1
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Galaz-Montoya JG. The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography. Front Mol Biosci 2024; 11:1390858. [PMID: 38868297 PMCID: PMC11167099 DOI: 10.3389/fmolb.2024.1390858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near-atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing toward delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET enables the visualization of cellular and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly enhanced and supported by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by "big data" in cryoET of tissues, cells, and macromolecules, offering the promise of enabling novel, quantitative insights into disease processes, which may translate into the clinic and lead to improved diagnostics and targeted therapeutics.
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Affiliation(s)
- Jesús G. Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, United States
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2
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Van Veen D, Galaz-Montoya JG, Shen L, Baldwin P, Chaudhari AS, Lyumkis D, Schmid MF, Chiu W, Pauly J. Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. Int J Mol Sci 2024; 25:5473. [PMID: 38791508 PMCID: PMC11121946 DOI: 10.3390/ijms25105473] [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: 04/10/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3-20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.
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Affiliation(s)
- Dave Van Veen
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA;
| | - Jesús G. Galaz-Montoya
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; (J.G.G.-M.); (W.C.)
| | - Liyue Shen
- Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Philip Baldwin
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA 92037, USA;
| | | | - Dmitry Lyumkis
- Department of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA 92037, USA;
- Graduate School of Biological Sciences, University of California San Diego, La Jolla, CA 92037, USA
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA;
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; (J.G.G.-M.); (W.C.)
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA;
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John Pauly
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA;
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3
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Van Veen D, Galaz-Montoya JG, Shen L, Baldwin P, Chaudhari AS, Lyumkis D, Schmid MF, Chiu W, Pauly J. Missing Wedge Completion via Unsupervised Learning with Coordinate Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589090. [PMID: 38712113 PMCID: PMC11071277 DOI: 10.1101/2024.04.12.589090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3 - 20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.
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Affiliation(s)
- Dave Van Veen
- Dept. of Electrical Engineering, Stanford University
| | | | - Liyue Shen
- Dept. of Electrical and Computer Engineering, University of Michigan
| | - Philip Baldwin
- Dept. of Biochemistry and Molecular Pharmacology, Baylor College of Medicine
- Dept. of Genetics, The Salk Institute for Biological Sciences
| | | | - Dmitry Lyumkis
- Dept. of Genetics, The Salk Institute for Biological Sciences
- Graduate School of Biological Sciences, University of California San Diego
| | - Michael F. Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory
| | - Wah Chiu
- Dept. of Bioengineering, Stanford University
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory
- Dept. of Microbiology and Immunology, Stanford University
| | - John Pauly
- Dept. of Electrical Engineering, Stanford University
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4
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Collier CP, Bolmatov D, Elkins JG, Katsaras J. Nanoscopic lipid domains determined by microscopy and neutron scattering. Methods 2024; 223:127-135. [PMID: 38331125 DOI: 10.1016/j.ymeth.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. In this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes.
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Affiliation(s)
- Charles P Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dima Bolmatov
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Neutron Scattering Division, Oak Ridge National Laboratorry, Oak Ridege, TN, USA
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5
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Ochner H, Bharat TAM. Charting the molecular landscape of the cell. Structure 2023; 31:1297-1305. [PMID: 37699393 PMCID: PMC7615466 DOI: 10.1016/j.str.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023]
Abstract
Biological function of macromolecules is closely tied to their cellular location, as well as to interactions with other molecules within the native environment of the cell. Therefore, to obtain detailed mechanistic insights into macromolecular functionality, one of the outstanding targets for structural biology is to produce an atomic-level understanding of the cell. One structural biology technique that has already been used to directly derive atomic models of macromolecules from cells, without any additional external information, is electron cryotomography (cryoET). In this perspective article, we discuss possible routes to chart the molecular landscape of the cell by advancing cryoET imaging as well as by embedding cryoET into correlative imaging workflows.
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Affiliation(s)
- Hannah Ochner
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK.
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6
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Laurent T, Carlson LA. The organization of double-stranded RNA in the chikungunya virus replication organelle. PLoS Negl Trop Dis 2023; 17:e0011404. [PMID: 37406010 DOI: 10.1371/journal.pntd.0011404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/22/2023] [Indexed: 07/07/2023] Open
Abstract
Alphaviruses are mosquito-borne, positive-sense single-stranded RNA viruses. Amongst the alphaviruses, chikungunya virus is notable as a large source of human illness, especially in tropical and subtropical regions. When they invade a cell, alphaviruses generate dedicated organelles for viral genome replication, so-called spherules. Spherules form as outward-facing buds at the plasma membrane, and it has recently been shown that the thin membrane neck that connects this membrane bud with the cytoplasm is guarded by a two-megadalton protein complex that contains all the enzymatic functions necessary for RNA replication. The lumen of the spherules contains a single copy of the negative-strand template RNA, present in a duplex with newly synthesized positive-sense RNA. Less is known about the organization of this double-stranded RNA as compared to the protein components of the spherule. Here, we analyzed cryo-electron tomograms of chikungunya virus spherules in terms of the organization of the double-stranded RNA replication intermediate. We find that the double-stranded RNA has a shortened apparent persistence length as compared to unconstrained double-stranded RNA. Around half of the genome is present in either of five conformations identified by subtomogram classification, each representing a relatively straight segment of ~25-32 nm. Finally, the RNA occupies the spherule lumen at a homogeneous density, but has a preferred orientation to be perpendicular to a vector pointing from the membrane neck towards the spherule center. Taken together, this analysis lays another piece of the puzzle of the highly coordinated alphavirus genome replication.
