights into structural cell biology.
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Pierson J, Vos M, McIntosh JR, Peters PJ. Perspectives on electron cryo-tomography of vitreous cryo-sections. JOURNAL OF ELECTRON MICROSCOPY 2011; 60 Suppl 1:S93-100. [PMID: 21844602 PMCID: PMC3156678 DOI: 10.1093/jmicro/dfr014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A major objective of modern structural biology is to appreciate the cellular organization by elucidating the spatial arrangement of macromolecular complexes within a cell. Cryogenic sample preparation, combined with cryo-ultramicrotomy, enables large cells and pieces of biological tissues to be thinned for electron cryo-tomography, which provides a three-dimensional view of the biological sample. There are, however, limitations associated with the technique that must be realized, addressed and overcome for the procedure to become mainstream. Here, we provide perspectives on the continued advancements in cryogenic sample preparation for vitreous cryo-sectioning, image collection and post-image processing that have expanded the attainable information limit within the three-dimensional reconstructions of cells and pieces of biological tissues.
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Affiliation(s)
- Jason Pierson
- Division of Cell Biology II, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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Bouchet-Marquis C, Hoenger A. Cryo-electron tomography on vitrified sections: a critical analysis of benefits and limitations for structural cell biology. Micron 2010; 42:152-62. [PMID: 20675145 DOI: 10.1016/j.micron.2010.07.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 06/29/2010] [Accepted: 07/02/2010] [Indexed: 11/28/2022]
Abstract
The technology to produce cryo-electron tomography on vitrified sections is now a few years old and some specialised labs worldwide have gathered sufficient experience so that it is justified at this point to critically analyse its usefulness for cellular and molecular biology, and make predictions on how the method might develop from here. Remarkably, the production of vitrified sections has been introduced some 40 years ago (the very origin dates back to Christensen, 1971, and McDowall et al., 1983). However, the real breakthrough came between 2002 and 2004 when the groups of Jacques Dubochet and Carmen Manella independently resurrected the vitrified sectioning technology from its sleeping beauty state. And despite its hooks and hurdles a beauty indeed it is! When aiming at the right subjects the results obtained by vitrified sectioning and soon after by cryo-electron tomography exceeded all expectations. Molecular details of intracellular structures were imaged with never before seen clarity in a comparable setting, and the structural preservation of macromolecular assemblies within cells was stunning. However, as with every progress, the great results we now have with vitrified sectioning come at a price. The sectioning procedure and handling of vitrified sections is tricky and requires substantial training and experience. Once frozen, the specimens cannot be manipulated anymore (e.g., by staining or immuno-labelling). The contrast, as with all true cryo-EM approaches, is produced solely by small density differences between cytosol and macromolecular assemblies, membranes, or nucleic acid structures (e.g., ribosomes, nucleosomes, inner nuclear structures, etc.). Vitrified sectioning should not be seen as a competition to the more established plastic-section tomography, but constitutes an excellent complement, filling in high-resolution detail in the overview of cellular architecture. Here we critically compare the benefits and limitations of vitrified sectioning for its application to modern structural cell biology.
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Affiliation(s)
- Cédric Bouchet-Marquis
- The Boulder Laboratory for 3-D Microscopy of Cells, Univ. of Colorado at Boulder, MCD-Biology, Boulder, CO 80309-0347, USA.
