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Held RG, Liang J, Brunger AT. Nanoscale architecture of synaptic vesicles and scaffolding complexes revealed by cryo-electron tomography. Proc Natl Acad Sci U S A 2024; 121:e2403136121. [PMID: 38923992 PMCID: PMC11228483 DOI: 10.1073/pnas.2403136121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
The spatial distribution of proteins and their arrangement within the cellular ultrastructure regulates the opening of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors in response to glutamate release at the synapse. Fluorescence microscopy imaging revealed that the postsynaptic density (PSD) and scaffolding proteins in the presynaptic active zone (AZ) align across the synapse to form a trans-synaptic "nanocolumn," but the relation to synaptic vesicle release sites is uncertain. Here, we employ focused-ion beam (FIB) milling and cryoelectron tomography to image synapses under near-native conditions. Improved image contrast, enabled by FIB milling, allows simultaneous visualization of supramolecular nanoclusters within the AZ and PSD and synaptic vesicles. Surprisingly, membrane-proximal synaptic vesicles, which fuse to release glutamate, are not preferentially aligned with AZ or PSD nanoclusters. These synaptic vesicles are linked to the membrane by peripheral protein densities, often consistent in size and shape with Munc13, as well as globular densities bridging the synaptic vesicle and plasma membrane, consistent with prefusion complexes of SNAREs, synaptotagmins, and complexin. Monte Carlo simulations of synaptic transmission events using biorealistic models guided by our tomograms predict that clustering AMPARs within PSD nanoclusters increases the variability of the postsynaptic response but not its average amplitude. Together, our data support a model in which synaptic strength is tuned at the level of single vesicles by the spatial relationship between scaffolding nanoclusters and single synaptic vesicle fusion sites.
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Affiliation(s)
- Richard G. Held
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
| | - Jiahao Liang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
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2
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Wang C, Jiang W, Leitz J, Yang K, Esquivies L, Wang X, Shen X, Held RG, Adams DJ, Basta T, Hampton L, Jian R, Jiang L, Stowell MHB, Baumeister W, Guo Q, Brunger AT. Structure and topography of the synaptic V-ATPase-synaptophysin complex. Nature 2024; 631:899-904. [PMID: 38838737 PMCID: PMC11269182 DOI: 10.1038/s41586-024-07610-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024]
Abstract
Synaptic vesicles are organelles with a precisely defined protein and lipid composition1,2, yet the molecular mechanisms for the biogenesis of synaptic vesicles are mainly unknown. Here we discovered a well-defined interface between the synaptic vesicle V-ATPase and synaptophysin by in situ cryo-electron tomography and single-particle cryo-electron microscopy of functional synaptic vesicles isolated from mouse brains3. The synaptic vesicle V-ATPase is an ATP-dependent proton pump that establishes the proton gradient across the synaptic vesicle, which in turn drives the uptake of neurotransmitters4,5. Synaptophysin6 and its paralogues synaptoporin7 and synaptogyrin8 belong to a family of abundant synaptic vesicle proteins whose function is still unclear. We performed structural and functional studies of synaptophysin-knockout mice, confirming the identity of synaptophysin as an interaction partner with the V-ATPase. Although there is little change in the conformation of the V-ATPase upon interaction with synaptophysin, the presence of synaptophysin in synaptic vesicles profoundly affects the copy number of V-ATPases. This effect on the topography of synaptic vesicles suggests that synaptophysin assists in their biogenesis. In support of this model, we observed that synaptophysin-knockout mice exhibit severe seizure susceptibility, suggesting an imbalance of neurotransmitter release as a physiological consequence of the absence of synaptophysin.
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Affiliation(s)
- Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Wenhong Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Kailu Yang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Xing Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiaotao Shen
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Stanford, CA, USA
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Richard G Held
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Daniel J Adams
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Tamara Basta
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Lucas Hampton
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Stanford, CA, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Stanford University, Stanford, CA, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Wolfgang Baumeister
- Department of Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Department of Structural Biology, Stanford University, Stanford, CA, USA.
- Department of Photon Science, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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3
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Gee CW, Andersen-Ranberg J, Boynton E, Rosen RZ, Jorgens D, Grob P, Holman HYN, Niyogi KK. Implicating the red body of Nannochloropsis in forming the recalcitrant cell wall polymer algaenan. Nat Commun 2024; 15:5456. [PMID: 38937455 PMCID: PMC11211512 DOI: 10.1038/s41467-024-49277-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Stramenopile algae contribute significantly to global primary productivity, and one class, Eustigmatophyceae, is increasingly studied for applications in high-value lipid production. Yet much about their basic biology remains unknown, including the nature of an enigmatic, pigmented globule found in vegetative cells. Here, we present an in-depth examination of this "red body," focusing on Nannochloropsis oceanica. During the cell cycle, the red body forms adjacent to the plastid, but unexpectedly it is secreted and released with the autosporangial wall following cell division. Shed red bodies contain antioxidant ketocarotenoids, and overexpression of a beta-carotene ketolase results in enlarged red bodies. Infrared spectroscopy indicates long-chain, aliphatic lipids in shed red bodies and cell walls, and UHPLC-HRMS detects a C32 alkyl diol, a potential precursor of algaenan, a recalcitrant cell wall polymer. We propose that the red body transports algaenan precursors from plastid to apoplast to be incorporated into daughter cell walls.
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Affiliation(s)
- Christopher W Gee
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Johan Andersen-Ranberg
- University of Copenhagen, Department of Plant and Environmental Sciences, Frederiksberg, DK-1871, Denmark
| | - Ethan Boynton
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Rachel Z Rosen
- Department of Chemistry, University of California, Berkeley, CA, 94702, USA
| | - Danielle Jorgens
- Electron Microscope Laboratory, University of California, Berkeley, CA, 94720, USA
| | - Patricia Grob
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- California Institute of Quantitative Biosciences, University of California, Berkeley, CA, 94720, USA
| | - Hoi-Ying N Holman
- Electron Microscope Laboratory, University of California, Berkeley, CA, 94720, USA
| | - Krishna K Niyogi
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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4
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Martin-Solana E, Casado-Zueras L, Torres TE, Goya GF, Fernandez-Fernandez MR, Fernandez JJ. Disruption of the mitochondrial network in a mouse model of Huntington's disease visualized by in-tissue multiscale 3D electron microscopy. Acta Neuropathol Commun 2024; 12:88. [PMID: 38840253 PMCID: PMC11151585 DOI: 10.1186/s40478-024-01802-2] [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: 04/04/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by an expanded CAG repeat in the coding sequence of huntingtin protein. Initially, it predominantly affects medium-sized spiny neurons (MSSNs) of the corpus striatum. No effective treatment is still available, thus urging the identification of potential therapeutic targets. While evidence of mitochondrial structural alterations in HD exists, previous studies mainly employed 2D approaches and were performed outside the strictly native brain context. In this study, we adopted a novel multiscale approach to conduct a comprehensive 3D in situ structural analysis of mitochondrial disturbances in a mouse model of HD. We investigated MSSNs within brain tissue under optimal structural conditions utilizing state-of-the-art 3D imaging technologies, specifically FIB/SEM for the complete imaging of neuronal somas and Electron Tomography for detailed morphological examination, and image processing-based quantitative analysis. Our findings suggest a disruption of the mitochondrial network towards fragmentation in HD. The network of interlaced, slim and long mitochondria observed in healthy conditions transforms into isolated, swollen and short entities, with internal cristae disorganization, cavities and abnormally large matrix granules.
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Affiliation(s)
- Eva Martin-Solana
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | | | - Teobaldo E Torres
- Advanced Microscopy Laboratory, University of Zaragoza, Zaragoza, Spain
- Instituto de Nanociencia y Materiales de Aragon (INMA), CSIC-Universidad de Zaragoza, 50018, Zaragoza, Spain
- Department of Condensed Matter Physics, University of Zaragoza, Zaragoza, Spain
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Gerardo F Goya
- Instituto de Nanociencia y Materiales de Aragon (INMA), CSIC-Universidad de Zaragoza, 50018, Zaragoza, Spain
- Department of Condensed Matter Physics, University of Zaragoza, Zaragoza, Spain
| | | | - Jose-Jesus Fernandez
- Spanish National Research Council (CSIC, CINN), Health Research Institute of Asturias (ISPA), 33011, Oviedo, Spain.
