1
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Maurer VJ, Siggel M, Kosinski J. What shapes template-matching performance in cryogenic electron tomography in situ? Acta Crystallogr D Struct Biol 2024; 80:410-420. [PMID: 38805246 PMCID: PMC11154592 DOI: 10.1107/s2059798324004303] [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: 02/22/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
The detection of specific biological macromolecules in cryogenic electron tomography data is frequently approached by applying cross-correlation-based 3D template matching. To reduce computational cost and noise, high binning is used to aggregate voxels before template matching. This remains a prevalent practice in both practical applications and methods development. Here, the relation between template size, shape and angular sampling is systematically evaluated to identify ribosomes in a ground-truth annotated data set. It is shown that at the commonly used binning, a detailed subtomogram average, a sphere and a heart emoji result in near-identical performance. These findings indicate that with current template-matching practices macromolecules can only be detected with high precision if their shape and size are sufficiently different from the background. Using theoretical considerations, the experimental results are rationalized and it is discussed why primarily low-frequency information remains at high binning and that template matching fails to be accurate because similarly shaped and sized macromolecules have similar low-frequency spectra. These challenges are discussed and potential enhancements for future template-matching methodologies are proposed.
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Affiliation(s)
- Valentin J. Maurer
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, 22607 Hamburg, Germany
| | - Marc Siggel
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, 22607 Hamburg, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, 22607 Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Notkestrasse 85, 22607 Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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2
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Eckstein N, Bates AS, Champion A, Du M, Yin Y, Schlegel P, Lu AKY, Rymer T, Finley-May S, Paterson T, Parekh R, Dorkenwald S, Matsliah A, Yu SC, McKellar C, Sterling A, Eichler K, Costa M, Seung S, Murthy M, Hartenstein V, Jefferis GSXE, Funke J. Neurotransmitter classification from electron microscopy images at synaptic sites in Drosophila melanogaster. Cell 2024; 187:2574-2594.e23. [PMID: 38729112 PMCID: PMC11106717 DOI: 10.1016/j.cell.2024.03.016] [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: 04/02/2023] [Revised: 10/04/2023] [Accepted: 03/13/2024] [Indexed: 05/12/2024]
Abstract
High-resolution electron microscopy of nervous systems has enabled the reconstruction of synaptic connectomes. However, we do not know the synaptic sign for each connection (i.e., whether a connection is excitatory or inhibitory), which is implied by the released transmitter. We demonstrate that artificial neural networks can predict transmitter types for presynapses from electron micrographs: a network trained to predict six transmitters (acetylcholine, glutamate, GABA, serotonin, dopamine, octopamine) achieves an accuracy of 87% for individual synapses, 94% for neurons, and 91% for known cell types across a D. melanogaster whole brain. We visualize the ultrastructural features used for prediction, discovering subtle but significant differences between transmitter phenotypes. We also analyze transmitter distributions across the brain and find that neurons that develop together largely express only one fast-acting transmitter (acetylcholine, glutamate, or GABA). We hope that our publicly available predictions act as an accelerant for neuroscientific hypothesis generation for the fly.
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Affiliation(s)
- Nils Eckstein
- HHMI Janelia Research Campus, Ashburn, VA, USA; Institute of Neuroinformatics UZH/ETHZ, Zurich, Switzerland
| | - Alexander Shakeel Bates
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Centre for Neural Circuits and Behaviour, The University of Oxford, Tinsley Building, Mansfield Road, Oxford OX1 3SR, UK; Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew Champion
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Michelle Du
- HHMI Janelia Research Campus, Ashburn, VA, USA
| | - Yijie Yin
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Philipp Schlegel
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | - Sven Dorkenwald
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Arie Matsliah
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Szi-Chieh Yu
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Claire McKellar
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Amy Sterling
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Katharina Eichler
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Marta Costa
- Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Sebastian Seung
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Mala Murthy
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Volker Hartenstein
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gregory S X E Jefferis
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK; Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Jan Funke
- HHMI Janelia Research Campus, Ashburn, VA, USA.
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3
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Nogales E, Mahamid J. Bridging structural and cell biology with cryo-electron microscopy. Nature 2024; 628:47-56. [PMID: 38570716 DOI: 10.1038/s41586-024-07198-2] [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: 07/18/2023] [Accepted: 02/13/2024] [Indexed: 04/05/2024]
Abstract
Most life scientists would agree that understanding how cellular processes work requires structural knowledge about the macromolecules involved. For example, deciphering the double-helical nature of DNA revealed essential aspects of how genetic information is stored, copied and repaired. Yet, being reductionist in nature, structural biology requires the purification of large amounts of macromolecules, often trimmed off larger functional units. The advent of cryogenic electron microscopy (cryo-EM) greatly facilitated the study of large, functional complexes and generally of samples that are hard to express, purify and/or crystallize. Nevertheless, cryo-EM still requires purification and thus visualization outside of the natural context in which macromolecules operate and coexist. Conversely, cell biologists have been imaging cells using a number of fast-evolving techniques that keep expanding their spatial and temporal reach, but always far from the resolution at which chemistry can be understood. Thus, structural and cell biology provide complementary, yet unconnected visions of the inner workings of cells. Here we discuss how the interplay between cryo-EM and cryo-electron tomography, as a connecting bridge to visualize macromolecules in situ, holds great promise to create comprehensive structural depictions of macromolecules as they interact in complex mixtures or, ultimately, inside the cell itself.
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Affiliation(s)
- Eva Nogales
- Molecular and Cell Biology Department, Institute for Quantitative Biomedicine, University of California, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Berkeley, CA, USA.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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4
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Collette D, Dunlap D, Finzi L. Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo. Int J Mol Sci 2023; 24:17502. [PMID: 38139331 PMCID: PMC10744201 DOI: 10.3390/ijms242417502] [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: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.
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Affiliation(s)
| | | | - Laura Finzi
- Department of Physics, College of Arts & Sciences, Emory University, Atlanta, GA 30322, USA; (D.C.); (D.D.)