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Affiliation(s)
- Timothée Laurent
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå, Sweden
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå, Sweden
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7
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Dudek NK, Galaz-Montoya JG, Shi H, Mayer M, Danita C, Celis AI, Viehboeck T, Wu GH, Behr B, Bulgheresi S, Huang KC, Chiu W, Relman DA. Previously uncharacterized rectangular bacterial structures in the dolphin mouth. Nat Commun 2023; 14:2098. [PMID: 37055390 PMCID: PMC10102025 DOI: 10.1038/s41467-023-37638-y] [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: 11/01/2021] [Accepted: 03/23/2023] [Indexed: 04/15/2023] Open
Abstract
Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.
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Affiliation(s)
- Natasha K Dudek
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Quantori, Cambridge, MA, 02142, USA
| | | | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Megan Mayer
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Cristina Danita
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Arianna I Celis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tobias Viehboeck
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, and Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Gong-Her Wu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Barry Behr
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Silvia Bulgheresi
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, 94304, USA.
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8
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Danita C, Chiu W, Galaz-Montoya JG. Efficient manual annotation of cryogenic electron tomograms using IMOD. STAR Protoc 2022; 3:101658. [PMID: 36097385 PMCID: PMC9463458 DOI: 10.1016/j.xpro.2022.101658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/28/2022] [Accepted: 08/01/2022] [Indexed: 11/24/2022] Open
Abstract
Annotation highlights and segmentation isolates features in cryogenic electron tomograms to improve visualization and quantification of features (for example, their size and abundance, and spatial relationships with other features), facilitating phenotypic structural analyses of cellular tomograms. Here, we present a manual annotation protocol using the open-source software IMOD and describe segmentation of three types of common cellular features: membranes, large globules, and filaments. IMOD’s interpolation function can improve the speed of manual annotation up to an order of magnitude. Interpolation between sparsely annotated slices speeds up manual annotation Manual annotation differentiates between similar features in different contexts Turning annotations into segmentations shows actual data instead of representations of it
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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9
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Wang H, Liu L, Wang J, Li C, Hou J, Zheng K. The Development of iDPC-STEM and Its Application in Electron Beam Sensitive Materials. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123829. [PMID: 35744947 PMCID: PMC9231126 DOI: 10.3390/molecules27123829] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022]
Abstract
The main aspects of material research: material synthesis, material structure, and material properties, are interrelated. Acquiring atomic structure information of electron beam sensitive materials by electron microscope, such as porous zeolites, organic-inorganic hybrid perovskites, metal-organic frameworks, is an important and challenging task. The difficulties in characterization of the structures will inevitably limit the optimization of their synthesis methods and further improve their performance. The emergence of integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM), a STEM characterization technique capable of obtaining images with high signal-to-noise ratio under lower doses, has made great breakthroughs in the atomic structure characterization of these materials. This article reviews the developments and applications of iDPC-STEM in electron beam sensitive materials, and provides an outlook on its capabilities and development.
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10
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Böhning J, Bharat TAM, Collins SM. Compressed sensing for electron cryotomography and high-resolution subtomogram averaging of biological specimens. Structure 2022; 30:408-417.e4. [PMID: 35051366 PMCID: PMC8919266 DOI: 10.1016/j.str.2021.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/21/2021] [Accepted: 12/22/2021] [Indexed: 11/07/2022]
Abstract
Cryoelectron tomography (cryo-ET) and subtomogram averaging (STA) allow direct visualization and structural studies of biological macromolecules in their native cellular environment, in situ. Often, low signal-to-noise ratios in tomograms, low particle abundance within the cell, and low throughput in typical cryo-ET workflows severely limit the obtainable structural information. To help mitigate these limitations, here we apply a compressed sensing approach using 3D second-order total variation (CS-TV2) to tomographic reconstruction. We show that CS-TV2 increases the signal-to-noise ratio in tomograms, enhancing direct visualization of macromolecules, while preserving high-resolution information up to the secondary structure level. We show that, particularly with small datasets, CS-TV2 allows improvement of the resolution of STA maps. We further demonstrate that the CS-TV2 algorithm is applicable to cellular specimens, leading to increased visibility of molecular detail within tomograms. This work highlights the potential of compressed sensing-based reconstruction algorithms for cryo-ET and in situ structural biology. Compressed sensing (CS-TV2) for cryo-ET using 3D second-order total variation CS-TV2 increases signal contrast while retaining high-resolution information Improved subtomogram averaging from CS-TV2 reconstructions of small datasets Increased contrast and detail in CS-TV2 reconstructions of cellular specimens
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Affiliation(s)
- Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Sean M Collins
- School of Chemical and Process Engineering & School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.
