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Lin HH, Wang CH, Huang SH, Lin SY, Kato T, Namba K, Hosogi N, Song C, Murata K, Yen CH, Hsu TL, Wong CH, Wu YM, Tu IP, Chang WH. Use of phase plate cryo-EM reveals conformation diversity of therapeutic IgG with 50 kDa Fab fragment resolved below 6 Å. Sci Rep 2024; 14:14079. [PMID: 38890341 PMCID: PMC11189423 DOI: 10.1038/s41598-024-62045-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
While cryogenic electron microscopy (cryo-EM) is fruitfully used for harvesting high-resolution structures of sizable macromolecules, its application to small or flexible proteins composed of small domains like immunoglobulin (IgG) remain challenging. Here, we applied single particle cryo-EM to Rituximab, a therapeutic IgG mediating anti-tumor toxicity, to explore its solution conformations. We found Rituximab molecules exhibited aggregates in cryo-EM specimens contrary to its solution behavior, and utilized a non-ionic detergent to successfully disperse them as isolated particles amenable to single particle analysis. As the detergent adversely reduced the protein-to-solvent contrast, we employed phase plate contrast to mitigate the impaired protein visibility. Assisted by phase plate imaging, we obtained a canonical three-arm IgG structure with other structures displaying variable arm densities co-existing in solution, affirming high flexibility of arm-connecting linkers. Furthermore, we showed phase plate imaging enables reliable structure determination of Fab to sub-nanometer resolution from ab initio, yielding a characteristic two-lobe structure that could be unambiguously docked with crystal structure. Our findings revealed conformation diversity of IgG and demonstrated phase plate was viable for cryo-EM analysis of small proteins without symmetry. This work helps extend cryo-EM boundaries, providing a valuable imaging and structural analysis framework for macromolecules with similar challenging features.
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Affiliation(s)
- Hsin-Hung Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Academia Sinica Cryo-EM Facility, Academia Sinica, Taipei, Taiwan
| | - Shih-Hsin Huang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Sung-Yao Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, Japan
- Institute of Protein Research, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, Japan
| | - Naoki Hosogi
- JEOL Ltd., 1-2 Musashino 3-chome, Akishima, Tokyo, Japan
| | - Chihong Song
- Exploratory Research Center on Life and Living Systems (ExCELLS) and National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, 38 Nishigonaka Myodaiji, Okazaki, Aichi, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS) and National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, 38 Nishigonaka Myodaiji, Okazaki, Aichi, Japan
| | | | - Tsui-Ling Hsu
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Huey Wong
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Min Wu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Cryo-EM Facility, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan.
- Genomic Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Physics, Academia Sinica, Taipei, Taiwan.
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2
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Xue H, Zhang M, Liu J, Wang J, Ren G. Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination. Front Chem 2022; 10:889203. [PMID: 36110139 PMCID: PMC9468540 DOI: 10.3389/fchem.2022.889203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022] Open
Abstract
To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.
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Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianjun Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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3
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Zhang Y, Lu PH, Rotunno E, Troiani F, van Schayck JP, Tavabi AH, Dunin-Borkowski RE, Grillo V, Peters PJ, Ravelli RBG. Single-particle cryo-EM: alternative schemes to improve dose efficiency. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1343-1356. [PMID: 34475283 PMCID: PMC8415325 DOI: 10.1107/s1600577521007931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Imaging of biomolecules by ionizing radiation, such as electrons, causes radiation damage which introduces structural and compositional changes of the specimen. The total number of high-energy electrons per surface area that can be used for imaging in cryogenic electron microscopy (cryo-EM) is severely restricted due to radiation damage, resulting in low signal-to-noise ratios (SNR). High resolution details are dampened by the transfer function of the microscope and detector, and are the first to be lost as radiation damage alters the individual molecules which are presumed to be identical during averaging. As a consequence, radiation damage puts a limit on the particle size and sample heterogeneity with which electron microscopy (EM) can deal. Since a transmission EM (TEM) image is formed from the scattering process of the electron by the specimen interaction potential, radiation damage is inevitable. However, we can aim to maximize the information transfer for a given dose and increase the SNR by finding alternatives to the conventional phase-contrast cryo-EM techniques. Here some alternative transmission electron microscopy techniques are reviewed, including phase plate, multi-pass transmission electron microscopy, off-axis holography, ptychography and a quantum sorter. Their prospects for providing more or complementary structural information within the limited lifetime of the sample are discussed.
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Affiliation(s)
- Yue Zhang
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
| | - Peng-Han Lu
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Enzo Rotunno
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/A, I-41125 Modena, Italy
| | - Filippo Troiani
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/A, I-41125 Modena, Italy
| | - J. Paul van Schayck
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
| | - Amir H. Tavabi
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Rafal E. Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, Jülich 52425, Germany
| | - Vincenzo Grillo
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/A, I-41125 Modena, Italy
| | - Peter J. Peters
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
| | - Raimond B. G. Ravelli
- Maastricht Multimodal Molecular Imaging Institute, Division of Nanoscopy, Maastricht University, Universiteitssingel 50, Maastricht 6229 ER, The Netherlands
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4
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von Loeffelholz O, Klaholz BP. Setup and Troubleshooting of Volta Phase Plate Cryo-EM Data Collection. Methods Mol Biol 2021; 2305:291-299. [PMID: 33950395 DOI: 10.1007/978-1-0716-1406-8_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Cryo electron microscopy (cryo-EM) has become a method of choice in structural biology to analyze isolated complexes and cellular structures. This implies adequate imaging of the specimen and advanced image-processing methods to obtain high-resolution 3D reconstructions. The use of a Volta phase plate in cryo-EM drastically increases the image contrast while being able to record images at high acceleration voltage and close to focus, i.e., at conditions where high-resolution information is best preserved. During image processing, higher contrast images can be aligned and classified better than lower quality ones resulting in increased data quality and the need for less data. Here, we give step-by-step guidelines on how to set up high-quality VPP cryo-EM single particle data collections, as exemplified by human ribosome data acquired during a one-day data collection session. Further, we describe specific technical details in image processing that differ from conventional single particle cryo-EM data analysis.
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Affiliation(s)
- Ottilie von Loeffelholz
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France. .,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France. .,Université de Strasbourg, Strasbourg, France.
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5
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Malac M, Hettler S, Hayashida M, Kano E, Egerton RF, Beleggia M. Phase plates in the transmission electron microscope: operating principles and applications. Microscopy (Oxf) 2020; 70:75-115. [DOI: 10.1093/jmicro/dfaa070] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/30/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023] Open
Abstract
Abstract
In this paper, we review the current state of phase plate imaging in a transmission electron microscope. We focus especially on the hole-free phase plate design, also referred to as the Volta phase plate. We discuss the implementation, operating principles and applications of phase plate imaging. We provide an imaging theory that accounts for inelastic scattering in both the sample and in the hole-free phase plate.