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5
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Lucas BA, Himes BA, Grigorieff N. Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias. eLife 2023; 12:RP90486. [PMID: 38010355 PMCID: PMC10681363 DOI: 10.7554/elife.90486] [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] [Indexed: 11/29/2023] Open
Abstract
Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and cellular background (Lucas et al., 2021; Lucas et al., 2022). Here, we show that once localized, these particles may be averaged together to generate high-resolution 3D reconstructions. However, regions included in the template may suffer from template bias, leading to inflated resolution estimates and making the interpretation of high-resolution features unreliable. We evaluate conditions that minimize template bias while retaining the benefits of high-precision localization, and we show that molecular features not present in the template can be reconstructed at high resolution from targets found by 2DTM, extending prior work at low-resolution. Moreover, we present a quantitative metric for template bias to aid the interpretation of 3D reconstructions calculated with particles localized using high-resolution templates and fine angular sampling.
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Affiliation(s)
- Bronwyn A Lucas
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Department of Molecular and Cell Biology, University of California BerkeleyBerkeleyUnited States
- Center for Computational Biology, University of California BerkeleyBerkeleyUnited States
| | - Benjamin A Himes
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Nikolaus Grigorieff
- RNA Therapeutics Institute, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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6
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Zhu D, Cao D, Zhang X. Virus structures revealed by advanced cryoelectron microscopy methods. Structure 2023; 31:1348-1359. [PMID: 37797619 DOI: 10.1016/j.str.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/07/2023]
Abstract
Before the resolution revolution, cryoelectron microscopy (cryo-EM) single-particle analysis (SPA) already achieved resolutions beyond 4 Å for certain icosahedral viruses, enabling ab initio atomic model building of these viruses. As the only samples that achieved such high resolution at that time, cryo-EM method development was closely intertwined with the improvement of reconstructions of symmetrical viruses. Viral morphology exhibits significant diversity, ranging from small to large, uniform to non-uniform, and from containing single symmetry to multiple symmetries. Furthermore, viruses undergo conformational changes during their life cycle. Several methods, such as asymmetric reconstruction, Ewald sphere correction, cryoelectron tomography (cryo-ET), and sub-tomogram averaging (STA), have been developed and applied to determine virus structures in vivo and in vitro. This review outlines current advanced cryo-EM methods for high-resolution structure determination of viruses and summarizes accomplishments obtained with these approaches. Moreover, persisting challenges in comprehending virus structures are discussed and we propose potential solutions.
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Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Chaillet ML, van der Schot G, Gubins I, Roet S, Veltkamp RC, Förster F. Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms. Int J Mol Sci 2023; 24:13375. [PMID: 37686180 PMCID: PMC10487639 DOI: 10.3390/ijms241713375] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Cryo-electron tomography provides 3D images of macromolecules in their cellular context. To detect macromolecules in tomograms, template matching (TM) is often used, which uses 3D models that are often reliable for substantial parts of the macromolecules. However, the extent of rotational searches in particle detection has not been investigated due to computational limitations. Here, we provide a GPU implementation of TM as part of the PyTOM software package, which drastically speeds up the orientational search and allows for sampling beyond the Crowther criterion within a feasible timeframe. We quantify the improvements in sensitivity and false-discovery rate for the examples of ribosome identification and detection. Sampling at the Crowther criterion, which was effectively impossible with CPU implementations due to the extensive computation times, allows for automated extraction with high sensitivity. Consequently, we also show that an extensive angular sample renders 3D TM sensitive to the local alignment of tilt series and damage induced by focused ion beam milling. With this new release of PyTOM, we focused on integration with other software packages that support more refined subtomogram-averaging workflows. The automated classification of ribosomes by TM with appropriate angular sampling on locally corrected tomograms has a sufficiently low false-discovery rate, allowing for it to be directly used for high-resolution averaging and adequate sensitivity to reveal polysome organization.
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Affiliation(s)
- Marten L. Chaillet
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
| | - Gijs van der Schot
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
| | - Ilja Gubins
- Department of Information and Computing Sciences, Utrecht University, 3584 CC Utrecht, The Netherlands; (I.G.); (R.C.V.)
| | - Sander Roet
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
| | - Remco C. Veltkamp
- Department of Information and Computing Sciences, Utrecht University, 3584 CC Utrecht, The Netherlands; (I.G.); (R.C.V.)
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.L.C.); (G.v.d.S.); (S.R.)
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8
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Lucas BA. Visualizing everything, everywhere, all at once: Cryo-EM and the new field of structureomics. Curr Opin Struct Biol 2023; 81:102620. [PMID: 37279614 DOI: 10.1016/j.sbi.2023.102620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023]
Abstract
Twenty years ago, the release of the first draft of the human genome sequence instigated a paradigm shift in genomics and molecular biology. Arguably, structural biology is entering an analogous era, with availability of an experimentally determined or predicted molecular model for almost every protein-coding gene from many genomes-producing a reference "structureome". Structural predictions require experimental validation and not all proteins conform to a single structure, making any reference structureome necessarily incomplete. Despite these limitations, a reference structureome can be used to characterize cell state in more detail than by quantifying sequence or expression levels alone. Cryogenic electron microscopy (cryo-EM) is a method that can generate atomic resolution views of molecules and cells frozen in place. In this perspective I consider how emerging cryo-EM methods are contributing to the new field of structureomics.
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Affiliation(s)
- Bronwyn A Lucas
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA.
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9
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Ravindran S. QnAs with Nikolaus Grigorieff. Proc Natl Acad Sci U S A 2023; 120:e2308656120. [PMID: 37459533 PMCID: PMC10372658 DOI: 10.1073/pnas.2308656120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
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10
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Zhang K, Lucas B, Grigorieff N. Exploring the Limits of 2D Template Matching for Detecting Targets in Cellular Cryo-EM Images. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:931. [PMID: 37613706 DOI: 10.1093/micmic/ozad067.462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Kexin Zhang
- The University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, MA, USA
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Bronwyn Lucas
- Department of Molecular & Cell Biology, The University of California, Berkeley, Berkeley, CA, USA
| | - Nikolaus Grigorieff
- The University of Massachusetts Chan Medical School, RNA Therapeutics Institute, Worcester, MA, USA
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
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11
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Abstract
Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.