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5
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Nakamura K, Aoyama-Ishiwatari S, Nagao T, Paaran M, Obara CJ, Sakurai-Saito Y, Johnston J, Du Y, Suga S, Tsuboi M, Nakakido M, Tsumoto K, Kishi Y, Gotoh Y, Kwak C, Rhee HW, Seo JK, Kosako H, Potter C, Carragher B, Lippincott-Schwartz J, Polleux F, Hirabayashi Y. PDZD8-FKBP8 tethering complex at ER-mitochondria contact sites regulates mitochondrial complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.22.554218. [PMID: 38895210 PMCID: PMC11185567 DOI: 10.1101/2023.08.22.554218] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identified the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-Electron Microscopy (Cryo-EM) tomography, and correlative light-EM (CLEM). Single molecule tracking revealed highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and capture at MERCS. Overexpression of FKBP8 was sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrated their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.
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6
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Schneider J, Jasnin M. Molecular architecture of the actin cytoskeleton: From single cells to whole organisms using cryo-electron tomography. Curr Opin Cell Biol 2024; 88:102356. [PMID: 38608425 DOI: 10.1016/j.ceb.2024.102356] [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: 02/01/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024]
Abstract
Cryo-electron tomography (cryo-ET) has begun to provide intricate views of cellular architecture at unprecedented resolutions. Considerable efforts are being made to further optimize and automate the cryo-ET workflow, from sample preparation to data acquisition and analysis, to enable visual proteomics inside of cells. Here, we will discuss the latest advances in cryo-ET that go hand in hand with their application to the actin cytoskeleton. The development of deep learning tools for automated annotation of tomographic reconstructions and the serial lift-out sample preparation procedure will soon make it possible to perform high-resolution structural biology in a whole new range of samples, from multicellular organisms to organoids and tissues.
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Affiliation(s)
- Jonathan Schneider
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Helmholtz Pioneer Campus, Helmholtz Munich, 85764 Neuherberg, Germany
| | - Marion Jasnin
- Helmholtz Pioneer Campus, Helmholtz Munich, 85764 Neuherberg, Germany; Department of Chemistry, Technical University of Munich, 85748 Garching, Germany.
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7
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Siggel M, Jensen RK, Maurer VJ, Mahamid J, Kosinski J. ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data. J Struct Biol 2024; 216:108067. [PMID: 38367824 DOI: 10.1016/j.jsb.2024.108067] [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: 07/12/2023] [Revised: 01/17/2024] [Accepted: 02/03/2024] [Indexed: 02/19/2024]
Abstract
Cellular cryo-electron tomography (cryo-ET) has emerged as a key method to unravel the spatial and structural complexity of cells in their near-native state at unprecedented molecular resolution. To enable quantitative analysis of the complex shapes and morphologies of lipid membranes, the noisy three-dimensional (3D) volumes must be segmented. Despite recent advances, this task often requires considerable user intervention to curate the resulting segmentations. Here, we present ColabSeg, a Python-based tool for processing, visualizing, editing, and fitting membrane segmentations from cryo-ET data for downstream analysis. ColabSeg makes many well-established algorithms for point-cloud processing easily available to the broad community of structural biologists for applications in cryo-ET through its graphical user interface (GUI). We demonstrate the usefulness of the tool with a range of use cases and biological examples. Finally, for a large Mycoplasma pneumoniae dataset of 50 tomograms, we show how ColabSeg enables high-throughput membrane segmentation, which can be used as valuable training data for fully automated convolutional neural network (CNN)-based segmentation.
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Affiliation(s)
- Marc Siggel
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestrasse 85, Hamburg 20607, Germany; Centre of Structural Systems Biology (CSSB), Notkestrasse 85, Hamburg 20607, Germany
| | - Rasmus K Jensen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Valentin J Maurer
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestrasse 85, Hamburg 20607, Germany; Centre of Structural Systems Biology (CSSB), Notkestrasse 85, Hamburg 20607, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg 69117, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestrasse 85, Hamburg 20607, Germany; Centre of Structural Systems Biology (CSSB), Notkestrasse 85, Hamburg 20607, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, Meyerhofstrasse 1, Heidelberg 69117, Germany.
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8
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Zhao DY, Bäuerlein FJB, Saha I, Hartl FU, Baumeister W, Wilfling F. Autophagy preferentially degrades non-fibrillar polyQ aggregates. Mol Cell 2024; 84:1980-1994.e8. [PMID: 38759629 DOI: 10.1016/j.molcel.2024.04.018] [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: 08/08/2023] [Revised: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
Aggregation of proteins containing expanded polyglutamine (polyQ) repeats is the cytopathologic hallmark of a group of dominantly inherited neurodegenerative diseases, including Huntington's disease (HD). Huntingtin (Htt), the disease protein of HD, forms amyloid-like fibrils by liquid-to-solid phase transition. Macroautophagy has been proposed to clear polyQ aggregates, but the efficiency of aggrephagy is limited. Here, we used cryo-electron tomography to visualize the interactions of autophagosomes with polyQ aggregates in cultured cells in situ. We found that an amorphous aggregate phase exists next to the radially organized polyQ fibrils. Autophagosomes preferentially engulfed this amorphous material, mediated by interactions between the autophagy receptor p62/SQSTM1 and the non-fibrillar aggregate surface. In contrast, amyloid fibrils excluded p62 and evaded clearance, resulting in trapping of autophagic structures. These results suggest that the limited efficiency of autophagy in clearing polyQ aggregates is due to the inability of autophagosomes to interact productively with the non-deformable, fibrillar disease aggregates.
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Affiliation(s)
- Dorothy Y Zhao
- Max Planck Institute of Biochemistry, Molecular Machines and Signaling, 82152 Martinsried, Germany; Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, 60438 Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Felix J B Bäuerlein
- Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; University Medical Center Göttingen, Institute of Neuropathology, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Itika Saha
- Max Planck Institute of Biochemistry, Cellular Biochemistry, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - F Ulrich Hartl
- Max Planck Institute of Biochemistry, Cellular Biochemistry, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Florian Wilfling
- Max Planck Institute of Biochemistry, Molecular Machines and Signaling, 82152 Martinsried, Germany; Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, 60438 Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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9
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Gaifas L, Kirchner MA, Timmins J, Gutsche I. Blik is an extensible 3D visualisation tool for the annotation and analysis of cryo-electron tomography data. PLoS Biol 2024; 22:e3002447. [PMID: 38687779 PMCID: PMC11268629 DOI: 10.1371/journal.pbio.3002447] [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: 11/08/2023] [Revised: 07/24/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Powerful, workflow-agnostic and interactive visualisation is essential for the ad hoc, human-in-the-loop workflows typical of cryo-electron tomography (cryo-ET). While several tools exist for visualisation and annotation of cryo-ET data, they are often integrated as part of monolithic processing pipelines, or focused on a specific task and offering limited reusability and extensibility. With each software suite presenting its own pros and cons and tools tailored to address specific challenges, seamless integration between available pipelines is often a difficult task. As part of the effort to enable such flexibility and move the software ecosystem towards a more collaborative and modular approach, we developed blik, an open-source napari plugin for visualisation and annotation of cryo-ET data (source code: https://github.com/brisvag/blik). blik offers fast, interactive, and user-friendly 3D visualisation thanks to napari, and is built with extensibility and modularity at the core. Data is handled and exposed through well-established scientific Python libraries such as numpy arrays and pandas dataframes. Reusable components (such as data structures, file read/write, and annotation tools) are developed as independent Python libraries to encourage reuse and community contribution. By easily integrating with established image analysis tools-even outside of the cryo-ET world-blik provides a versatile platform for interacting with cryo-ET data. On top of core visualisation features-interactive and simultaneous visualisation of tomograms, particle picks, and segmentations-blik provides an interface for interactive tools such as manual, surface-based and filament-based particle picking, and image segmentation, as well as simple filtering tools. Additional self-contained napari plugins developed as part of this work also implement interactive plotting and selection based on particle features, and label interpolation for easier segmentation. Finally, we highlight the differences with existing software and showcase blik's applicability in biological research.
