251
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Danev R, Yanagisawa H, Kikkawa M. Cryo-Electron Microscopy Methodology: Current Aspects and Future Directions. Trends Biochem Sci 2019; 44:837-848. [PMID: 31078399 DOI: 10.1016/j.tibs.2019.04.008] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 01/01/2023]
Abstract
Cryo-electron microscopy (cryo-EM) has emerged as a powerful structure determination technique. Its most prolific branch is single particle analysis (SPA), a method being used in a growing number of laboratories worldwide to determine high-resolution protein structures. Cryo-electron tomography (cryo-ET) is another powerful approach that enables visualization of protein complexes in their native cellular environment. Despite the wide-ranging success of cryo-EM, there are many methodological aspects that could be improved. Those include sample preparation, sample screening, data acquisition, image processing, and structure validation. Future developments will increase the reliability and throughput of the technique and reduce the cost and skill level barrier for its adoption.
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Affiliation(s)
- Radostin Danev
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Haruaki Yanagisawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Kikkawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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252
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Weiner A, Enninga J. The Pathogen–Host Interface in Three Dimensions: Correlative FIB/SEM Applications. Trends Microbiol 2019; 27:426-439. [DOI: 10.1016/j.tim.2018.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/17/2022]
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253
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Markova EA, Zanetti G. Visualizing membrane trafficking through the electron microscope: cryo-tomography of coat complexes. Acta Crystallogr D Struct Biol 2019; 75:467-474. [PMID: 31063149 PMCID: PMC6503763 DOI: 10.1107/s2059798319005011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/12/2019] [Indexed: 11/23/2022] Open
Abstract
Coat proteins mediate vesicular transport between intracellular compartments, which is essential for the distribution of molecules within the eukaryotic cell. The global arrangement of coat proteins on the membrane is key to their function, and cryo-electron tomography and subtomogram averaging have been used to study membrane-bound coat proteins, providing crucial structural insight. This review outlines a workflow for the structural elucidation of coat proteins, incorporating recent developments in the collection and processing of cryo-electron tomography data. Recent work on coat protein I, coat protein II and retromer performed on in vitro reconstitutions or in situ is summarized. These studies have answered long-standing questions regarding the mechanisms of membrane binding, polymerization and assembly regulation of coat proteins.
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Affiliation(s)
- Evgenia A. Markova
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
| | - Giulia Zanetti
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
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254
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Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Curr Opin Struct Biol 2019; 58:1-9. [PMID: 31005754 DOI: 10.1016/j.sbi.2019.03.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 01/03/2023]
Abstract
Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein's location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA.
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Affiliation(s)
- Florian Km Schur
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria.
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255
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Kizilyaprak C, Stierhof YD, Humbel BM. Volume microscopy in biology: FIB-SEM tomography. Tissue Cell 2019; 57:123-128. [DOI: 10.1016/j.tice.2018.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/30/2018] [Accepted: 09/20/2018] [Indexed: 01/10/2023]
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256
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Ognjenović J, Grisshammer R, Subramaniam S. Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies. Annu Rev Biomed Eng 2019; 21:395-415. [PMID: 30892930 DOI: 10.1146/annurev-bioeng-060418-052453] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In recent years, cryo electron microscopy (cryo-EM) technology has been transformed with the development of better instrumentation, direct electron detectors, improved methods for specimen preparation, and improved software for data analysis. Analyses using single-particle cryo-EM methods have enabled determination of structures of proteins with sizes smaller than 100 kDa and resolutions of ∼2 Å in some cases. The use of electron tomography combined with subvolume averaging is beginning to allow the visualization of macromolecular complexes in their native environment in unprecedented detail. As a result of these advances, solutions to many intractable challenges in structural and cell biology, such as analysis of highly dynamic soluble and membrane-embedded protein complexes or partially ordered protein aggregates, are now within reach. Recent reports of structural studies of G protein-coupled receptors, spliceosomes, and fibrillar specimens illustrate the progress that has been made using cryo-EM methods, and are the main focus of this review.
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Affiliation(s)
- Jana Ognjenović
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20814, USA; ,
| | - Reinhard Grisshammer
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20814, USA; ,
| | - Sriram Subramaniam
- University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada;
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257
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Voigt F, Zhang H, Cui XA, Triebold D, Liu AX, Eglinger J, Lee ES, Chao JA, Palazzo AF. Single-Molecule Quantification of Translation-Dependent Association of mRNAs with the Endoplasmic Reticulum. Cell Rep 2019; 21:3740-3753. [PMID: 29281824 DOI: 10.1016/j.celrep.2017.12.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 09/29/2017] [Accepted: 12/04/2017] [Indexed: 10/25/2022] Open
Abstract
It is well established that mRNAs encoding secretory or membrane-bound proteins are translated on the surface of the endoplasmic reticulum (ER). The extent to which mRNAs that encode cytosolic proteins associate with the ER, however, remains controversial. To address this question, we quantified the number of cytosolic protein-encoding mRNAs that co-localize with the ER using single-molecule RNA imaging in fixed and living cells. We found that a small but significant number of mRNAs that encode cytosolic proteins associate with the ER and show that this interaction is translation dependent. Furthermore, we demonstrate that cytosolic protein-encoding transcripts can remain on the ER with dwell times consistent with multiple rounds of translation and have higher ribosome occupancies than transcripts translated in the cytosol. These results advance our understanding of the diversity and dynamics of localized translation on the ER.
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Affiliation(s)
- Franka Voigt
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Hui Zhang
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada
| | - Xianying A Cui
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada
| | - Désirée Triebold
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland
| | - Ai Xin Liu
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada
| | - Jan Eglinger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Eliza S Lee
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
| | - Alexander F Palazzo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, MSB Room 5336, Toronto, ON M5S 1A8, Canada.
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258
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Xu M, Singla J, Tocheva EI, Chang YW, Stevens RC, Jensen GJ, Alber F. De Novo Structural Pattern Mining in Cellular Electron Cryotomograms. Structure 2019; 27:679-691.e14. [PMID: 30744995 DOI: 10.1016/j.str.2019.01.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/16/2022]
Abstract
Electron cryotomography enables 3D visualization of cells in a near-native state at molecular resolution. The produced cellular tomograms contain detailed information about a plethora of macromolecular complexes, their structures, abundances, and specific spatial locations in the cell. However, extracting this information in a systematic way is very challenging, and current methods usually rely on individual templates of known structures. Here, we propose a framework called "Multi-Pattern Pursuit" for de novo discovery of different complexes from highly heterogeneous sets of particles extracted from entire cellular tomograms without using information of known structures. These initially detected structures can then serve as input for more targeted refinement efforts. Our tests on simulated and experimental tomograms show that our automated method is a promising tool for supporting large-scale template-free visual proteomics analysis.