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11
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Perspective: Emerging strategies for determining atomic-resolution structures of macromolecular complexes within cells. J Struct Biol 2021; 214:107827. [PMID: 34915129 PMCID: PMC8978977 DOI: 10.1016/j.jsb.2021.107827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 11/28/2022]
Abstract
In principle, electron cryo-tomography (cryo-ET) of thin portions of cells provides high-resolution images of the three-dimensional spatial arrangement of all members of the proteome. In practice, however, radiation damage creates a tension between recording images at many different tilt angles, but at correspondingly reduced exposure levels, versus limiting the number of tilt angles in order to improve the signal-to-noise ratio (SNR). Either way, it is challenging to read the available information out at the level of atomic structure. Here, we first review work that explores the optimal strategy for data collection, which currently seems to favor the use of a limited angular range for tilting the sample or even the use of a single image to record the high-resolution information. Looking then to the future, we point to the alternative of so-called “deconvolution microscopy”, which may be applied to tilt-series or optically-sectioned, focal series data. Recording data as a focal series has the advantage that little or no translational alignment of frames might be needed, and a three-dimensional reconstruction might require only 2/3 the number of images as does standard tomography. We also point to the unexploited potential of phase plates to increase the contrast, and thus to reduce the electron exposure levels while retaining the ability align and merge the data. In turn, using much lower exposures per image could have the advantage that high-resolution information is retained throughout the full data-set, whether recorded as a tilt series or a focal series of images.
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12
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Zeng X, Howe G, Xu M. End-to-end robust joint unsupervised image alignment and clustering. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON COMPUTER VISION 2021; 2021:3834-3846. [PMID: 35392630 PMCID: PMC8986091 DOI: 10.1109/iccv48922.2021.00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Computing dense pixel-to-pixel image correspondences is a fundamental task of computer vision. Often, the objective is to align image pairs from the same semantic category for manipulation or segmentation purposes. Despite achieving superior performance, existing deep learning alignment methods cannot cluster images; consequently, clustering and pairing images needed to be a separate laborious and expensive step. Given a dataset with diverse semantic categories, we propose a multi-task model, Jim-Net, that can directly learn to cluster and align images without any pixel-level or image-level annotations. We design a pair-matching alignment unsupervised training algorithm that selectively matches and aligns image pairs from the clustering branch. Our unsupervised Jim-Net achieves comparable accuracy with state-of-the-art supervised methods on benchmark 2D image alignment dataset PF-PASCAL. Specifically, we apply Jim-Net to cryo-electron tomography, a revolutionary 3D microscopy imaging technique of native subcellular structures. After extensive evaluation on seven datasets, we demonstrate that Jim-Net enables systematic discovery and recovery of representative macromolecular structures in situ, which is essential for revealing molecular mechanisms underlying cellular functions. To our knowledge, Jim-Net is the first end-to-end model that can simultaneously align and cluster images, which significantly improves the performance as compared to performing each task alone.