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Affiliation(s)
- Lindsey N Young
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth Villa
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA
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12
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Russo CJ, Dickerson JL, Naydenova K. Cryomicroscopy in situ: what is the smallest molecule that can be directly identified without labels in a cell? Faraday Discuss 2022; 240:277-302. [PMID: 35913392 PMCID: PMC9642008 DOI: 10.1039/d2fd00076h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Electron cryomicroscopy (cryoEM) has made great strides in the last decade, such that the atomic structure of most biological macromolecules can, at least in principle, be determined. Major technological advances - in electron imaging hardware, data analysis software, and cryogenic specimen preparation technology - continue at pace and contribute to the exponential growth in the number of atomic structures determined by cryoEM. It is now conceivable that within the next decade we will have structures for hundreds of thousands of unique protein and nucleic acid molecular complexes. But the answers to many important questions in biology would become obvious if we could identify these structures precisely inside cells with quantifiable error. In the context of an abundance of known structures, it is appropriate to consider the current state of electron cryomicroscopy for frozen specimens prepared directly from cells, and try to answer to the question of the title, both now and in the foreseeable future.
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Affiliation(s)
- Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Joshua L Dickerson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Katerina Naydenova
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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13
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Lucas BA, Zhang K, Loerch S, Grigorieff N. In situ single particle classification reveals distinct 60S maturation intermediates in cells. eLife 2022; 11:79272. [PMID: 36005291 PMCID: PMC9444246 DOI: 10.7554/elife.79272] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Previously we showed that high-resolution template matching can localize ribosomes in two-dimensional electron cryo-microscopy (cryo-EM) images of untilted Mycoplasma pneumoniae cells with high precision (Lucas et al., 2021). Here we show that comparing the signal-to-noise ratio (SNR) observed with 2DTM using different templates relative to the same cellular target can correct for local variation in noise and differentiate related complexes in focused ion beam (FIB)-milled cell sections. We use a maximum likelihood approach to define the probability of each particle belonging to each class, thereby establishing a statistic to describe the confidence of our classification. We apply this method in two contexts to locate and classify related intermediate states of 60S ribosome biogenesis in the Saccharomyces cerevisiae cell nucleus. In the first, we separate the nuclear pre-60S population from the cytoplasmic mature 60S population, using the subcellular localization to validate assignment. In the second, we show that relative 2DTM SNRs can be used to separate mixed populations of nuclear pre-60S that are not visually separable. 2DTM can distinguish related molecular populations without the need to generate 3D reconstructions from the data to be classified, permitting classification even when only a few target particles exist in a cell.
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Affiliation(s)
- Bronwyn A Lucas
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Kexin Zhang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Sarah Loerch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, United States
| | - Nikolaus Grigorieff
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
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14
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Vilas JL, Carazo JM, Sorzano COS. Emerging Themes in CryoEM─Single Particle Analysis Image Processing. Chem Rev 2022; 122:13915-13951. [PMID: 35785962 PMCID: PMC9479088 DOI: 10.1021/acs.chemrev.1c00850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is an interdisciplinary field that takes advantage of advances in biochemistry, physics, and image processing, among other disciplines. Innovations in these three basic pillars have contributed to the boosting of CryoEM in the past decade. This work reviews the main contributions in image processing to the current reconstruction workflow of single particle analysis (SPA) by CryoEM. Our review emphasizes the time evolution of the algorithms across the different steps of the workflow differentiating between two groups of approaches: analytical methods and deep learning algorithms. We present an analysis of the current state of the art. Finally, we discuss the emerging problems and challenges still to be addressed in the evolution of CryoEM image processing methods in SPA.
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Affiliation(s)
- Jose Luis Vilas
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Jose Maria Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Carlos Oscar S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
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15
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Dickerson JL, Lu PH, Hristov D, Dunin-Borkowski RE, Russo CJ. Imaging biological macromolecules in thick specimens: The role of inelastic scattering in cryoEM. Ultramicroscopy 2022; 237:113510. [PMID: 35367900 PMCID: PMC9355893 DOI: 10.1016/j.ultramic.2022.113510] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/24/2022] [Accepted: 03/06/2022] [Indexed: 11/17/2022]
Abstract
We investigate potential improvements in using electron cryomicroscopy to image thick specimens with high-resolution phase contrast imaging. In particular, using model experiments, electron scattering theory, Monte Carlo and multislice simulations, we determine the potential for improving electron cryomicrographs of proteins within a cell using chromatic aberration (Cc) correction. We show that inelastically scattered electrons lose a quantifiable amount of spatial coherence as they transit the specimen, yet can be used to enhance the signal from thick biological specimens (in the 1000 to 5000 Å range) provided they are imaged close to focus with an achromatic lens. This loss of information quantified here, which we call "specimen induced decoherence", is a fundamental limit on imaging biological molecules in situ. We further show that with foreseeable advances in transmission electron microscope technology, it should be possible to directly locate and uniquely identify sub-100 kDa proteins without the need for labels, in a vitrified specimen taken from a cell.
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Affiliation(s)
- Joshua L Dickerson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Peng-Han Lu
- Ernst Ruska-Centrum für Mikroskopie und Spektroskopie mit Elektronen, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Dilyan Hristov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Rafal E Dunin-Borkowski
- Ernst Ruska-Centrum für Mikroskopie und Spektroskopie mit Elektronen, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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16
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Calcraft T, Rosenthal PB. Cryogenic electron microscopy approaches that combine images and tilt series. Microscopy (Oxf) 2022; 71:i15-i22. [PMID: 35275182 PMCID: PMC8855521 DOI: 10.1093/jmicro/dfab053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/29/2021] [Accepted: 01/28/2022] [Indexed: 11/12/2022] Open
Abstract
Cryogenic electron microscopy can be widely applied to biological specimens from the molecular to the cellular scale. In single-particle analysis, 3D structures may be obtained in high resolution by averaging 2D images of single particles in random orientations. For pleomorphic specimens, structures may be obtained by recording the tilt series of a single example of the specimen and calculating tomograms. Where many copies of a single structure such as a protein or nucleic acid assembly are present within the tomogram, averaging of the sub-volumes (subtomogram averaging) has been successfully applied. The choice of data collection method for any given specimen may depend on the structural question of interest and is determined by the radiation sensitivity of the specimen. Here, we survey some recent developments on the use of hybrid methods for recording and analysing data from radiation-sensitive biological specimens. These include single-particle reconstruction from 2D images where additional views are recorded at a single tilt angle of the specimen and methods where image tilt series, initially used for tomogram reconstruction, are processed as individual single-particle images. There is a continuum of approaches now available to maximize structural information obtained from the specimen.