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Chen S, McDowall A, Dobro MJ, Briegel A, Ladinsky M, Shi J, Tocheva EI, Beeby M, Pilhofer M, Ding HJ, Li Z, Gan L, Morris DM, Jensen GJ. Electron cryotomography of bacterial cells. J Vis Exp 2010:1943. [PMID: 20461053 PMCID: PMC3149996 DOI: 10.3791/1943] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While much is already known about the basic metabolism of bacterial cells, many fundamental questions are still surprisingly unanswered, including for instance how they generate and maintain specific cell shapes, establish polarity, segregate their genomes, and divide. In order to understand these phenomena, imaging technologies are needed that bridge the resolution gap between fluorescence light microscopy and higher-resolution methods such as X-ray crystallography and NMR spectroscopy. Electron cryotomography (ECT) is an emerging technology that does just this, allowing the ultrastructure of cells to be visualized in a near-native state, in three dimensions (3D), with "macromolecular" resolution (~4nm).1, 2 In ECT, cells are imaged in a vitreous, "frozen-hydrated" state in a cryo transmission electron microscope (cryoTEM) at low temperature (< -180°C). For slender cells (up to ~500 nm in thickness3), intact cells are plunge-frozen within media across EM grids in cryogens such as ethane or ethane/propane mixtures. Thicker cells and biofilms can also be imaged in a vitreous state by first "high-pressure freezing" and then, "cryo-sectioning" them. A series of two-dimensional projection images are then collected through the sample as it is incrementally tilted along one or two axes. A three-dimensional reconstruction, or "tomogram" can then be calculated from the images. While ECT requires expensive instrumentation, in recent years, it has been used in a few labs to reveal the structures of various external appendages, the structures of different cell envelopes, the positions and structures of cytoskeletal filaments, and the locations and architectures of large macromolecular assemblies such as flagellar motors, internal compartments and chemoreceptor arrays.1, 2 In this video article we illustrate how to image cells with ECT, including the processes of sample preparation, data collection, tomogram reconstruction, and interpretation of the results through segmentation and in some cases correlation with light microscopy.
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Affiliation(s)
- Songye Chen
- Division of Biology, California Institute of Technology - Caltech.
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Tucker JD, Siebert CA, Escalante M, Adams PG, Olsen JD, Otto C, Stokes DL, Hunter CN. Membrane invagination in Rhodobacter sphaeroides is initiated at curved regions of the cytoplasmic membrane, then forms both budded and fully detached spherical vesicles. Mol Microbiol 2010; 76:833-47. [PMID: 20444085 DOI: 10.1111/j.1365-2958.2010.07153.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The purple phototrophic bacteria synthesize an extensive system of intracytoplasmic membranes (ICM) in order to increase the surface area for absorbing and utilizing solar energy. Rhodobacter sphaeroides cells contain curved membrane invaginations. In order to study the biogenesis of ICM in this bacterium mature (ICM) and precursor (upper pigmented band - UPB) membranes were purified and compared at the single membrane level using electron, atomic force and fluorescence microscopy, revealing fundamental differences in their morphology, protein organization and function. Cryo-electron tomography demonstrates the complexity of the ICM of Rba. sphaeroides. Some ICM vesicles have no connection with other structures, others are found nearer to the cytoplasmic membrane (CM), often forming interconnected structures that retain a connection to the CM, and possibly having access to the periplasmic space. Near-spherical single invaginations are also observed, still attached to the CM by a 'neck'. Small indents of the CM are also seen, which are proposed to give rise to the UPB precursor membranes upon cell disruption. 'Free-living' ICM vesicles, which possess all the machinery for converting light energy into ATP, can be regarded as bacterial membrane organelles.
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Affiliation(s)
- Jaimey D Tucker
- Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Firth Court, Sheffield S10 2TN, UK
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Daum B, Nicastro D, Austin J, McIntosh JR, Kühlbrandt W. Arrangement of photosystem II and ATP synthase in chloroplast membranes of spinach and pea. THE PLANT CELL 2010; 22:1299-312. [PMID: 20388855 PMCID: PMC2879734 DOI: 10.1105/tpc.109.071431] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 03/03/2010] [Accepted: 03/29/2010] [Indexed: 05/17/2023]
Abstract
We used cryoelectron tomography to reveal the arrangements of photosystem II (PSII) and ATP synthase in vitreous sections of intact chloroplasts and plunge-frozen suspensions of isolated thylakoid membranes. We found that stroma and grana thylakoids are connected at the grana margins by staggered lamellar membrane protrusions. The stacking repeat of grana membranes in frozen-hydrated chloroplasts is 15.7 nm, with a 4.5-nm lumenal space and a 3.2-nm distance between the flat stromal surfaces. The chloroplast ATP synthase is confined to minimally curved regions at the grana end membranes and stroma lamellae, where it covers 20% of the surface area. In total, 85% of the ATP synthases are monomers and the remainder form random assemblies of two or more copies. Supercomplexes of PSII and light-harvesting complex II (LHCII) occasionally form ordered arrays in appressed grana thylakoids, whereas this order is lost in destacked membranes. In the ordered arrays, each membrane on either side of the stromal gap contains a two-dimensional crystal of supercomplexes, with the two lattices arranged such that PSII cores, LHCII trimers, and minor LHCs each face a complex of the same kind in the opposite membrane. Grana formation is likely to result from electrostatic interactions between these complexes across the stromal gap.