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13
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Han R, Li L, Yang P, Zhang F, Gao X. A novel constrained reconstruction model towards high-resolution subtomogram averaging. Bioinformatics 2021; 37:1616-1626. [PMID: 31617571 DOI: 10.1093/bioinformatics/btz787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/12/2019] [Accepted: 10/14/2019] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION Electron tomography (ET) offers a unique capacity to image biological structures in situ. However, the resolution of ET reconstructed tomograms is not comparable to that of the single-particle cryo-EM. If many copies of the object of interest are present in the tomograms, their structures can be reconstructed in the tomogram, picked, aligned and averaged to increase the signal-to-noise ratio and improve the resolution, which is known as the subtomogram averaging. To date, the resolution improvement of the subtomogram averaging is still limited because each reconstructed subtomogram is of low reconstruction quality due to the missing wedge issue. RESULTS In this article, we propose a novel computational model, the constrained reconstruction model (CRM), to better recover the information from the multiple subtomograms and compensate for the missing wedge issue in each of them. CRM is supposed to produce a refined reconstruction in the final turn of subtomogram averaging after alignment, instead of directly taking the average. We first formulate the averaging method and our CRM as linear systems, and prove that the solution space of CRM is no larger, and in practice much smaller, than that of the averaging method. We then propose a sparse Kaczmarz algorithm to solve the formulated CRM, and further extend the solution to the simultaneous algebraic reconstruction technique (SART). Experimental results demonstrate that CRM can significantly alleviate the missing wedge issue and improve the final reconstruction quality. In addition, our model is robust to the number of images in each tilt series, the tilt range and the noise level. AVAILABILITY AND IMPLEMENTATION The codes of CRM-SIRT and CRM-SART are available at https://github.com/icthrm/CRM. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Renmin Han
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Lun Li
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, 100190 Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng Yang
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Fa Zhang
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, 100190 Beijing, China
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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14
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Cryo-electron tomography provides topological insights into mutant huntingtin exon 1 and polyQ aggregates. Commun Biol 2021; 4:849. [PMID: 34239038 PMCID: PMC8266869 DOI: 10.1038/s42003-021-02360-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/15/2021] [Indexed: 01/27/2023] Open
Abstract
Huntington disease (HD) is a neurodegenerative trinucleotide repeat disorder caused by an expanded poly-glutamine (polyQ) tract in the mutant huntingtin (mHTT) protein. The formation and topology of filamentous mHTT inclusions in the brain (hallmarks of HD implicated in neurotoxicity) remain elusive. Using cryo-electron tomography and subtomogram averaging, here we show that mHTT exon 1 and polyQ-only aggregates in vitro are structurally heterogenous and filamentous, similar to prior observations with other methods. Yet, we find filaments in both types of aggregates under ~2 nm in width, thinner than previously reported, and regions forming large sheets. In addition, our data show a prevalent subpopulation of filaments exhibiting a lumpy slab morphology in both aggregates, supportive of the polyQ core model. This provides a basis for future cryoET studies of various aggregated mHTT and polyQ constructs to improve their structure-based modeling as well as their identification in cells without fusion tags.
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15
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Wensel TG, Potter VL, Moye A, Zhang Z, Robichaux MA. Structure and dynamics of photoreceptor sensory cilia. Pflugers Arch 2021; 473:1517-1537. [PMID: 34050409 DOI: 10.1007/s00424-021-02564-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023]
Abstract
The rod and cone photoreceptor cells of the vertebrate retina have highly specialized structures that enable them to carry out their function of light detection over a broad range of illumination intensities with optimized spatial and temporal resolution. Most prominent are their unusually large sensory cilia, consisting of outer segments packed with photosensitive disc membranes, a connecting cilium with many features reminiscent of the primary cilium transition zone, and a pair of centrioles forming a basal body which serves as the platform upon which the ciliary axoneme is assembled. These structures form a highway through which an enormous flux of material moves on a daily basis to sustain the continual turnover of outer segment discs and the energetic demands of phototransduction. After decades of study, the details of the fine structure and distribution of molecular components of these structures are still incompletely understood, but recent advances in cellular imaging techniques and animal models of inherited ciliary defects are yielding important new insights. This knowledge informs our understanding both of the mechanisms of trafficking and assembly and of the pathophysiological mechanisms of human blinding ciliopathies.
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Affiliation(s)
- Theodore G Wensel
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology and Developmental Biology Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Valencia L Potter
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology and Developmental Biology Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program (MSTP), Baylor College of Medicine, Houston, TX, 77030, USA
| | - Abigail Moye
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhixian Zhang
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael A Robichaux
- Departments of Ophthalmology and Biochemistry, West Virginia University, Morgantown, WV, USA
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16
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Lévy D, Di Cicco A, Bertin A, Dezi M. [Cryo-electron microcopy for a new vision of the cell and its components]. Med Sci (Paris) 2021; 37:379-385. [PMID: 33908856 DOI: 10.1051/medsci/2021034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) is a technique for imaging biological samples that plays a central role in structural biology, with high impact on research fields such as cell and developmental biology, bioinformatics, cell physics and applied mathematics. It allows the determination of structures of purified proteins within cells. This review describes the main recent advances in cryo-EM, illustrated by examples of proteins of biomedical interest, and the avenues for future development.