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Affiliation(s)
- Marek Malac
- NRC-NANO, National Research Council, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Simon Hettler
- Laboratorio de Microscopías Avanzadas (LMA), Instituto de Nanociencia y Materiales de Aragon (INMA), Universidad de Zaragoza, Campus Río Ebro, 50018 Zaragoza, España
| | - Misa Hayashida
- NRC-NANO, National Research Council, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Emi Kano
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Ray F Egerton
- Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Marco Beleggia
- DTU Nanolab, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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6
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Supramolecular tholos-like architecture constituted by archaeal proteins without functional annotation. Sci Rep 2020; 10:1540. [PMID: 32001743 PMCID: PMC6992696 DOI: 10.1038/s41598-020-58371-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/14/2020] [Indexed: 11/08/2022] Open
Abstract
Euryarchaeal genomes encode proteasome-assembling chaperone homologs, PbaA and PbaB, although archaeal proteasome formation is a chaperone-independent process. Homotetrameric PbaB functions as a proteasome activator, while PbaA forms a homopentamer that does not interact with the proteasome. Notably, PbaA forms a complex with PF0014, an archaeal protein without functional annotation. In this study, based on our previous research on PbaA crystal structure, we performed an integrative analysis of the supramolecular structure of the PbaA/PF0014 complex using native mass spectrometry, solution scattering, high-speed atomic force microscopy, and electron microscopy. The results indicated that this highly thermostable complex constitutes ten PbaA and ten PF0014 molecules, which are assembled into a dumbbell-shaped structure. Two PbaA homopentameric rings correspond to the dumbbell plates, with their N-termini located outside of the plates and C-terminal segments left mobile. Furthermore, mutant PbaA lacking the mobile C-terminal segment retained the ability to form a complex with PF0014, allowing 3D modeling of the complex. The complex shows a five-column tholos-like architecture, in which each column comprises homodimeric PF0014, harboring a central cavity, which can potentially accommodate biomacromolecules including proteins. Our findings provide insight into the functional roles of Pba family proteins, offering a novel framework for designing functional protein cages.
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7
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Lü Y, Zeng X, Zhao X, Li S, Li H, Gao X, Xu M. Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization. BMC Bioinformatics 2019; 20:443. [PMID: 31455212 PMCID: PMC6712796 DOI: 10.1186/s12859-019-3003-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 07/19/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryo-electron tomography (Cryo-ET) is an imaging technique used to generate three-dimensional structures of cellular macromolecule complexes in their native environment. Due to developing cryo-electron microscopy technology, the image quality of three-dimensional reconstruction of cryo-electron tomography has greatly improved. However, cryo-ET images are characterized by low resolution, partial data loss and low signal-to-noise ratio (SNR). In order to tackle these challenges and improve resolution, a large number of subtomograms containing the same structure needs to be aligned and averaged. Existing methods for refining and aligning subtomograms are still highly time-consuming, requiring many computationally intensive processing steps (i.e. the rotations and translations of subtomograms in three-dimensional space). RESULTS In this article, we propose a Stochastic Average Gradient (SAG) fine-grained alignment method for optimizing the sum of dissimilarity measure in real space. We introduce a Message Passing Interface (MPI) parallel programming model in order to explore further speedup. CONCLUSIONS We compare our stochastic average gradient fine-grained alignment algorithm with two baseline methods, high-precision alignment and fast alignment. Our SAG fine-grained alignment algorithm is much faster than the two baseline methods. Results on simulated data of GroEL from the Protein Data Bank (PDB ID:1KP8) showed that our parallel SAG-based fine-grained alignment method could achieve close-to-optimal rigid transformations with higher precision than both high-precision alignment and fast alignment at a low SNR (SNR=0.003) with tilt angle range ±60∘ or ±40∘. For the experimental subtomograms data structures of GroEL and GroEL/GroES complexes, our parallel SAG-based fine-grained alignment can achieve higher precision and fewer iterations to converge than the two baseline methods.
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Affiliation(s)
- Yongchun Lü
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent Information Processing, CAS, Beijing, China
| | - Xiangrui Zeng
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| | - Xiaofang Zhao
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
| | - Shirui Li
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent Information Processing, CAS, Beijing, China
| | - Hua Li
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Computing Technology of the Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Intelligent Information Processing, CAS, Beijing, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
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8
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Wang HW, Fan X. Challenges and opportunities in cryo-EM with phase plate. Curr Opin Struct Biol 2019; 58:175-182. [PMID: 31374473 DOI: 10.1016/j.sbi.2019.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022]
Abstract
Not long after the invention of transmission electron microscope (TEM), phase plate was proposed as a novel electron-optical apparatus at the back-focal plane of the objective lens to modulate the magnified specimen images with enhanced contrast, especially in cryo-electron microscopy (cryo-EM) application of biological specimens. In the past two decades, novel phase plates of different kinds were designed and fabricated for cryo-EM application. Some of them such as the Volta phase plate have already been proved very useful in single particle cryo-EM and cryo-electron tomography (cryo-ET) analysis. In this review, we discuss the current progress, challenges and opportunities of cryo-EM with phase plate.
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Affiliation(s)
- Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Xiao Fan
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
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9
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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: 32] [Impact Index Per Article: 6.4] [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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10
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Tsunoda J, Song C, Imai FL, Takagi J, Ueno H, Murata T, Iino R, Murata K. Off-axis rotor in Enterococcus hirae V-ATPase visualized by Zernike phase plate single-particle cryo-electron microscopy. Sci Rep 2018; 8:15632. [PMID: 30353110 PMCID: PMC6199243 DOI: 10.1038/s41598-018-33977-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
EhV-ATPase is an ATP-driven Na+ pump in the eubacteria Enterococcus hirae (Eh). Here, we present the first entire structure of detergent-solubilized EhV-ATPase by single-particle cryo-electron microscopy (cryo-EM) using Zernike phase plate. The cryo-EM map dominantly showed one of three catalytic conformations in this rotary enzyme. To further stabilize the originally heterogeneous structure caused by the ATP hydrolysis states of the V1-ATPases, a peptide epitope tag system was adopted, in which the inserted peptide epitope sequence interfered with rotation of the central rotor by binding the Fab. As a result, the map unexpectedly showed another catalytic conformation of EhV-ATPase. Interestingly, these two conformations identified with and without Fab conversely coincided with those of the minor state 2 and the major state 1 of Thermus thermophilus V/A-ATPase, respectively. The most prominent feature in EhV-ATPase was the off-axis rotor, where the cytoplasmic V1 domain was connected to the transmembrane Vo domain through the off-axis central rotor. Furthermore, compared to the structure of ATP synthases, the larger size of the interface between the transmembrane a-subunit and c-ring of EhV-ATPase would be more advantageous for active ion pumping.
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Affiliation(s)
- Jun Tsunoda
- The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.,National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Chihong Song
- National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Fabiana Lica Imai
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, 263-8522, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, 3-2 Suita, Osaka, 565-0871, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, University of Tokyo, Tokyo, 113-8656, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, 263-8522, Japan.,JST, PRESTO, Inage, Chiba, 263-8522, Japan
| | - Ryota Iino
- The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.,Institute for Molecular Science, Okazaki, Aichi, 444-8787, Japan
| | - Kazuyoshi Murata
- The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan. .,National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan.