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Affiliation(s)
- Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Jitin Singla
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Elitza I Tocheva
- Department of Microbiology and Immunology, Life Sciences Institute, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raymond C Stevens
- Department of Biological Sciences and Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA
| | - Frank Alber
- Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA; Quantitative and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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259
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Tuijtel MW, Koster AJ, Jakobs S, Faas FGA, Sharp TH. Correlative cryo super-resolution light and electron microscopy on mammalian cells using fluorescent proteins. Sci Rep 2019; 9:1369. [PMID: 30718653 PMCID: PMC6362030 DOI: 10.1038/s41598-018-37728-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/12/2018] [Indexed: 11/22/2022] Open
Abstract
Sample fixation by vitrification is critical for the optimal structural preservation of biomolecules and subsequent high-resolution imaging by cryo-correlative light and electron microscopy (cryoCLEM). There is a large resolution gap between cryo fluorescence microscopy (cryoFLM), ~400-nm, and the sub-nanometre resolution achievable with cryo-electron microscopy (cryoEM), which hinders interpretation of cryoCLEM data. Here, we present a general approach to increase the resolution of cryoFLM using cryo-super-resolution (cryoSR) microscopy that is compatible with successive cryoEM investigation in the same region. We determined imaging parameters to avoid devitrification of the cryosamples without the necessity for cryoprotectants. Next, we examined the applicability of various fluorescent proteins (FPs) for single-molecule localisation cryoSR microscopy and found that all investigated FPs display reversible photoswitchable behaviour, and demonstrated cryoSR on lipid nanotubes labelled with rsEGFP2 and rsFastLime. Finally, we performed SR-cryoCLEM on mammalian cells expressing microtubule-associated protein-2 fused to rsEGFP2 and performed 3D cryo-electron tomography on the localised areas. The method we describe exclusively uses commercially available equipment to achieve a localisation precision of 30-nm. Furthermore, all investigated FPs displayed behaviour compatible with cryoSR microscopy, making this technique broadly available without requiring specialised equipment and will improve the applicability of this emerging technique for cellular and structural biology.
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Affiliation(s)
- Maarten W Tuijtel
- Section Electron Microscopy, Dept. of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Abraham J Koster
- Section Electron Microscopy, Dept. of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
- NeCEN, Gorlaeus Laboratories, Leiden University, 2333 CC, Leiden, The Netherlands
| | - Stefan Jakobs
- Max Planck Institute for Biophysical Chemistry, Dept. of NanoBiophotonics and University Medical Center of Göttingen, Dept. of Neurology, Am Faßberg 11, 37077, Göttingen, Germany
| | - Frank G A Faas
- Section Electron Microscopy, Dept. of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
| | - Thomas H Sharp
- Section Electron Microscopy, Dept. of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.
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260
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Ader NR, Hoffmann PC, Ganeva I, Borgeaud AC, Wang C, Youle RJ, Kukulski W. Molecular and topological reorganizations in mitochondrial architecture interplay during Bax-mediated steps of apoptosis. eLife 2019; 8:40712. [PMID: 30714902 PMCID: PMC6361589 DOI: 10.7554/elife.40712] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/22/2019] [Indexed: 12/25/2022] Open
Abstract
During apoptosis, Bcl-2 proteins such as Bax and Bak mediate the release of pro-apoptotic proteins from the mitochondria by clustering on the outer mitochondrial membrane and thereby permeabilizing it. However, it remains unclear how outer membrane openings form. Here, we combined different correlative microscopy and electron cryo-tomography approaches to visualize the effects of Bax activity on mitochondria in human cells. Our data show that Bax clusters localize near outer membrane ruptures of highly variable size. Bax clusters contain structural elements suggesting a higher order organization of their components. Furthermore, unfolding of inner membrane cristae is coupled to changes in the supramolecular assembly of ATP synthases, particularly pronounced at membrane segments exposed to the cytosol by ruptures. Based on our results, we propose a comprehensive model in which molecular reorganizations of the inner membrane and sequestration of outer membrane components into Bax clusters interplay in the formation of outer membrane ruptures. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
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Affiliation(s)
- Nicholas R Ader
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Iva Ganeva
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Alicia C Borgeaud
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Chunxin Wang
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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261
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Collection of Continuous Rotation MicroED Data from Ion Beam-Milled Crystals of Any Size. Structure 2019; 27:545-548.e2. [PMID: 30661853 DOI: 10.1016/j.str.2018.12.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/19/2018] [Accepted: 12/05/2018] [Indexed: 11/22/2022]
Abstract
Microcrystal electron diffraction (MicroED) allows for macromolecular structure solution from nanocrystals. To create crystals of suitable size for MicroED data collection, sample preparation typically involves sonication or pipetting a slurry of crystals from a crystallization drop. The resultant crystal fragments are fragile and the quality of the data that can be obtained from them is sensitive to subsequent sample preparation for cryoelectron microscopy as interactions in the water-air interface can damage crystals during blotting. Here, we demonstrate the use of a focused ion beam to generate lamellae of macromolecular protein crystals for continuous rotation MicroED that are of ideal thickness, easy to locate, and require no blotting optimization. In this manner, crystals of nearly any size may be scooped and milled to desired dimensions prior to data collection, thus streamlining the methodology for sample preparation for MicroED.
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262
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Weber MS, Wojtynek M, Medalia O. Cellular and Structural Studies of Eukaryotic Cells by Cryo-Electron Tomography. Cells 2019; 8:E57. [PMID: 30654455 PMCID: PMC6356268 DOI: 10.3390/cells8010057] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 11/23/2022] Open
Abstract
The architecture of protein assemblies and their remodeling during physiological processes is fundamental to cells. Therefore, providing high-resolution snapshots of macromolecular complexes in their native environment is of major importance for understanding the molecular biology of the cell. Cellular structural biology by means of cryo-electron tomography (cryo-ET) offers unique insights into cellular processes at an unprecedented resolution. Recent technological advances have enabled the detection of single impinging electrons and improved the contrast of electron microscopic imaging, thereby significantly increasing the sensitivity and resolution. Moreover, various sample preparation approaches have paved the way to observe every part of a eukaryotic cell, and even multicellular specimens, under the electron beam. Imaging of macromolecular machineries at high resolution directly within their native environment is thereby becoming reality. In this review, we discuss several sample preparation and labeling techniques that allow the visualization and identification of macromolecular assemblies in situ, and demonstrate how these methods have been used to study eukaryotic cellular landscapes.