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Affiliation(s)
- Daniel Lévy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 168, Laboratoire Physico- Chimie Curie, 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Aurélie Di Cicco
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 168, Laboratoire Physico- Chimie Curie, 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Aurélie Bertin
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 168, Laboratoire Physico- Chimie Curie, 11 rue Pierre et Marie Curie, 75005 Paris, France
| | - Manuela Dezi
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR 168, Laboratoire Physico- Chimie Curie, 11 rue Pierre et Marie Curie, 75005 Paris, France
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17
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Chreifi G, Chen S, Jensen GJ. Rapid tilt-series method for cryo-electron tomography: Characterizing stage behavior during FISE acquisition. J Struct Biol 2021; 213:107716. [PMID: 33713788 DOI: 10.1016/j.jsb.2021.107716] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
We and others recently developed rapid tilt-series acquisition methods for cryo-electron tomography on a Titan Krios G3i equipped with a single axis holder and a K-series direct electron detector and showed that one of these, the fast-incremental single exposure (FISE) method, significantly accelerates tilt-series acquisition when compared to traditional methods while preserving the quality of the images. Here, we characterize the behavior of our single axis holder in detail during a FISE experiment to optimally balance data quality with speed. We explain our methodology in detail so others can characterize their own stages, and conclude with recommendations for projects with different resolution goals.
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Affiliation(s)
- Georges Chreifi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Songye Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States; Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States; Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States; Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84604, United States.
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18
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Baldwin PR, Lyumkis D. Tools for visualizing and analyzing Fourier space sampling in Cryo-EM. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 160:53-65. [PMID: 32645314 PMCID: PMC7785567 DOI: 10.1016/j.pbiomolbio.2020.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022]
Abstract
A complete understanding of how an orientation distribution contributes to a cryo-EM reconstruction remains lacking. It is necessary to begin critically assessing the set of views to gain an understanding of its effect on experimental reconstructions. Toward that end, we recently suggested that the type of orientation distribution may alter resolution measures in a systematic manner. We introduced the sampling compensation factor (SCF), which incorporates how the collection geometry might change the spectral signal-to-noise ratio (SSNR), irrespective of the other experimental aspects. We show here that knowledge of the sampling restricted to spherical surfaces of sufficiently large radii in Fourier space is equivalent to knowledge of the set of projection views. Moreover, the SCF geometrical factor may be calculated from one such surface. To aid cryo-EM practitioners, we developed a graphical user interface (GUI) tool that evaluates experimental orientation distributions. The GUI returns plots of projection directions, sampling constrained to the surface of a sphere, the SCF value, the fraction of the empty region of Fourier space, and a histogram of the sampling values over the points on a sphere. Finally, a fixed tilt angle may be incorporated to determine how tilting the grid during collection may improve the distribution of views and Fourier space sampling. We advocate this simple conception of sampling and the use of such tools as a complement to the distribution of views to capture the different aspects of the effect of projection directions on cryo-EM reconstructions.
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Affiliation(s)
- Philip R Baldwin
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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19
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Fake It 'Till You Make It-The Pursuit of Suitable Membrane Mimetics for Membrane Protein Biophysics. Int J Mol Sci 2020; 22:ijms22010050. [PMID: 33374526 PMCID: PMC7793082 DOI: 10.3390/ijms22010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022] Open
Abstract
Membrane proteins evolved to reside in the hydrophobic lipid bilayers of cellular membranes. Therefore, membrane proteins bridge the different aqueous compartments separated by the membrane, and furthermore, dynamically interact with their surrounding lipid environment. The latter not only stabilizes membrane proteins, but directly impacts their folding, structure and function. In order to be characterized with biophysical and structural biological methods, membrane proteins are typically extracted and subsequently purified from their native lipid environment. This approach requires that lipid membranes are replaced by suitable surrogates, which ideally closely mimic the native bilayer, in order to maintain the membrane proteins structural and functional integrity. In this review, we survey the currently available membrane mimetic environments ranging from detergent micelles to bicelles, nanodiscs, lipidic-cubic phase (LCP), liposomes, and polymersomes. We discuss their respective advantages and disadvantages as well as their suitability for downstream biophysical and structural characterization. Finally, we take a look at ongoing methodological developments, which aim for direct in-situ characterization of membrane proteins within native membranes instead of relying on membrane mimetics.
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20
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Chen Q, Dwyer C, Sheng G, Zhu C, Li X, Zheng C, Zhu Y. Imaging Beam-Sensitive Materials by Electron Microscopy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1907619. [PMID: 32108394 DOI: 10.1002/adma.201907619] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/20/2019] [Indexed: 05/15/2023]
Abstract
Electron microscopy allows the extraction of multidimensional spatiotemporally correlated structural information of diverse materials down to atomic resolution, which is essential for figuring out their structure-property relationships. Unfortunately, the high-energy electrons that carry this important information can cause damage by modulating the structures of the materials. This has become a significant problem concerning the recent boost in materials science applications of a wide range of beam-sensitive materials, including metal-organic frameworks, covalent-organic frameworks, organic-inorganic hybrid materials, 2D materials, and zeolites. To this end, developing electron microscopy techniques that minimize the electron beam damage for the extraction of intrinsic structural information turns out to be a compelling but challenging need. This article provides a comprehensive review on the revolutionary strategies toward the electron microscopic imaging of beam-sensitive materials and associated materials science discoveries, based on the principles of electron-matter interaction and mechanisms of electron beam damage. Finally, perspectives and future trends in this field are put forward.