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Affiliation(s)
- Lorenzo Gaifas
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Moritz A. Kirchner
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Joanna Timmins
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- Department of Chemistry, Umeå University, Umeå, Sweden
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10
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Kraus F, He Y, Swarup S, Overmyer KA, Jiang Y, Brenner J, Capitanio C, Bieber A, Jen A, Nightingale NM, Anderson BJ, Lee C, Paulo JA, Smith IR, Plitzko JM, Schulman BA, Wilfling F, Coon JJ, Wade Harper J. Lysosomal storage disease proteo/lipidomic profiling using nMOST links ferritinophagy with mitochondrial iron deficiencies in cells lacking NPC2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586828. [PMID: 38585873 PMCID: PMC10996675 DOI: 10.1101/2024.03.26.586828] [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
Lysosomal storage diseases (LSDs) comprised ~50 monogenic diseases characterized by the accumulation of cellular material in lysosomes and associated defects in lysosomal function, but systematic molecular phenotyping is lacking. Here, we develop a nanoflow-based multi-omic single-shot technology (nMOST) workflow allowing simultaneously quantify HeLa cell proteomes and lipidomes from more than two dozen LSD mutants, revealing diverse molecular phenotypes. Defects in delivery of ferritin and its autophagic receptor NCOA4 to lysosomes (ferritinophagy) were pronounced in NPC2-/- cells, which correlated with increased lyso-phosphatidylcholine species and multi-lamellar membrane structures visualized by cryo-electron-tomography. Ferritinophagy defects correlated with loss of mitochondrial cristae, MICOS-complex components, and electron transport chain complexes rich in iron-sulfur cluster proteins. Strikingly, mitochondrial defects were alleviated when iron was provided through the transferrin system. This resource reveals how defects in lysosomal function can impact mitochondrial homeostasis in trans and highlights nMOST as a discovery tool for illuminating molecular phenotypes across LSDs.
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Affiliation(s)
- Felix Kraus
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- equal contribution
| | - Yuchen He
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- equal contribution
| | - Sharan Swarup
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- equal contribution
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yizhi Jiang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Johann Brenner
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
- CryoEM Technology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Cristina Capitanio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anna Bieber
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicole M Nightingale
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Benton J Anderson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chan Lee
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ian R Smith
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jürgen M Plitzko
- CryoEM Technology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Brenda A Schulman
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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11
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Diep DTV, Collado J, Hugenroth M, Fausten RM, Percifull L, Wälte M, Schuberth C, Schmidt O, Fernández-Busnadiego R, Bohnert M. A metabolically controlled contact site between vacuoles and lipid droplets in yeast. Dev Cell 2024; 59:740-758.e10. [PMID: 38367622 DOI: 10.1016/j.devcel.2024.01.016] [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: 04/26/2023] [Revised: 11/17/2023] [Accepted: 01/18/2024] [Indexed: 02/19/2024]
Abstract
The lipid droplet (LD) organization proteins Ldo16 and Ldo45 affect multiple aspects of LD biology in yeast. They are linked to the LD biogenesis machinery seipin, and their loss causes defects in LD positioning, protein targeting, and breakdown. However, their molecular roles remained enigmatic. Here, we report that Ldo16/45 form a tether complex with Vac8 to create vacuole lipid droplet (vCLIP) contact sites, which can form in the absence of seipin. The phosphatidylinositol transfer protein (PITP) Pdr16 is a further vCLIP-resident recruited specifically by Ldo45. While only an LD subpopulation is engaged in vCLIPs at glucose-replete conditions, nutrient deprivation results in vCLIP expansion, and vCLIP defects impair lipophagy upon prolonged starvation. In summary, Ldo16/45 are multifunctional proteins that control the formation of a metabolically regulated contact site. Our studies suggest a link between LD biogenesis and breakdown and contribute to a deeper understanding of how lipid homeostasis is maintained during metabolic challenges.
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Affiliation(s)
- Duy Trong Vien Diep
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Javier Collado
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany
| | - Marie Hugenroth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Rebecca Martina Fausten
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Louis Percifull
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Mike Wälte
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany
| | - Christian Schuberth
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter Innsbruck, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Rubén Fernández-Busnadiego
- Institute of Neuropathology, University Medical Center Göttingen, 37099 Göttingen, Germany; Cluster of Excellence "Multiscale Imaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany; Faculty of Physics, University of Göttingen, Göttingen 37077, Germany
| | - Maria Bohnert
- Institute of Cell Dynamics and Imaging, University of Münster, Von-Esmarch-Strasse 56, 48149 Münster, Germany; Cells in Motion Interfaculty Centre (CiM), University of Münster, Münster, Germany.
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12
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Fedry J, Silva J, Vanevic M, Fronik S, Mechulam Y, Schmitt E, des Georges A, Faller WJ, Förster F. Visualization of translation reorganization upon persistent ribosome collision stress in mammalian cells. Mol Cell 2024; 84:1078-1089.e4. [PMID: 38340715 PMCID: PMC7615912 DOI: 10.1016/j.molcel.2024.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/06/2023] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Aberrantly slow ribosomes incur collisions, a sentinel of stress that triggers quality control, signaling, and translation attenuation. Although each collision response has been studied in isolation, the net consequences of their collective actions in reshaping translation in cells is poorly understood. Here, we apply cryoelectron tomography to visualize the translation machinery in mammalian cells during persistent collision stress. We find that polysomes are compressed, with up to 30% of ribosomes in helical polysomes or collided disomes, some of which are bound to the stress effector GCN1. The native collision interface extends beyond the in vitro-characterized 40S and includes the L1 stalk and eEF2, possibly contributing to translocation inhibition. The accumulation of unresolved tRNA-bound 80S and 60S and aberrant 40S configurations identifies potentially limiting steps in collision responses. Our work provides a global view of the translation machinery in response to persistent collisions and a framework for quantitative analysis of translation dynamics in situ.
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Affiliation(s)
- Juliette Fedry
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands; MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
| | - Joana Silva
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mihajlo Vanevic
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Stanley Fronik
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Amédée des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA; Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA; Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CG Utrecht, the Netherlands
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13
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Zeng X, Ding Y, Zhang Y, Uddin MR, Dabouei A, Xu M. DUAL: deep unsupervised simultaneous simulation and denoising for cryo-electron tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.02.583135. [PMID: 38496657 PMCID: PMC10942334 DOI: 10.1101/2024.03.02.583135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Recent biotechnological developments in cryo-electron tomography allow direct visualization of native sub-cellular structures with unprecedented details and provide essential information on protein functions/dysfunctions. Denoising can enhance the visualization of protein structures and distributions. Automatic annotation via data simulation can ameliorate the time-consuming manual labeling of large-scale datasets. Here, we combine the two major cryo-ET tasks together in DUAL, by a specific cyclic generative adversarial network with novel noise disentanglement. This enables end-to-end unsupervised learning that requires no labeled data for training. The denoising branch outperforms existing works and substantially improves downstream particle picking accuracy on benchmark datasets. The simulation branch provides learning-based cryo-ET simulation for the first time and generates synthetic tomograms indistinguishable from experimental ones. Through comprehensive evaluations, we showcase the effectiveness of DUAL in detecting macromolecular complexes across a wide range of molecular weights in experimental datasets. The versatility of DUAL is expected to empower cryo-ET researchers by improving visual interpretability, enhancing structural detection accuracy, expediting annotation processes, facilitating cross-domain model adaptability, and compensating for missing wedge artifacts. Our work represents a significant advancement in the unsupervised mining of protein structures in cryo-ET, offering a multifaceted tool that facilitates cryo-ET research.
