1
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Zens B, Fäßler F, Hansen JM, Hauschild R, Datler J, Hodirnau VV, Zheden V, Alanko J, Sixt M, Schur FK. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. J Cell Biol 2024; 223:e202309125. [PMID: 38506714 PMCID: PMC10955043 DOI: 10.1083/jcb.202309125] [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: 09/26/2023] [Revised: 02/19/2024] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.
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Affiliation(s)
- Bettina Zens
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Florian Fäßler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jesse M. Hansen
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Robert Hauschild
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Julia Datler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | | | - Vanessa Zheden
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jonna Alanko
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Michael Sixt
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Florian K.M. Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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2
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Lee HE, Jung M, Choi K, Jang JH, Hwang SK, Chae S, Lee JH, Mun JY. L-serine restored lysosomal failure in cells derived from patients with BPAN reducing iron accumulation with eliminating lipofuscin. Free Radic Biol Med 2024; 221:273-282. [PMID: 38740102 DOI: 10.1016/j.freeradbiomed.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Defective mitochondria and autophagy, as well as accumulation of lipid and iron in WDR45 mutant fibroblasts, is related to beta-propeller protein-associated neurodegeneration (BPAN). In this study, we found that enlarged lysosomes in cells derived from patients with BPAN had low enzyme activity, and most of the enlarged lysosomes had an accumulation of iron and oxidized lipid. Cryo-electron tomography revealed elongated lipid accumulation, and spectrometry-based elemental analysis showed that lysosomal iron and oxygen accumulation superimposed with lipid aggregates. Lysosomal lipid aggregates superimposed with autofluorescence as free radical generator, lipofuscin. To eliminate free radical stress by iron accumulation in cells derived from patients with BPAN, we investigated the effects of the iron chelator, 2,2'-bipyridine (bipyridyl, BIP). To study whether the defects in patient-derived cells can be rescued by an iron chelator BIP, we tested whether the level of iron and reactive oxygen species (ROS) in the cells and genes related to oxidative stress were rescued BIP treatment. Although BIP treatment decreased some iron accumulation in the cytoplasm and mitochondria, the accumulation of iron in the lysosomes and levels of cellular ROS were unaffected. In addition, the change of specific RNA levels related to free radical stress in patient fibroblasts was not rescued by BIP. To alleviate free radical stress, we investigated whether l-serine can regulate abnormal structures in cells derived from patients with BPAN through the regulation of free radical stress. l-serine treatment alleviated increase of enlarged lysosomes and iron accumulation and rescued impaired lysosomal activity by reducing oxidized lipid accumulation in the lysosomes of the cells. Lamellated lipids in the lysosomes of the cells were identified as lipofuscin through correlative light and electron microscopy, and l-serine treatment reduced the increase of lipofuscin. These data suggest that l-serine reduces oxidative stress-mediated lysosomal lipid oxidation and iron accumulation by rescuing lysosomal activity.
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Affiliation(s)
- Hye Eun Lee
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, South Korea; School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Kiju Choi
- Division of Structural Biology, Baobab AiBIO, Incheon, South Korea
| | - Jae Hyuck Jang
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea; Electron Microscopy Group for Materials Science, Korea Basic Science Institute, Daejeon, South Korea
| | - Su-Kyeong Hwang
- Department of Pediatrics, School of Medicine, Kyungpook National University, Daegu, South Korea; Astrogen Inc., Techno-Building 313, Kyungpook National University, Daegu, 41566, South Korea
| | - Sehyun Chae
- Division of Chemical Engineering and Bioengineering, College of Art, Culture and Engineering, Kangwon National University, Chuncheon, 24341, South Korea
| | - Jae-Hyeok Lee
- Department of Neurology, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan, 50612, South Korea; Medical Research Institute, Pusan National University School of Medicine, Yangsan, 50612, South Korea.
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, South Korea.
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3
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Khanna K, Welch MD. Cryo-electron tomography of stationary phase Burkholderia thailandensis. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001178. [PMID: 38725941 PMCID: PMC11079643 DOI: 10.17912/micropub.biology.001178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024]
Abstract
Burkholderia species belonging to the pseudomallei group include significant human and animal pathogens as well as the non-pathogenic species Burkholderia thailandensis . These bacteria co-opt the host cell machinery for their replication and spread between host cells. Thus, it is of interest to understand the structural features of these cells that contribute to host cell colonization and virulence. This study provides high-resolution cryo-electron tomograms of stationary phase Burkholderia thailandensis . It reveals the presence of compact nucleoids and storage granules, as well as examples of the type III secretion system and chemoreceptor arrays. The data can be used to investigate the near-atomic structure of stationary-phase bacterial macromolecules, such as ribosomes.
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Affiliation(s)
- Kanika Khanna
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States
| | - Matthew D. Welch
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States
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4
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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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5
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Comet M, Dijkman PM, Boer Iwema R, Franke T, Masiulis S, Schampers R, Raschdorf O, Grollios F, Pryor EE, Drulyte I. Tomo Live: an on-the-fly reconstruction pipeline to judge data quality for cryo-electron tomography workflows. Acta Crystallogr D Struct Biol 2024; 80:247-258. [PMID: 38512070 PMCID: PMC10994173 DOI: 10.1107/s2059798324001840] [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: 10/31/2023] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
Data acquisition and processing for cryo-electron tomography can be a significant bottleneck for users. To simplify and streamline the cryo-ET workflow, Tomo Live, an on-the-fly solution that automates the alignment and reconstruction of tilt-series data, enabling real-time data-quality assessment, has been developed. Through the integration of Tomo Live into the data-acquisition workflow for cryo-ET, motion correction is performed directly after each of the acquired tilt angles. Immediately after the tilt-series acquisition has completed, an unattended tilt-series alignment and reconstruction into a 3D volume is performed. The results are displayed in real time in a dedicated remote web platform that runs on the microscope hardware. Through this web platform, users can review the acquired data (aligned stack and 3D volume) and several quality metrics that are obtained during the alignment and reconstruction process. These quality metrics can be used for fast feedback for subsequent acquisitions to save time. Parameters such as Alignment Accuracy, Deleted Tilts and Tilt Axis Correction Angle are visualized as graphs and can be used as filters to export only the best tomograms (raw data, reconstruction and intermediate data) for further processing. Here, the Tomo Live algorithms and workflow are described and representative results on several biological samples are presented. The Tomo Live workflow is accessible to both expert and non-expert users, making it a valuable tool for the continued advancement of structural biology, cell biology and histology.
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Affiliation(s)
- Maxime Comet
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Patricia M. Dijkman
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Reint Boer Iwema
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Tilman Franke
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Simonas Masiulis
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Ruud Schampers
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Oliver Raschdorf
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Fanis Grollios
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Edward E. Pryor
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Ieva Drulyte
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
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6
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Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. The Molecular Architecture of the Nuclear Basket. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587068. [PMID: 38586009 PMCID: PMC10996695 DOI: 10.1101/2024.03.27.587068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of Nups in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.
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Affiliation(s)
- Digvijay Singh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Neelesh Soni
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Farhaz Shaikh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeleine Duquette
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergey Suslov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kelly Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
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7
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Esser TK, Böhning J, Önür A, Chinthapalli DK, Eriksson L, Grabarics M, Fremdling P, Konijnenberg A, Makarov A, Botman A, Peter C, Benesch JLP, Robinson CV, Gault J, Baker L, Bharat TAM, Rauschenbach S. Cryo-EM of soft-landed β-galactosidase: Gas-phase and native structures are remarkably similar. SCIENCE ADVANCES 2024; 10:eadl4628. [PMID: 38354247 PMCID: PMC10866560 DOI: 10.1126/sciadv.adl4628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
Native mass spectrometry (MS) has become widely accepted in structural biology, providing information on stoichiometry, interactions, homogeneity, and shape of protein complexes. Yet, the fundamental assumption that proteins inside the mass spectrometer retain a structure faithful to native proteins in solution remains a matter of intense debate. Here, we reveal the gas-phase structure of β-galactosidase using single-particle cryo-electron microscopy (cryo-EM) down to 2.6-Å resolution, enabled by soft landing of mass-selected protein complexes onto cold transmission electron microscopy (TEM) grids followed by in situ ice coating. We find that large parts of the secondary and tertiary structure are retained from the solution. Dehydration-driven subunit reorientation leads to consistent compaction in the gas phase. By providing a direct link between high-resolution imaging and the capability to handle and select protein complexes that behave problematically in conventional sample preparation, the approach has the potential to expand the scope of both native mass spectrometry and cryo-EM.