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Affiliation(s)
- Qiaoli Chen
- Center for Electron Microscopy, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Christian Dwyer
- Department of Physics, Arizona State University, Tempe, AZ, 85287-1504, USA
| | - Guan Sheng
- Advanced Membranes and Porous Materials Center, Physical Science and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Chongzhi Zhu
- Center for Electron Microscopy, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaonian Li
- Center for Electron Microscopy, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Changlin Zheng
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, 200438, China
| | - Yihan Zhu
- Center for Electron Microscopy, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, 310014, China
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21
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Unravelling the Stability and Capsid Dynamics of the Three Virions of Brome Mosaic Virus Assembled Autonomously In Vivo. J Virol 2020; 94:JVI.01794-19. [PMID: 31996436 DOI: 10.1128/jvi.01794-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022] Open
Abstract
Viral capsids are dynamic assemblies that undergo controlled conformational transitions to perform various biological functions. The replication-derived four-molecule RNA progeny of Brome mosaic virus (BMV) is packaged by a single capsid protein (CP) into three types of morphologically indistinguishable icosahedral virions with T=3 quasisymmetry. Type 1 (B1V) and type 2 (B2V) virions package genomic RNA1 and RNA2, respectively, while type 3 (B3+4V) virions copackage genomic RNA3 (B3) and its subgenomic RNA4 (sgB4). In this study, the application of a robust Agrobacterium-mediated transient expression system allowed us to assemble each virion type separately in planta Experimental approaches analyzing the morphology, size, and electrophoretic mobility failed to distinguish between the virion types. Thermal denaturation analysis and protease-based peptide mass mapping experiments were used to analyze stability and the conformational dynamics of the individual virions, respectively. The crystallographic structure of the BMV capsid shows four trypsin cleavage sites (K65, R103, K111, and K165 on the CP subunits) exposed on the exterior of the capsid. Irrespective of the digestion time, while retaining their capsid structural integrity, B1V and B2V released a single peptide encompassing amino acids 2 to 8 of the N-proximal arginine-rich RNA binding motif. In contrast, B3+4V capsids were unstable with trypsin, releasing several peptides in addition to the peptides encompassing four predicted sites exposed on the capsid exterior. These results, demonstrating qualitatively different dynamics for the three types of BMV virions, suggest that the different RNA genes they contain may have different translational timing and efficiency and may even impart different structures to their capsids.IMPORTANCE The majority of viruses contain RNA genomes protected by a shell of capsid proteins. Although crystallographic studies show that viral capsids are static structures, accumulating evidence suggests that, in solution, virions are highly dynamic assemblies. The three genomic RNAs (RNA1, -2, and -3) and a single subgenomic RNA (RNA4) of Brome mosaic virus (BMV), an RNA virus pathogenic to plants, are distributed among three physically homogeneous virions. This study examines the thermal stability by differential scanning fluorimetry (DSF) and capsid dynamics by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analyses following trypsin digestion of the three virions assembled separately in vivo using the Agrobacterium-mediated transient expression approach. The results provide compelling evidence that virions packaging genomic RNA1 and -2 are distinct from those copackaging RNA3 and -4 in their stability and dynamics, suggesting that RNA-dependent capsid dynamics play an important biological role in the viral life cycle.
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22
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Liu Y, Yuan B, Peng L, Zhao J, Cheng B, Huang Y, Zheng X, Zhou Y, Xiang S, Zhu L, Wu Y. Single-particle analysis of urea amidolyase reveals its molecular mechanism. Protein Sci 2020; 29:1242-1249. [PMID: 32105377 DOI: 10.1002/pro.3847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 11/08/2022]
Abstract
Urea amidolyase (UA), a bifunctional enzyme that is widely distributed in bacteria, fungi, algae, and plants, plays a pivotal role in the recycling of nitrogen in the biosphere. Its substrate urea is ultimately converted to ammonium, via successive catalysis at the C-terminal urea carboxylase (UC) domain and followed by the N-terminal allophanate hydrolyse (AH) domain. Although our previous studies have shown that Kluyveromyces lactis UA (KlUA) functions efficiently as a homodimer, the architecture of the full-length enzyme remains unresolved. Thus how the biotin carboxyl carrier protein (BCCP) domain is transferred within the UC domain remains unclear. Here we report the structures of full-length KlUA in its homodimer form in three different functional states by negatively-stained single-particle electron microscopy. We report here that the ADP-bound structure with or without urea shows two possible locations of BCCP with preferred asymmetry, and that when BCCP is attached to the carboxyl transferase domain of one monomer, it is attached to the biotin carboxylase domain in the second domain. Based on this observation, we propose a BCCP-swinging model for biotin-dependent carboxylation mechanism of this enzyme.