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Affiliation(s)
- Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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17
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Klykov O, Kopylov M, Carragher B, Heck AJ, Noble AJ, Scheltema RA. Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. Mol Cell 2022; 82:285-303. [PMID: 35063097 PMCID: PMC8842845 DOI: 10.1016/j.molcel.2021.12.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Combining diverse experimental structural and interactomic methods allows for the construction of comprehensible molecular encyclopedias of biological systems. Typically, this involves merging several independent approaches that provide complementary structural and functional information from multiple perspectives and at different resolution ranges. A particularly potent combination lies in coupling structural information from cryoelectron microscopy or tomography (cryo-EM or cryo-ET) with interactomic and structural information from mass spectrometry (MS)-based structural proteomics. Cryo-EM/ET allows for sub-nanometer visualization of biological specimens in purified and near-native states, while MS provides bioanalytical information for proteins and protein complexes without introducing additional labels. Here we highlight recent achievements in protein structure and interactome determination using cryo-EM/ET that benefit from additional MS analysis. We also give our perspective on how combining cryo-EM/ET and MS will continue bridging gaps between molecular and cellular studies by capturing and describing 3D snapshots of proteomes and interactomes.
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Affiliation(s)
- Oleg Klykov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Mykhailo Kopylov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bridget Carragher
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Alex J Noble
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Corresponding author for cryo-EM/ET/FIB-SEM: Alex J. Noble, tel: (+1) 212-939-0660;
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands,Corresponding author for MS: Richard A. Scheltema, tel: (+31) 30 253 6804;
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18
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Lees JA, Dias JM, Han S. Applications of Cryo-EM in small molecule and biologics drug design. Biochem Soc Trans 2021; 49:2627-2638. [PMID: 34812853 PMCID: PMC8786282 DOI: 10.1042/bst20210444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 02/03/2023]
Abstract
Electron cryo-microscopy (cryo-EM) is a powerful technique for the structural characterization of biological macromolecules, enabling high-resolution analysis of targets once inaccessible to structural interrogation. In recent years, pharmaceutical companies have begun to utilize cryo-EM for structure-based drug design. Structural analysis of integral membrane proteins, which comprise a large proportion of druggable targets and pose particular challenges for X-ray crystallography, by cryo-EM has enabled insights into important drug target families such as G protein-coupled receptors (GPCRs), ion channels, and solute carrier (SLCs) proteins. Structural characterization of biologics, such as vaccines, viral vectors, and gene therapy agents, has also become significantly more tractable. As a result, cryo-EM has begun to make major impacts in bringing critical therapeutics to market. In this review, we discuss recent instructive examples of impacts from cryo-EM in therapeutics design, focusing largely on its implementation at Pfizer. We also discuss the opportunities afforded by emerging technological advances in cryo-EM, and the prospects for future development of the technique.
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Affiliation(s)
- Joshua A. Lees
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, U.S.A
| | - Joao M. Dias
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, U.S.A
| | - Seungil Han
- Discovery Sciences, Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, U.S.A
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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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20
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Determining structures in a native environment using single-particle cryoelectron microscopy images. ACTA ACUST UNITED AC 2021; 2:100166. [PMID: 34632438 PMCID: PMC8488058 DOI: 10.1016/j.xinn.2021.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/21/2021] [Indexed: 12/05/2022]
Abstract
Cryo-electron tomography is a powerful tool for structure determination in the native environment. However, this method requires the acquisition of tilt series, which is time-consuming and severely slows structure determination. By treating the densities of non-target protein as non-Gaussian noise, we developed a new target function that greatly improves the efficiency of recognizing the target protein in a single cryo-electron microscopy image. Moreover, we developed a sorting function that effectively eliminates the model dependence and improved the resolution during the subsequent structure refinement procedure. By eliminating model bias, our method allows using homolog proteins as models to recognize the target proteins in a complex context. Together, we developed an in situ single-particle analysis method. Our method was successfully applied to solve structures of glycoproteins on the surface of a non-icosahedral virus and Rubisco inside the carboxysome. Both data were collected within 24 h, thus allowing fast and simple structural determination. Structures could be achieved when proteins are overlapped with surroundings free of tilt series The particle detection efficiency is significantly improved Allowing the usage of homolog proteins as templates The throughput of structure determination is remarkably enhanced
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21
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Himes B, Grigorieff N. Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation. IUCRJ 2021; 8:943-953. [PMID: 34804546 PMCID: PMC8562658 DOI: 10.1107/s2052252521008538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Image simulation plays a central role in the development and practice of high-resolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in experimental images remains challenging, especially for amorphous samples. Current state-of-the-art simulators apply post hoc scaling to approximate empirical solvent contrast, attenuated image intensity due to specimen thickness and amplitude contrast. This practice fails for images that require spatially variable scaling, e.g. simulations of a crowded or cellular environment. Modeling both the signal and the noise accurately is necessary to simulate images of biological specimens with contrast that is correct on an absolute scale. The 'frozen plasmon' method is introduced to explicitly model spatially variable inelastic scattering processes in cryo-EM specimens. This approach produces amplitude contrast that depends on the atomic composition of the specimen, reproduces the total inelastic mean free path as observed experimentally and allows for the incorporation of radiation damage in the simulation. These improvements are quantified using the matched filter concept to compare simulation and experiment. The frozen plasmon method, in combination with a new mathematical formulation for accurately sampling the tabulated atomic scattering potentials onto a Cartesian grid, is implemented in the open-source software package cisTEM.
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Affiliation(s)
- Benjamin Himes
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Nikolaus Grigorieff
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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22
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Bäuerlein FJB, Baumeister W. Towards Visual Proteomics at High Resolution. J Mol Biol 2021; 433:167187. [PMID: 34384780 DOI: 10.1016/j.jmb.2021.167187] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/24/2022]
Abstract
Traditionally, structural biologists approach the complexity of cellular proteomes in a reductionist manner. Proteomes are fractionated, their molecular components purified and studied one-by-one using the experimental methods for structure determination at their disposal. Visual proteomics aims at obtaining a holistic picture of cellular proteomes by studying them in situ, ideally in unperturbed cellular environments. The method that enables doing this at highest resolution is cryo-electron tomography. It allows to visualize cellular landscapes with molecular resolution generating maps or atlases revealing the interaction networks which underlie cellular functions in health and in disease states. Current implementations of cryo ET do not yet realize the full potential of the method in terms of resolution and interpretability. To this end, further improvements in technology and methodology are needed. This review describes the state of the art as well as measures which we expect will help overcoming current limitations.