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Affiliation(s)
- Tim K. Esser
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Thermo Fisher Scientific, 1 Boundary Park, Hemel Hempstead, Hertfordshire HP2 7GE, UK
| | - Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Alpcan Önür
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Dinesh K. Chinthapalli
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Lukas Eriksson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Marko Grabarics
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Alexander Makarov
- Thermo Fisher Scientific, Bremen 28199, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Aurelien Botman
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz 78457, Germany
| | - Justin L. P. Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Lindsay Baker
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Stephan Rauschenbach
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, UK
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8
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Bauda E, Gallet B, Moravcova J, Effantin G, Chan H, Novacek J, Jouneau PH, Rodrigues CDA, Schoehn G, Moriscot C, Morlot C. Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography. Nat Commun 2024; 15:1376. [PMID: 38355696 PMCID: PMC10867305 DOI: 10.1038/s41467-024-45770-6] [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: 09/06/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
Bacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography on lamellae generated by cryo-focused ion beam micromachining provides insights into the ultrastructural organization of Bacillus subtilis sporangia. The reconstructed tomograms reveal that early during sporulation, the chromosome in the forespore adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a stack of amorphous or structured layers with distinct electron density, dimensions and organization. By analyzing mutant strains using cryo-electron tomography and transmission electron microscopy on resin sections, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of coat morphogenetic proteins.
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Affiliation(s)
- Elda Bauda
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Benoit Gallet
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | - Jana Moravcova
- CEITEC-Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | | | - Helena Chan
- University of Technology Sydney, 2007, Ultimo, NSW, Australia
| | - Jiri Novacek
- CEITEC-Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | | | | | - Guy Schoehn
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France
| | | | - Cecile Morlot
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000, Grenoble, France.
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9
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Li W, Li A, Yu B, Zhang X, Liu X, White KL, Stevens RC, Baumeister W, Sali A, Jasnin M, Sun L. In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography. Nat Commun 2024; 15:1311. [PMID: 38346988 PMCID: PMC10861521 DOI: 10.1038/s41467-024-45648-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
Actin mediates insulin secretion in pancreatic β-cells through remodeling. Hampered by limited resolution, previous studies have offered an ambiguous depiction as depolymerization and repolymerization. We report the in situ structure of actin remodeling in INS-1E β-cells during glucose-stimulated insulin secretion at nanoscale resolution. After remodeling, the actin filament network at the cell periphery exhibits three marked differences: 12% of actin filaments reorient quasi-orthogonally to the ventral membrane; the filament network mainly remains as cell-stabilizing bundles but partially reconfigures into a less compact arrangement; actin filaments anchored to the ventral membrane reorganize from a "netlike" to a "blooming" architecture. Furthermore, the density of actin filaments and microtubules around insulin secretory granules decreases, while actin filaments and microtubules become more densely packed. The actin filament network after remodeling potentially precedes the transport and release of insulin secretory granules. These findings advance our understanding of actin remodeling and its role in glucose-stimulated insulin secretion.
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Affiliation(s)
- Weimin Li
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Angdi Li
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Bing Yu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiaoxiao Zhang
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Xiaoyan Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Kate L White
- Department of Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, 90089, USA
| | - Raymond C Stevens
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wolfgang Baumeister
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.
| | - Andrej Sali
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Marion Jasnin
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764, Neuherberg, Germany.
- Department of Chemistry, Technical University of Munich, 85748, Garching, Germany.
| | - Liping Sun
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
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10
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Fry MY, Navarro PP, Hakim P, Ananda VY, Qin X, Landoni JC, Rath S, Inde Z, Lugo CM, Luce BE, Ge Y, McDonald JL, Ali I, Ha LL, Kleinstiver BP, Chan DC, Sarosiek KA, Chao LH. In situ architecture of Opa1-dependent mitochondrial cristae remodeling. EMBO J 2024; 43:391-413. [PMID: 38225406 PMCID: PMC10897290 DOI: 10.1038/s44318-024-00027-2] [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: 01/14/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024] Open
Abstract
Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms in the mitochondrion, a membrane-anchored long form (l-Opa1) and a processed short form (s-Opa1). The mechanisms for how Opa1 influences cristae shape have remained unclear due to lack of native three-dimensional views of cristae. We perform in situ cryo-electron tomography of cryo-focused ion beam milled mouse embryonic fibroblasts with defined Opa1 states to understand how each form of Opa1 influences cristae architecture. In our tomograms, we observe a variety of cristae shapes with distinct trends dependent on s-Opa1:l-Opa1 balance. Increased l-Opa1 levels promote cristae stacking and elongated mitochondria, while increased s-Opa1 levels correlated with irregular cristae packing and round mitochondria shape. Functional assays indicate a role for l-Opa1 in wild-type apoptotic and calcium handling responses, and show a compromised respiratory function under Opa1 imbalance. In summary, we provide three-dimensional visualization of cristae architecture to reveal relationships between mitochondrial ultrastructure and cellular function dependent on Opa1-mediated membrane remodeling.
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Affiliation(s)
- Michelle Y Fry
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Pusparanee Hakim
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Virly Y Ananda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Xingping Qin
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Molecular and Integrative Physiological Sciences (MIPS) Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Lab of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Juan C Landoni
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sneha Rath
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Zintis Inde
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Molecular and Integrative Physiological Sciences (MIPS) Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Lab of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Bridget E Luce
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Yifan Ge
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Interdisciplinary Research Center of Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, Shanghai, China
| | - Julie L McDonald
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ilzat Ali
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Leillani L Ha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - David C Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kristopher A Sarosiek
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Molecular and Integrative Physiological Sciences (MIPS) Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Lab of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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11
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Asarnow D, Becker VA, Bobe D, Dubbledam C, Johnston JD, Kopylov M, Lavoie NR, Li Q, Mattingly JM, Mendez JH, Paraan M, Turner J, Upadhye V, Walsh RM, Gupta M, Eng ET. Recent advances in infectious disease research using cryo-electron tomography. Front Mol Biosci 2024; 10:1296941. [PMID: 38288336 PMCID: PMC10822977 DOI: 10.3389/fmolb.2023.1296941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/07/2023] [Indexed: 01/31/2024] Open
Abstract
With the increasing spread of infectious diseases worldwide, there is an urgent need for novel strategies to combat them. Cryogenic sample electron microscopy (cryo-EM) techniques, particularly electron tomography (cryo-ET), have revolutionized the field of infectious disease research by enabling multiscale observation of biological structures in a near-native state. This review highlights the recent advances in infectious disease research using cryo-ET and discusses the potential of this structural biology technique to help discover mechanisms of infection in native environments and guiding in the right direction for future drug discovery.
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Affiliation(s)
- Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, WA, United States
| | - Vada A. Becker
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States
| | - Daija Bobe
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Charlie Dubbledam
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jake D. Johnston
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, United States
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Nathalie R. Lavoie
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, MA, United States
| | - Qiuye Li
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Jacob M. Mattingly
- Department of Chemistry, College of Arts and Sciences, Emory University, Atlanta, GA, United States
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Mohammadreza Paraan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
| | - Jack Turner
- European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Viraj Upadhye
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
| | - Richard M. Walsh
- Harvard Cryo-Electron Microscopy Center for Structural Biology and Harvard Medical School, Boston, MA, United States
| | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, United States
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States
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12
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Raveh B, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP, Cowburn D, Sali A. Integrative spatiotemporal map of nucleocytoplasmic transport. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573409. [PMID: 38260487 PMCID: PMC10802240 DOI: 10.1101/2023.12.31.573409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The Nuclear Pore Complex (NPC) facilitates rapid and selective nucleocytoplasmic transport of molecules as large as ribosomal subunits and viral capsids. It is not clear how key emergent properties of this transport arise from the system components and their interactions. To address this question, we constructed an integrative coarse-grained Brownian dynamics model of transport through a single NPC, followed by coupling it with a kinetic model of Ran-dependent transport in an entire cell. The microscopic model parameters were fitted to reflect experimental data and theoretical information regarding the transport, without making any assumptions about its emergent properties. The resulting reductionist model is validated by reproducing several features of transport not used for its construction, such as the morphology of the central transporter, rates of passive and facilitated diffusion as a function of size and valency, in situ radial distributions of pre-ribosomal subunits, and active transport rates for viral capsids. The model suggests that the NPC functions essentially as a virtual gate whose flexible phenylalanine-glycine (FG) repeat proteins raise an entropy barrier to diffusion through the pore. Importantly, this core functionality is greatly enhanced by several key design features, including 'fuzzy' and transient interactions, multivalency, redundancy in the copy number of FG nucleoporins, exponential coupling of transport kinetics and thermodynamics in accordance with the transition state theory, and coupling to the energy-reliant RanGTP concentration gradient. These design features result in the robust and resilient rate and selectivity of transport for a wide array of cargo ranging from a few kilodaltons to megadaltons in size. By dissecting these features, our model provides a quantitative starting point for rationally modulating the transport system and its artificial mimics.