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11
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Dai W, Chen M, Myers C, Ludtke SJ, Pettitt BM, King JA, Schmid MF, Chiu W. Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. J Mol Biol 2018; 430:4156-4167. [PMID: 30138616 DOI: 10.1016/j.jmb.2018.08.013.visualizing] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/29/2018] [Accepted: 08/13/2018] [Indexed: 05/19/2023]
Abstract
Cyanobacteria are photosynthetic organisms responsible for ~25% of the organic carbon fixation on earth. A key step in carbon fixation is catalyzed by ribulose bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme in the biosphere. Applying Zernike phase-contrast electron cryo-tomography and automated annotation, we identified individual RuBisCO molecules and their assembly intermediates leading to the formation of carboxysomes inside Syn5 cyanophage infected cyanobacteria Synechococcus sp. WH8109 cells. Surprisingly, more RuBisCO molecules were found to be present as cytosolic free-standing complexes or clusters than as packaged assemblies inside carboxysomes. Cytosolic RuBisCO clusters and partially assembled carboxysomes identified in the cell tomograms support a concurrent assembly model involving both the protein shell and the enclosed RuBisCO. In mature carboxysomes, RuBisCO is neither randomly nor strictly icosahedrally packed within protein shells of variable sizes. A time-averaged molecular dynamics simulation showed a semi-liquid probability distribution of the RuBisCO in carboxysomes and correlated well with carboxysome subtomogram averages. Our structural observations reveal the various stages of RuBisCO assemblies, which could be important for understanding cellular function.
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Affiliation(s)
- Wei Dai
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Muyuan Chen
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Myers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven J Ludtke
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA; Departments of Bioengineering and of Microbiology and Immunoplogy, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
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12
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Dai W, Chen M, Myers C, Ludtke SJ, Pettitt BM, King JA, Schmid MF, Chiu W. Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. J Mol Biol 2018; 430:4156-4167. [PMID: 30138616 DOI: 10.1016/j.jmb.2018.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/29/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria are photosynthetic organisms responsible for ~25% of the organic carbon fixation on earth. A key step in carbon fixation is catalyzed by ribulose bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme in the biosphere. Applying Zernike phase-contrast electron cryo-tomography and automated annotation, we identified individual RuBisCO molecules and their assembly intermediates leading to the formation of carboxysomes inside Syn5 cyanophage infected cyanobacteria Synechococcus sp. WH8109 cells. Surprisingly, more RuBisCO molecules were found to be present as cytosolic free-standing complexes or clusters than as packaged assemblies inside carboxysomes. Cytosolic RuBisCO clusters and partially assembled carboxysomes identified in the cell tomograms support a concurrent assembly model involving both the protein shell and the enclosed RuBisCO. In mature carboxysomes, RuBisCO is neither randomly nor strictly icosahedrally packed within protein shells of variable sizes. A time-averaged molecular dynamics simulation showed a semi-liquid probability distribution of the RuBisCO in carboxysomes and correlated well with carboxysome subtomogram averages. Our structural observations reveal the various stages of RuBisCO assemblies, which could be important for understanding cellular function.
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Affiliation(s)
- Wei Dai
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Muyuan Chen
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Myers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven J Ludtke
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA; Departments of Bioengineering and of Microbiology and Immunoplogy, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
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13
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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: 1.3] [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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14
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Murata K, Kaneko Y. Visualization of DNA Compaction in Cyanobacteria by High-voltage Cryo-electron Tomography. J Vis Exp 2018. [PMID: 30080205 PMCID: PMC6126509 DOI: 10.3791/57197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
This protocol describes how to visualize the transient DNA compaction in cyanobacteria. DNA compaction is a dramatic cytoplasmic event recently found to occur in some cyanobacteria before cell division. However, due to the large cell size and the transient character, it is difficult to investigate the structure in detail. To overcome the difficulties, first, DNA compaction is reproducibly produced in the cyanobacterium Synechococcus elongatus PCC 7942 by synchronous culture using 12 h each light/dark cycle. Second, DNA compaction is monitored by fluorescence microscopy and captured by rapid freezing. Third, the detailed structure of DNA compacted cells is visualized in three dimensions (3D) by high voltage cryo-electron tomography. This set of methods is widely applicable to investigate transient structures in bacteria, e.g. cell division, chromosome segregation, phage infection etc., which are monitored by fluorescence microscopy and directly visualized by cryo-electron tomography at appropriate time points.
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Affiliation(s)
| | - Yasuko Kaneko
- Graduate School of Science and Engineering, Saitama University
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15
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Xu M, Chai X, Muthakana H, Liang X, Yang G, Zeev-Ben-Mordehai T, Xing EP. Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms. Bioinformatics 2018; 33:i13-i22. [PMID: 28881965 PMCID: PMC5946875 DOI: 10.1093/bioinformatics/btx230] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Motivation Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and their spatial organizations inside single cells. However, high degree of structural complexity together with practical imaging limitations makes the systematic de novo discovery of structures within cells challenging. It would likely require averaging and classifying millions of subtomograms potentially containing hundreds of highly heterogeneous structural classes. Although it is no longer difficult to acquire CECT data containing such amount of subtomograms due to advances in data acquisition automation, existing computational approaches have very limited scalability or discrimination ability, making them incapable of processing such amount of data. Results To complement existing approaches, in this article we propose a new approach for subdividing subtomograms into smaller but relatively homogeneous subsets. The structures in these subsets can then be separately recovered using existing computation intensive methods. Our approach is based on supervised structural feature extraction using deep learning, in combination with unsupervised clustering and reference-free classification. Our experiments show that, compared with existing unsupervised rotation invariant feature and pose-normalization based approaches, our new approach achieves significant improvements in both discrimination ability and scalability. More importantly, our new approach is able to discover new structural classes and recover structures that do not exist in training data. Availability and Implementation Source code freely available at http://www.cs.cmu.edu/∼mxu1/software. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaoqi Chai
- Biomedical Engineering Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Hariank Muthakana
- Computer Science Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaodan Liang
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ge Yang
- Biomedical Engineering Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tzviya Zeev-Ben-Mordehai
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Eric P Xing
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA, USA
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16
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Cyrklaff M, Frischknecht F, Kudryashev M. Functional insights into pathogen biology from 3D electron microscopy. FEMS Microbiol Rev 2018; 41:828-853. [PMID: 28962014 DOI: 10.1093/femsre/fux041] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/25/2017] [Indexed: 01/10/2023] Open
Abstract
In recent years, novel imaging approaches revolutionised our understanding of the cellular and molecular biology of microorganisms. These include advances in fluorescent probes, dynamic live cell imaging, superresolution light and electron microscopy. Currently, a major transition in the experimental approach shifts electron microscopy studies from a complementary technique to a method of choice for structural and functional analysis. Here we review functional insights into the molecular architecture of viruses, bacteria and parasites as well as interactions with their respective host cells gained from studies using cryogenic electron tomography and related methodologies.
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Affiliation(s)
- Marek Cyrklaff
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt, Max-von-Laue Strasse 17, 60438 Frankfurt, Germany
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17
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Okamoto K, Miyazaki N, Song C, Maia FRNC, Reddy HKN, Abergel C, Claverie JM, Hajdu J, Svenda M, Murata K. Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy. Sci Rep 2017; 7:13291. [PMID: 29038566 PMCID: PMC5643343 DOI: 10.1038/s41598-017-13390-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 09/22/2017] [Indexed: 12/23/2022] Open
Abstract
The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 μm in length and 0.9 μm in diameter. These particles show significant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo-tomography (cryo-ET) and energy-filtered cryo-EM. We detected a previously undescribed low-density outer layer covering the tegument and a periodical structuring of the fibres in the striated apical cork. Energy-filtered Zernike phase-contrast cryo-EM images show distinct substructures inside the particles, implicating an internal compartmentalisation. The density of the interior volume of Pithovirus particles is three quarters lower than that of the Mimivirus. However, it is remarkably high given that the 600 kbp Pithovirus genome is only half the size of the Mimivirus genome and is packaged in a volume up to 100 times larger. These observations suggest that the interior is densely packed with macromolecules in addition to the genomic nucleic acid.