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Affiliation(s)
- Felix J B Bäuerlein
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany; Georg-August-University, Institute for Neuropathology, Robert-Koch-Strasse 40, 37075 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany.
| | - Wolfgang Baumeister
- Max-Planck-Institute of Biochemistry, Department for Molecular Structural Biology, Am Klopferspitz 18, 82152 Planegg, Germany.
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23
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Abstract
The application of cryo-correlative light and cryo-electron microscopy (cryo-CLEM) gives us a way to locate structures of interest in the electron microscope. In brief, the structures of interest are fluorescently tagged, and images from the cryo-fluorescent microscope (cryo-FM) maps are superimposed on those from the cryo-electron microscope (cryo-EM). By enhancing cryo-FM to include single-molecule localization microscopy (SMLM), we can achieve much better localization. The introduction of cryo-SMLM increased the yield of photons from fluorophores, which can benefit localization efforts. Dahlberg and Moerner (2021, Annual Review of Physical Chemistry, 72, 253-278) have a recent broad and elegant review of super-resolution cryo-CLEM. This paper focuses on cryo(F)PALM/STORM for the cryo-electron tomography community. I explore the current challenges to increase the accuracy of localization by SMLM and the mapping of those positions onto cryo-EM images and maps. There is much to consider: we need to know if the excitation of fluorophores damages the structures we seek to visualize. We need to determine if higher numerical aperture (NA) objectives, which add complexity to image analysis but increase resolution and the efficiency of photon collection, are better than lower NA objectives, which pose fewer problems. We need to figure out the best way to determine the axial position of fluorophores. We need to have better ways of aligning maps determined by FM with those determined by EM. We need to improve the instrumentation to be easier to use, more accurate, and ice-contamination free. The bottom line is that we have more work to do.
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24
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Lucas BA, Himes BA, Xue L, Grant T, Mahamid J, Grigorieff N. Locating macromolecular assemblies in cells by 2D template matching with cisTEM. eLife 2021; 10:e68946. [PMID: 34114559 PMCID: PMC8219381 DOI: 10.7554/elife.68946] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022] Open
Abstract
For a more complete understanding of molecular mechanisms, it is important to study macromolecules and their assemblies in the broader context of the cell. This context can be visualized at nanometer resolution in three dimensions (3D) using electron cryo-tomography, which requires tilt series to be recorded and computationally aligned, currently limiting throughput. Additionally, the high-resolution signal preserved in the raw tomograms is currently limited by a number of technical difficulties, leading to an increased false-positive detection rate when using 3D template matching to find molecular complexes in tomograms. We have recently described a 2D template matching approach that addresses these issues by including high-resolution signal preserved in single-tilt images. A current limitation of this approach is the high computational cost that limits throughput. We describe here a GPU-accelerated implementation of 2D template matching in the image processing software cisTEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydrated Mycoplasma pneumoniae cells with high precision and sensitivity, demonstrating that this is a versatile tool for in situ visual proteomics and in situ structure determination. We benchmark the results with 3D template matching of tomograms acquired on identical sample locations and identify strengths and weaknesses of both techniques, which offer complementary information about target localization and identity.
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Affiliation(s)
- Bronwyn A Lucas
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Benjamin A Himes
- Howard Hughes Medical Institute, RNA Therapeutics Institute, The University of Massachusetts Medical SchoolWorcesterUnited States
| | - Liang Xue
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of BiosciencesHeidelbergGermany
| | - Timothy Grant
- Howard Hughes Medical Institute, Janelia Research CampusAshburnUnited States
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Nikolaus Grigorieff
- Howard Hughes Medical Institute, RNA Therapeutics Institute, The University of Massachusetts Medical SchoolWorcesterUnited States
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25
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Li X, Park D, Chang Y, Radhakrishnan A, Wu H, Wang P, Liu J. A mammalian system for high-resolution imaging of intact cells by cryo-electron tomography. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 160:87-96. [PMID: 33058942 DOI: 10.1016/j.pbiomolbio.2020.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/17/2020] [Accepted: 09/20/2020] [Indexed: 10/23/2022]
Abstract
Mammalian cells contain an elaborate network of organelles and molecular machines that orchestrate essential cellular processes. Visualization of this network at a molecular level is vital for understanding these cellular processes. Here we present a model system based on nerve growth factor (NGF)-differentiated PC12 cells (PC12+) and suitable for high resolution imaging of organelles and molecular machines in situ. We detail an optimized imaging pipeline that effectively combines correlative light and electron microscopy (CLEM), cryo-focused ion beam (cryo-FIB), cryo-electron tomography (cryo-ET), and sub-tomogram averaging to produce three-dimensional and molecular resolution snapshots of organelles and molecular machines in near-native cellular environments. Our studies demonstrate that cryo-ET imaging of PC12+ systems provides an accessible and highly efficient avenue for dissecting specific cellular processes in mammalian cells at high resolution.
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Affiliation(s)
- Xia Li
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA; Institute of Special Environmental Medicine and Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, 226000, China.
| | - Donghyun Park
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA
| | - Yunjie Chang
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA
| | | | - Hangjun Wu
- Center of Cryo Electron Microscopy and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Pei Wang
- Institute of Biophysics, Chinese Academy of Science, Beijing, 100101, China
| | - Jun Liu
- Department of Microbial Pathogenesis and Microbial Science Institute, Yale School of Medicine, New Haven, CT, 06516, USA.
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26
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The In Situ Structure of Parkinson's Disease-Linked LRRK2. Cell 2020; 182:1508-1518.e16. [PMID: 32783917 DOI: 10.1016/j.cell.2020.08.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 05/28/2020] [Accepted: 07/31/2020] [Indexed: 12/31/2022]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of familial Parkinson's disease. LRRK2 is a multi-domain protein containing a kinase and GTPase. Using correlative light and electron microscopy, in situ cryo-electron tomography, and subtomogram analysis, we reveal a 14-Å structure of LRRK2 bearing a pathogenic mutation that oligomerizes as a right-handed double helix around microtubules, which are left-handed. Using integrative modeling, we determine the architecture of LRRK2, showing that the GTPase and kinase are in close proximity, with the GTPase closer to the microtubule surface, whereas the kinase is exposed to the cytoplasm. We identify two oligomerization interfaces mediated by non-catalytic domains. Mutation of one of these abolishes LRRK2 microtubule-association. Our work demonstrates the power of cryo-electron tomography to generate models of previously unsolved structures in their cellular environment.