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13
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Berkamp S, Daviran D, Smeets M, Caignard A, Jani RA, Sundermeyer P, Jonker C, Gerlach S, Hoffmann B, Lau K, Sachse C. Correlative Light and Electron Cryo-Microscopy Workflow Combining Micropatterning, Ice Shield, and an In-Chamber Fluorescence Light Microscope. Bio Protoc 2023; 13:e4901. [PMID: 38156035 PMCID: PMC10751236 DOI: 10.21769/bioprotoc.4901] [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: 08/10/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 12/30/2023] Open
Abstract
In situ cryo-electron tomography (cryo-ET) is the most current, state-of-the-art technique to study cell machinery in its hydrated near-native state. The method provides ultrastructural details at sub-nanometer resolution for many components within the cellular context. Making use of recent advances in sample preparation techniques and combining this method with correlative light and electron microscopy (CLEM) approaches have enabled targeted molecular visualization. Nevertheless, the implementation has also added to the complexity of the workflow and introduced new obstacles in the way of streamlining and achieving high throughput, sample yield, and sample quality. Here, we report a detailed protocol by combining multiple newly available technologies to establish an integrated, high-throughput, optimized, and streamlined cryo-CLEM workflow for improved sample yield. Key features • PRIMO micropatterning allows precise cell positioning and maximum number of cell targets amenable to thinning with cryo focused-ion-beam-scanning electron microscopy. • CERES ice shield ensures that the lamellae remain free of ice contamination during the batch milling process. • METEOR in-chamber fluorescence microscope facilitates the targeted cryo focused-ion-beam (cryo FIB) milling of these targets. • Combining the three technologies into one cryo-CLEM workflow maximizes sample yield, throughput, and efficiency. Graphical overview.
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Affiliation(s)
- Sabrina Berkamp
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-6: Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
| | | | | | | | | | - Pia Sundermeyer
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-6: Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
| | | | - Sven Gerlach
- Institute of Biological Information Processing, IBI-2: Mechanobiology Forschungszentrum Jülich, Jülich, Germany
| | - Bernd Hoffmann
- Institute of Biological Information Processing, IBI-2: Mechanobiology Forschungszentrum Jülich, Jülich, Germany
| | | | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing, IBI-6: Structural Cell Biology, Forschungszentrum Jülich, Jülich, Germany
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
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14
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Woods EV, Kim SH, El-Zoka AA, Stephenson LT, Gault B. Scalable substrate development for aqueous sample preparation for atom probe tomography. J Microsc 2023. [PMID: 38115688 DOI: 10.1111/jmi.13255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
Reliable and consistent preparation of atom probe tomography (APT) specimens from aqueous and hydrated biological specimens remains a significant challenge. One particularly difficult process step is the use of a focused ion beam (FIB) instrument for preparing the required needle-shaped specimen, typically involving a 'lift-out' procedure of a small sample of material. Here, two alternative substrate designs are introduced that enable using FIB only for sharpening, along with example APT datasets. The first design is a laser-cut FIB-style half-grid close to those used for transmission electron microscopy (TEM) that can be used in a grid holder compatible with APT pucks. The second design is a larger, standalone self-supporting substrate called a 'crown', with several specimen positions, which self-aligns in APT pucks, prepared by electrical discharge machining (EDM). Both designs are made nanoporous, to provide strength to the liquid-substrate interface, using chemical and vacuum dealloying. Alpha brass, a simple, widely available, lower-cost alternative to previously proposed substrates, was selected for this work. The resulting designs and APT data are presented and suggestions are provided to help drive wider community adoption.
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Affiliation(s)
- Eric V Woods
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
| | - Se-Ho Kim
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials Science and Engineering, Korea University, Seoul, Republic of Korea
| | - Ayman A El-Zoka
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
| | - L T Stephenson
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, New South Wales, Australia
| | - B Gault
- Department Mikrostrukturphysik und Legierungsdesign, Max-Planck-Institut für Eisenforschung, Düsseldorf, Germany
- Department of Materials, Royal School of Mines, Imperial College London, London, UK
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15
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Weber N, Hinks B, Jensen J, Lidahl T, Mendonça L. Sample Preparation for In Situ Cryotomography of Mammalian Cells. J Vis Exp 2023:10.3791/65697. [PMID: 38163272 PMCID: PMC10921979 DOI: 10.3791/65697] [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] [Indexed: 01/03/2024] Open
Abstract
In situ cellular cryotomography is a powerful technique for studying complex objects in their native frozen-hydrated cellular context, making it highly relevant to cellular biology and virology. The potential of combining cryotomography with other microscopy modalities makes it a perfect technique for integrative and correlative imaging. However, sample preparation for in situ cellular tomography is not straightforward, as cells do not readily attach and stretch over the electron microscopy grid. Additionally, the grids themselves are fragile and can break if handled too forcefully, resulting in the loss of imageable areas. The geometry of tissue culture dishes can also pose a challenge when manipulating the grids with tweezers. Here, we describe the tips and tricks to overcome these (and other) challenges and prepare good-quality samples for in situ cellular cryotomography and correlative imaging of adherent mammalian cells. With continued advances in cryomicroscopy technology, this technique holds enormous promise for advancing our understanding of complex biological systems.
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Affiliation(s)
- Noah Weber
- College of Liberal Arts, University of Minnesota; Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota
| | - Brennan Hinks
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota; College of Biological Sciences, University of Minnesota
| | - Jacob Jensen
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota
| | - Thomas Lidahl
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota; College of Biological Sciences, University of Minnesota
| | - Luiza Mendonça
- Department of Biochemistry, Molecular Biology and Biophysics, Medical School, University of Minnesota;
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16
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Fry MY, Navarro PP, Hakim P, Ananda VY, Qin X, Landoni JC, Rath S, Inde Z, Lugo CM, Luce BE, Ge Y, McDonald JL, Ali I, Ha LL, Kleinstiver BP, Chan DC, Sarosiek KA, Chao LH. In situ architecture of Opa1-dependent mitochondrial cristae remodeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524176. [PMID: 36711707 PMCID: PMC9882235 DOI: 10.1101/2023.01.16.524176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms in the mitochondrion, a membrane-anchored long form (l-Opa1) and a processed short form (s-Opa1). The mechanisms for how Opa1 influences cristae shape have remained unclear due to lack of native three-dimensional views of cristae. We perform in situ cryo-electron tomography of cryo-focused ion beam milled mouse embryonic fibroblasts with defined Opa1 states to understand how each form of Opa1 influences cristae architecture. In our tomograms, we observe a variety of cristae shapes with distinct trends dependent on s-Opa1:l-Opa1 balance. Increased l-Opa1 levels promote cristae stacking and elongated mitochondria while increased s-Opa1 levels correlated with irregular cristae packing and round mitochondria shape. Functional assays indicate a role for l-Opa1 in wild-type apoptotic and calcium handling responses, and compromised respiratory function under Opa1 imbalance. In summary, we provide three-dimensional visualization of cristae architecture to reveal relationships between mitochondrial ultrastructure and cellular function dependent on Opa1-mediated membrane remodeling.
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Affiliation(s)
- Michelle Y. Fry
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Paula P. Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Pusparanee Hakim
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
| | - Virly Y. Ananda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
| | - Xingping Qin
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- Molecular and Integrative Physiological Sciences (MIPS) Program, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Juan C. Landoni
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sneha Rath
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
| | - Zintis Inde
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
- Molecular and Integrative Physiological Sciences (MIPS) Program, Harvard T.H. Chan School of Public Health, Boston, USA
| | | | - Bridget E. Luce
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
| | - Yifan Ge
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
- Current address: Interdisciplinary Research Center of Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Science, China
| | - Julie L. McDonald
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
- Current address: Massachusetts Institute of Technology, Biology, Cambridge, USA
| | - Ilzat Ali
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Leillani L. Ha
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Department of Pathology, Massachusetts General Hospital, Boston, USA
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
- Department of Pathology, Massachusetts General Hospital, Boston, USA
- Department of Pathology, Harvard Medical School, Boston, USA
| | - David C. Chan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA
| | - Kristopher A. Sarosiek
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, USA
- Molecular and Integrative Physiological Sciences (MIPS) Program, Harvard T.H. Chan School of Public Health, Boston, USA
- Lab of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Luke H. Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, USA
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17
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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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18
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Pi H, Sun R, McBride JR, Kruse ARS, Gibson-Corley KN, Krystofiak ES, Nicholson MR, Spraggins JM, Zhou Q, Skaar EP. Clostridioides difficile ferrosome organelles combat nutritional immunity. Nature 2023; 623:1009-1016. [PMID: 37968387 PMCID: PMC10822667 DOI: 10.1038/s41586-023-06719-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 10/05/2023] [Indexed: 11/17/2023]
Abstract
Iron is indispensable for almost all forms of life but toxic at elevated levels1-4. To survive within their hosts, bacterial pathogens have evolved iron uptake, storage and detoxification strategies to maintain iron homeostasis1,5,6. Recent studies showed that three Gram-negative environmental anaerobes produce iron-containing ferrosome granules7,8. However, it remains unclear whether ferrosomes are generated exclusively by Gram-negative bacteria. The Gram-positive bacterium Clostridioides difficile is the leading cause of nosocomial and antibiotic-associated infections in the USA9. Here we report that C. difficile undergoes an intracellular iron biomineralization process and stores iron in membrane-bound ferrosome organelles containing non-crystalline iron phosphate biominerals. We found that a membrane protein (FezA) and a P1B6-ATPase transporter (FezB), repressed by both iron and the ferric uptake regulator Fur, are required for ferrosome formation and play an important role in iron homeostasis during transition from iron deficiency to excess. Additionally, ferrosomes are often localized adjacent to cellular membranes as shown by cryo-electron tomography. Furthermore, using two mouse models of C. difficile infection, we demonstrated that the ferrosome system is activated in the inflamed gut to combat calprotectin-mediated iron sequestration and is important for bacterial colonization and survival during C. difficile infection.