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Affiliation(s)
- Xiangrui Zeng
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Yizhe Ding
- Department of Statistics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yueqian Zhang
- School of Electrical and Electronic Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Mostofa Rafid Uddin
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Ali Dabouei
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Min Xu
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
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14
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Hoyer MJ, Capitanio C, Smith IR, Paoli JC, Bieber A, Jiang Y, Paulo JA, Gonzalez-Lozano MA, Baumeister W, Wilfling F, Schulman BA, Harper JW. Combinatorial selective ER-phagy remodels the ER during neurogenesis. Nat Cell Biol 2024; 26:378-392. [PMID: 38429475 PMCID: PMC10940164 DOI: 10.1038/s41556-024-01356-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 01/11/2024] [Indexed: 03/03/2024]
Abstract
The endoplasmic reticulum (ER) employs a diverse proteome landscape to orchestrate many cellular functions, ranging from protein and lipid synthesis to calcium ion flux and inter-organelle communication. A case in point concerns the process of neurogenesis, where a refined tubular ER network is assembled via ER shaping proteins into the newly formed neuronal projections to create highly polarized dendrites and axons. Previous studies have suggested a role for autophagy in ER remodelling, as autophagy-deficient neurons in vivo display axonal ER accumulation within synaptic boutons, and the membrane-embedded ER-phagy receptor FAM134B has been genetically linked with human sensory and autonomic neuropathy. However, our understanding of the mechanisms underlying selective removal of the ER and the role of individual ER-phagy receptors is limited. Here we combine a genetically tractable induced neuron (iNeuron) system for monitoring ER remodelling during in vitro differentiation with proteomic and computational tools to create a quantitative landscape of ER proteome remodelling via selective autophagy. Through analysis of single and combinatorial ER-phagy receptor mutants, we delineate the extent to which each receptor contributes to both the magnitude and selectivity of ER protein clearance. We define specific subsets of ER membrane or lumenal proteins as preferred clients for distinct receptors. Using spatial sensors and flux reporters, we demonstrate receptor-specific autophagic capture of ER in axons, and directly visualize tubular ER membranes within autophagosomes in neuronal projections by cryo-electron tomography. This molecular inventory of ER proteome remodelling and versatile genetic toolkit provide a quantitative framework for understanding the contributions of individual ER-phagy receptors for reshaping ER during cell state transitions.
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Affiliation(s)
- Melissa J Hoyer
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Cristina Capitanio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ian R Smith
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Velia Therapeutics, San Diego, CA, USA
| | - Julia C Paoli
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Anna Bieber
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Yizhi Jiang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Miguel A Gonzalez-Lozano
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Wolfgang Baumeister
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Wilfling
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Brenda A Schulman
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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15
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Zhu S, Bradfield CJ, Maminska A, Park ES, Kim BH, Kumar P, Huang S, Kim M, Zhang Y, Bewersdorf J, MacMicking JD. Native architecture of a human GBP1 defense complex for cell-autonomous immunity to infection. Science 2024; 383:eabm9903. [PMID: 38422126 DOI: 10.1126/science.abm9903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
All living organisms deploy cell-autonomous defenses to combat infection. In plants and animals, large supramolecular complexes often activate immune proteins for protection. In this work, we resolved the native structure of a massive host-defense complex that polymerizes 30,000 guanylate-binding proteins (GBPs) over the surface of gram-negative bacteria inside human cells. Construction of this giant nanomachine took several minutes and remained stable for hours, required guanosine triphosphate hydrolysis, and recruited four GBPs plus caspase-4 and Gasdermin D as a cytokine and cell death immune signaling platform. Cryo-electron tomography suggests that GBP1 can adopt an extended conformation for bacterial membrane insertion to establish this platform, triggering lipopolysaccharide release that activated coassembled caspase-4. Our "open conformer" model provides a dynamic view into how the human GBP1 defense complex mobilizes innate immunity to infection.
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Affiliation(s)
- Shiwei Zhu
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Clinton J Bradfield
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Agnieszka Maminska
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Eui-Soon Park
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Bae-Hoon Kim
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Pradeep Kumar
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shuai Huang
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Minjeong Kim
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Nanobiology Institute, West Haven, CT 06477, USA
| | - John D MacMicking
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510, USA
- Yale Systems Biology Institute, West Haven, CT 06477, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
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16
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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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17
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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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18
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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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19
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Nesterov SV, Plokhikh KS, Chesnokov YM, Mustafin DA, Goleva TN, Rogov AG, Vasilov RG, Yaguzhinsky LS. Safari with an Electron Gun: Visualization of Protein and Membrane Interactions in Mitochondria in Natural Environment. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:257-268. [PMID: 38622094 DOI: 10.1134/s0006297924020068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 04/17/2024]
Abstract
This paper presents new structural data about mitochondria using correlative light and electron microscopy (CLEM) and cryo-electron tomography. These state-of-the-art structural biology methods allow studying biological objects at nanometer scales under natural conditions. Non-invasiveness of these methods makes them comparable to observing animals in their natural environment on a safari. The paper highlights two areas of research that can only be accomplished using these methods. The study visualized location of the Aβ42 amyloid aggregates in relation to mitochondria to test a hypothesis of development of mitochondrial dysfunction in Alzheimer's disease. The results showed that the Aβ42 aggregates do not interact with mitochondria, although some of them are closely located. Therefore, the study demonstrated that mitochondrial dysfunction is not directly associated with the effects of aggregates on mitochondrial structure. Other processes should be considered as sources of mitochondrial dysfunction. Second unique area presented in this work is high-resolution visualization of the mitochondrial membranes and proteins in them. Analysis of the cryo-ET data reveals toroidal holes in the lamellar structures of cardiac mitochondrial cristae, where ATP synthases are located. The study proposes a new mechanism for sorting and clustering protein complexes in the membrane based on topology. According to this suggestion, position of the OXPHOS system proteins in the membrane is determined by its curvature. High-resolution tomography expands and complements existing ideas about the structural and functional organization of mitochondria. This makes it possible to study the previously inaccessible structural interactions of proteins with each other and with membranes in vivo.
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Affiliation(s)
- Semen V Nesterov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia.
| | | | - Yuriy M Chesnokov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Denis A Mustafin
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Tatyana N Goleva
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Anton G Rogov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Raif G Vasilov
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Lev S Yaguzhinsky
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
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20
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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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21
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Plokhikh KS, Nesterov SV, Chesnokov YM, Rogov AG, Kamyshinsky RA, Vasiliev AL, Yaguzhinsky LS, Vasilov RG. Association of 2-oxoacid dehydrogenase complexes with respirasomes in mitochondria. FEBS J 2024; 291:132-141. [PMID: 37789611 DOI: 10.1111/febs.16965] [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: 03/02/2023] [Revised: 08/14/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
In the present study, cryo-electron tomography was used to investigate the localization of 2-oxoacid dehydrogenase complexes (OADCs) in cardiac mitochondria and mitochondrial inner membrane samples. Two classes of ordered OADC inner cores with different symmetries were distinguished and their quaternary structures modeled. One class corresponds to pyruvate dehydrogenase complexes and the other to dehydrogenase complexes of α-ketoglutarate and branched-chain α-ketoacids. OADCs were shown to be localized in close proximity to membrane-embedded respirasomes, as observed both in densely packed lamellar cristae of cardiac mitochondria and in ruptured mitochondrial samples where the dense packing is absent. This suggests the specificity of the OADC-respirasome interaction, which allows localized NADH/NAD+ exchange between OADCs and complex I of the respiratory chain. The importance of this local coupling is based on OADCs being the link between respiration, glycolysis and amino acid metabolism. The coupling of these basic metabolic processes can vary in different tissues and conditions and may be involved in the development of various pathologies. The present study shows that this important and previously missing parameter of mitochondrial complex coupling can be successfully assessed using cryo-electron tomography.
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Affiliation(s)
- Konstantin S Plokhikh
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Semen V Nesterov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Yuriy M Chesnokov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Anton G Rogov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
| | - Roman A Kamyshinsky
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
| | - Aleksandr L Vasiliev
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Lev S Yaguzhinsky
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Belozersky Research Institute for Physico-Chemical Biology, Lomonosov Moscow State University, Russia
| | - Raif G Vasilov
- Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow, Russia
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22
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Karki S, Javanainen M, Rehan S, Tranter D, Kellosalo J, Huiskonen JT, Happonen L, Paavilainen V. Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. EMBO Rep 2023; 24:e57910. [PMID: 37983950 DOI: 10.15252/embr.202357910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. Here, we present the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by cryogenic electron microscopy (cryo-EM). Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions.