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27
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Abstract
Single-particle electron cryomicroscopy (cryo-EM) is an increasingly popular technique for elucidating the three-dimensional structure of proteins and other biologically significant complexes at near-atomic resolution. It is an imaging method that does not require crystallization and can capture molecules in their native states. In single-particle cryo-EM, the three-dimensional molecular structure needs to be determined from many noisy two-dimensional tomographic projections of individual molecules, whose orientations and positions are unknown. The high level of noise and the unknown pose parameters are two key elements that make reconstruction a challenging computational problem. Even more challenging is the inference of structural variability and flexible motions when the individual molecules being imaged are in different conformational states. This review discusses computational methods for structure determination by single-particle cryo-EM and their guiding principles from statistical inference, machine learning, and signal processing that also play a significant role in many other data science applications.
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Affiliation(s)
- Amit Singer
- Department of Mathematics and Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08544, USA
| | - Fred J Sigworth
- Departments of Cellular and Molecular Physiology, Biomedical Engineering, and Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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28
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Kaelber JT, Jiang W, Weaver SC, Auguste AJ, Chiu W. Arrangement of the Polymerase Complexes inside a Nine-Segmented dsRNA Virus. Structure 2020; 28:604-612.e3. [PMID: 32049031 PMCID: PMC7289189 DOI: 10.1016/j.str.2020.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 12/18/2019] [Accepted: 01/17/2020] [Indexed: 12/15/2022]
Abstract
Members of the family Reoviridae package several copies of the viral polymerase complex into their capsid to carry out replication and transcription within viral particles. Classical single-particle reconstruction encounters difficulties resolving structures such as the intraparticle polymerase complex because refinement can converge to an incorrect map and because the map could depict a nonrepresentative subset of particles or an average of heterogeneous particles. Using the nine-segmented Fako virus, we tested hypotheses for the arrangement and number of polymerase complexes within the virion by measuring how well each hypothesis describes the set of cryoelectron microscopy images of individual viral particles. We find that the polymerase complex in Fako virus binds at ten possible sites despite having only nine genome segments. A single asymmetric configuration describes the arrangement of these complexes in both virions and genome-free capsids. Similarities between the arrangements of Reoviridae with 9, 10, and 11 segments indicate the generalizability of this architecture.
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Affiliation(s)
- Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Scott C Weaver
- Institute for Human Infections and Immunity, World Reference Center for Emerging Viruses and Arboviruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Albert J Auguste
- Institute for Human Infections and Immunity, World Reference Center for Emerging Viruses and Arboviruses, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Department of Entomology, Fralin Life Science Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Wah Chiu
- Department of Bioengineering, Department of Microbiology and Immunology, and James H. Clark Center, Stanford University, Stanford, CA, USA
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29
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McCafferty CL, Verbeke EJ, Marcotte EM, Taylor DW. Structural Biology in the Multi-Omics Era. J Chem Inf Model 2020; 60:2424-2429. [PMID: 32129623 PMCID: PMC7254829 DOI: 10.1021/acs.jcim.9b01164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Indexed: 12/12/2022]
Abstract
Rapid developments in cryogenic electron microscopy have opened new avenues to probe the structures of protein assemblies in their near native states. Recent studies have begun applying single -particle analysis to heterogeneous mixtures, revealing the potential of structural-omics approaches that combine the power of mass spectrometry and electron microscopy. Here we highlight advances and challenges in sample preparation, data processing, and molecular modeling for handling increasingly complex mixtures. Such advances will help structural-omics methods extend to cellular-level models of structural biology.
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Affiliation(s)
- Caitlyn L. McCafferty
- Department
of Molecular Biosciences, University of
Texas at Austin, Austin, Texas 78712, United States
| | - Eric J. Verbeke
- Department
of Molecular Biosciences, University of
Texas at Austin, Austin, Texas 78712, United States
| | - Edward M. Marcotte
- Department
of Molecular Biosciences, University of
Texas at Austin, Austin, Texas 78712, United States
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Systems and Synthetic Biology, University
of Texas at Austin, Austin, Texas 78712, United States
| | - David W. Taylor
- Department
of Molecular Biosciences, University of
Texas at Austin, Austin, Texas 78712, United States
- Institute
for Cellular and Molecular Biology, University
of Texas at Austin, Austin, Texas 78712, United States
- Center
for Systems and Synthetic Biology, University
of Texas at Austin, Austin, Texas 78712, United States
- LIVESTRONG
Cancer Institutes, Dell Medical School, Austin, Texas 78712, United States
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30
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Song K, Shang Z, Fu X, Lou X, Grigorieff N, Nicastro D. In situ structure determination at nanometer resolution using TYGRESS. Nat Methods 2020; 17:201-208. [PMID: 31768058 PMCID: PMC7004880 DOI: 10.1038/s41592-019-0651-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/20/2019] [Accepted: 10/11/2019] [Indexed: 02/06/2023]
Abstract
The resolution of subtomogram averages calculated from cryo-electron tomograms (cryo-ET) of crowded cellular environments is often limited owing to signal loss in, and misalignment of, the subtomograms. By contrast, single-particle cryo-electron microscopy (SP-cryo-EM) routinely reaches near-atomic resolution of isolated complexes. We report a method called 'tomography-guided 3D reconstruction of subcellular structures' (TYGRESS) that is a hybrid of cryo-ET and SP-cryo-EM, and is able to achieve close-to-nanometer resolution of complexes inside crowded cellular environments. TYGRESS combines the advantages of SP-cryo-EM (images with good signal-to-noise ratio and contrast, as well as minimal radiation damage) and subtomogram averaging (three-dimensional alignment of macromolecules in a complex sample). Using TYGRESS, we determined the structure of the intact ciliary axoneme with up to resolution of 12 Å. These results reveal many structural details that were not visible by cryo-ET alone. TYGRESS is generally applicable to cellular complexes that are amenable to subtomogram averaging.