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Affiliation(s)
- Hualiang Pi
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Rong Sun
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James R McBride
- Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN, USA
| | - Angela R S Kruse
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Katherine N Gibson-Corley
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Evan S Krystofiak
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Maribeth R Nicholson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiangjun Zhou
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt Kennedy Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University, Nashville, TN, USA.
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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19
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Woldeyes RA, Nishiga M, Vander Roest AS, Engel L, Giri P, Montenegro GC, Wu AC, Dunn AR, Spudich JA, Bernstein D, Schmid MF, Wu JC, Chiu W. Cryo-electron tomography reveals the structural diversity of cardiac proteins in their cellular context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564098. [PMID: 37961228 PMCID: PMC10634850 DOI: 10.1101/2023.10.26.564098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Cardiovascular diseases are a leading cause of death worldwide, but our understanding of the underlying mechanisms is limited, in part because of the complexity of the cellular machinery that controls the heart muscle contraction cycle. Cryogenic electron tomography (cryo-ET) provides a way to visualize diverse cellular machinery while preserving contextual information like subcellular localization and transient complex formation, but this approach has not been widely applied to the study of heart muscle cells (cardiomyocytes). Here, we deploy a platform for studying cardiovascular disease by combining cryo-ET with human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). After developing a cryo-ET workflow for visualizing macromolecules in hiPSC-CMs, we reconstructed sub-nanometer resolution structures of the human thin filament, a central component of the contractile machinery. We also visualized a previously unobserved organization of a regulatory complex that connects muscle contraction to calcium signaling (the troponin complex), highlighting the value of our approach for interrogating the structures of cardiac proteins in their cellular context.
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Affiliation(s)
- Rahel A. Woldeyes
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Masataka Nishiga
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alison S. Vander Roest
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Engineering, University of Michigan, MI, USA
| | - Leeya Engel
- Faculty of Mechanical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Prerna Giri
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Andrew C. Wu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Alexander R. Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - James A. Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Bernstein
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael F. Schmid
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
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20
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Yang JE, Larson MR, Sibert BS, Kim JY, Parrell D, Sanchez JC, Pappas V, Kumar A, Cai K, Thompson K, Wright ER. Correlative montage parallel array cryo-tomography for in situ structural cell biology. Nat Methods 2023; 20:1537-1543. [PMID: 37723245 PMCID: PMC10555823 DOI: 10.1038/s41592-023-01999-5] [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: 01/07/2022] [Accepted: 08/08/2023] [Indexed: 09/20/2023]
Abstract
Imaging large fields of view while preserving high-resolution structural information remains a challenge in low-dose cryo-electron tomography. Here we present robust tools for montage parallel array cryo-tomography (MPACT) tailored for vitrified specimens. The combination of correlative cryo-fluorescence microscopy, focused-ion-beam milling, substrate micropatterning, and MPACT supports studies that contextually define the three-dimensional architecture of cells. To further extend the flexibility of MPACT, tilt series may be processed in their entirety or as individual tiles suitable for sub-tomogram averaging, enabling efficient data processing and analysis.
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Affiliation(s)
- Jie E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Matthew R Larson
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Joseph Y Kim
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
| | - Daniel Parrell
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | - Juan C Sanchez
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Biophysics Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Victoria Pappas
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Biophysics Graduate Program, University of Wisconsin, Madison, WI, USA
| | - Anil Kumar
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Kai Cai
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Keith Thompson
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, USA.
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA.
- Morgridge Institute for Research, Madison, WI, USA.
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21
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Thongchol J, Lill Z, Hoover Z, Zhang J. Recent Advances in Structural Studies of Single-Stranded RNA Bacteriophages. Viruses 2023; 15:1985. [PMID: 37896763 PMCID: PMC10610835 DOI: 10.3390/v15101985] [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: 08/07/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Positive-sense single-stranded RNA (ssRNA) bacteriophages (phages) were first isolated six decades ago. Since then, extensive research has been conducted on these ssRNA phages, particularly those infecting E. coli. With small genomes of typically 3-4 kb that usually encode four essential proteins, ssRNA phages employ a straightforward infectious cycle involving host adsorption, genome entry, genome replication, phage assembly, and host lysis. Recent advancements in metagenomics and transcriptomics have led to the identification of ~65,000 sequences from ssRNA phages, expanding our understanding of their prevalence and potential hosts. This review article illuminates significant investigations into ssRNA phages, with a focal point on their structural aspects, providing insights into the various stages of their infectious cycle.
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Affiliation(s)
| | | | | | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; (J.T.); (Z.L.); (Z.H.)
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22
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Sanchez Carrillo IB, Hoffmann PC, Barff T, Beck M, Germain H. Preparing Arabidopsis thaliana root protoplasts for cryo electron tomography. FRONTIERS IN PLANT SCIENCE 2023; 14:1261180. [PMID: 37810374 PMCID: PMC10556516 DOI: 10.3389/fpls.2023.1261180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
The use of protoplasts in plant biology has become a convenient tool for the application of transient gene expression. This model system has allowed the study of plant responses to biotic and abiotic stresses, protein location and trafficking, cell wall dynamics, and single-cell transcriptomics, among others. Although well-established protocols for isolating protoplasts from different plant tissues are available, they have never been used for studying plant cells using cryo electron microscopy (cryo-EM) and cryo electron tomography (cryo-ET). Here we describe a workflow to prepare root protoplasts from Arabidopsis thaliana plants for cryo-ET. The process includes protoplast isolation and vitrification on EM grids, and cryo-focused ion beam milling (cryo-FIB), with the aim of tilt series acquisition. The whole workflow, from growing the plants to the acquisition of the tilt series, may take a few months. Our protocol provides a novel application to use plant protoplasts as a tool for cryo-ET.
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Affiliation(s)
| | - Patrick C. Hoffmann
- Department of Molecular Sociology, Max-Planck-Institute for Biophysics, Frankfurt, Germany
| | - Teura Barff
- Department of Chemistry, Biochemistry, and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Martin Beck
- Department of Molecular Sociology, Max-Planck-Institute for Biophysics, Frankfurt, Germany
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Hugo Germain
- Department of Chemistry, Biochemistry, and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
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23
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Skoupý R, Boltje DB, Slouf M, Mrázová K, Láznička T, Taisne CM, Krzyžánek V, Hoogenboom JP, Jakobi AJ. Robust Local Thickness Estimation of Sub-Micrometer Specimen by 4D-STEM. SMALL METHODS 2023; 7:e2300258. [PMID: 37248805 DOI: 10.1002/smtd.202300258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/21/2023] [Indexed: 05/31/2023]
Abstract
A quantitative four-dimensional scanning transmission electron microscopy (4D-STEM) imaging technique (q4STEM) for local thickness estimation across amorphous specimen such as obtained by focused ion beam (FIB)-milling of lamellae for (cryo-)TEM analysis is presented. This study is based on measuring spatially resolved diffraction patterns to obtain the angular distribution of electron scattering, or the ratio of integrated virtual dark and bright field STEM signals, and their quantitative evaluation using Monte Carlo simulations. The method is independent of signal intensity calibrations and only requires knowledge of the detector geometry, which is invariant for a given instrument. This study demonstrates that the method yields robust thickness estimates for sub-micrometer amorphous specimen using both direct detection and light conversion 2D-STEM detectors in a coincident FIB-SEM and a conventional SEM. Due to its facile implementation and minimal dose reauirements, it is anticipated that this method will find applications for in situ thickness monitoring during lamella fabrication of beam-sensitive materials.