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Affiliation(s)
- Ying Liu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Bin Yuan
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Liang Peng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jing Zhao
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Bin Cheng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yuhua Huang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xinxing Zheng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yuerong Zhou
- College of Marine and Biochemical Engineering, Fujian Normal University, Fuzhou, China
| | - Song Xiang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, Tianjin, China
| | - Li Zhu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yi Wu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
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23
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Abstract
Cryo-electron tomography (cryo-ET) allows three-dimensional (3D) visualization of frozen-hydrated biological samples, such as protein complexes and cell organelles, in near-native environments at nanometer scale. Protein complexes that are present in multiple copies in a set of tomograms can be extracted, mutually aligned, and averaged to yield a signal-enhanced 3D structure up to sub-nanometer or even near-atomic resolution. This technique, called subtomogram averaging (StA), is powered by improvements in EM hardware and image processing software. Importantly, StA provides unique biological insights into the structure and function of cellular machinery in close-to-native contexts. In this chapter, we describe the principles and key steps of StA. We briefly cover sample preparation and data collection with an emphasis on image processing procedures related to tomographic reconstruction, subtomogram alignment, averaging, and classification. We conclude by summarizing current limitations and future directions of this technique with a focus on high-resolution StA.
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Yi X, Verbeke EJ, Chang Y, Dickinson DJ, Taylor DW. Electron microscopy snapshots of single particles from single cells. J Biol Chem 2018; 294:1602-1608. [PMID: 30541924 PMCID: PMC6364765 DOI: 10.1074/jbc.ra118.006686] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/07/2018] [Indexed: 12/15/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) has become an indispensable tool for structural studies of biological macromolecules. Two additional predominant methods are available for studying the architectures of multiprotein complexes: 1) single-particle analysis of purified samples and 2) tomography of whole cells or cell sections. The former can produce high-resolution structures but is limited to highly purified samples, whereas the latter can capture proteins in their native state but has a low signal-to-noise ratio and yields lower-resolution structures. Here, we present a simple, adaptable method combining microfluidic single-cell extraction with single-particle analysis by EM to characterize protein complexes from individual Caenorhabditis elegans embryos. Using this approach, we uncover 3D structures of ribosomes directly from single embryo extracts. Moreover, we investigated structural dynamics during development by counting the number of ribosomes per polysome in early and late embryos. This approach has significant potential applications for counting protein complexes and studying protein architectures from single cells in developmental, evolutionary, and disease contexts.
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Affiliation(s)
- Xiunan Yi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Eric J Verbeke
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Yiran Chang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| | - Daniel J Dickinson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712.
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712; LIVESTRONG Cancer Institute, Dell Medical School, Austin, Texas 78712.
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25
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Melia CE, Bharat TAM. Locating macromolecules and determining structures inside bacterial cells using electron cryotomography. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:973-981. [PMID: 29908328 PMCID: PMC6052677 DOI: 10.1016/j.bbapap.2018.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Electron cryotomography (cryo-ET) is an imaging technique uniquely suited to the study of bacterial ultrastructure and cell biology. Recent years have seen a surge in structural and cell biology research on bacteria using cryo-ET. This research has driven major technical developments in the field, with applications emerging to address a wide range of biological questions. In this review, we explore the diversity of cryo-ET approaches used for structural and cellular microbiology, with a focus on in situ localization and structure determination of macromolecules. The first section describes strategies employed to locate target macromolecules within large cellular volumes. Next, we explore methods to study thick specimens by sample thinning. Finally, we review examples of macromolecular structure determination in a cellular context using cryo-ET. The examples outlined serve as powerful demonstrations of how the cellular location, structure, and function of any bacterial macromolecule of interest can be investigated using cryo-ET.
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Affiliation(s)
- Charlotte E Melia
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Central Oxford Structural and Molecular Imaging Centre, University of Oxford, Oxford OX1 3RE, United Kingdom.