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Affiliation(s)
- Miriam Sarah Weber
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland.
| | - Matthias Wojtynek
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland.
- Department of Biology, Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland.
| | - Ohad Medalia
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland.
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84120, Israel.
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263
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Lopez-Garrido J, Ojkic N, Khanna K, Wagner FR, Villa E, Endres RG, Pogliano K. Chromosome Translocation Inflates Bacillus Forespores and Impacts Cellular Morphology. Cell 2019; 172:758-770.e14. [PMID: 29425492 DOI: 10.1016/j.cell.2018.01.027] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/16/2017] [Accepted: 01/18/2018] [Indexed: 01/14/2023]
Abstract
The means by which the physicochemical properties of different cellular components together determine bacterial cell shape remain poorly understood. Here, we investigate a programmed cell-shape change during Bacillus subtilis sporulation, when a rod-shaped vegetative cell is transformed to an ovoid spore. Asymmetric cell division generates a bigger mother cell and a smaller, hemispherical forespore. The septum traps the forespore chromosome, which is translocated to the forespore by SpoIIIE. Simultaneously, forespore size increases as it is reshaped into an ovoid. Using genetics, timelapse microscopy, cryo-electron tomography, and mathematical modeling, we demonstrate that forespore growth relies on membrane synthesis and SpoIIIE-mediated chromosome translocation, but not on peptidoglycan or protein synthesis. Our data suggest that the hydrated nucleoid swells and inflates the forespore, displacing ribosomes to the cell periphery, stretching septal peptidoglycan, and reshaping the forespore. Our results illustrate how simple biophysical interactions between core cellular components contribute to cellular morphology.
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Affiliation(s)
- Javier Lopez-Garrido
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nikola Ojkic
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; Centre for Integrative Systems Biology and Bioinformatics, London SW7 2AZ, UK
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Felix R Wagner
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert G Endres
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; Centre for Integrative Systems Biology and Bioinformatics, London SW7 2AZ, UK.
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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264
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High Rac1 activity is functionally translated into cytosolic structures with unique nanoscale cytoskeletal architecture. Proc Natl Acad Sci U S A 2019; 116:1267-1272. [PMID: 30630946 DOI: 10.1073/pnas.1808830116] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rac1 activation is at the core of signaling pathways regulating polarized cell migration. So far, it has not been possible to directly explore the structural changes triggered by Rac1 activation at the molecular level. Here, through a multiscale imaging workflow that combines biosensor imaging of Rac1 dynamics with electron cryotomography, we identified, within the crowded environment of eukaryotic cells, a unique nanoscale architecture of a flexible, signal-dependent actin structure. In cell regions with high Rac1 activity, we found a structural regime that spans from the ventral membrane up to a height of ∼60 nm above that membrane, composed of directionally unaligned, densely packed actin filaments, most shorter than 150 nm. This unique Rac1-induced morphology is markedly different from the dendritic network architecture in which relatively short filaments emanate from existing, longer actin filaments. These Rac1-mediated scaffold assemblies are devoid of large macromolecules such as ribosomes or other filament types, which are abundant at the periphery and within the remainder of the imaged volumes. Cessation of Rac1 activity induces a complete and rapid structural transition, leading to the absence of detectable remnants of such structures within 150 s, providing direct structural evidence for rapid actin filament network turnover induced by GTPase signaling events. It is tempting to speculate that this highly dynamical nanoscaffold system is sensitive to local spatial cues, thus serving to support the formation of more complex actin filament architectures-such as those mandated by epithelial-mesenchymal transition, for example-or resetting the region by completely dissipating.
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265
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266
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Beckers M, Jakobi AJ, Sachse C. Thresholding of cryo-EM density maps by false discovery rate control. IUCRJ 2019; 6:18-33. [PMID: 30713700 PMCID: PMC6327189 DOI: 10.1107/s2052252518014434] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/12/2018] [Indexed: 05/31/2023]
Abstract
Cryo-EM now commonly generates close-to-atomic resolution as well as intermediate resolution maps from macromolecules observed in isolation and in situ. Interpreting these maps remains a challenging task owing to poor signal in the highest resolution shells and the necessity to select a threshold for density analysis. In order to facilitate this process, a statistical framework for the generation of confidence maps by multiple hypothesis testing and false discovery rate (FDR) control has been developed. In this way, three-dimensional confidence maps contain signal separated from background noise in the form of local detection rates of EM density values. It is demonstrated that confidence maps and FDR-based thresholding can be used for the interpretation of near-atomic resolution single-particle structures as well as lower resolution maps determined by subtomogram averaging. Confidence maps represent a conservative way of interpreting molecular structures owing to minimized noise. At the same time they provide a detection error with respect to background noise, which is associated with the density and is particularly beneficial for the interpretation of weaker cryo-EM densities in cases of conformational flexibility and lower occupancy of bound molecules and ions in the structure.
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Affiliation(s)
- Maximilian Beckers
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Faculty of Biosciences, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Arjen J. Jakobi
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Hamburg Unit c/o DESY, Notkestrasse 85, 22607 Hamburg, Germany
- The Hamburg Centre for Ultrafast Imaging (CUI), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, 52425 Jülich, Germany
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267
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Adivarahan S, Zenklusen D. Lessons from (pre-)mRNA Imaging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:247-284. [DOI: 10.1007/978-3-030-31434-7_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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268
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Lang S, Nguyen D, Pfeffer S, Förster F, Helms V, Zimmermann R. Functions and Mechanisms of the Human Ribosome-Translocon Complex. Subcell Biochem 2019; 93:83-141. [PMID: 31939150 DOI: 10.1007/978-3-030-28151-9_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane of the endoplasmic reticulum (ER) in human cells harbors the protein translocon, which facilitates membrane insertion and translocation of almost every newly synthesized polypeptide targeted to organelles of the secretory pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins, which are associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, Sec61 channel opening and closing, and modification of precursor polypeptides in transit through the Sec61 complex. Recently, cryoelectron tomography of translocons in native ER membranes has given unprecedented insights into the architecture and dynamics of the native, ribosome-associated translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion or translocation of newly synthesized polypeptides as well as the possible roles of the Sec61 channel as a passive ER calcium leak channel and regulator of ATP/ADP exchange between cytosol and ER.
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Affiliation(s)
- Sven Lang
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany.