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Affiliation(s)
- Kenta Okamoto
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.
| | - Naoyuki Miyazaki
- National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan
| | - Chihong Song
- National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan
| | - Filipe R N C Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Hemanth K N Reddy
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Chantal Abergel
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, 13288, France
| | - Jean-Michel Claverie
- Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille, 13288, France.,Assistance Publique des Hôpitaux de Marseille. La Timone, 13005, Marseille, France
| | - Janos Hajdu
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden.,Institute of Physics AS CR, v.v.i., Na Slovance 2, 18221, Prague 8, Czech Republic
| | - Martin Svenda
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-75124, Uppsala, Sweden
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585, Japan.
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18
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Near-Atomic Resolution Structure Determination in Over-Focus with Volta Phase Plate by Cs-Corrected Cryo-EM. Structure 2017; 25:1623-1630.e3. [DOI: 10.1016/j.str.2017.08.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/25/2017] [Accepted: 08/15/2017] [Indexed: 11/21/2022]
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19
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Danev R, Baumeister W. Expanding the boundaries of cryo-EM with phase plates. Curr Opin Struct Biol 2017; 46:87-94. [DOI: 10.1016/j.sbi.2017.06.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 10/19/2022]
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20
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Chua EYD, Sandin S. Advances in phase plate cryo-EM imaging of DNA and nucleosomes. Nucleus 2017; 8:275-278. [PMID: 28340334 PMCID: PMC5499919 DOI: 10.1080/19491034.2017.1287643] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 01/23/2017] [Indexed: 11/11/2022] Open
Abstract
Contrast in electron cryo-microscopy (cryo-EM) is limited by the weak phase and radiation sensitive nature of biologic samples embedded in vitrified ice. We have recently shown that a new contrast enhancement technique utilizing the Volta phase plate can be combined with single particle analysis to determine the structure of a small chromatin complex, the nucleosome core particle, at near-atomic resolution. Here, we discuss advantages and limitations of the technique in terms of data collection, particle detection, and visualization of individual DNA molecules and higher-order chromatin structure.
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Affiliation(s)
- Eugene Y. D. Chua
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sara Sandin
- School of Biological Sciences, Nanyang Technological University, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore
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21
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Wadell C, Inagaki S, Nakamura T, Shi J, Nakamura Y, Sannomiya T. Nanocuvette: A Functional Ultrathin Liquid Container for Transmission Electron Microscopy. ACS NANO 2017; 11:1264-1272. [PMID: 28135067 DOI: 10.1021/acsnano.6b05007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Advances in TEM techniques have spurred a renewed interest in a wide variety of research fields. A rather recent track within these endeavors is the use of TEM for in situ imaging in liquids. In this article, we show the fabrication of a liquid cell for TEM observations which we call the nanocuvette. The structure consists of a nanohole film sandwiched by carbon films, sealing liquid in the holes. The hole film can be produced using a variety of materials, tailored for the desired application. Since the fabrication is based on self-assembly, it is both cheap and straightforward. Compared to previously reported liquid cells, this structure allows for thinner liquid layers with better controlled cell structures, making it possible to achieve a high resolution even at lower acceleration voltages and electron doses. We demonstrate a resolution corresponding to an information transfer up to ∼2 nm at 100 kV for molecular imaging. Apart from the advantages arising from the thin liquid layer, the nanocuvette also enables the possibility to study liquid-solid interfaces at the side walls of the nanoholes. We illustrate the possibilities of the nanocuvette by studying several model systems: electron beam induced growth dynamics of silver nanoparticles in salt solution, polymer deposition from solution, and imaging of nonstained antibodies in solution. Finally, we show how the inclusion of a plasmonically active gold layer in the nanocuvette structure enables optical confirmation of successful liquid encapsulation prior to TEM studies. The nanocuvette provides an easily fabricated and flexible platform which can help further the understanding of reactions, processes, and conformation of molecules and atoms in liquid environments.
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Affiliation(s)
- Carl Wadell
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Satoshi Inagaki
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Tomiro Nakamura
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Ji Shi
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Yoshio Nakamura
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
| | - Takumi Sannomiya
- Department of Materials Science and Engineering, School of Materials and Chemical Technologies, Tokyo Institute of Technology , 4259 Nagatsuta, Midoriku, Yokohama 226-8503 Japan
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22
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Grange M, Vasishtan D, Grünewald K. Cellular electron cryo tomography and in situ sub-volume averaging reveal the context of microtubule-based processes. J Struct Biol 2017; 197:181-190. [PMID: 27374320 PMCID: PMC5287354 DOI: 10.1016/j.jsb.2016.06.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/27/2016] [Accepted: 06/28/2016] [Indexed: 11/27/2022]
Abstract
Electron cryo-tomography (cryoET) is currently the only technique that allows the direct observation of proteins in their native cellular environment. Sub-volume averaging of electron tomograms offers a route to increase the signal-to-noise of repetitive biological structures, such improving the information content and interpretability of tomograms. We discuss the potential for sub-volume averaging in highlighting and investigating specific processes in situ, focusing on microtubule structure and viral infection. We show that (i) in situ sub-volume averaging from single tomograms can guide and complement segmentation of biological features, (ii) the in situ determination of the structure of individual viruses is possible as they infect a cell, and (iii) novel, transient processes can be imaged with high levels of detail.
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Affiliation(s)
- Michael Grange
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Daven Vasishtan
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom.
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23
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Orlov I, Myasnikov AG, Andronov L, Natchiar SK, Khatter H, Beinsteiner B, Ménétret JF, Hazemann I, Mohideen K, Tazibt K, Tabaroni R, Kratzat H, Djabeur N, Bruxelles T, Raivoniaina F, Pompeo LD, Torchy M, Billas I, Urzhumtsev A, Klaholz BP. The integrative role of cryo electron microscopy in molecular and cellular structural biology. Biol Cell 2016; 109:81-93. [PMID: 27730650 DOI: 10.1111/boc.201600042] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 01/10/2023]
Abstract
After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo-EM) is now heading off at unprecedented speed towards high-resolution analysis of biological objects of various sizes. This 'revolution in resolution' is happening largely thanks to new developments of new-generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo-EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo-EM in synergy with other methods such as X-ray crystallography, fluorescence imaging or focussed-ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi-scale and multi-resolution approaches allow integrating molecular and cellular levels when applied to purified or in situ macromolecular complexes, thus illustrating the trend of the field towards cellular structural biology.
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Affiliation(s)
- Igor Orlov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexander G Myasnikov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Heena Khatter
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Brice Beinsteiner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Jean-François Ménétret
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Kareem Mohideen
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Karima Tazibt
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Rachel Tabaroni
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Hanna Kratzat
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Nadia Djabeur
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Tatiana Bruxelles
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Finaritra Raivoniaina
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Lorenza di Pompeo
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Morgan Torchy
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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24
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The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes. Sci Rep 2016; 6:33170. [PMID: 27616740 PMCID: PMC5018817 DOI: 10.1038/srep33170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/23/2016] [Indexed: 01/10/2023] Open
Abstract
Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 Å resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 Å resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short “plug” structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts.