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26
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Jin J, Galaz-Montoya JG, Sherman MB, Sun SY, Goldsmith CS, O'Toole ET, Ackerman L, Carlson LA, Weaver SC, Chiu W, Simmons G. Neutralizing Antibodies Inhibit Chikungunya Virus Budding at the Plasma Membrane. Cell Host Microbe 2018; 24:417-428.e5. [PMID: 30146390 DOI: 10.1016/j.chom.2018.07.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/05/2018] [Accepted: 07/26/2018] [Indexed: 01/29/2023]
Abstract
Neutralizing antibodies (NAbs) are traditionally thought to inhibit virus infection by preventing virion entry into target cells. In addition, antibodies can engage Fc receptors (FcRs) on immune cells to activate antiviral responses. We describe a mechanism by which NAbs inhibit chikungunya virus (CHIKV), the most common alphavirus infecting humans, by preventing virus budding from infected human cells and activating IgG-specific Fcγ receptors. NAbs bind to CHIKV glycoproteins on the infected cell surface and induce glycoprotein coalescence, preventing budding of nascent virions and leaving structurally heterogeneous nucleocapsids arrested in the cytosol. Furthermore, NAbs induce clustering of CHIKV replication spherules at sites of budding blockage. Functionally, these densely packed glycoprotein-NAb complexes on infected cells activate Fcγ receptors, inducing a strong, antibody-dependent, cell-mediated cytotoxicity response from immune effector cells. Our findings describe a triply functional antiviral pathway for NAbs that might be broadly applicable across virus-host systems, suggesting avenues for therapeutic innovation through antibody design.
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Affiliation(s)
- Jing Jin
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Jesús G Galaz-Montoya
- Departments of Bioengineering, Microbiology and Immunology, and Photon Science, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Stella Y Sun
- Departments of Bioengineering, Microbiology and Immunology, and Photon Science, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Cynthia S Goldsmith
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Eileen T O'Toole
- Boulder Laboratory for 3-D Electron Microscopy of Cells, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Larry Ackerman
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Scott C Weaver
- Institute for Human Infections and Immunity and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Wah Chiu
- Departments of Bioengineering, Microbiology and Immunology, and Photon Science, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Graham Simmons
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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27
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Dutta M. Recent Advances in Single Particle Cryo-electron Microscopy and Cryo-electron Tomography to Determine the Structures of Biological Macromolecules. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0087-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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28
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IgG Antibody 3D Structures and Dynamics. Antibodies (Basel) 2018; 7:antib7020018. [PMID: 31544870 PMCID: PMC6698877 DOI: 10.3390/antib7020018] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/19/2022] Open
Abstract
Antibodies are vital for human health because of their ability to function as nature's drugs by protecting the body from infection. In recent decades, antibodies have been used as pharmaceutics for targeted therapy in patients with cancer, autoimmune diseases, and cardiovascular diseases. Capturing the dynamic structure of antibodies and characterizing antibody fluctuation is critical for gaining a deeper understanding of their structural characteristics and for improving drug development. Current techniques for studying three-dimensional (3D) structural heterogeneity and variability of proteins have limitations in ascertaining the dynamic structural behavior of antibodies and antibody-antigen complexes. Here, we review current techniques used to study antibody structures with a focus on the recently developed individual-particle electron tomography (IPET) technique. IPET, as a particle-by-particle methodology for 3D structural characterization, has shown advantages in studying structural variety and conformational changes of antibodies, providing direct imaging data for biomolecular engineering to improve development and clinical application of synthetic antibodies.
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Abstract
Experimental methods for the characterization of protein complexes have been instrumental in achieving our current understanding of the protein universe and continue to progress with each year that passes. In this chapter, we review some of the most important tools and techniques in the field, covering the important points in X-ray crystallography, cryo-electron microscopy, NMR spectroscopy, and mass spectrometry. Novel developments are making it possible to study large protein complexes at near-atomic resolutions, and we also now have the ability to study the dynamics and assembly pathways of protein complexes across a range of sizes.
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Affiliation(s)
- Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
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Johnston CM, Krafft AJ, Russe MF, Rog-Zielinska EA. A new look at the heart-novel imaging techniques. Herzschrittmacherther Elektrophysiol 2017; 29:14-23. [PMID: 29242981 DOI: 10.1007/s00399-017-0546-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/24/2017] [Indexed: 01/20/2023]
Abstract
The development and successful implementation of cutting-edge imaging technologies to visualise cardiac anatomy and function is a key component of effective diagnostic efforts in cardiology. Here, we describe a number of recent exciting advances in the field of cardiology spanning from macro- to micro- to nano-scales of observation, including magnetic resonance imaging, computed tomography, optical mapping, photoacoustic imaging, and electron tomography. The methodologies discussed are currently making the transition from scientific research to routine clinical use, albeit at different paces. We discuss the most likely trajectory of this transition into clinical research and standard diagnostics, and highlight the key challenges and opportunities associated with each of the methodologies.
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Affiliation(s)
- C M Johnston
- Institute for Experimental Cardiovascular Medicine, University Heart Center, Medical Center - University of Freiburg, and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - A J Krafft
- Department of Radiology, Medical Physics, Medical Center - Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - M F Russe
- Department of Radiology, Medical Center - Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - E A Rog-Zielinska
- Institute for Experimental Cardiovascular Medicine, University Heart Center, Medical Center - University of Freiburg, and Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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