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- ZMBH, 69120, Heidelberg, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Richard Zimmermann
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany
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269
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Structural studies of the spliceosome: past, present and future perspectives. Biochem Soc Trans 2018; 46:1407-1422. [PMID: 30420411 DOI: 10.1042/bst20170240] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/18/2022]
Abstract
The spliceosome is a multi-subunit RNA-protein complex involved in the removal of non-coding segments (introns) from between the coding regions (exons) in precursors of messenger RNAs (pre-mRNAs). Intron removal proceeds via two transesterification reactions, occurring between conserved sequences at intron-exon junctions. A tightly regulated, hierarchical assembly with a multitude of structural and compositional rearrangements posed a great challenge for structural studies of the spliceosome. Over the years, X-ray crystallography dominated the field, providing valuable high-resolution structural information that was mostly limited to individual proteins and smaller sub-complexes. Recent developments in the field of cryo-electron microscopy allowed the visualisation of fully assembled yeast and human spliceosomes, providing unprecedented insights into substrate recognition, catalysis, and active site formation. This has advanced our mechanistic understanding of pre-mRNA splicing enormously.
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270
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Enzymatic complexes across scales. Essays Biochem 2018; 62:501-514. [PMID: 30315098 PMCID: PMC6204551 DOI: 10.1042/ebc20180008] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/12/2018] [Accepted: 09/13/2018] [Indexed: 02/07/2023]
Abstract
An unprecedented opportunity to integrate ~100 years of meticulous in vitro biomolecular research is currently provided in the light of recent advances in methods to visualize closer-to-native architectures of biomolecular machines, and metabolic enzymes in particular. Traditional views of enzymes, namely biomolecular machines, only partially explain their role, organization and kinetics in the cellular milieu. Enzymes self- or hetero-associate, form fibers, may bind to membranes or cytoskeletal elements, have regulatory roles, associate into higher order assemblies (metabolons) or even actively participate in phase-separated membraneless organelles, and all the above in a transient, temporal and spatial manner in response to environmental changes or structural/functional changes of their assemblies. Here, we focus on traditional and emerging concepts in cellular biochemistry and discuss new opportunities in bridging structural, molecular and cellular analyses for metabolic pathways, accumulated over the years, highlighting functional aspects of enzymatic complexes discussed across different levels of spatial resolution.
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271
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The Structural and Functional Organization of Ribosomal Compartment in the Cell: A Mystery or a Reality? Trends Biochem Sci 2018; 43:938-950. [PMID: 30337135 DOI: 10.1016/j.tibs.2018.09.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 11/23/2022]
Abstract
Great progress has been made toward solving the atomic structure of the ribosome, which is the main biosynthetic machine in cells, but we still do not have a full picture of exactly how cellular ribosomes function. Based on the analysis of crystallographic and electron microscopy data, we propose a basic model of the structural organization of ribosomes into a compartment. This compartment is regularly formed by arrays of ribosomal tetramers made up of two dimers that are actually facing in opposite directions. The compartment functions as the main 'factory' for the production of cellular proteins. The model is consistent with the existing biochemical and genetic data. We also consider the functional connections of such a compartment with cellular transcription and ribosomal biogenesis.
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272
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Pfeffer S, Mahamid J. Unravelling molecular complexity in structural cell biology. Curr Opin Struct Biol 2018; 52:111-118. [PMID: 30339965 DOI: 10.1016/j.sbi.2018.08.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/18/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Recent technological breakthroughs propelled electron microscopy of frozen hydrated specimens (cryo-EM) followed by single-particle analysis (SPA) to become a widely applied approach for obtaining near-atomic resolution structures of purified macromolecules. In parallel, ongoing developments on sample preparation are increasingly successful in bringing molecular views into cell biology. Cryo-electron tomography (cryo-ET) has so far served as the main imaging modality employed in these efforts towards obtaining three-dimensional (3D) volumes of heterogeneous molecular assemblies. We review the state-of-the-art in cryo-ET and computational processing and describe the current opportunities and frontiers for in-cell applications.
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Affiliation(s)
- Stefan Pfeffer
- Centre for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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273
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Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S, Ramakrishnan V, Hegde RS. ZNF598 Is a Quality Control Sensor of Collided Ribosomes. Mol Cell 2018; 72:469-481.e7. [PMID: 30293783 PMCID: PMC6224477 DOI: 10.1016/j.molcel.2018.08.037] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 08/07/2018] [Accepted: 08/22/2018] [Indexed: 01/30/2023]
Abstract
Aberrantly slow translation elicits quality control pathways initiated by the ubiquitin ligase ZNF598. How ZNF598 discriminates physiologic from pathologic translation complexes and ubiquitinates stalled ribosomes selectively is unclear. Here, we find that the minimal unit engaged by ZNF598 is the collided di-ribosome, a molecular species that arises when a trailing ribosome encounters a slower leading ribosome. The collided di-ribosome structure reveals an extensive 40S-40S interface in which the ubiquitination targets of ZNF598 reside. The paucity of 60S interactions allows for different ribosome rotation states, explaining why ZNF598 recognition is indifferent to how the leading ribosome has stalled. The use of ribosome collisions as a proxy for stalling allows the degree of tolerable slowdown to be tuned by the initiation rate on that mRNA; hence, the threshold for triggering quality control is substrate specific. These findings illustrate how higher-order ribosome architecture can be exploited by cellular factors to monitor translation status. ZNF598 is a direct sensor of ribosome collisions incurred by many unrelated causes The minimal target recognized and ubiquitinated by ZNF598 is a collided di-ribosome Collided di-ribosome structure shows that ZNF598 ubiquitin sites are near the interface Collisions are required to terminally arrest translation in ZNF598-dependent manner
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Affiliation(s)
| | | | - Zhewang Lin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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274
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Hanske J, Sadian Y, Müller CW. The cryo-EM resolution revolution and transcription complexes. Curr Opin Struct Biol 2018; 52:8-15. [PMID: 30015202 PMCID: PMC6302067 DOI: 10.1016/j.sbi.2018.07.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/25/2018] [Accepted: 07/02/2018] [Indexed: 01/22/2023]
Abstract
Direct electron detector technology combined with improved imaging processing procedures has dramatically increased the resolution that can be obtained by single-particle cryo-electron microscopy and cryo-electron tomography. These developments-often referred to as the `resolution revolution' in cryo-EM-have had a profound impact on the structural biology of transcription as they allow the determination of atomic or near-atomic resolution structures of very large, flexible and often transient transcription complexes that in many cases had resisted crystal structure determination for decades. In this review, we will discuss recent advances and breakthroughs in the structural biology of transcription complexes enabled by the revolution in cryo-electron microscopy with particular focus on eukaryotic RNA polymerases and their pre-initiation complexes, but also chromatin remodelers and epigenetic regulators.