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Affiliation(s)
- Sudeep Karki
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Matti Javanainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Shahid Rehan
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Protein Biochemistry and Structural Biology, Omass Therapeutics Ltd, Oxford, UK
| | - Dale Tranter
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juho Kellosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juha T Huiskonen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ville Paavilainen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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23
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Mann D, Fromm SA, Martinez-Sanchez A, Gopaldass N, Choy R, Mayer A, Sachse C. Atg18 oligomer organization in assembled tubes and on lipid membrane scaffolds. Nat Commun 2023; 14:8086. [PMID: 38057304 DOI: 10.1038/s41467-023-43460-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/09/2023] [Indexed: 12/08/2023] Open
Abstract
Autophagy-related protein 18 (Atg18) participates in the elongation of early autophagosomal structures in concert with Atg2 and Atg9 complexes. How Atg18 contributes to the structural coordination of Atg2 and Atg9 at the isolation membrane remains to be understood. Here, we determined the cryo-EM structures of Atg18 organized in helical tubes, Atg18 oligomers in solution as well as on lipid membrane scaffolds. The helical assembly is composed of Atg18 tetramers forming a lozenge cylindrical lattice with remarkable structural similarity to the COPII outer coat. When reconstituted with lipid membranes, using subtomogram averaging we determined tilted Atg18 dimer structures bridging two juxtaposed lipid membranes spaced apart by 80 Å. Moreover, lipid reconstitution experiments further delineate the contributions of Atg18's FRRG motif and the amphipathic helical extension in membrane interaction. The observed structural plasticity of Atg18's oligomeric organization and membrane binding properties provide a molecular framework for the positioning of downstream components of the autophagy machinery.
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Affiliation(s)
- Daniel Mann
- Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
- Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
| | - Simon A Fromm
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio Martinez-Sanchez
- Department of Information and Communications Engineering, Faculty of Computers Sciences, University of Murcia, Murcia, Spain
| | - Navin Gopaldass
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Ramona Choy
- Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
- Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
| | - Andreas Mayer
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Carsten Sachse
- Ernst-Ruska Centre 3/Structural Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany.
- Institute for Biological Information Processing 6/Structural Cellular Biology, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany.
- Department of Biology, Heinrich Heine University, Universitätsstr. 1, Düsseldorf, Germany.
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24
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Fung HKH, Hayashi Y, Salo VT, Babenko A, Zagoriy I, Brunner A, Ellenberg J, Müller CW, Cuylen-Haering S, Mahamid J. Genetically encoded multimeric tags for subcellular protein localization in cryo-EM. Nat Methods 2023; 20:1900-1908. [PMID: 37932397 PMCID: PMC10703698 DOI: 10.1038/s41592-023-02053-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
Cryo-electron tomography (cryo-ET) allows for label-free high-resolution imaging of macromolecular assemblies in their native cellular context. However, the localization of macromolecules of interest in tomographic volumes can be challenging. Here we present a ligand-inducible labeling strategy for intracellular proteins based on fluorescent, 25-nm-sized, genetically encoded multimeric particles (GEMs). The particles exhibit recognizable structural signatures, enabling their automated detection in cryo-ET data by convolutional neural networks. The coupling of GEMs to green fluorescent protein-tagged macromolecules of interest is triggered by addition of a small-molecule ligand, allowing for time-controlled labeling to minimize disturbance to native protein function. We demonstrate the applicability of GEMs for subcellular-level localization of endogenous and overexpressed proteins across different organelles in human cells using cryo-correlative fluorescence and cryo-ET imaging. We describe means for quantifying labeling specificity and efficiency, and for systematic optimization for rare and abundant protein targets, with emphasis on assessing the potential effects of labeling on protein function.
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Affiliation(s)
- Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Yuki Hayashi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Veijo T Salo
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anastasiia Babenko
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- University of Heidelberg, Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Brunner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Sara Cuylen-Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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25
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Liu J, Li Z, Li M, Du W, Baumeister W, Yang J, Guo Q. Vimentin regulates nuclear segmentation in neutrophils. Proc Natl Acad Sci U S A 2023; 120:e2307389120. [PMID: 37983515 PMCID: PMC10691343 DOI: 10.1073/pnas.2307389120] [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: 05/03/2023] [Accepted: 10/11/2023] [Indexed: 11/22/2023] Open
Abstract
Granulocytes are indispensable for various immune responses. Unlike other cell types in the body, the nuclei of granulocytes, particularly neutrophils, are heavily segmented into multiple lobes. Although this distinct morphological feature has long been observed, the underlying mechanism remains incompletely characterized. In this study, we utilize cryo-electron tomography to examine the nuclei of mouse neutrophils, revealing the cytoplasmic enrichment of intermediate filaments on the concave regions of the nuclear envelope. Aided by expression profiling and immuno-electron microscopy, we then elucidate that the intermediate-filament protein vimentin is responsible for such perinuclear structures. Of importance, exogenously expressed vimentin in nonimmune cells is sufficient to form cytoplasmic filaments wrapping on the concave nuclear surface. Moreover, genetic deletion of the protein causes a significant reduction of the number of nuclear lobes in neutrophils and eosinophils, mimicking the hematological condition of the Pelger-Huët anomaly. These results have uncovered a new component establishing the nuclear segmentation of granulocytes.
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Affiliation(s)
- Jiaqi Liu
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing100871, China
| | - Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Meijing Li
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried82152, Germany
| | - Wenjing Du
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Changping Laboratory, Beijing102206, China
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried82152, Germany
| | - Jing Yang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing100871, China
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
- IDG/McGovern Institute for Brain Research, Peking University, Beijing100871, China
- Peking University Third Hospital Cancer Center, Beijing100191, China
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen518055, China
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing100871, China
- Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
- Changping Laboratory, Beijing102206, China
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26
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Liu Y, Zhai H, Alemayehu H, Boulanger J, Hopkins LJ, Borgeaud AC, Heroven C, Howe JD, Leigh KE, Bryant CE, Modis Y. Cryo-electron tomography of NLRP3-activated ASC complexes reveals organelle co-localization. Nat Commun 2023; 14:7246. [PMID: 37945612 PMCID: PMC10636019 DOI: 10.1038/s41467-023-43180-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023] Open
Abstract
NLRP3 induces caspase-1-dependent pyroptotic cell death to drive inflammation. Aberrant activity of NLRP3 occurs in many human diseases. NLRP3 activation induces ASC polymerization into a single, micron-scale perinuclear punctum. Higher resolution imaging of this signaling platform is needed to understand how it induces pyroptosis. Here, we apply correlative cryo-light microscopy and cryo-electron tomography to visualize ASC/caspase-1 in NLRP3-activated cells. The puncta are composed of branched ASC filaments, with a tubular core formed by the pyrin domain. Ribosomes and Golgi-like or endosomal vesicles permeate the filament network, consistent with roles for these organelles in NLRP3 activation. Mitochondria are not associated with ASC but have outer-membrane discontinuities the same size as gasdermin D pores, consistent with our data showing gasdermin D associates with mitochondria and contributes to mitochondrial depolarization.
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Affiliation(s)
- Yangci Liu
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Haoming Zhai
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Helen Alemayehu
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Jérôme Boulanger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Lee J Hopkins
- Department of Medicine, University of Cambridge, Box 157, Level 5, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
- Wren Therapeutics, Clarendon House, Clarendon Road, Cambridge, CB2 8FH, UK
| | - Alicia C Borgeaud
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Christina Heroven
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonathan D Howe
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Kendra E Leigh
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK
| | - Clare E Bryant
- Department of Medicine, University of Cambridge, Box 157, Level 5, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK.
| | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge, CB2 0AW, UK.
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27
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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: 3] [Impact Index Per Article: 3.0] [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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Legal T, Parra M, Tong M, Black CS, Joachimiak E, Valente-Paterno M, Lechtreck K, Gaertig J, Bui KH. CEP104/FAP256 and associated cap complex maintain stability of the ciliary tip. J Cell Biol 2023; 222:e202301129. [PMID: 37756660 PMCID: PMC10522465 DOI: 10.1083/jcb.202301129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 07/13/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Cilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest of the cilium. Here, we used cryo-electron tomography and subtomogram averaging to obtain the structure of the ciliary tip of the ciliate Tetrahymena thermophila. We show that the microtubules at the tip are highly crosslinked with each other and stabilized by luminal proteins, plugs, and cap proteins at the plus ends. In the tip region, the central pair lacks typical projections and twists significantly. By analyzing cells lacking a ciliary tip-enriched protein CEP104/FAP256 by cryo-electron tomography and proteomics, we discovered candidates for the central pair cap complex and explained the potential functions of CEP104/FAP256. These data provide new insights into the function of the ciliary tip and the mechanisms of ciliary assembly and length regulation.