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Affiliation(s)
- Radim Skoupý
- Institute of Scientific Instruments, Czech Academy of Sciences, Brno, 61264, CZ
- Department of Bionanoscience, Delft University of Technology, Delft, 2628 CD, NL
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2628 CJ, NL
- Department of Imaging Physics, Delft University of Technology, Delft, 2628 CJ, NL
| | - Daan B Boltje
- Department of Imaging Physics, Delft University of Technology, Delft, 2628 CJ, NL
| | - Miroslav Slouf
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, 162 00, CZ
| | - Kateřina Mrázová
- Institute of Scientific Instruments, Czech Academy of Sciences, Brno, 61264, CZ
| | - Tomáš Láznička
- Institute of Scientific Instruments, Czech Academy of Sciences, Brno, 61264, CZ
| | - Clémence M Taisne
- Department of Bionanoscience, Delft University of Technology, Delft, 2628 CD, NL
| | - Vladislav Krzyžánek
- Institute of Scientific Instruments, Czech Academy of Sciences, Brno, 61264, CZ
| | - Jacob P Hoogenboom
- Department of Imaging Physics, Delft University of Technology, Delft, 2628 CJ, NL
| | - Arjen J Jakobi
- Department of Bionanoscience, Delft University of Technology, Delft, 2628 CD, NL
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24
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Huang Y, Zhang Y, Ni T. Towards in situ high-resolution imaging of viruses and macromolecular complexes using cryo-electron tomography. J Struct Biol 2023; 215:108000. [PMID: 37467823 DOI: 10.1016/j.jsb.2023.108000] [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: 04/25/2023] [Revised: 07/15/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Cryo-electron tomography and subtomogram averaging are rising and fast-evolving imaging techniques to study biological events, providing structural information at an unprecedented resolution while preserving spatial correlation in their native contexts. The latest technology and methodology development ranging from sample preparation to data collection and data processing, has enabled significant advancement in its applications to various biological systems. This review provides an overview of the current technology development enabling high-resolution structural study in situ, highlighting the use of a priori information of biological samples to assess the quality of subtomogram averaging pipeline. We exemplify the applications of this technique to understanding viruses and principles of macromolecule assembly using different biological systems, ranging from in vitro to in situ samples, which provide structural information at different resolutions and contexts.
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Affiliation(s)
- Yixin Huang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Yu Zhang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Tao Ni
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region.
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25
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Watanabe R, Saphire EO. The in situ Structural Approach to Reveal the Filovirus Budding Mechanism. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:900-901. [PMID: 37613812 DOI: 10.1093/micmic/ozad067.447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Reika Watanabe
- La Jolla Institute for Immunology, Center for Infectious Disease and Vaccine Research, La Jolla, CA, United States
| | - Erica Ollmann Saphire
- La Jolla Institute for Immunology, Center for Infectious Disease and Vaccine Research, La Jolla, CA, United States
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26
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Rice G, Wagner T, Stabrin M, Sitsel O, Prumbaum D, Raunser S. TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining. Nat Methods 2023:10.1038/s41592-023-01878-z. [PMID: 37188953 DOI: 10.1038/s41592-023-01878-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volumes are still needed. Detailed analysis of macromolecules through subtomogram averaging requires particles to first be localized within the tomogram volume, a task complicated by several factors including a low signal to noise ratio and crowding of the cellular space. Available methods for this task suffer either from being error prone or requiring manual annotation of training data. To assist in this crucial particle picking step, we present TomoTwin: an open source general picking model for cryogenic-electron tomograms based on deep metric learning. By embedding tomograms in an information-rich, high-dimensional space that separates macromolecules according to their three-dimensional structure, TomoTwin allows users to identify proteins in tomograms de novo without manually creating training data or retraining the network to locate new proteins.
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Affiliation(s)
- Gavin Rice
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Markus Stabrin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel Prumbaum
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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27
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Wozny MR, Di Luca A, Morado DR, Picco A, Khaddaj R, Campomanes P, Ivanović L, Hoffmann PC, Miller EA, Vanni S, Kukulski W. In situ architecture of the ER-mitochondria encounter structure. Nature 2023:10.1038/s41586-023-06050-3. [PMID: 37165187 DOI: 10.1038/s41586-023-06050-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane biogenesis that rely on lipid exchange via membrane contact sites1-3, but the underpinning mechanisms remain poorly understood. In yeast, tethering and lipid transfer between the two organelles is mediated by the endoplasmic reticulum-mitochondria encounter structure (ERMES), a four-subunit complex of unresolved stoichiometry and architecture4-6. Here we determined the molecular organization of ERMES within Saccharomyces cerevisiae cells using integrative structural biology by combining quantitative live imaging, cryo-correlative microscopy, subtomogram averaging and molecular modelling. We found that ERMES assembles into approximately 25 discrete bridge-like complexes distributed irregularly across a contact site. Each bridge consists of three synaptotagmin-like mitochondrial lipid binding protein domains oriented in a zig-zag arrangement. Our molecular model of ERMES reveals a pathway for lipids. These findings resolve the in situ supramolecular architecture of a major inter-organelle lipid transfer machinery and provide a basis for the mechanistic understanding of lipid fluxes in eukaryotic cells.
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Affiliation(s)
- Michael R Wozny
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Andrea Di Luca
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Dustin R Morado
- MRC Laboratory of Molecular Biology, Cambridge, UK
- SciLifeLab, Solna, Sweden
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrea Picco
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Rasha Khaddaj
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Lazar Ivanović
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Patrick C Hoffmann
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
| | - Wanda Kukulski
- MRC Laboratory of Molecular Biology, Cambridge, UK.
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
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28
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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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29
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Li Z, Du W, Yang J, Lai DH, Lun ZR, Guo Q. Cryo-Electron Tomography of Toxoplasma gondii Indicates That the Conoid Fiber May Be Derived from Microtubules. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206595. [PMID: 36840635 DOI: 10.1002/advs.202206595] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/04/2023] [Indexed: 05/18/2023]
Abstract
Toxoplasma gondii (T. gondii) is the causative agent of toxoplasmosis and can infect numerous warm-blooded animals. An improved understanding of the fine structure of this parasite can help elucidate its replication mechanism. Previous studies have resolved the ultrastructure of the cytoskeleton using purified samples, which eliminates their cellular context. Here the application of cryo-electron tomography to visualize T. gondii tachyzoites in their native state is reported. The fine structure and cellular distribution of the cytoskeleton are resolved and analyzed at nanometer resolution. Additionally, the tachyzoite structural characteristics are annotated during its endodyogeny for the first time. By comparing the structural features in mature tachyzoites and their daughter buds, it is proposed that the conoid fiber of the Apicomplexa originates from microtubules. This work represents the detailed molecular anatomy of T. gondii, particularly during the budding replication stage of tachyzoite, and provides a reference for further studies of this fascinating organism.
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Affiliation(s)
- Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Wenjing Du
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Jiong Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - De-Hua Lai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Zhao-Rong Lun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, 100871, P. R. China
- Changping Laboratory, Yard 28, Science Park Road, Beijing, 102206, P. R. China
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30
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Lobato-Márquez D, Conesa JJ, López-Jiménez AT, Divine ME, Pruneda JN, Mostowy S. Septins and K63 ubiquitin chains are present in separate bacterial microdomains during autophagy of entrapped Shigella. J Cell Sci 2023; 136:jcs261139. [PMID: 36939083 PMCID: PMC10264824 DOI: 10.1242/jcs.261139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/21/2023] Open
Abstract
During host cell invasion, Shigella escapes to the cytosol and polymerizes actin for cell-to-cell spread. To restrict cell-to-cell spread, host cells employ cell-autonomous immune responses including antibacterial autophagy and septin cage entrapment. How septins interact with the autophagy process to target Shigella for destruction is poorly understood. Here, we employed a correlative light and cryo-soft X-ray tomography (cryo-SXT) pipeline to study Shigella septin cage entrapment in its near-native state. Quantitative cryo-SXT showed that Shigella fragments mitochondria and enabled visualization of X-ray-dense structures (∼30 nm resolution) surrounding Shigella entrapped in septin cages. Using Airyscan confocal microscopy, we observed lysine 63 (K63)-linked ubiquitin chains decorating septin-cage-entrapped Shigella. Remarkably, septins and K63 chains are present in separate bacterial microdomains, indicating they are recruited separately during antibacterial autophagy. Cryo-SXT and live-cell imaging revealed an interaction between septins and LC3B-positive membranes during autophagy of Shigella. Together, these findings demonstrate how septin-caged Shigella are targeted for autophagy and provide fundamental insights into autophagy-cytoskeleton interactions.