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Affiliation(s)
- Jonas Hanske
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Yashar Sadian
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christoph W Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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275
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Celli F, Petitalot A, Samson C, Theillet FX, Zinn-Justin S. 1H, 13C and 15N backbone resonance assignment of the lamin C-terminal region specific to prelamin A. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:225-229. [PMID: 29582385 DOI: 10.1007/s12104-018-9813-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/20/2018] [Indexed: 06/08/2023]
Abstract
Lamins are the main components of the nucleoskeleton. They form a protein meshwork that underlies the inner nuclear membrane. Mutations in the LMNA gene coding for A-type lamins (lamins A and C) cause a large panel of human diseases, referred to as laminopathies. These diseases include muscular dystrophies, lipodystrophies and premature aging diseases. Lamin A exhibits a C-terminal region that is different from lamin C and is post-translationally modified. It is produced as prelamin A and it is then farnesylated, cleaved, carboxymethylated and cleaved again in order to become mature lamin A. In patients with the severe Hutchinson-Gilford progeria syndrome, a specific single point mutation in LMNA leads to an aberrant splicing of the LMNA gene preventing the post-translational processing of prelamin A. This leads to the accumulation of a permanently farnesylated lamin A mutant lacking 50 amino acids named progerin. We here report the NMR 1H, 15N, 13CO, 13Cα and 13Cβ chemical shift assignment of the C-terminal region that is specific to prelamin A, from amino acid 567 to amino acid 664. We also report the NMR 1H, 15N, 13CO, 13Cα and 13Cβ chemical shift assignment of the C-terminal region of the progerin variant, from amino acid 567 to amino acid 614. Analysis of these chemical shift data confirms that both prelamin A and progerin C-terminal domains are largely disordered and identifies a common partially populated α-helix from amino acid 576 to amino acid 585. This helix is well conserved from fishes to mammals.
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Affiliation(s)
- Florian Celli
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ambre Petitalot
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Camille Samson
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - François-Xavier Theillet
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sophie Zinn-Justin
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
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276
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Electron microscopy of Chaetomium pom152 shows the assembly of ten-bead string. Cell Discov 2018; 4:56. [PMID: 30245846 PMCID: PMC6141588 DOI: 10.1038/s41421-018-0057-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 11/08/2022] Open
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277
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Nguyen D, Stutz R, Schorr S, Lang S, Pfeffer S, Freeze HH, Förster F, Helms V, Dudek J, Zimmermann R. Proteomics reveals signal peptide features determining the client specificity in human TRAP-dependent ER protein import. Nat Commun 2018; 9:3765. [PMID: 30217974 PMCID: PMC6138672 DOI: 10.1038/s41467-018-06188-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 08/23/2018] [Indexed: 12/22/2022] Open
Abstract
In mammalian cells, one-third of all polypeptides are transported into or across the ER membrane via the Sec61 channel. While the Sec61 complex facilitates translocation of all polypeptides with amino-terminal signal peptides (SP) or transmembrane helices, the Sec61-auxiliary translocon-associated protein (TRAP) complex supports translocation of only a subset of precursors. To characterize determinants of TRAP substrate specificity, we here systematically identify TRAP-dependent precursors by analyzing cellular protein abundance changes upon TRAP depletion using quantitative label-free proteomics. The results are validated in independent experiments by western blotting, quantitative RT-PCR, and complementation analysis. The SPs of TRAP clients exhibit above-average glycine-plus-proline content and below-average hydrophobicity as distinguishing features. Thus, TRAP may act as SP receptor on the ER membrane’s cytosolic face, recognizing precursor polypeptides with SPs of high glycine-plus-proline content and/or low hydrophobicity, and triggering substrate-specific opening of the Sec61 channel through interactions with the ER-lumenal hinge of Sec61α. While Sec61 enables ER import of all polypeptides with N-terminal signal peptides, only selected clients are accepted for TRAP-assisted ER import. Here, the authors use a proteomics approach to characterize TRAP-dependent clients, identifying signal peptide features that govern recognition by TRAP.
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Affiliation(s)
- Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Regine Stutz
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany
| | - Stefan Schorr
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany
| | - Stefan Pfeffer
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, 82152, Martinsried, Germany
| | - Hudson H Freeze
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany.
| | - Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany.
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany.
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278
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Englmeier R, Förster F. Cryo-electron tomography for the structural study of mitochondrial translation. Tissue Cell 2018; 57:129-138. [PMID: 30197222 DOI: 10.1016/j.tice.2018.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/29/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Cryo-electron tomography (cryo-ET) enables the three-dimensional (3D) structural characterization of macromolecular complexes in their physiological environment. Thus, cryo-ET is uniquely suited to study the structural basis of biomolecular processes that are extremely difficult or even impossible to reconstitute using purified components. Translation of mitochondrial genes, which occurs in the secluded interior of mitochondria, falls into this category. Here, we describe the principles of cryo-ET in the context of mitochondrial translation and outline recent developments and challenges of the method. The 3D image of a frozen-hydrated biological sample is computed from its 2D projections, which are acquired using a transmission electron microscope. In conjunction with automated detection of different copies of the molecule of interest and averaging of the corresponding subtomograms, cryo-ET enables macromolecular structure determination in the native environment (i.e. in situ) at sub-nanometer resolution. The preservation of the native environment furthermore allows the extraction of contextual information about the molecules, including the location of specific molecules with respect to membranes, their relative positioning and the spatial organization with respect to other types of macromolecules. Recent preparative developments extend the field of application of cryo-ET from isolated organelles to cultured eukaryotic cells and even tissue, making the traditional borders between molecular and cellular structural biology disappear.
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Affiliation(s)
- Robert Englmeier
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands.
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279
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Arifulin EA, Musinova YR, Vassetzky YS, Sheval EV. Mobility of Nuclear Components and Genome Functioning. BIOCHEMISTRY (MOSCOW) 2018; 83:690-700. [PMID: 30195325 DOI: 10.1134/s0006297918060068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell nucleus is characterized by strong compartmentalization of structural components in its three-dimensional space. Certain genomic functions are accompanied by changes in the localization of chromatin loci and nuclear bodies. Here we review recent data on the mobility of nuclear components and the role of this mobility in genome functioning.