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Affiliation(s)
- Bertram Daum
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Daniela Nicastro
- Biology Department, Brandeis University, Waltham, Massachusetts 02453
| | - Jotham Austin
- Advanced Electron Microscopy Facility, University of Chicago, Chicago, Illinois 60637
| | | | - Werner Kühlbrandt
- Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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Kirmse R, Bouchet-Marquis C, Page C, Hoenger A. Three-dimensional cryo-electron microscopy on intermediate filaments. Methods Cell Biol 2010; 96:565-89. [PMID: 20869538 DOI: 10.1016/s0091-679x(10)96023-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Together with microtubules and actin filaments (F-actin), intermediate filaments (IFs) form the cytoskeleton of metazoan cells. However, unlike the other two entities that are extremely conserved, IFs are much more diverse and are grouped into five different families. In contrast to microtubules and F-actin, IFs do not exhibit a polarity, which may be the reason that no molecular motors travel along them. The molecular structure of IFs is less well resolved than that of the other cytoskeletal systems. This is partially due to their functional variability, tissue-specific expression, and their intrinsic structural properties. IFs are composed mostly of relatively smooth protofibrils formed by antiparallel arranged α-helical coiled-coil bundles flanked by small globular domains at either end. These features make them difficult to study by various electron microscopy methods or atomic force microscopy (AFM). Furthermore, the elongated shape of monomeric or dimeric IF units interferes with the formation of highly ordered three-dimensional (3-D) crystals suitable for atomic resolution crystallography. So far, most of the data we currently have on IF macromolecular structures come from electron microscopy of negatively stained samples, and fragmented α-helical coiled-coil units solved by X-ray diffraction. In addition, AFM allows the observation of the dynamic states of IFs in solution and delivers a new view into the assembly properties of IFs. Here, we discuss the applicability of cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) for the field. Both methods are strongly related and have only recently been applied to IFs. However, cryo-EM revealed distinct new features within IFs that have not been seen before, and cryo-ET adds a 3-D view of IFs revealing the path and number of protofilaments within the various IF assemblies.
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Affiliation(s)
- Robert Kirmse
- The Boulder Laboratory for 3-D Microscopy of Cells, University of Colorado at Boulder, Boulder, Colorado 80309-0347, USA
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Abstract
Some bacteria are amongst the most important model organisms for biology and medicine. Here we review how electron microscopes have been used to image bacterial cells, summarizing the technical details of the various methods, the advantages and disadvantages of each, and the major biological insights that have been obtained. Three specific example structures, "mesosomes," "cytoskeletal filaments," and "nucleoid," are used to illustrate how methodological advances have shaped our understanding of bacterial ultrastructure. Methods that involve dehydration and metal stains are widely practiced and have revealed many ultrastructural features, but they can generate misleading artifacts and have failed to preserve important structures such as the bacterial cytoskeleton. The invention of cryo-electron microscopy, which allows bacterial cells to be imaged in a frozen-hydrated, near-native state without the need for dehydration and stains, has now led to important new insights. Efforts to identify structures and localize specific proteins in cryo-EM images are summarized.
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Hoenger A, McIntosh JR. Probing the macromolecular organization of cells by electron tomography. Curr Opin Cell Biol 2009; 21:89-96. [PMID: 19185480 DOI: 10.1016/j.ceb.2008.12.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 11/24/2022]
Abstract
A major goal in cell biology is to understand the functional organization of macromolecular complexes in vivo. Electron microscopy is helping cell biologists to achieve this goal, thanks to its ability to resolve structural details in the nanometer range. While issues related to specimen preparation, imaging, and image interpretation make this approach to cell architecture difficult, recent improvements in methods, equipment, and software have facilitated the study of both important macromolecular complexes and comparatively large volumes from cellular specimens. Here, we describe recent progress in electron microscopy of cells and the ways in which the relevant methodologies are helping to elucidate cell architecture.