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Affiliation(s)
- Thibault Legal
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Mireya Parra
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Maxwell Tong
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Corbin S. Black
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Melissa Valente-Paterno
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Jacek Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
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Hou Z, Nightingale F, Zhu Y, MacGregor-Chatwin C, Zhang P. Structure of native chromatin fibres revealed by Cryo-ET in situ. Nat Commun 2023; 14:6324. [PMID: 37816746 PMCID: PMC10564948 DOI: 10.1038/s41467-023-42072-1] [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: 08/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023] Open
Abstract
The structure of chromatin plays pivotal roles in regulating gene transcription, DNA replication and repair, and chromosome segregation. This structure, however, remains elusive. Here, using cryo-FIB and cryo-ET, we delineate the 3D architecture of native chromatin fibres in intact interphase human T-lymphoblasts and determine the in situ structures of nucleosomes in different conformations. These chromatin fibres are not structured as uniform 30 nm one-start or two-start filaments but are composed of relaxed, variable zigzag organizations of nucleosomes connected by straight linker DNA. Nucleosomes with little H1 and linker DNA density are distributed randomly without any spatial preference. This work will inspire future high-resolution investigations on native chromatin structures in situ at both a single-nucleosome level and a population level under many different cellular conditions in health and disease.
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Affiliation(s)
- Zhen Hou
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Frank Nightingale
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
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30
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Maeda G, Baba M, Baba N. Semiautomatic contour tracking method for biological object segmentation in thin-section electron microscope images with modified zero DC component-type Gabor wavelets. Microscopy (Oxf) 2023; 72:433-445. [PMID: 36852576 DOI: 10.1093/jmicro/dfad018] [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: 12/13/2022] [Revised: 02/01/2023] [Accepted: 02/22/2023] [Indexed: 03/01/2023] Open
Abstract
In electron microscopic image processing, artificial intelligence (AI) is a powerful method for segmentation. Because creating training data remains time-consuming and burdensome, a simple and accurate segmentation tool, which is effective and does not rely on manual drawings, is necessary to create training data for AI and to support immediate image analysis. A Gabor wavelet-based contour tracking method has been devised as a step toward realizing such a tool. Although many papers on Gabor filter-based and Gabor filter bank-based texture segmentations have been published, previous studies did not apply the Gabor wavelet-based method to straightforwardly detect membrane-like ridges and step edges for segmentation because earlier works used a nonzero DC component-type Gabor wavelets. The DC component has a serious flaw in such detection. Although the DC component can be removed by a formula that satisfies the wavelet theory or by a log-Gabor function, this is not practical for the proposed scheme. Herein, we devised modified zero DC component-type Gabor wavelets. The proposed method can practically confine a wavelet within a small image area. This type of Gabor wavelet can appropriately track various contours of organelles appearing in thin-section transmission electron microscope images prepared by the freeze-substitution fixation method. The proposed method not only more accurately tracks ridge and step edge contours but also tracks pattern boundary contours consisting of slightly different image patterns. Simulations verified these results.
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Affiliation(s)
- Gen Maeda
- Major of Informatics, Graduate School, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Misuzu Baba
- Research Institute for Science and Technology, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Norio Baba
- Major of Informatics, Graduate School, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
- Research Institute for Science and Technology, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
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31
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Wu Y, Qin C, Du W, Guo Z, Chen L, Guo Q. A practical multicellular sample preparation pipeline broadens the application of in situ cryo-electron tomography. J Struct Biol 2023; 215:107971. [PMID: 37201639 DOI: 10.1016/j.jsb.2023.107971] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/28/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
The structural studies of macromolecules in their physiological context, particularly in tissue, is constrained by the bottleneck of sample preparation. In this study, we present a practical pipeline for preparing multicellular samples for cryo-electron tomography. The pipeline comprises sample isolation, vitrification, and lift-out-based lamella preparation using commercially available instruments. We demonstrate the efficacy of our pipeline by visualizing pancreatic β cells from mouse islets at the molecular level. This pipeline enables the determination of the properties of insulin crystals in situ for the first time, using unperturbed samples.
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Affiliation(s)
- Yichun Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China
| | - Changdong Qin
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjing Du
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China
| | - Zhenxi Guo
- School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Center for Life Sciences, College of Future Technology, Peking University, Beijing 100871, China
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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32
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Kiewisz R, Fabig G, Müller-Reichert T, Bepler T. Automated Segmentation of 3D Cytoskeletal Filaments from Electron Micrographs with TARDIS. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:970-972. [PMID: 37613687 DOI: 10.1093/micmic/ozad067.485] [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)
- Robert Kiewisz
- Simons Machine Learning Center/New York Structural Biology Center, New York, New York, USA
- Biocomputing Unit/Centro Nacional de Biotecnologia, Madrid, Cantoblanco, Spain
| | - Gunar Fabig
- Faculty of Medicine Carl Gustav Carus/Technische Universität Dresden, Dresden, Saxony, Germany
| | - Thomas Müller-Reichert
- Faculty of Medicine Carl Gustav Carus/Technische Universität Dresden, Dresden, Saxony, Germany
| | - Tristan Bepler
- Simons Machine Learning Center/New York Structural Biology Center, New York, New York, USA
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33
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Yang J, Vrbovská V, Franke T, Sibert B, Larson M, Hall A, Rigort A, Mitchels J, Wright ER. Integrated Fluorescence Microscopy (iFLM) for Cryo-FIB-milling and In-situ Cryo-ET. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548578. [PMID: 37502891 PMCID: PMC10369943 DOI: 10.1101/2023.07.11.548578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Correlative cryo-FLM-FIB milling is a powerful sample preparation technique for in situ cryo-ET. However, correlative workflows that incorporate precise targeting remain challenging. Here, we demonstrate the development and use of an integrated Fluorescence Light Microscope (iFLM) module within a cryo-FIB-SEM to enable a coordinate-based two-point 3D correlative workflow. The iFLM guided targeting of regions of interest coupled with an automated milling process of the cryo-FIB-SEM instrument allows for the efficient preparation of 9-12 ∼200 nm thick lamellae within 24 hours. Using regular and montage-cryo-ET data collection schemes, we acquired data from FIB-milled lamellae of HeLa cells to examine cellular ultrastructure. Overall, this workflow facilitates on-the-fly targeting and automated FIB-milling of cryo-preserved cells, bacteria, and possibly high pressure frozen tissue, to produce lamellae for downstream cryo-ET data collection.