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25
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Abstract
AbstractThere has been enormous progress during the last few years in the determination of three-dimensional biological structures by single particle electron cryomicroscopy (cryoEM), allowing maps to be obtained with higher resolution and from fewer images than required previously. This is due principally to the introduction of a new type of direct electron detector that has 2- to 3-fold higher detective quantum efficiency than available previously, and to the improvement of the computational algorithms for image processing. In spite of the great strides that have been made, quantitative analysis shows that there are still significant gains to be made provided that the problems associated with image degradation can be solved, possibly by minimising beam-induced specimen movement and charge build up during imaging. If this can be achieved, it should be possible to obtain near atomic resolution structures of smaller single particles, using fewer images and resolving more conformational states than at present, thus realising the full potential of the method. The recent popularity of cryoEM for molecular structure determination also highlights the need for lower cost microscopes, so we encourage development of an inexpensive, 100 keV electron cryomicroscope with a high-brightness field emission gun to make the method accessible to individual groups or institutions that cannot afford the investment and running costs of a state-of-the-art 300 keV installation. A key requisite for successful high-resolution structure determination by cryoEM includes interpretation of images and optimising the biochemistry and grid preparation to obtain nicely distributed macromolecules of interest. We thus include in this review a gallery of cryoEM micrographs that shows illustrative examples of single particle images of large and small macromolecular complexes.
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26
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Abstract
Cryo-electron tomography (cryo-ET) allows 3D volumes to be reconstructed from a set of 2D projection images of a tilted biological sample. It allows densities to be resolved in 3D that would otherwise overlap in 2D projection images. Cryo-ET can be applied to resolve structural features in complex native environments, such as within the cell. Analogous to single-particle reconstruction in cryo-electron microscopy, structures present in multiple copies within tomograms can be extracted, aligned, and averaged, thus increasing the signal-to-noise ratio and resolution. This reconstruction approach, termed subtomogram averaging, can be used to determine protein structures in situ. It can also be applied to facilitate more conventional 2D image analysis approaches. In this chapter, we provide an introduction to cryo-ET and subtomogram averaging. We describe the overall workflow, including tomographic data collection, preprocessing, tomogram reconstruction, subtomogram alignment and averaging, classification, and postprocessing. We consider theoretical issues and practical considerations for each step in the workflow, along with descriptions of recent methodological advances and remaining limitations.
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Affiliation(s)
- W Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - J A G Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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27
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Hollow Cone Electron Imaging for Single Particle 3D Reconstruction of Proteins. Sci Rep 2016; 6:27701. [PMID: 27292544 PMCID: PMC4904375 DOI: 10.1038/srep27701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/19/2016] [Indexed: 11/08/2022] Open
Abstract
The main bottlenecks for high-resolution biological imaging in electron microscopy are radiation sensitivity and low contrast. The phase contrast at low spatial frequencies can be enhanced by using a large defocus but this strongly reduces the resolution. Recently, phase plates have been developed to enhance the contrast at small defocus but electrical charging remains a problem. Single particle cryo-electron microscopy is mostly used to minimize the radiation damage and to enhance the resolution of the 3D reconstructions but it requires averaging images of a massive number of individual particles. Here we present a new route to achieve the same goals by hollow cone dark field imaging using thermal diffuse scattered electrons giving about a 4 times contrast increase as compared to bright field imaging. We demonstrate the 3D reconstruction of a stained GroEL particle can yield about 13.5 Å resolution but using a strongly reduced number of images.
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28
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Oikonomou CM, Chang YW, Jensen GJ. A new view into prokaryotic cell biology from electron cryotomography. Nat Rev Microbiol 2016; 14:205-20. [PMID: 26923112 PMCID: PMC5551487 DOI: 10.1038/nrmicro.2016.7] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electron cryotomography (ECT) enables intact cells to be visualized in 3D in an essentially native state to 'macromolecular' (∼4 nm) resolution, revealing the basic architectures of complete nanomachines and their arrangements in situ. Since its inception, ECT has advanced our understanding of many aspects of prokaryotic cell biology, from morphogenesis to subcellular compartmentalization and from metabolism to complex interspecies interactions. In this Review, we highlight how ECT has provided structural and mechanistic insights into the physiology of bacteria and archaea and discuss prospects for the future.
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Affiliation(s)
- Catherine M Oikonomou
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Yi-Wei Chang
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
| | - Grant J Jensen
- Howard Hughes Medical Institute; Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA
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29
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Grillo V, Harris J, Gazzadi GC, Balboni R, Mafakheri E, Dennis MR, Frabboni S, Boyd RW, Karimi E. Generation and application of bessel beams in electron microscopy. Ultramicroscopy 2016; 166:48-60. [PMID: 27203186 DOI: 10.1016/j.ultramic.2016.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 03/15/2016] [Accepted: 03/23/2016] [Indexed: 10/22/2022]
Abstract
We report a systematic treatment of the holographic generation of electron Bessel beams, with a view to applications in electron microscopy. We describe in detail the theory underlying hologram patterning, as well as the actual electron-optical configuration used experimentally. We show that by optimizing our nanofabrication recipe, electron Bessel beams can be generated with relative efficiencies reaching 37±3%. We also demonstrate by tuning various hologram parameters that electron Bessel beams can be produced with many visible rings, making them ideal for interferometric applications, or in more highly localized forms with fewer rings, more suitable for imaging. We describe the settings required to tune beam localization in this way, and explore beam and hologram configurations that allow the convergences and topological charges of electron Bessel beams to be controlled. We also characterize the phase structure of the Bessel beams generated with our technique, using a simulation procedure that accounts for imperfections in the hologram manufacturing process.
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Affiliation(s)
- Vincenzo Grillo
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/a, I-41125 Modena, Italy; CNR-IMEM, Parco Area delle Scienze 37/A, I-43124 Parma, Italy.