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Affiliation(s)
- Damián Lobato-Márquez
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - José Javier Conesa
- MISTRAL beamline, ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Ana Teresa López-Jiménez
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Michael E. Divine
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jonathan N. Pruneda
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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31
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Berger C, Premaraj N, Ravelli RBG, Knoops K, López-Iglesias C, Peters PJ. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat Methods 2023; 20:499-511. [PMID: 36914814 DOI: 10.1038/s41592-023-01783-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.
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Affiliation(s)
- Casper Berger
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Navya Premaraj
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Kèvin Knoops
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Carmen López-Iglesias
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
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32
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Klein S, Golani G, Lolicato F, Lahr C, Beyer D, Herrmann A, Wachsmuth-Melm M, Reddmann N, Brecht R, Hosseinzadeh M, Kolovou A, Makroczyova J, Peterl S, Schorb M, Schwab Y, Brügger B, Nickel W, Schwarz US, Chlanda P. IFITM3 blocks influenza virus entry by sorting lipids and stabilizing hemifusion. Cell Host Microbe 2023; 31:616-633.e20. [PMID: 37003257 DOI: 10.1016/j.chom.2023.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/15/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023]
Abstract
Interferon-induced transmembrane protein 3 (IFITM3) inhibits the entry of numerous viruses through undefined molecular mechanisms. IFITM3 localizes in the endosomal-lysosomal system and specifically affects virus fusion with target cell membranes. We found that IFITM3 induces local lipid sorting, resulting in an increased concentration of lipids disfavoring viral fusion at the hemifusion site. This increases the energy barrier for fusion pore formation and the hemifusion dwell time, promoting viral degradation in lysosomes. In situ cryo-electron tomography captured IFITM3-mediated arrest of influenza A virus membrane fusion. Observation of hemifusion diaphragms between viral particles and late endosomal membranes confirmed hemifusion stabilization as a molecular mechanism of IFITM3. The presence of the influenza fusion protein hemagglutinin in post-fusion conformation close to hemifusion sites further indicated that IFITM3 does not interfere with the viral fusion machinery. Collectively, these findings show that IFITM3 induces lipid sorting to stabilize hemifusion and prevent virus entry into target cells.
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Affiliation(s)
- Steffen Klein
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Gonen Golani
- BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany; Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany; Department of Physics, University of Helsinki, Helsinki, Finland
| | - Carmen Lahr
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Daniel Beyer
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Alexia Herrmann
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Nina Reddmann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Romy Brecht
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Mehdi Hosseinzadeh
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Androniki Kolovou
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Sarah Peterl
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Martin Schorb
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Yannick Schwab
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany
| | - Ulrich S Schwarz
- BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany; Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; BioQuant Center for Quantitative Biology, Heidelberg University, 69120 Heidelberg, Germany.
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33
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Berger C, Dumoux M, Glen T, Yee NBY, Mitchels JM, Patáková Z, Darrow MC, Naismith JH, Grange M. Plasma FIB milling for the determination of structures in situ. Nat Commun 2023; 14:629. [PMID: 36746945 PMCID: PMC9902539 DOI: 10.1038/s41467-023-36372-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Structural biology studies inside cells and tissues require methods to thin vitrified specimens to electron transparency. Until now, focused ion beams based on gallium have been used. However, ion implantation, changes to surface chemistry and an inability to access high currents limit gallium application. Here, we show that plasma-coupled ion sources can produce cryogenic lamellae of vitrified human cells in a robust and automated manner, with quality sufficient for pseudo-atomic structure determination. Lamellae were produced in a prototype microscope equipped for long cryogenic run times (> 1 week) and with multi-specimen support fully compatible with modern-day transmission electron microscopes. We demonstrate that plasma ion sources can be used for structural biology within cells, determining a structure in situ to 4.9 Å, and characterise the resolution dependence on particle distance from the lamella edge. We describe a workflow upon which different plasmas can be examined to further streamline lamella fabrication.
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Affiliation(s)
- Casper Berger
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, United Kingdom
| | - Maud Dumoux
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Thomas Glen
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Neville B-Y Yee
- Artificial Intelligence & Informatics, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - John M Mitchels
- Thermo Fisher Scientific Brno s.r.o, Brno, 627 00, Czech Republic
| | - Zuzana Patáková
- Thermo Fisher Scientific Brno s.r.o, Brno, 627 00, Czech Republic
| | - Michele C Darrow
- Artificial Intelligence & Informatics, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, United Kingdom
| | - Michael Grange
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom. .,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, United Kingdom.
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34
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High-speed laser writing of structural colors for full-color inkless printing. Nat Commun 2023; 14:565. [PMID: 36732539 PMCID: PMC9894925 DOI: 10.1038/s41467-023-36275-9] [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: 08/22/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023] Open
Abstract
It is a formidable challenge to simultaneously achieve wide-gamut, high-resolution, high-speed while low-cost manufacturability, long-term stability, and viewing-angle independence in structural colors for practical applications. The conventional nanofabrication techniques fail to match the requirement in low-cost, large-scale and flexible manufacturing. Processing by pulsed lasers can achieve high throughput while suffering from a narrow gamut of ~15% sRGB or angle-dependent colors. Here, we demonstrate an all-in-one solution for ultrafast laser-produced structural colors on ultrathin hybrid films that comprise an absorbent dielectric TiAlN layer coating on a metallic TiN layer. Under laser irradiation, the absorption behaviours of the TiAlN-TiN hybrid films are tailored by photothermal-induced oxidation on the topmost TiAlN. The oxidized films exhibit double-resonance absorption, which is due to the non-trivial phase shifts both at the oxide-TiAlN interface, and at the TiAlN-TiN interface. By varying the accumulated laser fluence to modulate the oxidation depth, angle-robust structural colors with unprecedented large-gamut of ~90% sRGB are obtained. The highest printing speed reaches 10 cm2/s and the highest resolution exceeds 10000 dpi. The durability of the laser-printed colors is confirmed by fastness examination, including salt spray, double-85, light bleaching, and adhesion tests. These features render our technique to be competitive for industrial applications.
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35
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Huang G, Zeng C, Shi Y. Structure of the nuclear pore complex goes atomic. Curr Opin Struct Biol 2023; 78:102523. [PMID: 36641895 DOI: 10.1016/j.sbi.2022.102523] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 01/14/2023]
Abstract
The nuclear pore complex (NPC) is a supra-molecular assembly that mediates substance and information flow across the nuclear envelope (NE). Due to its extraordinary size and complexity, the NPC remains one of the most challenging tasks in structural elucidation at atomic resolution. Recent breakthroughs in cryo-electron microscopy (cryo-EM) reconstruction, Machine Learning empowered structure prediction and biochemical reconstitution have combined to yield molecular models of the NPC at unprecedented accuracy. Furthermore, in cellulo cryo-electron tomography (cryo-ET) structures reveal substantial structural dynamics of the NPC. These advances shed light on the organizational principles and functions of the NPC.
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Affiliation(s)
- Gaoxingyu Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China.
| | - Chao Zeng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China.
| | - Yigong Shi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Beijing Advanced Innovation Center for Structural Biology & Advanced Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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36
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de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli CE, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck M, Diz-Muñoz A, Kreshuk A, Mahamid J, Zaugg JB. Convolutional networks for supervised mining of molecular patterns within cellular context. Nat Methods 2023; 20:284-294. [PMID: 36690741 PMCID: PMC9911354 DOI: 10.1038/s41592-022-01746-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/02/2022] [Indexed: 01/24/2023]
Abstract
Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community.