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Affiliation(s)
- E A Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Y R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, 94805, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Y S Vassetzky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, 94805, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia.,UMR8126, CNRS, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, 94805, France
| | - E V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, 94805, France
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280
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Melia CE, Bharat TAM. Locating macromolecules and determining structures inside bacterial cells using electron cryotomography. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:973-981. [PMID: 29908328 PMCID: PMC6052677 DOI: 10.1016/j.bbapap.2018.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Electron cryotomography (cryo-ET) is an imaging technique uniquely suited to the study of bacterial ultrastructure and cell biology. Recent years have seen a surge in structural and cell biology research on bacteria using cryo-ET. This research has driven major technical developments in the field, with applications emerging to address a wide range of biological questions. In this review, we explore the diversity of cryo-ET approaches used for structural and cellular microbiology, with a focus on in situ localization and structure determination of macromolecules. The first section describes strategies employed to locate target macromolecules within large cellular volumes. Next, we explore methods to study thick specimens by sample thinning. Finally, we review examples of macromolecular structure determination in a cellular context using cryo-ET. The examples outlined serve as powerful demonstrations of how the cellular location, structure, and function of any bacterial macromolecule of interest can be investigated using cryo-ET.
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Affiliation(s)
- Charlotte E Melia
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Central Oxford Structural and Molecular Imaging Centre, University of Oxford, Oxford OX1 3RE, United Kingdom.
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281
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From the resolution revolution to evolution: structural insights into the evolutionary relationships between vesicle coats and the nuclear pore. Curr Opin Struct Biol 2018; 52:32-40. [PMID: 30103204 DOI: 10.1016/j.sbi.2018.07.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 11/22/2022]
Abstract
Nuclear pores and coated vesicles are elaborate multi-component protein complexes that oligomerize on membranes, and stabilize or induce membrane curvature. Their components, nucleoporins and coat proteins, respectively, share similar structural folds and some principles of how they interact with membranes. The protocoatomer hypothesis postulates that this is due to divergent evolution from a common ancestor. It therefore has been suggested that nucleoporins and coat proteins have similar higher order architectures. Here, we review recent work that relied on technical advances in cryo-electron microscopy and integrative structural biology to take a fresh look on how these proteins form membrane coats in situ. We discuss the relationship between the architectures of nuclear pores and coated vesicles, and their evolutionary origins.
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282
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Cai S, Böck D, Pilhofer M, Gan L. The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin. Mol Biol Cell 2018; 29:2450-2457. [PMID: 30091658 PMCID: PMC6233054 DOI: 10.1091/mbc.e18-05-0331] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The in situ three-dimensional organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography to determine the in situ structures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.
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Affiliation(s)
- Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Désirée Böck
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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283
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Revisiting Centrioles in Nematodes-Historic Findings and Current Topics. Cells 2018; 7:cells7080101. [PMID: 30096824 PMCID: PMC6115991 DOI: 10.3390/cells7080101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 01/02/2023] Open
Abstract
Theodor Boveri is considered as the “father” of centrosome biology. Boveri’s fundamental findings have laid the groundwork for decades of research on centrosomes. Here, we briefly review his early work on centrosomes and his first description of the centriole. Mainly focusing on centriole structure, duplication, and centriole assembly factors in C. elegans, we will highlight the role of this model in studying germ line centrosomes in nematodes. Last but not least, we will point to future directions of the C. elegans centrosome field.
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284
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Greenan GA, Keszthelyi B, Vale RD, Agard DA. Insights into centriole geometry revealed by cryotomography of doublet and triplet centrioles. eLife 2018; 7:36851. [PMID: 30080137 PMCID: PMC6110610 DOI: 10.7554/elife.36851] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/03/2018] [Indexed: 12/31/2022] Open
Abstract
Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being defined at increasing resolution, centriolar structure remains poorly understood. Here, we used electron cryo-tomography to determine the structure of mammalian (triplet) and Drosophila (doublet) centrioles. Mammalian centrioles have two distinct domains: a 200 nm proximal core region connected by A-C linkers, and a distal domain where the C-tubule is incomplete and a pair of novel linkages stabilize the assembly producing a geometry more closely resembling the ciliary axoneme. Drosophila centrioles resemble the mammalian core, but with their doublet microtubules linked through the A tubules. The commonality of core-region length, and the abrupt transition in mammalian centrioles, suggests a conserved length-setting mechanism. The unexpected linker diversity suggests how unique centriolar architectures arise in different tissues and organisms.
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Affiliation(s)
- Garrett A Greenan
- Department of Biochemistry and Biophysics, University of California, San Francisco, United States.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, United States.,Howard Hughes Medical Institute, San Francisco, United States
| | - Bettina Keszthelyi
- Department of Biochemistry and Biophysics, University of California, San Francisco, United States.,Howard Hughes Medical Institute, San Francisco, United States
| | - Ronald D Vale
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, United States.,Howard Hughes Medical Institute, San Francisco, United States
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, United States.,Howard Hughes Medical Institute, San Francisco, United States
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285
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Dillard RS, Hampton CM, Strauss JD, Ke Z, Altomara D, Guerrero-Ferreira RC, Kiss G, Wright ER. Biological Applications at the Cutting Edge of Cryo-Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:406-419. [PMID: 30175702 PMCID: PMC6265046 DOI: 10.1017/s1431927618012382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is a powerful tool for macromolecular to near-atomic resolution structure determination in the biological sciences. The specimen is maintained in a near-native environment within a thin film of vitreous ice and imaged in a transmission electron microscope. The images can then be processed by a number of computational methods to produce three-dimensional information. Recent advances in sample preparation, imaging, and data processing have led to tremendous growth in the field of cryo-EM by providing higher resolution structures and the ability to investigate macromolecules within the context of the cell. Here, we review developments in sample preparation methods and substrates, detectors, phase plates, and cryo-correlative light and electron microscopy that have contributed to this expansion. We also have included specific biological applications.
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Affiliation(s)
- Rebecca S Dillard
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Cheri M Hampton
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Joshua D Strauss
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Zunlong Ke
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Deanna Altomara
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Ricardo C Guerrero-Ferreira
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Gabriella Kiss
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Elizabeth R Wright
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
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286
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Dutta M. Recent Advances in Single Particle Cryo-electron Microscopy and Cryo-electron Tomography to Determine the Structures of Biological Macromolecules. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0087-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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287
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Robust workflow and instrumentation for cryo-focused ion beam milling of samples for electron cryotomography. Ultramicroscopy 2018; 190:1-11. [DOI: 10.1016/j.ultramic.2018.04.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/28/2018] [Accepted: 04/04/2018] [Indexed: 01/11/2023]
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288
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Fine details in complex environments: the power of cryo-electron tomography. Biochem Soc Trans 2018; 46:807-816. [PMID: 29934301 PMCID: PMC6103461 DOI: 10.1042/bst20170351] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/09/2018] [Accepted: 05/11/2018] [Indexed: 01/10/2023]
Abstract
Cryo-electron tomography (CET) is uniquely suited to obtain structural information from a wide range of biological scales, integrating and bridging knowledge from molecules to cells. In particular, CET can be used to visualise molecular structures in their native environment. Depending on the experiment, a varying degree of resolutions can be achieved, with the first near-atomic molecular structures becoming recently available. The power of CET has increased significantly in the last 5 years, in parallel with improvements in cryo-EM hardware and software that have also benefited single-particle reconstruction techniques. In this review, we cover the typical CET pipeline, starting from sample preparation, to data collection and processing, and highlight in particular the recent developments that support structural biology in situ. We provide some examples that highlight the importance of structure determination of molecules embedded within their native environment, and propose future directions to improve CET performance and accessibility.