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Affiliation(s)
- Kangkang Song
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhiguo Shang
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaofeng Fu
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Biological Science Imaging Resource, Florida State University, Tallahassee, FL, USA
| | - Xiaochu Lou
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikolaus Grigorieff
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Daniela Nicastro
- Departments of Cell Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms. Nat Methods 2020; 17:209-216. [PMID: 31907446 DOI: 10.1038/s41592-019-0675-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/11/2019] [Indexed: 01/12/2023]
Abstract
With faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography provides an accurate representation of molecular architecture of cells. However, detection and precise localization of macromolecular complexes within cellular environments is aggravated by the presence of many molecular species and molecular crowding. We developed a template-free image processing procedure for accurate tracing of complex networks of densities in cryo-electron tomograms, a comprehensive and automated detection of heterogeneous membrane-bound complexes and an unsupervised classification (PySeg). Applications to intact cells and isolated endoplasmic reticulum (ER) allowed us to detect and classify small protein complexes. This classification provided sufficiently homogeneous particle sets and initial references to allow subsequent de novo subtomogram averaging. Spatial distribution analysis showed that ER complexes have different localization patterns forming nanodomains. Therefore, this procedure allows a comprehensive detection and structural analysis of complexes in situ.
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32
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Classification of Single Particles from Human Cell Extract Reveals Distinct Structures. Cell Rep 2019; 24:259-268.e3. [PMID: 29972786 PMCID: PMC6109231 DOI: 10.1016/j.celrep.2018.06.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/09/2018] [Accepted: 06/05/2018] [Indexed: 01/27/2023] Open
Abstract
Multi-protein complexes are necessary for nearly all cellular processes, and understanding their structure is required for elucidating their function. Current high-resolution strategies in structural biology are effective but lag behind other fields (e.g., genomics and proteomics) due to their reliance on purified samples rather than heterogeneous mixtures. Here, we present a method combining single-particle analysis by electron microscopy with protein identification by mass spectrometry to structurally characterize macromolecular complexes from human cell extract. We identify HSP60 through two-dimensional classification and obtain three-dimensional structures of native proteasomes directly from ab initio classification of a heterogeneous mixture of protein complexes. In addition, we reveal an ∼1-MDa-size structure of unknown composition and reference our proteomics data to suggest possible identities. Our study shows the power of using a shotgun approach to electron microscopy (shotgun EM) when coupled with mass spectrometry as a tool to uncover the structures of macromolecular machines.
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Tegunov D, Cramer P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat Methods 2019; 16:1146-1152. [PMID: 31591575 PMCID: PMC6858868 DOI: 10.1038/s41592-019-0580-y] [Citation(s) in RCA: 629] [Impact Index Per Article: 125.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/21/2019] [Indexed: 12/22/2022]
Abstract
The acquisition of cryo-electron microscopy (cryo-EM) data from biological specimens must be tightly coupled to data preprocessing to ensure the best data quality and microscope usage. Here we describe Warp, a software that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Warp corrects micrographs for global and local motion, estimates the local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. The software further includes deep-learning-based models for accurate particle picking and image denoising. The output from Warp can be fed into established programs for particle classification and 3D-map refinement. Our benchmarks show improvement in the nominal resolution, which went from 3.9 Å to 3.2 Å, of a published cryo-EM data set for influenza virus hemagglutinin. Warp is easy to install from http://github.com/cramerlab/warp and computationally inexpensive, and has an intuitive, streamlined user interface.
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Affiliation(s)
- Dimitry Tegunov
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany.
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In situ structures of RNA-dependent RNA polymerase inside bluetongue virus before and after uncoating. Proc Natl Acad Sci U S A 2019; 116:16535-16540. [PMID: 31350350 DOI: 10.1073/pnas.1905849116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bluetongue virus (BTV), a major threat to livestock, is a multilayered, nonturreted member of the Reoviridae, a family of segmented dsRNA viruses characterized by endogenous RNA transcription through an RNA-dependent RNA polymerase (RdRp). To date, the structure of BTV RdRp has been unknown, limiting our mechanistic understanding of BTV transcription and hindering rational drug design effort targeting this essential enzyme. Here, we report the in situ structures of BTV RdRp VP1 in both the triple-layered virion and double-layered core, as determined by cryo-electron microscopy (cryoEM) and subparticle reconstruction. BTV RdRp has 2 unique motifs not found in other viral RdRps: a fingernail, attached to the conserved fingers subdomain, and a bundle of 3 helices: 1 from the palm subdomain and 2 from the N-terminal domain. BTV RdRp VP1 is anchored to the inner surface of the capsid shell via 5 asymmetrically arranged N termini of the inner capsid shell protein VP3A around the 5-fold axis. The structural changes of RdRp VP1 and associated capsid shell proteins between BTV virions and cores suggest that the detachment of the outer capsid proteins VP2 and VP5 during viral entry induces both global movements of the inner capsid shell and local conformational changes of the N-terminal latch helix (residues 34 to 51) of 1 inner capsid shell protein VP3A, priming RdRp VP1 within the capsid for transcription. Understanding this mechanism in BTV also provides general insights into RdRp activation and regulation during viral entry of other multilayered, nonturreted dsRNA viruses.
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35
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In situ Structure of Rotavirus VP1 RNA-Dependent RNA Polymerase. J Mol Biol 2019; 431:3124-3138. [PMID: 31233764 DOI: 10.1016/j.jmb.2019.06.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/07/2019] [Accepted: 06/14/2019] [Indexed: 02/03/2023]
Abstract
Rotaviruses, like other non-enveloped, double-strand RNA viruses, package an RNA-dependent RNA polymerase (RdRp) with each duplex of their segmented genomes. Rotavirus cell entry results in loss of an outer protein layer and delivery into the cytosol of an intact, inner capsid particle (the "double-layer particle," or DLP). The RdRp, designated VP1, is active inside the DLP; each VP1 achieves many rounds of mRNA transcription from its associated genome segment. Previous work has shown that one VP1 molecule lies close to each 5-fold axis of the icosahedrally symmetric DLP, just beneath the inner surface of its protein shell, embedded in tightly packed RNA. We have determined a high-resolution structure for the rotavirus VP1 RdRp in situ, by local reconstruction of density around individual 5-fold positions. We have analyzed intact virions ("triple-layer particles"), non-transcribing DLPs and transcribing DLPs. Outer layer dissociation enables the DLP to synthesize RNA, in vitro as well as in vivo, but appears not to induce any detectable structural change in the RdRp. Addition of NTPs, Mg2+, and S-adenosylmethionine, which allows active transcription, results in conformational rearrangements, in both VP1 and the DLP capsid shell protein, that allow a transcript to exit the polymerase and the particle. The position of VP1 (among the five symmetrically related alternatives) at one vertex does not correlate with its position at other vertices. This stochastic distribution of site occupancies limits long-range order in the 11-segment, double-strand RNA genome.