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Affiliation(s)
- Irene de Teresa-Trueba
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Computer Science and Artificial Intelligence Lab, ENGIE Lab Crigen, Stains, France
| | - Sara K. Goetz
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Alexander Mattausch
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Frosina Stojanovska
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Christian E. Zimmerli
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Mauricio Toro-Nahuelpan
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Santiago GmbH & Co. KG, Willich, Germany
| | - Dorothy W. C. Cheng
- grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fergus Tollervey
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Constantin Pape
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7450.60000 0001 2364 4210Present Address: Institute for Computer Science, Universität Göttingen, Göttingen, Germany
| | - Martin Beck
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Alba Diz-Muñoz
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna Kreshuk
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Judith B. Zaugg
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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37
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Nicolas WJ, Jensen GJ, Meyerowitz EM. Focused Ion Beam Milling and Cryo-electron Tomography Methods to Study the Structure of the Primary Cell Wall in Allium cepa. Bio Protoc 2022; 12:e4559. [PMID: 36561119 PMCID: PMC9729855 DOI: 10.21769/bioprotoc.4559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/07/2022] [Accepted: 10/12/2022] [Indexed: 12/12/2022] Open
Abstract
Cryo-electron tomography (cryo-ET) is a formidable technique to observe the inner workings of vitrified cells at a nanometric resolution in near-native conditions and in three-dimensions. One consequent drawback of this technique is the sample thickness, for two reasons: i) achieving proper vitrification of the sample gets increasingly difficult with sample thickness, and ii) cryo-ET relies on transmission electron microscopy (TEM), requiring thin samples for proper electron transmittance (<500 nm). For samples exceeding this thickness limit, thinning methods can be used to render the sample amenable for cryo-ET. Cryo-focused ion beam (cryo-FIB) milling is one of them and despite having hugely benefitted the fields of animal cell biology, virology, microbiology, and even crystallography, plant cells are still virtually unexplored by cryo-ET, in particular because they are generally orders of magnitude bigger than bacteria, viruses, or animal cells (at least 10 μm thick) and difficult to process by cryo-FIB milling. Here, we detail a preparation method where abaxial epidermal onion cell wall peels are separated from the epidermal cells and subsequently plunge frozen, cryo-FIB milled, and screened by cryo-ET in order to acquire high resolution tomographic data for analyzing the organization of the cell wall. This protocol was validated in: Curr Biol (2022), DOI: 10.1016/j.cub.2022.04.024.
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Affiliation(s)
- William J. Nicolas
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
,
California Institute of Technology, 1200 E California bvd, Pasadena, CA 91125, USA
,
*For correspondence:
| | - Grant J. Jensen
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
,
California Institute of Technology, 1200 E California bvd, Pasadena, CA 91125, USA
| | - Elliot M. Meyerowitz
- Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, USA
,
California Institute of Technology, 1200 E California bvd, Pasadena, CA 91125, USA
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38
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Zabeo D, Davies KM. Studying membrane modulation mechanisms by electron cryo-tomography. Curr Opin Struct Biol 2022; 77:102464. [PMID: 36174286 DOI: 10.1016/j.sbi.2022.102464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022]
Abstract
Membrane modulation is a key part of cellular life. Critical to processes like energy production, cell division, trafficking, migration and even pathogen entry, defects in membrane modulation are often associated with diseases. Studying the molecular mechanisms of membrane modulation is challenging due to the highly dynamic nature of the oligomeric assemblies involved, which adopt multiple conformations depending on the precise event they are participating in. With the development of electron cryo-tomography and subtomogram averaging, many of these challenges are being resolved as it is now possible to observe complex macromolecular assemblies inside a cell at nanometre to sub-nanometre resolutions. Here, we review the different ways electron cryo-tomography is being used to help uncover the molecular mechanisms used by cells to shape their membranes.
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Affiliation(s)
- Davide Zabeo
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Karen M Davies
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
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39
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Guaita M, Watters SC, Loerch S. Recent advances and current trends in cryo-electron microscopy. Curr Opin Struct Biol 2022; 77:102484. [PMID: 36323134 DOI: 10.1016/j.sbi.2022.102484] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/13/2022] [Accepted: 09/21/2022] [Indexed: 12/14/2022]
Abstract
All steps of cryogenic electron-microscopy (cryo-EM) workflows have rapidly evolved over the last decade. Advances in both single-particle analysis (SPA) cryo-EM and cryo-electron tomography (cryo-ET) have facilitated the determination of high-resolution biomolecular structures that are not tractable with other methods. However, challenges remain. For SPA, these include improved resolution in an additional dimension: time. For cryo-ET, these include accessing difficult-to-image areas of a cell and finding rare molecules. Finally, there is a need for automated and faster workflows, as many projects are limited by throughput. Here, we review current developments in SPA cryo-EM and cryo-ET that push these boundaries. Collectively, these advances are poised to propel our spatial and temporal understanding of macromolecular processes.
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Affiliation(s)
- Margherita Guaita
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Scott C Watters
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA
| | - Sarah Loerch
- University of California, Santa Cruz, Department of Chemistry and Biochemistry, Santa Cruz, CA, USA.
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40
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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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41
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Long DM, Singh MK, Small KA, Watt J. Cryo-FIB for TEM investigation of soft matter and beam sensitive energy materials. NANOTECHNOLOGY 2022; 33:503001. [PMID: 36121746 DOI: 10.1088/1361-6528/ac92eb] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/18/2022] [Indexed: 06/15/2023]
Abstract
Primarily driven by structural biology, the rapid advances in cryogenic electron microscopy techniques are now being adopted and applied by materials scientists. Samples that inherently have electron transparency can be rapidly frozen (vitrified) in amorphous ice and imaged directly on a cryogenic transmission electron microscopy (cryo-TEM), however this is not the case for many important materials systems, which can consist of layered structures, embedded architectures, or be contained within a device. Cryogenic focused ion beam (cryo-FIB) lift-out procedures have recently been developed to extract intact regions and interfaces of interest, that can then be thinned to electron transparency and transferred to the cryo-TEM for characterization. Several detailed studies have been reported demonstrating the cryo-FIB lift-out procedure, however due to its relative infancy in materials science improvements are still required to ensure the technique becomes more accessible and routinely successful. Here, we review recent results on the preparation of cryo-TEM lamellae using cryo-FIB and show that the technique is broadly applicable to a range of soft matter and beam sensitive energy materials. We then present a tutorial that can guide the materials scientist through the cryo-FIB lift-out process, highlighting recent methodological advances that address the most common failure points of the technique, such as needle attachment, lift-out and transfer, and final thinning.
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Affiliation(s)
- Daniel M Long
- Sandia National Laboratories, Albuquerque, NM 87123, United States of America
| | - Manish Kumar Singh
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Kathryn A Small
- Sandia National Laboratories, Albuquerque, NM 87123, United States of America
| | - John Watt
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
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42
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Lasker K, Boeynaems S, Lam V, Scholl D, Stainton E, Briner A, Jacquemyn M, Daelemans D, Deniz A, Villa E, Holehouse AS, Gitler AD, Shapiro L. The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems. Nat Commun 2022; 13:5643. [PMID: 36163138 PMCID: PMC9512792 DOI: 10.1038/s41467-022-33221-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Intracellular phase separation is emerging as a universal principle for organizing biochemical reactions in time and space. It remains incompletely resolved how biological function is encoded in these assemblies and whether this depends on their material state. The conserved intrinsically disordered protein PopZ forms condensates at the poles of the bacterium Caulobacter crescentus, which in turn orchestrate cell-cycle regulating signaling cascades. Here we show that the material properties of these condensates are determined by a balance between attractive and repulsive forces mediated by a helical oligomerization domain and an expanded disordered region, respectively. A series of PopZ mutants disrupting this balance results in condensates that span the material properties spectrum, from liquid to solid. A narrow range of condensate material properties supports proper cell division, linking emergent properties to organismal fitness. We use these insights to repurpose PopZ as a modular platform for generating tunable synthetic condensates in human cells. “Intracellular phase separation is emerging as a universal principle for organizing biochemical reactions in time and space. Here the authors show that PopZ condensate dynamics support cell division and using PopZ modular architecture, the tunable PopTag platform was developed to enable designer condensates.”
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Affiliation(s)
- Keren Lasker
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vinson Lam
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Scholl
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emma Stainton
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam Briner
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), The University of Queensland, Brisbane, QLD, Australia
| | - Maarten Jacquemyn
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, KU Leuven, Leuven, Belgium
| | - Ashok Deniz
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elizabeth Villa
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, MO, USA.,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
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43
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Navarro PP, Vettiger A, Ananda VY, Llopis PM, Allolio C, Bernhardt TG, Chao LH. Cell wall synthesis and remodelling dynamics determine division site architecture and cell shape in Escherichia coli. Nat Microbiol 2022; 7:1621-1634. [PMID: 36097171 PMCID: PMC9519445 DOI: 10.1038/s41564-022-01210-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 07/21/2022] [Indexed: 01/19/2023]
Abstract
The bacterial division apparatus catalyses the synthesis and remodelling of septal peptidoglycan (sPG) to build the cell wall layer that fortifies the daughter cell poles. Understanding of this essential process has been limited by the lack of native three-dimensional views of developing septa. Here, we apply state-of-the-art cryogenic electron tomography (cryo-ET) and fluorescence microscopy to visualize the division site architecture and sPG biogenesis dynamics of the Gram-negative bacterium Escherichia coli. We identify a wedge-like sPG structure that fortifies the ingrowing septum. Experiments with strains defective in sPG biogenesis revealed that the septal architecture and mode of division can be modified to more closely resemble that of other Gram-negative (Caulobacter crescentus) or Gram-positive (Staphylococcus aureus) bacteria, suggesting that a conserved mechanism underlies the formation of different septal morphologies. Finally, analysis of mutants impaired in amidase activation (ΔenvC ΔnlpD) showed that cell wall remodelling affects the placement and stability of the cytokinetic ring. Taken together, our results support a model in which competition between the cell elongation and division machineries determines the shape of cell constrictions and the poles they form. They also highlight how the activity of the division system can be modulated to help generate the diverse array of shapes observed in the bacterial domain.