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289
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Mosalaganti S, Kosinski J, Albert S, Schaffer M, Strenkert D, Salomé PA, Merchant SS, Plitzko JM, Baumeister W, Engel BD, Beck M. In situ architecture of the algal nuclear pore complex. Nat Commun 2018; 9:2361. [PMID: 29915221 PMCID: PMC6006428 DOI: 10.1038/s41467-018-04739-y] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/23/2018] [Indexed: 12/19/2022] Open
Abstract
Nuclear pore complexes (NPCs) span the nuclear envelope and mediate nucleocytoplasmic exchange. They are a hallmark of eukaryotes and deeply rooted in the evolutionary origin of cellular compartmentalization. NPCs have an elaborate architecture that has been well studied in vertebrates. Whether this architecture is unique or varies significantly in other eukaryotic kingdoms remains unknown, predominantly due to missing in situ structural data. Here, we report the architecture of the algal NPC from the early branching eukaryote Chlamydomonas reinhardtii and compare it to the human NPC. We find that the inner ring of the Chlamydomonas NPC has an unexpectedly large diameter, and the outer rings exhibit an asymmetric oligomeric state that has not been observed or predicted previously. Our study provides evidence that the NPC is subject to substantial structural variation between species. The divergent and conserved features of NPC architecture provide insights into the evolution of the nucleocytoplasmic transport machinery.
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Affiliation(s)
- Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Center for Structural Systems Biology (CSSB), Notkestrasse 85, 22607, Hamburg, Germany
| | - Sahradha Albert
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Daniela Strenkert
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Patrice A Salomé
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Sabeeha S Merchant
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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290
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The application of CorrSight™ in correlative light and electron microscopy of vitrified biological specimens. BIOPHYSICS REPORTS 2018. [DOI: 10.1007/s41048-018-0059-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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291
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Medeiros JM, Böck D, Pilhofer M. Imaging bacteria inside their host by cryo-focused ion beam milling and electron cryotomography. Curr Opin Microbiol 2018; 43:62-68. [DOI: 10.1016/j.mib.2017.12.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 11/28/2022]
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292
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Expanding horizons of cryo-tomography to larger volumes. Curr Opin Microbiol 2018; 43:155-161. [DOI: 10.1016/j.mib.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/02/2018] [Accepted: 01/03/2018] [Indexed: 12/18/2022]
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293
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Spectral comparisons of mammalian cells and intact organelles by solid-state NMR. J Struct Biol 2018; 206:49-54. [PMID: 29859329 DOI: 10.1016/j.jsb.2018.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/15/2018] [Accepted: 05/25/2018] [Indexed: 01/18/2023]
Abstract
Whole-cell protein profiling, spatial localization, and quantification of activities such as gene transcription and protein translation are possible with modern biochemical and biophysical techniques. Yet, addressing questions of overall compositional changes within a cell - capturing the relative amounts of protein and ribosomal RNA levels and lipid content simultaneously - would require extractions and purifications with caveats due to isolation yields and detection methods. A holistic view of cellular composition would aid in the study of cellular composition and function. Here, solid state NMR is used to identify 13C NMR signatures for cellular organelles in HeLa cells without the use of any isotopic labeling. Comparisons are made with carbon spectra of subcellular assemblies including DNA, lipids, ribosomes, nuclei and mitochondria. Whole-cell comparisons are made with different mammalian cells lines, with red blood cells that lack nuclei and organelles, and with Gram-negative and Gram-positive bacteria. Furthermore, treatment of mammalian cells with cycloheximide, a commonly used protein synthesis inhibitor, revealed unanticipated changes consistent with a significant increase in protein glycosylation, obvious at the whole cell level. Thus, we demonstrate that solid-state NMR serves as a unique analytical tool to catalog and compare the ratios of distinct carbon types in cells and serves as a discovery tool to reveal the workings of inhibitors such as cycloheximide on whole-cell biochemistry.
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294
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Nitta R, Imasaki T, Nitta E. Recent progress in structural biology: lessons from our research history. Microscopy (Oxf) 2018; 67:4996565. [PMID: 29771342 DOI: 10.1093/jmicro/dfy022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/25/2018] [Indexed: 11/13/2022] Open
Abstract
The recent 'resolution revolution' in structural analyses of cryo-electron microscopy (cryo-EM) has drastically changed the research strategy for structural biology. In addition to X-ray crystallography and nuclear magnetic resonance spectroscopy, cryo-EM has achieved the structural analysis of biological molecules at near-atomic resolution, resulting in the Nobel Prize in Chemistry 2017. The effect of this revolution has spread within the biology and medical science fields affecting everything from basic research to pharmaceutical development by visualizing atomic structure. As we have used cryo-EM as well as X-ray crystallography since 2000 to elucidate the molecular mechanisms of the fundamental phenomena in the cell, here we review our research history and summarize our findings. In the first half of the review, we describe the structural mechanisms of microtubule-based motility of molecular motor kinesin by using a joint cryo-EM and X-ray crystallography method. In the latter half, we summarize our structural studies on transcriptional regulation by X-ray crystallography of in vitro reconstitution of a multi-protein complex.
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Affiliation(s)
- Ryo Nitta
- Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
- RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tsuyoshi Imasaki
- Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
- RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Eriko Nitta
- Division of Structural Medicine and Anatomy, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
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295
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Electron cryomicroscopy as a powerful tool in biomedical research. J Mol Med (Berl) 2018; 96:483-493. [PMID: 29730699 PMCID: PMC5988769 DOI: 10.1007/s00109-018-1640-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/05/2018] [Accepted: 04/11/2018] [Indexed: 01/08/2023]
Abstract
A human cell is a precisely regulated system that relies on the complex interaction of molecules. Structural insights into the cellular machinery at the atomic level allow us to understand the underlying regulatory mechanism and provide us with a roadmap for the development of novel drugs to fight diseases. Facilitated by recent technological breakthroughs, the Nobel prize-winning technique electron cryomicroscopy (cryo-EM) has become a versatile and extremely powerful tool to solve routinely near-atomic resolution three-dimensional protein structures. Consequently, it has become the focus of attention for structure-based drug design. In this review, we describe the basics of cryo-EM and highlight its growing role in biomedical research. Furthermore, we discuss latest developments as well as future perspectives.