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Affiliation(s)
- Andreas Hoenger
- Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells and Molecules, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
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Millen JI, Pierson J, Kvam E, Olsen LJ, Goldfarb DS. The luminal N-terminus of yeast Nvj1 is an inner nuclear membrane anchor. Traffic 2008; 9:1653-64. [PMID: 18694438 DOI: 10.1111/j.1600-0854.2008.00789.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The endoplasmic reticulum (ER) in Saccharomyces cerevisiae is largely divided between perinuclear and cortical compartments. Yeast Nvj1 localizes exclusively to small patches on the perinuclear ER where it interacts with Vac8 in the vacuole membrane to form nucleus-vacuole (NV) junctions. Three regions of Nvj1 mediate the biogenesis of NV junctions. A membrane-spanning domain targets the protein to the ER. The C-terminus binds Vac8 in the vacuole membrane, which induces the clustering of both proteins into NV junctions. The luminal N-terminus is required for strict perinuclear localization. Three-dimensional cryo-electron tomography reveals that Nvj1 clamps the separation between the two nuclear membranes to half the width of bulk nuclear envelope. The N-terminus contains a hydrophobic sequence bracketed by basic residues that resembles outer mitochondrial membrane signal-anchors. The hydrophobic sequence can be scrambled or reversed without affecting function. Mutations that reduce the hydrophobicity of the core sequence or affect the distribution of basic residues cause mislocalization to the cortical ER. We conclude that the N-terminus of Nvj1 is a retention sequence that bridges the perinuclear lumen and inserts into the inner nuclear membrane.
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Affiliation(s)
- Jonathan I Millen
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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Schwartz CL, Sarbash VI, Ataullakhanov FI, McIntosh JR, Nicastro D. Cryo-fluorescence microscopy facilitates correlations between light and cryo-electron microscopy and reduces the rate of photobleaching. J Microsc 2007; 227:98-109. [PMID: 17845705 DOI: 10.1111/j.1365-2818.2007.01794.x] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence light microscopy (LM) has many advantages for the study of cell organization. Specimen preparation is easy and relatively inexpensive, and the use of appropriate tags gives scientists the ability to visualize specific proteins of interest. LM is, however, limited in resolution, so when one is interested in ultrastructure, one must turn to electron microscopy (EM), even though this method presents problems of its own. The biggest difficulty with cellular EM is its limited utility in localizing macromolecules of interest while retaining good structural preservation. We have built a cryo-light microscope stage that allows us to generate LM images of vitreous samples prepared for cryo-EM. Correlative LM and EM allows one to find areas of particular interest by using fluorescent proteins or vital dyes as markers within vitrified samples. Once located, the sample can be placed in the EM for further study at higher resolution. An additional benefit of the cryo-LM stage is that photobleaching is slower at cryogenic temperatures (-140 degrees C) than at room temperature.
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Affiliation(s)
- Cindi L Schwartz
- Boulder Laboratory for 3D Electron Microscopy of Cells, University of Colorado, Department of Molecular, Cellular, and Developmental Biology, Boulder, CO, USA
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Midgley PA, Ward EPW, Hungría AB, Thomas JM. Nanotomography in the chemical, biological and materials sciences. Chem Soc Rev 2007; 36:1477-94. [PMID: 17660880 DOI: 10.1039/b701569k] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nanotomography is a technique of growing importance in the investigation of the shape, size, distribution and elemental composition of a wide variety of materials that are of central interest to investigators in the physical and biological sciences. Nanospatial factors often hold the key to a deeper understanding of the properties of matter at the nanoscale level. With recent advances in tomography, it is possible to achieve experimental resolution in the nanometre range, and to determine with elemental specificity the three-dimensional distribution of materials. This critical review deals principally with electron tomography, but it also outlines the power and future potential of transmission X-ray tomography, and alludes to other related techniques.
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Affiliation(s)
- Paul A Midgley
- Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge, UK CB2 3QZ.
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