| | - Jérémie Harris
- Department of Physics, University of Ottawa, 25 Templeton St., Ottawa, Ontario, Canada K1N 6N5
| | - Gian Carlo Gazzadi
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/a, I-41125 Modena, Italy
| | | | - Erfan Mafakheri
- Dipartimento di Fisica Informatica e Matematica, Università di Modena e Reggio Emilia, via G Campi 213/a, I-41125 Modena, Italy
| | - Mark R Dennis
- H.H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, United Kingdom
| | - Stefano Frabboni
- CNR-Istituto Nanoscienze, Centro S3, Via G Campi 213/a, I-41125 Modena, Italy; Dipartimento di Fisica Informatica e Matematica, Università di Modena e Reggio Emilia, via G Campi 213/a, I-41125 Modena, Italy
| | - Robert W Boyd
- Department of Physics, University of Ottawa, 25 Templeton St., Ottawa, Ontario, Canada K1N 6N5
| | - Ebrahim Karimi
- Department of Physics, University of Ottawa, 25 Templeton St., Ottawa, Ontario, Canada K1N 6N5
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30
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Danev R, Baumeister W. Cryo-EM single particle analysis with the Volta phase plate. eLife 2016; 5. [PMID: 26949259 PMCID: PMC4850076 DOI: 10.7554/elife.13046] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 03/03/2016] [Indexed: 12/12/2022] Open
Abstract
We present a method for in-focus data acquisition with a phase plate that enables near-atomic resolution single particle reconstructions. Accurate focusing is the determining factor for obtaining high quality data. A double-area focusing strategy was implemented in order to achieve the required precision. With this approach we obtained a 3.2 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome. The phase plate matches or slightly exceeds the performance of the conventional defocus approach. Spherical aberration becomes a limiting factor for achieving resolutions below 3 Å with in-focus phase plate images. The phase plate could enable single particle analysis of challenging samples in terms of small size, heterogeneity and flexibility that are difficult to solve by the conventional defocus approach. DOI:http://dx.doi.org/10.7554/eLife.13046.001 One way of investigating how proteins and other biological molecules work is to look at their structure. Light microscopes cannot produce detailed enough images to fully reveal these structures, and so a technique called cryo-electron microscopy is often used instead. In this technique, a biological sample is frozen to the temperature of liquid nitrogen and a beam of electrons is fired at it to create an image. By taking many of these images and then subjecting them to computer processing it is possible to reconstruct the three-dimensional structure of the molecule. Frozen biological samples are essentially transparent to the electron beam used in an electron microscope. To view samples, researchers therefore use a method called phase contrast, which relies on a property of the electron beam (called its phase) changing as the beam passes through the sample. The traditional “defocus” method of producing phase contrast from electron microscopy relies on processing a series of slightly out-of-focus images of the sample. Phase plates are add-on devices that are commonly used in light microscopes to produce phase contrast. For many years now, attempts have been made to produce a working phase plate for electron microscopes. However, an effective plate, called the Volta phase plate, has only recently been developed. Danev and Baumeister have now evaluated how well the Volta phase plate performs during the analysis of a single, relatively large protein. This molecule is considered ‘easy’ to analyze using cryo-electron microscopy as relatively few microscopic images need to be recorded to solve the protein’s structure. Danev and Baumeister found that the Volta phase plate matched or slightly exceeded the performance of the traditional defocus method of producing phase contrast, depending on how many images were used to analyze the protein. This is the first time that a phase plate has matched the performance of the defocus method. A future challenge will be to make the experimental procedures and the software involved in using the Volta phase plate more user-friendly. The phase plate also needs to be tested with more ‘difficult’ samples, such as small proteins and samples whose structure could not be established using the defocus method of producing phase contrast. DOI:http://dx.doi.org/10.7554/eLife.13046.002
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Affiliation(s)
- Radostin Danev
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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31
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Thompson RF, Walker M, Siebert CA, Muench SP, Ranson NA. An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology. Methods 2016; 100:3-15. [PMID: 26931652 PMCID: PMC4854231 DOI: 10.1016/j.ymeth.2016.02.017] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/11/2016] [Accepted: 02/25/2016] [Indexed: 11/22/2022] Open
Abstract
Transmission electron microscopy (EM) is a versatile technique that can be used to image biological specimens ranging from intact eukaryotic cells to individual proteins >150 kDa. There are several strategies for preparing samples for imaging by EM, including negative staining and cryogenic freezing. In the last few years, cryo-EM has undergone a ‘resolution revolution’, owing to both advances in imaging hardware, image processing software, and improvements in sample preparation, leading to growing number of researchers using cryo-EM as a research tool. However, cryo-EM is still a rapidly growing field, with unique challenges. Here, we summarise considerations for imaging of a range of specimens from macromolecular complexes to cells using EM.
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Affiliation(s)
- Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Matt Walker
- MLW Consulting, 11 Race Hill, Launceston, Cornwall PL15 9BB, United Kingdom
| | - C Alistair Siebert
- Electron Bio-Imaging Centre, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Stephen P Muench
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
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32
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Majorovits E, Angert I, Kaiser U, Schröder RR. Benefits and Limitations of Low-kV Macromolecular Imaging of Frozen-Hydrated Biological Samples. Biophys J 2016; 110:776-84. [PMID: 26910420 DOI: 10.1016/j.bpj.2016.01.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
Object contrast is one of the most important parameters of macromolecular imaging. Low-voltage transmission electron microscopy has shown an increased atom contrast for carbon materials, indicating that amplitude contrast contributions increase at a higher rate than phase contrast and inelastic scattering. Here, we studied image contrast using ice-embedded tobacco mosaic virus particles as test samples at 20-80 keV electron energy. The particles showed the expected increase in contrast for lower energies, but at the same time the 2.3-nm-resolution measure decayed more rapidly. We found a pronounced signal loss below 60 keV, and therefore we conclude that increased inelastic scattering counteracts increased amplitude contrast. This model also implies that as long as the amplitude contrast does not increase with resolution, beam damage and multiple scattering will always win over increased contrast at the lowest energies. Therefore, we cannot expect that low-energy imaging of conventionally prepared samples would provide better data than state-of-the-art 200-300 keV imaging.
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Affiliation(s)
| | | | | | - Rasmus R Schröder
- Centre for Advanced Materials, Universität Heidelberg, Heidelberg, Germany; Cryo Electron Microscopy, CellNetworks, BioQuant, Universitätsklinikum Heidelberg, Heidelberg, Germany.
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33
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Volta phase plate cryo-EM of the small protein complex Prx3. Nat Commun 2016; 7:10534. [PMID: 26817416 PMCID: PMC4738354 DOI: 10.1038/ncomms10534] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/23/2015] [Indexed: 12/25/2022] Open
Abstract
Cryo-EM of large, macromolecular assemblies has seen a significant increase in the numbers of high-resolution structures since the arrival of direct electron detectors. However, sub-nanometre resolution cryo-EM structures are rare compared with crystal structure depositions, particularly for relatively small particles (<400 kDa). Here we demonstrate the benefits of Volta phase plates for single-particle analysis by time-efficient cryo-EM structure determination of 257 kDa human peroxiredoxin-3 dodecamers at 4.4 Å resolution. The Volta phase plate improves the applicability of cryo-EM for small molecules and accelerates structure determination. Although the resolution achievable with cryo-EM can now rival crystallography, its application to small protein assemblies remains challenging. Here the authors demonstrate the use of the Volta phase plate for single particle analysis and its potential for the study of small specimens.
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34
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Rhinow D. Towards an optimum design for thin film phase plates. Ultramicroscopy 2016; 160:1-6. [DOI: 10.1016/j.ultramic.2015.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 08/27/2015] [Accepted: 09/03/2015] [Indexed: 01/18/2023]
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35
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Irobalieva RN, Martins B, Medalia O. Cellular structural biology as revealed by cryo-electron tomography. J Cell Sci 2016; 129:469-76. [DOI: 10.1242/jcs.171967] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
ABSTRACT
Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.