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Affiliation(s)
- Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Andrea Vettiger
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Virly Y Ananda
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Christoph Allolio
- Faculty of Mathematics and Physics, Mathematical Institute, Charles University, Prague, Czech Republic
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
| | - Luke H Chao
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. .,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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44
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Luo Y, Paunesku T, Antipova O, Liu Y, Zaluzec NJ, Di Z, Woloschak G, Chen S. A reliable workflow for improving nanoscale X-ray fluorescence tomographic analysis on nanoparticle-treated HeLa cells. Metallomics 2022; 14:mfac025. [PMID: 35751648 PMCID: PMC9434635 DOI: 10.1093/mtomcs/mfac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/13/2022] [Indexed: 11/19/2022]
Abstract
Scanning X-ray fluorescence (XRF) tomography provides powerful characterization capabilities in evaluating elemental distribution and differentiating their inter- and intra-cellular interactions in a three-dimensional (3D) space. Scanning XRF tomography encounters practical challenges from the sample itself, where the range of rotation angles is limited by geometric constraints, involving sample substrates or nearby features either blocking or converging into the field of view. This study aims to develop a reliable and efficient workflow that can (1) expand the experimental window for nanoscale tomographic analysis of local areas of interest within a laterally extended specimen, and (2) bridge 3D analysis at micrometer and nanoscales on the same specimen. We demonstrate the workflow using a specimen of HeLa cells exposed to iron oxide core and titanium dioxide shell (Fe3O4/TiO2) nanocomposites. The workflow utilizes iterative and multiscale XRF data collection with intermediate sample processing by focused ion beam (FIB) sample preparation between measurements at different length scales. Initial assessment combined with precise sample manipulation via FIB allows direct removal of sample regions that are obstacles to both incident X-ray beam and outgoing XRF signals, which considerably improves the subsequent nanoscale tomography analysis. This multiscale analysis workflow has advanced bio-nanotechnology studies by providing deep insights into the interaction between nanocomposites and single cells at a subcellular level as well as statistical assessments from measuring a population of cells.
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Affiliation(s)
- Yanqi Luo
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Tatjana Paunesku
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Olga Antipova
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Yuzi Liu
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Nestor J Zaluzec
- Photon Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Zichao Di
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Gayle Woloschak
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Si Chen
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
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45
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Kralt A, Wojtynek M, Fischer JS, Agote-Aran A, Mancini R, Dultz E, Noor E, Uliana F, Tatarek-Nossol M, Antonin W, Onischenko E, Medalia O, Weis K. An amphipathic helix in Brl1 is required for nuclear pore complex biogenesis in S. cerevisiae. eLife 2022; 11:78385. [PMID: 36000978 PMCID: PMC9402233 DOI: 10.7554/elife.78385] [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: 03/04/2022] [Accepted: 08/03/2022] [Indexed: 12/28/2022] Open
Abstract
The nuclear pore complex (NPC) is the central portal for macromolecular exchange between the nucleus and cytoplasm. In all eukaryotes, NPCs assemble into an intact nuclear envelope (NE) during interphase, but the process of NPC biogenesis remains poorly characterized. Furthermore, little is known about how NPC assembly leads to the fusion of the outer and inner NE, and no factors have been identified that could trigger this event. Here, we characterize the transmembrane protein Brl1 as an NPC assembly factor required for NE fusion in budding yeast. Brl1 preferentially associates with NPC assembly intermediates and its depletion halts NPC biogenesis, leading to NE herniations that contain inner and outer ring nucleoporins but lack the cytoplasmic export platform. Furthermore, we identify an essential amphipathic helix in the luminal domain of Brl1 that mediates interactions with lipid bilayers. Mutations in this amphipathic helix lead to NPC assembly defects, and cryo-electron tomography analyses reveal multilayered herniations of the inner nuclear membrane with NPC-like structures at the neck, indicating a failure in NE fusion. Taken together, our results identify a role for Brl1 in NPC assembly and suggest a function of its amphipathic helix in mediating the fusion of the inner and outer nuclear membranes.
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Affiliation(s)
- Annemarie Kralt
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Wojtynek
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.,Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Jonas S Fischer
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Arantxa Agote-Aran
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Roberta Mancini
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elisa Dultz
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Federico Uliana
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Evgeny Onischenko
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
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46
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Abstract
The three-dimensional organization of biomolecules important for the functioning of all living systems can be determined by cryo-electron tomography imaging under native biological contexts. Cryo-electron tomography is continually expanding and evolving, and the development of new methods that use the latest technology for sample thinning is enabling the visualization of ever larger and more complex biological systems, allowing imaging across scales. Quantitative cryo-electron tomography possesses the capability of visualizing the impact of molecular and environmental perturbations in subcellular structure and function to understand fundamental biological processes. This review provides an overview of current hardware and software developments that allow quantitative cryo-electron tomography studies and their limitations and how overcoming them may allow us to unleash the full power of cryo-electron tomography.
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Affiliation(s)
- Paula P Navarro
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Department of Genetics, Harvard Medical School, Boston, MA, United States
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47
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Piper SJ, Johnson RM, Wootten D, Sexton PM. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Chem Rev 2022; 122:13989-14017. [PMID: 35849490 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
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Affiliation(s)
- Sarah J Piper
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M Johnson
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Denise Wootten
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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48
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Revealing bacterial cell biology using cryo-electron tomography. Curr Opin Struct Biol 2022; 75:102419. [PMID: 35820259 DOI: 10.1016/j.sbi.2022.102419] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Visualizing macromolecules inside bacteria at a high spatial resolution has remained a challenge owing to their small size and limited resolution of optical microscopy techniques. Recent advances in cryo-electron tomography (cryo-ET) imaging methods have revealed the spatial and temporal assemblies of many macromolecules involved in different cellular processes in bacteria at a resolution of a few nanometers in their native milieu. Specifically, the application of cryo-focused ion beam (cryo-FIB) milling to thin bacterial specimens makes them amenable for high-resolution cryo-ET data collection. In this review, we highlight recent research in three emerging areas of bacterial cell biology that have benefited from the cryo-FIB-ET technology - cytoskeletal filament assembly, intracellular organelles, and multicellularity.
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49
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Lyons FMT, Gabriela M, Tham WH, Dietrich MH. Plasmodium 6-Cysteine Proteins: Functional Diversity, Transmission-Blocking Antibodies and Structural Scaffolds. Front Cell Infect Microbiol 2022; 12:945924. [PMID: 35899047 PMCID: PMC9309271 DOI: 10.3389/fcimb.2022.945924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
The 6-cysteine protein family is one of the most abundant surface antigens that are expressed throughout the Plasmodium falciparum life cycle. Many members of the 6-cysteine family have critical roles in parasite development across the life cycle in parasite transmission, evasion of the host immune response and host cell invasion. The common feature of the family is the 6-cysteine domain, also referred to as s48/45 domain, which is conserved across Aconoidasida. This review summarizes the current approaches for recombinant expression for 6-cysteine proteins, monoclonal antibodies against 6-cysteine proteins that block transmission and the growing collection of crystal structures that provide insights into the functional domains of this protein family.
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Affiliation(s)
- Frankie M. T. Lyons
- The Walter and Eliza Hall Institute of Medical Research, Infectious Diseases and Immune Defence Division, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Mikha Gabriela
- The Walter and Eliza Hall Institute of Medical Research, Infectious Diseases and Immune Defence Division, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Wai-Hong Tham
- The Walter and Eliza Hall Institute of Medical Research, Infectious Diseases and Immune Defence Division, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Melanie H. Dietrich
- The Walter and Eliza Hall Institute of Medical Research, Infectious Diseases and Immune Defence Division, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
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50
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Chua EYD, Mendez JH, Rapp M, Ilca SL, Tan YZ, Maruthi K, Kuang H, Zimanyi CM, Cheng A, Eng ET, Noble AJ, Potter CS, Carragher B. Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. Annu Rev Biochem 2022; 91:1-32. [PMID: 35320683 PMCID: PMC10393189 DOI: 10.1146/annurev-biochem-032620-110705] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.
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Affiliation(s)
- Eugene Y D Chua
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Joshua H Mendez
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Micah Rapp
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore;
- Disease Intervention Technology Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kashyap Maruthi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Christina M Zimanyi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Edward T Eng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Clinton S Potter
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Bridget Carragher
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
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