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Affiliation(s)
- Jae Yang
- 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 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
| | - Matthew 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
| | - Alex Hall
- Thermo Fisher Scientific Brno, Brno, Czech Republic
| | - Alex Rigort
- Thermo Fisher Scientific Brno, Brno, Czech Republic
| | | | - 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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34
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Kaplan M, Chang YW, Oikonomou CM, Nicolas WJ, Jewett AI, Kreida S, Dutka P, Rettberg LA, Maggi S, Jensen GJ. Bdellovibrio predation cycle characterized at nanometre-scale resolution with cryo-electron tomography. Nat Microbiol 2023; 8:1267-1279. [PMID: 37349588 PMCID: PMC11061892 DOI: 10.1038/s41564-023-01401-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/27/2023] [Indexed: 06/24/2023]
Abstract
Bdellovibrio bacteriovorus is a microbial predator that offers promise as a living antibiotic for its ability to kill Gram-negative bacteria, including human pathogens. Even after six decades of study, fundamental details of its predation cycle remain mysterious. Here we used cryo-electron tomography to comprehensively image the lifecycle of B. bacteriovorus at nanometre-scale resolution. With high-resolution images of predation in a native (hydrated, unstained) state, we discover several surprising features of the process, including macromolecular complexes involved in prey attachment/invasion and a flexible portal structure lining a hole in the prey peptidoglycan that tightly seals the prey outer membrane around the predator during entry. Unexpectedly, we find that B. bacteriovorus does not shed its flagellum during invasion, but rather resorbs it into its periplasm for degradation. Finally, following growth and division in the bdelloplast, we observe a transient and extensive ribosomal lattice on the condensed B. bacteriovorus nucleoid.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - William J Nicolas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrew I Jewett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stefan Kreida
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Przemysław Dutka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Stefano Maggi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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35
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett KD, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. Cell Rep 2023; 42:112432. [PMID: 37120812 PMCID: PMC10299810 DOI: 10.1016/j.celrep.2023.112432] [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: 12/14/2022] [Revised: 02/28/2023] [Accepted: 04/08/2023] [Indexed: 05/01/2023] Open
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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Affiliation(s)
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas G Laughlin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Amber Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kyle P Thomas
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika E Sy
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tara Spencer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aileen Asavavimol
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Allison Cafferata
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Mia Cameron
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Chiu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Demyan Davydov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Isha Desai
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gabriel Diaz
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Melissa Guereca
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kiley Hearst
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Leyi Huang
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Emily Jacobs
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika Johnson
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Samuel Kahn
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ryan Koch
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adamari Martinez
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Meliné Norquist
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tyler Pau
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gino Prasad
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Katrina Saam
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Milan Sandhu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Angel Jose Sarabia
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Siena Schumaker
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aaron Sonin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ariya Uyeno
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alison Zhao
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin Meyer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, 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
| | - Rachel Dutton
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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36
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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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37
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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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38
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Kim HHS, Uddin MR, Xu M, Chang YW. Computational Methods Toward Unbiased Pattern Mining and Structure Determination in Cryo-Electron Tomography Data. J Mol Biol 2023; 435:168068. [PMID: 37003470 PMCID: PMC10164694 DOI: 10.1016/j.jmb.2023.168068] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/19/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
Cryo-electron tomography can uniquely probe the native cellular environment for macromolecular structures. Tomograms feature complex data with densities of diverse, densely crowded macromolecular complexes, low signal-to-noise, and artifacts such as the missing wedge effect. Post-processing of this data generally involves isolating regions or particles of interest from tomograms, organizing them into related groups, and rendering final structures through subtomogram averaging. Template-matching and reference-based structure determination are popular analysis methods but are vulnerable to biases and can often require significant user input. Most importantly, these approaches cannot identify novel complexes that reside within the imaged cellular environment. To reliably extract and resolve structures of interest, efficient and unbiased approaches are therefore of great value. This review highlights notable computational software and discusses how they contribute to making automated structural pattern discovery a possibility. Perspectives emphasizing the importance of features for user-friendliness and accessibility are also presented.
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Affiliation(s)
- Hannah Hyun-Sook Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. https://twitter.com/hannahinthelab
| | - Mostofa Rafid Uddin
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA. https://twitter.com/duran_rafid
| | - Min Xu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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39
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Jung JH, Chen X, Reese TS. Cryo-EM tomography and automatic segmentation delineate modular structures in the postsynaptic density. Front Synaptic Neurosci 2023; 15:1123564. [PMID: 37091879 PMCID: PMC10117989 DOI: 10.3389/fnsyn.2023.1123564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/02/2023] [Indexed: 04/08/2023] Open
Abstract
Postsynaptic densities (PSDs) are large protein complexes associated with the postsynaptic membrane of excitatory synapses important for synaptic function including plasticity. Conventional electron microscopy (EM) typically depicts PSDs as compact disk-like structures of hundreds of nanometers in size. Biochemically isolated PSDs were also similar in dimension revealing a predominance of proteins with the ability to polymerize into an extensive scaffold; several EM studies noted their irregular contours with often small granular structures (<30 nm) and holes. Super-resolution light microscopy studies observed clusters of PSD elements and their activity-induced lateral movement. Furthermore, our recent EM study on PSD fractions after sonication observed PSD fragments (40–90 nm in size) separate from intact PSDs; however, such structures within PSDs remained unidentified. Here we examined isolated PSDs by cryo-EM tomography with our new approach of automatic segmentation that enables delineation of substructures and their quantitative analysis. The delineated substructures broadly varied in size, falling behind 30 nm or exceeding 100 nm and showed that a considerable portion of the substructures (>38%) in isolated PSDs was in the same size range as those fragments. Furthermore, substructures spanning the entire thickness of the PSD were found, large enough to contain both membrane-associated and cytoplasmic proteins of the PSD; interestingly, they were similar to nanodomains in frequency. The structures detected here appear to constitute the isolated PSD as modules of various compositions, and this modular nature may facilitate remodeling of the PSD for proper synaptic function and plasticity.
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40
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Barad BA, Medina M, Fuentes D, Wiseman RL, Grotjahn DA. Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline. J Cell Biol 2023; 222:e202204093. [PMID: 36786771 PMCID: PMC9960335 DOI: 10.1083/jcb.202204093] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/22/2022] [Accepted: 01/17/2023] [Indexed: 02/15/2023] Open
Abstract
Cellular cryo-electron tomography (cryo-ET) enables three-dimensional reconstructions of organelles in their native cellular environment at subnanometer resolution. However, quantifying ultrastructural features of pleomorphic organelles in three dimensions is challenging, as is defining the significance of observed changes induced by specific cellular perturbations. To address this challenge, we established a semiautomated workflow to segment organellar membranes and reconstruct their underlying surface geometry in cryo-ET. To complement this workflow, we developed an open-source suite of ultrastructural quantifications, integrated into a single pipeline called the surface morphometrics pipeline. This pipeline enables rapid modeling of complex membrane structures and allows detailed mapping of inter- and intramembrane spacing, curvedness, and orientation onto reconstructed membrane meshes, highlighting subtle organellar features that are challenging to detect in three dimensions and allowing for statistical comparison across many organelles. To demonstrate the advantages of this approach, we combine cryo-ET with cryo-fluorescence microscopy to correlate bulk mitochondrial network morphology (i.e., elongated versus fragmented) with membrane ultrastructure of individual mitochondria in the presence and absence of endoplasmic reticulum (ER) stress. Using our pipeline, we demonstrate ER stress promotes adaptive remodeling of ultrastructural features of mitochondria including spacing between the inner and outer membranes, local curvedness of the inner membrane, and spacing between mitochondrial cristae. We show that differences in membrane ultrastructure correlate to mitochondrial network morphologies, suggesting that these two remodeling events are coupled. Our pipeline offers opportunities for quantifying changes in membrane ultrastructure on a single-cell level using cryo-ET, opening new opportunities to define changes in ultrastructural features induced by diverse types of cellular perturbations.
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Affiliation(s)
- Benjamin A. Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Michaela Medina
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel Fuentes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - R. Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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41
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González-Ruiz V, Fernández-Fernández MR, Fernández JJ. Structure-preserving Gaussian denoising of FIB-SEM volumes. Ultramicroscopy 2023; 246:113674. [PMID: 36586197 DOI: 10.1016/j.ultramic.2022.113674] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022]
Abstract
FIB-SEM (Focused Ion Beam-Scanning Electron Microscopy) is an imaging technique that allows 3D ultrastructural analysis of cells and tissues at the nanoscale. The acquired FIB-SEM data are highly noisy, which makes denoising an essential step prior to volume interpretation. Gaussian filtering is a standard method in the field because it is fast and straightforward. However, it tends to blur the biological features due to its linear nature that ignores the rapid changes of the structures throughout the volume. To address this issue, we have developed a new approach to structure-preserving noise reduction for FIB-SEM. It has abilities to locally adapt the filtering to the biological structures while taking advantage of the simplicity of Gaussian filtering. It uses the Optical Flow (OF) to estimate the variations of the structural features across the volume, so that they are compensated before the subsequent filtering with a Gaussian function. As demonstrated qualitatively and objectively with datasets from different samples and acquired under different conditions, our denoising approach outperforms the standard Gaussian filtering and is competitive with state-of-the-art methods in terms of noise reduction and preservation of the sharpness of the structures.
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Affiliation(s)
- V González-Ruiz
- University of Almeria, Informatics Department, Agrifood Campus of International Excellence (ceiA3), Ctra. Sacramento, s/n, Almeria, 04120, Spain.
| | - M R Fernández-Fernández
- Spanish National Research Council (CINN-CSIC). Health Research Institute of Asturias (ISPA), Av Hospital Universitario s/n, Oviedo, 33011, Spain
| | - J J Fernández
- Spanish National Research Council (CINN-CSIC). Health Research Institute of Asturias (ISPA), Av Hospital Universitario s/n, Oviedo, 33011, Spain.