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Affiliation(s)
- Rossitza N. Irobalieva
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Bruno Martins
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva 84105, Israel
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36
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Murata K, Murata T, Ueno H, Iino R. C3-O-03Single particle 3D reconstruction ofEhV-ATPase by Zernike phase contrast cryo-electron microscopy equipped with a direct detector. Microscopy (Oxf) 2015. [DOI: 10.1093/jmicro/dfv190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Danev R, Khoshouei M, Baumeister W. A3Near-atomic Resolution Single Particle Analysis with the Volta Phase Plate. Microscopy (Oxf) 2015. [DOI: 10.1093/jmicro/dfv068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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38
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Developments in cryo-electron tomography for in situ structural analysis. Arch Biochem Biophys 2015; 581:78-85. [DOI: 10.1016/j.abb.2015.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/14/2015] [Accepted: 04/19/2015] [Indexed: 12/31/2022]
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39
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Kishchenko GP, Danev R, Fisher R, He J, Hsieh C, Marko M, Sui H. Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM. J Struct Biol 2015. [PMID: 26210582 DOI: 10.1016/j.jsb.2015.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Zernike phase-plate (ZPP) imaging greatly increases contrast in cryo-electron microscopy, however fringe artifacts appear in the images. A computational de-fringing method has been proposed, but it has not been widely employed, perhaps because the importance of de-fringing has not been clearly demonstrated. For testing purposes, we employed Zernike phase-plate imaging in a cryo-electron tomographic study of radial-spoke complexes attached to microtubule doublets. We found that the contrast enhancement by ZPP imaging made nonlinear denoising insensitive to the filtering parameters, such that simple low-frequency band-pass filtering made the same improvement in map quality. We employed sub-tomogram averaging, which compensates for the effect of the "missing wedge" and considerably improves map quality. We found that fringes (caused by the abrupt cut-on of the central hole in the phase plate) can lead to incorrect representation of a structure that is well-known from the literature. The expected structure was restored by amplitude scaling, as proposed in the literature. Our results show that de-fringing is an important part of image-processing for cryo-electron tomography of macromolecular complexes with ZPP imaging.
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Affiliation(s)
- Gregory P Kishchenko
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Radostin Danev
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Rebecca Fisher
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Jie He
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Chyongere Hsieh
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Michael Marko
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Haixin Sui
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States; Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY 12201, United States.
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Schröder RR. Advances in electron microscopy: A qualitative view of instrumentation development for macromolecular imaging and tomography. Arch Biochem Biophys 2015; 581:25-38. [PMID: 26032338 DOI: 10.1016/j.abb.2015.05.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/08/2015] [Accepted: 05/21/2015] [Indexed: 02/03/2023]
Abstract
Macromolecular imaging and tomography of ice embedded samples has developed into a mature imaging technology, in structural biology today widely referred to simply as cryo electron microscopy.(1) While the pioneers of the technique struggled with ill-suited instruments, state-of-the-art cryo microscopes are now readily available and an increasing number of groups are producing excellent high-resolution structural data of macromolecular complexes, of cellular organelles, or the morphology of whole cells. Instrumentation developers, however, are offering yet more novel electron optical devices, such as energy filters and monochromators, aberration correctors or physical phase plates. Here we discuss how current instrumentation has already changed cryo EM, and how newly available instrumentation - often developed in other fields of electron microscopy - may further develop the use and applicability of cryo EM to the imaging of single isolated macromolecules of smaller size or molecules embedded in a crowded cellular environment.
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Affiliation(s)
- Rasmus R Schröder
- Cryo Electron Microscopy, CellNetwork, BioQuant, Universitätsklinikum Heidelberg, Universität Heidelberg, Germany.
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Binshtein E, Ohi MD. Cryo-Electron Microscopy and the Amazing Race to Atomic Resolution. Biochemistry 2015; 54:3133-41. [DOI: 10.1021/acs.biochem.5b00114] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elad Binshtein
- Department of Cell and Developmental
Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Melanie D. Ohi
- Department of Cell and Developmental
Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
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42
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Single particle tomography in EMAN2. J Struct Biol 2015; 190:279-90. [PMID: 25956334 DOI: 10.1016/j.jsb.2015.04.016] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 11/22/2022]
Abstract
Single particle tomography (SPT or subtomogram averaging) offers a powerful alternative to traditional 2-D single particle reconstruction for studying conformationally or compositionally heterogeneous macromolecules. It can also provide direct observation (without labeling or staining) of complexes inside cells at nanometer resolution. The development of computational methods and tools for SPT remains an area of active research. Here we present the EMAN2.1 SPT toolbox, which offers a full SPT processing pipeline, from particle picking to post-alignment analysis of subtomogram averages, automating most steps. Different algorithm combinations can be applied at each step, providing versatility and allowing for procedural cross-testing and specimen-specific strategies. Alignment methods include all-vs-all, binary tree, iterative single-model refinement, multiple-model refinement, and self-symmetry alignment. An efficient angular search, Graphic Processing Unit (GPU) acceleration and both threaded and distributed parallelism are provided to speed up processing. Finally, automated simulations, per particle reconstruction of subtiltseries, and per-particle Contrast Transfer Function (CTF) correction have been implemented. Processing examples using both real and simulated data are shown for several structures.
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43
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Towards an optimum design for electrostatic phase plates. Ultramicroscopy 2015; 153:22-31. [PMID: 25697462 DOI: 10.1016/j.ultramic.2015.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/21/2015] [Accepted: 01/31/2015] [Indexed: 11/20/2022]
Abstract
Charging of physical phase plates is a problem that has prevented their routine use in transmission electron microscopy of weak-phase objects. In theory, electrostatic phase plates are superior to thin-film phase plates since they do not attenuate the scattered electron beam and allow freely adjustable phase shifts. Electrostatic phase plates consist of multiple layers of conductive and insulating materials, and are thus more prone to charging than thin-film phase plates, which typically consist of only one single layer of amorphous material. We have addressed the origins of charging of Boersch phase plates and show how it can be reduced. In particular, we have performed simulations and experiments to analyze the influence of the insulating Si3N4 layers and surface charges on electrostatic charging. To optimize the performance of electrostatic phase plates, it would be desirable to fabricate electrostatic phase plates, which (i) impart a homogeneous phase shift to the unscattered electrons, (ii) have a low cut-on frequency, (iii) expose as little material to the intense unscattered beam as possible, and (iv) can be additionally polished by a focused ion-beam instrument to eliminate carbon contamination accumulated during exposure to the unscattered electron beam (Walter et al., 2012, Ultramicroscopy, 116, 62-72). We propose a new type of electrostatic phase plate that meets the above requirements and would be superior to a Boersch phase plate. It consists of three free-standing coaxial rods converging in the center of an aperture (3-fold coaxial phase plate). Simulations and preliminary experiments with modified Boersch phase plates indicate that the fabrication of a 3-fold coaxial phase plate is feasible.
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Kirchenbuechler D, Mutsafi Y, Horowitz B, Levin-Zaidman S, Fass D, G. Wolf S, Elbaum M. Cryo-STEM Tomography of Intact Vitrified Fibroblasts. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.3.259] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Fu X, Himes BA, Ke D, Rice WJ, Ning J, Zhang P. Controlled bacterial lysis for electron tomography of native cell membranes. Structure 2014; 22:1875-1882. [PMID: 25456413 DOI: 10.1016/j.str.2014.09.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 09/22/2014] [Accepted: 09/27/2014] [Indexed: 11/16/2022]
Abstract
Cryo-electron tomography (cryoET) has become a powerful tool for direct visualization of 3D structures of native biological specimens at molecular resolution, but its application is limited to thin specimens (<300 nm). Recently, vitreous sectioning and cryoFIB milling technologies were developed to physically reduce the specimen thickness; however, cryoET analysis of membrane protein complexes within native cell membranes remains a great challenge. Here, we use phage ΦX174 lysis gene E to rapidly produce native, intact, bacterial cell membranes for high resolution cryoET. We characterized E gene-induced cell lysis using FIB/SEM and cryoEM and showed that the bacteria cytoplasm was largely depleted through spot lesion, producing ghosts with the cell membranes intact. We further demonstrated the utility of E-gene-induced lysis for cryoET using the bacterial chemotaxis receptor signaling complex array. The described method should have a broad application for structural and functional studies of native, intact cell membranes and membrane protein complexes.