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36
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Ding K, Celma CC, Zhang X, Chang T, Shen W, Atanasov I, Roy P, Zhou ZH. In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release. Nat Commun 2019; 10:2216. [PMID: 31101900 PMCID: PMC6525196 DOI: 10.1038/s41467-019-10236-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/25/2019] [Indexed: 01/11/2023] Open
Abstract
Transcribing and replicating a double-stranded genome require protein modules to unwind, transcribe/replicate nucleic acid substrates, and release products. Here we present in situ cryo-electron microscopy structures of rotavirus dsRNA-dependent RNA polymerase (RdRp) in two states pertaining to transcription. In addition to the previously discovered universal "hand-shaped" polymerase core domain shared by DNA polymerases and telomerases, our results show the function of N- and C-terminal domains of RdRp: the former opens the genome duplex to isolate the template strand; the latter splits the emerging template-transcript hybrid, guides genome reannealing to form a transcription bubble, and opens a capsid shell protein (CSP) to release the transcript. These two "helicase" domains also extensively interact with CSP, which has a switchable N-terminal helix that, like cellular transcriptional factors, either inhibits or promotes RdRp activity. The in situ structures of RdRp, CSP, and RNA in action inform mechanisms of not only transcription, but also replication.
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Affiliation(s)
- Ke Ding
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Cristina C Celma
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Xing Zhang
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Thomas Chang
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Wesley Shen
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Ivo Atanasov
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Polly Roy
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Z Hong Zhou
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA.
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37
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38
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Himes BA, Zhang P. emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging. Nat Methods 2018; 15:955-961. [PMID: 30349041 PMCID: PMC6281437 DOI: 10.1038/s41592-018-0167-z] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 07/25/2018] [Indexed: 11/17/2022]
Abstract
Macromolecular complexes are intrinsically flexible and often challenging to purify for structure determination by single particle cryoEM. Such complexes may be studied using cryo-electron tomography combined with sub-tomogram alignment and classification, which in exceptional cases reaches sub-nanometer resolution, yielding insight into structure-function relationships. Extending this approach to specimens that exhibit conformational or compositional heterogeneity, and that may be present at low abundance, remains challenging. To address this challenge, we developed emClarity (https://github.com/bHimes/emClarity/wiki), a GPU-accelerated image processing package, which features an iterative tomographic tilt-series refinement algorithm using sub-tomograms as fiducial markers and a 3D-samping function compensated, multi-scale Principle Component Analysis classification method. We demonstrate substantial improvements in the resolution of maps and in the separation of different functional states of macromolecular complexes, compared to those generated using current state-of-the-art software.
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Affiliation(s)
- Benjamin A Himes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA. .,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. .,Electron Bio-Imaging Centre, Diamond Light Source, Didcot, UK.
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39
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Pfeffer S, Mahamid J. Unravelling molecular complexity in structural cell biology. Curr Opin Struct Biol 2018; 52:111-118. [PMID: 30339965 DOI: 10.1016/j.sbi.2018.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/18/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Recent technological breakthroughs propelled electron microscopy of frozen hydrated specimens (cryo-EM) followed by single-particle analysis (SPA) to become a widely applied approach for obtaining near-atomic resolution structures of purified macromolecules. In parallel, ongoing developments on sample preparation are increasingly successful in bringing molecular views into cell biology. Cryo-electron tomography (cryo-ET) has so far served as the main imaging modality employed in these efforts towards obtaining three-dimensional (3D) volumes of heterogeneous molecular assemblies. We review the state-of-the-art in cryo-ET and computational processing and describe the current opportunities and frontiers for in-cell applications.
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Affiliation(s)
- Stefan Pfeffer
- Centre for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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40
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Kim LY, Rice WJ, Eng ET, Kopylov M, Cheng A, Raczkowski AM, Jordan KD, Bobe D, Potter CS, Carragher B. Benchmarking cryo-EM Single Particle Analysis Workflow. Front Mol Biosci 2018; 5:50. [PMID: 29951483 PMCID: PMC6009202 DOI: 10.3389/fmolb.2018.00050] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/08/2018] [Indexed: 11/17/2022] Open
Abstract
Cryo electron microscopy facilities running multiple instruments and serving users with varying skill levels need a robust and reliable method for benchmarking both the hardware and software components of their single particle analysis workflow. The workflow is complex, with many bottlenecks existing at the specimen preparation, data collection and image analysis steps; the samples and grid preparation can be of unpredictable quality, there are many different protocols for microscope and camera settings, and there is a myriad of software programs for analysis that can depend on dozens of settings chosen by the user. For this reason, we believe it is important to benchmark the entire workflow, using a standard sample and standard operating procedures, on a regular basis. This provides confidence that all aspects of the pipeline are capable of producing maps to high resolution. Here we describe benchmarking procedures using a test sample, rabbit muscle aldolase.
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Affiliation(s)
- Laura Y Kim
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - William J Rice
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Anchi Cheng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Ashleigh M Raczkowski
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Kelsey D Jordan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Daija Bobe
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Clinton S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
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41
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Erdmann PS, Plitzko JM, Baumeister W. Addressing cellular compartmentalization by in situ cryo-electron tomography. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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42
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Desselberger U. 7th European rotavirus biology conference, Cork/Ireland, 18–21 June 2017. Virus Res 2017; 240:197-199. [DOI: 10.1016/j.virusres.2017.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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43
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Single-protein detection by cryo-EM. Nat Methods 2017. [DOI: 10.1038/nmeth.4351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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