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296
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297
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Earnest TM, Cole JA, Luthey-Schulten Z. Simulating biological processes: stochastic physics from whole cells to colonies. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:052601. [PMID: 29424367 DOI: 10.1088/1361-6633/aaae2c] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge that give rise to the complex forms and behaviors we see in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recent years have seen stochastic modeling grow into a major subdiscipline within biological physics. Here we review some of the major advances that have shaped our understanding of stochasticity in biology. We begin with some historical context, outlining a string of important experimental results that motivated the development of stochastic modeling. We then embark upon a fairly rigorous treatment of the simulation methods that are currently available for the treatment of stochastic biological models, with an eye toward comparing and contrasting their realms of applicability, and the care that must be taken when parameterizing them. Following that, we describe how stochasticity impacts several key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, before considering how the functions may be coupled into a comprehensive model of a 'minimal cell'. Finally, we close with our expectation for the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches in order to understand life across a range of length and time scales.
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Affiliation(s)
- Tyler M Earnest
- Department of Chemistry, University of Illinois, Urbana, IL, 61801, United States of America. National Center for Supercomputing Applications, University of Illinois, Urbana, IL, 61801, United States of America
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298
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Chudinova EM, Nadezhdina ES. Interactions between the Translation Machinery and Microtubules. BIOCHEMISTRY (MOSCOW) 2018; 83:S176-S189. [PMID: 29544439 DOI: 10.1134/s0006297918140146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microtubules are components of eukaryotic cytoskeleton that are involved in the transport of various components from the nucleus to the cell periphery and back. They also act as a platform for assembly of complex molecular ensembles. Ribonucleoprotein (RNP) complexes, such as ribosomes and mRNPs, are transported over significant distances (e.g. to neuronal processes) along microtubules. The association of RNPs with microtubules and their transport along these structures are essential for compartmentalization of protein biosynthesis in cells. Microtubules greatly facilitate assembly of stress RNP granules formed by accumulation of translation machinery components during cell stress response. Microtubules are necessary for the cytoplasm-to-nucleus transport of proteins, including ribosomal proteins. At the same time, ribosomal proteins and RNA-binding proteins can influence cell mobility and cytoplasm organization by regulating microtubule dynamics. The molecular mechanisms underlying the association between the translation machinery components and microtubules have not been studied systematically; the results of such studies are mostly fragmentary. In this review, we attempt to fill this gap by summarizing and discussing the data on protein and RNA components of the translation machinery that directly interact with microtubules or microtubule motor proteins.
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Affiliation(s)
- E M Chudinova
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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299
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Grigoryev SA. Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles. Biophys J 2018; 114:2290-2297. [PMID: 29628212 DOI: 10.1016/j.bpj.2018.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/03/2018] [Accepted: 03/09/2018] [Indexed: 01/24/2023] Open
Abstract
The mechanism by which the "beads-on-a-string" nucleosome chain folds into various higher-order chromatin structures in eukaryotic cell nuclei is still poorly understood. The various models depicting higher-order chromatin as regular helical fibers and the very opposite "polymer melt" theory imply that interactions between nucleosome "beads" make the main contribution to the chromatin compaction. Other models in which the geometry of linker DNA "strings" entering and exiting the nucleosome define the three-dimensional structure predict that small changes in the linker DNA configuration may strongly affect nucleosome chain folding and chromatin higher-order structure. Among those studies, the cross-disciplinary approach pioneered by Jörg Langowski that combines computational modeling with biophysical and biochemical experiments was most instrumental for understanding chromatin higher-order structure in vitro. Strikingly, many recent studies, including genome-wide nucleosome interaction mapping and chromatin imaging, show an excellent agreement with the results of three-dimensional computational modeling based on the primary role of linker DNA geometry in chromatin compaction. This perspective relates nucleosome array models with experimental studies of nucleosome array folding in vitro and in situ. I argue that linker DNA configuration plays a key role in determining nucleosome chain flexibility, topology, and propensity for self-association, thus providing new implications for regulation of chromatin accessibility to DNA binding factors and RNA transcription machinery as well as long-range communications between distant genomic sites.
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Affiliation(s)
- Sergei A Grigoryev
- Department of Biochemistry & Molecular Biology, H171, Milton S. Hershey Medical Center, Penn State University College of Medicine, Hershey, Pennsylvania.
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300
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Lau C, Hunter MJ, Stewart A, Perozo E, Vandenberg JI. Never at rest: insights into the conformational dynamics of ion channels from cryo-electron microscopy. J Physiol 2018; 596:1107-1119. [PMID: 29377132 PMCID: PMC5878226 DOI: 10.1113/jp274888] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 12/27/2017] [Indexed: 01/04/2023] Open
Abstract
The tightly regulated opening and closure of ion channels underlies the electrical signals that are vital for a wide range of physiological processes. Two decades ago the first atomic level view of ion channel structures led to a detailed understanding of ion selectivity and conduction. In recent years, spectacular developments in the field of cryo-electron microscopy have resulted in cryo-EM superseding crystallography as the technique of choice for determining near-atomic resolution structures of ion channels. Here, we will review the recent developments in cryo-EM and its specific application to the study of ion channel gating. We will highlight the advantages and disadvantages of the current technology and where the field is likely to head in the next few years.
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Affiliation(s)
- Carus Lau
- Victor Chang Cardiac Research InstituteDarlinghurstNSW2010Australia
- St Vincent's Clinical SchoolUniversity of NSWDarlinghurstNSW2010Australia
| | - Mark J. Hunter
- Victor Chang Cardiac Research InstituteDarlinghurstNSW2010Australia
| | - Alastair Stewart
- Victor Chang Cardiac Research InstituteDarlinghurstNSW2010Australia
- St Vincent's Clinical SchoolUniversity of NSWDarlinghurstNSW2010Australia
| | - Eduardo Perozo
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIL60637USA
| | - Jamie I. Vandenberg
- Victor Chang Cardiac Research InstituteDarlinghurstNSW2010Australia
- St Vincent's Clinical SchoolUniversity of NSWDarlinghurstNSW2010Australia
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