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Affiliation(s)
- Xiaofeng Fu
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Benjamin A Himes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Danxia Ke
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - William J Rice
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - Jiying Ning
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Mechanical Engineering and Materials Science, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Whole-cell imaging of the budding yeast Saccharomyces cerevisiae by high-voltage scanning transmission electron tomography. Ultramicroscopy 2014; 146:39-45. [DOI: 10.1016/j.ultramic.2014.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/07/2014] [Accepted: 05/24/2014] [Indexed: 11/19/2022]
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Volta potential phase plate for in-focus phase contrast transmission electron microscopy. Proc Natl Acad Sci U S A 2014; 111:15635-40. [PMID: 25331897 DOI: 10.1073/pnas.1418377111] [Citation(s) in RCA: 321] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe a phase plate for transmission electron microscopy taking advantage of a hitherto-unknown phenomenon, namely a beam-induced Volta potential on the surface of a continuous thin film. The Volta potential is negative, indicating that it is not caused by beam-induced electrostatic charging. The film must be heated to ∼ 200 °C to prevent contamination and enable the Volta potential effect. The phase shift is created "on the fly" by the central diffraction beam eliminating the need for precise phase plate alignment. Images acquired with the Volta phase plate (VPP) show higher contrast and unlike Zernike phase plate images no fringing artifacts. Following installation into the microscope, the VPP has an initial settling time of about a week after which the phase shift behavior becomes stable. The VPP has a long service life and has been used for more than 6 mo without noticeable degradation in performance. The mechanism underlying the VPP is the same as the one responsible for the degradation over time of the performance of thin-film Zernike phase plates, but in the VPP it is used in a constructive way. The exact physics and/or chemistry behind the process causing the Volta potential are not fully understood, but experimental evidence suggests that radiation-induced surface modification combined with a chemical equilibrium between the surface and residual gases in the vacuum play an important role.
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Zernike phase-contrast electron cryotomography applied to marine cyanobacteria infected with cyanophages. Nat Protoc 2014; 9:2630-42. [PMID: 25321408 DOI: 10.1038/nprot.2014.176] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Advances in electron cryotomography have provided new opportunities to visualize the internal 3D structures of a bacterium. An electron microscope equipped with Zernike phase-contrast optics produces images with markedly increased contrast compared with images obtained by conventional electron microscopy. Here we describe a protocol to apply Zernike phase plate technology for acquiring electron tomographic tilt series of cyanophage-infected cyanobacterial cells embedded in ice, without staining or chemical fixation. We detail the procedures for aligning and assessing phase plates for data collection, and methods for obtaining 3D structures of cyanophage assembly intermediates in the host by subtomogram alignment, classification and averaging. Acquiring three or four tomographic tilt series takes ∼12 h on a JEM2200FS electron microscope. We expect this time requirement to decrease substantially as the technique matures. The time required for annotation and subtomogram averaging varies widely depending on the project goals and data volume.
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Chaturongakul S, Ounjai P. Phage-host interplay: examples from tailed phages and Gram-negative bacterial pathogens. Front Microbiol 2014; 5:442. [PMID: 25191318 PMCID: PMC4138488 DOI: 10.3389/fmicb.2014.00442] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/04/2014] [Indexed: 01/21/2023] Open
Abstract
Complex interactions between bacteriophages and their bacterial hosts play significant roles in shaping the structure of environmental microbial communities, not only by genetic transduction but also by modification of bacterial gene expression patterns. Survival of phages solely depends on their ability to infect their bacterial hosts, most importantly during phage entry. Successful dynamic adaptation of bacteriophages when facing selective pressures, such as host adaptation and resistance, dictates their abundance and diversification. Co-evolution of the phage tail fibers and bacterial receptors determine bacterial host ranges, mechanisms of phage entry, and other infection parameters. This review summarizes the current knowledge about the physical interactions between tailed bacteriophages and bacterial pathogens (e.g., Salmonella enterica and Pseudomonas aeruginosa) and the influences of the phage on host gene expression. Understanding these interactions can offer insights into phage-host dynamics and suggest novel strategies for the design of bacterial pathogen biological controls.
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Affiliation(s)
- Soraya Chaturongakul
- Department of Microbiology, Faculty of Science, Mahidol University Bangkok, Thailand ; Center for Emerging Bacterial Infections, Faculty of Science, Mahidol University Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University Bangkok, Thailand
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Structural analysis of respiratory syncytial virus reveals the position of M2-1 between the matrix protein and the ribonucleoprotein complex. J Virol 2014; 88:7602-17. [PMID: 24760890 DOI: 10.1128/jvi.00256-14] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Respiratory syncytial virus (RSV), a member of the Paramyxoviridae family of nonsegmented, negative-sense, single-stranded RNA genome viruses, is a leading cause of lower respiratory tract infections in infants, young children, and the elderly or immunocompromised. There are many open questions regarding the processes that regulate human RSV (hRSV) assembly and budding. Here, using cryo-electron tomography, we identified virus particles that were spherical, filamentous, and asymmetric in structure, all within the same virus preparation. The three particle morphologies maintained a similar organization of the surface glycoproteins, matrix protein (M), M2-1, and the ribonucleoprotein (RNP). RNP filaments were traced in three dimensions (3D), and their total length was calculated. The measurements revealed the inclusion of multiple full-length genome copies per particle. RNP was associated with the membrane whenever the M layer was present. The amount of M coverage ranged from 24% to 86% in the different morphologies. Using fluorescence light microscopy (fLM), direct stochastic optical reconstruction microscopy (dSTORM), and a proximity ligation assay (PLA), we provide evidence illustrating that M2-1 is located between RNP and M in isolated viral particles. In addition, regular spacing of the M2-1 densities was resolved when hRSV viruses were imaged using Zernike phase contrast (ZPC) cryo-electron tomography. Our studies provide a more complete characterization of the hRSV virion structure and substantiation that M and M2-1 regulate virus organization. IMPORTANCE hRSV is a leading cause of lower respiratory tract infections in infants and young children as well as elderly or immunocompromised individuals. We used cryo-electron tomography and Zernike phase contrast cryo-electron tomography to visualize populations of purified hRSV in 3D. We observed the three distinct morphologies, spherical, filamentous, and asymmetric, which maintained comparable organizational profiles. Depending on the virus morphology examined, the amount of M ranged from 24% to 86%. We complemented the cryo-imaging studies with fluorescence microscopy, dSTORM, and a proximity ligation assay to provide additional evidence that M2-1 is incorporated into viral particles and is positioned between M and RNP. The results highlight the impact of M and M2-1 on the regulation of hRSV organization.
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