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42
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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: 28] [Impact Index Per Article: 28.0] [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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43
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Ferreira JL, Pražák V, Vasishtan D, Siggel M, Hentzschel F, Binder AM, Pietsch E, Kosinski J, Frischknecht F, Gilberger TW, Grünewald K. Variable microtubule architecture in the malaria parasite. Nat Commun 2023; 14:1216. [PMID: 36869034 PMCID: PMC9984467 DOI: 10.1038/s41467-023-36627-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/09/2023] [Indexed: 03/05/2023] Open
Abstract
Microtubules are a ubiquitous eukaryotic cytoskeletal element typically consisting of 13 protofilaments arranged in a hollow cylinder. This arrangement is considered the canonical form and is adopted by most organisms, with rare exceptions. Here, we use in situ electron cryo-tomography and subvolume averaging to analyse the changing microtubule cytoskeleton of Plasmodium falciparum, the causative agent of malaria, throughout its life cycle. Unexpectedly, different parasite forms have distinct microtubule structures coordinated by unique organising centres. In merozoites, the most widely studied form, we observe canonical microtubules. In migrating mosquito forms, the 13 protofilament structure is further reinforced by interrupted luminal helices. Surprisingly, gametocytes contain a wide distribution of microtubule structures ranging from 13 to 18 protofilaments, doublets and triplets. Such a diversity of microtubule structures has not been observed in any other organism to date and is likely evidence of a distinct role in each life cycle form. This data provides a unique view into an unusual microtubule cytoskeleton of a relevant human pathogen.
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Affiliation(s)
- Josie L Ferreira
- Centre for Structural Systems Biology, Hamburg, Germany
- Leibniz Institute for Virology (LIV), Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | - Vojtěch Pražák
- Centre for Structural Systems Biology, Hamburg, Germany
- Leibniz Institute for Virology (LIV), Hamburg, Germany
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Daven Vasishtan
- Centre for Structural Systems Biology, Hamburg, Germany
- Leibniz Institute for Virology (LIV), Hamburg, Germany
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Marc Siggel
- Centre for Structural Systems Biology, Hamburg, Germany
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Franziska Hentzschel
- Integrative Parasitology, Centre for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
- German Center for Infection Research, DZIF Partner Site Heidelberg, Heidelberg, Germany
| | - Annika M Binder
- Integrative Parasitology, Centre for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Emma Pietsch
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Jan Kosinski
- Centre for Structural Systems Biology, Hamburg, Germany
- European Molecular Biology Laboratory, Hamburg, Germany
- Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Centre for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
- German Center for Infection Research, DZIF Partner Site Heidelberg, Heidelberg, Germany
| | - Tim W Gilberger
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Kay Grünewald
- Centre for Structural Systems Biology, Hamburg, Germany.
- Leibniz Institute for Virology (LIV), Hamburg, Germany.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- University of Hamburg, Hamburg, Germany.
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44
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy A, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett K, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529968. [PMID: 36865095 PMCID: PMC9980170 DOI: 10.1101/2023.02.24.529968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication encoded in the core genome are conserved among diverse chimalliviruses, and reveal that non-core components can confer intriguing variations on this replication mechanism. For instance, unlike previously studied nucleus-forming phages, RAY doesn't degrade the host genome, and its PhuZ homolog appears to form a five-stranded filament with a lumen. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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45
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Saha I, Yuste-Checa P, Da Silva Padilha M, Guo Q, Körner R, Holthusen H, Trinkaus VA, Dudanova I, Fernández-Busnadiego R, Baumeister W, Sanders DW, Gautam S, Diamond MI, Hartl FU, Hipp MS. The AAA+ chaperone VCP disaggregates Tau fibrils and generates aggregate seeds in a cellular system. Nat Commun 2023; 14:560. [PMID: 36732333 PMCID: PMC9894937 DOI: 10.1038/s41467-023-36058-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 01/13/2023] [Indexed: 02/04/2023] Open
Abstract
Amyloid-like aggregates of the microtubule-associated protein Tau are associated with several neurodegenerative disorders including Alzheimer's disease. The existence of cellular machinery for the removal of such aggregates has remained unclear, as specialized disaggregase chaperones are thought to be absent in mammalian cells. Here we show in cell culture and in neurons that the hexameric ATPase valosin-containing protein (VCP) is recruited to ubiquitylated Tau fibrils, resulting in their efficient disaggregation. Aggregate clearance depends on the functional cooperation of VCP with heat shock 70 kDa protein (Hsp70) and the ubiquitin-proteasome machinery. While inhibition of VCP activity stabilizes large Tau aggregates, disaggregation by VCP generates seeding-active Tau species as byproduct. These findings identify VCP as a core component of the machinery for the removal of neurodegenerative disease aggregates and suggest that its activity can be associated with enhanced aggregate spreading in tauopathies.
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Affiliation(s)
- Itika Saha
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Patricia Yuste-Checa
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Miguel Da Silva Padilha
- Molecular Neurodegeneration Group, Max Planck Institute for Biological Intelligence, 82152, Martinsried, Germany.,Department of Molecules - Signaling - Development, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152, Martinsried, Germany.,Center for Anatomy, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Qiang Guo
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Roman Körner
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Hauke Holthusen
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Victoria A Trinkaus
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Irina Dudanova
- Molecular Neurodegeneration Group, Max Planck Institute for Biological Intelligence, 82152, Martinsried, Germany.,Department of Molecules - Signaling - Development, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152, Martinsried, Germany.,Center for Anatomy, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Rubén Fernández-Busnadiego
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.,Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Institute of Neuropathology, University Medical Center Göttingen, 37099, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Wolfgang Baumeister
- Department of Structural Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - David W Sanders
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, 75390, TX, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Saurabh Gautam
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Boehringer Ingelheim International GmbH, 55216, Ingelheim, Germany.,ViraTherapeutics GmbH, 6063, Rum, Austria
| | - Marc I Diamond
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, 75390, TX, USA
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. .,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Mark S Hipp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany. .,School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany. .,Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan, 1, 9713 AV, Groningen, The Netherlands.
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46
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Exocytosis of the silicified cell wall of diatoms involves extensive membrane disintegration. Nat Commun 2023; 14:480. [PMID: 36717559 PMCID: PMC9886994 DOI: 10.1038/s41467-023-36112-z] [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: 08/04/2021] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Diatoms are unicellular algae characterized by silica cell walls. These silica elements are known to be formed intracellularly in membrane-bound silica deposition vesicles and exocytosed after completion. How diatoms maintain membrane homeostasis during the exocytosis of these large and rigid silica elements remains unknown. Here we study the membrane dynamics during cell wall formation and exocytosis in two model diatom species, using live-cell confocal microscopy, transmission electron microscopy and cryo-electron tomography. Our results show that during its formation, the mineral phase is in tight association with the silica deposition vesicle membranes, which form a precise mold of the delicate geometrical patterns. We find that during exocytosis, the distal silica deposition vesicle membrane and the plasma membrane gradually detach from the mineral and disintegrate in the extracellular space, without any noticeable endocytic retrieval or extracellular repurposing. We demonstrate that within the cell, the proximal silica deposition vesicle membrane becomes the new barrier between the cell and its environment, and assumes the role of a new plasma membrane. These results provide direct structural observations of diatom silica exocytosis, and point to an extraordinary mechanism in which membrane homeostasis is maintained by discarding, rather than recycling, significant membrane patches.
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47
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Legal T, Tong M, Black C, Valente Paterno M, Gaertig J, Bui KH. Molecular architecture of the ciliary tip revealed by cryo-electron tomography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522627. [PMID: 36711791 PMCID: PMC9881849 DOI: 10.1101/2023.01.03.522627] [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: 01/06/2023]
Abstract
Cilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest of the cilium. Here, we used cryo-electron tomography and subtomogram averaging to obtain the structure of the ciliary tip of the ciliate Tetrahymena thermophila. We show the microtubules in the tip are highly cross-linked with each other and stabilised by luminal proteins, plugs and cap proteins at the plus ends. In the tip region, the central pair lacks the typical projections and twists significantly. By analysing cells lacking a ciliary tip-enriched protein CEP104/FAP256 by cryo-electron tomography and proteomics, we discovered candidates for the central pair cap complex and explain potential functions of CEP104/FAP256. These data provide new insights into the function of the ciliary tip and inform about the mechanisms of ciliary assembly and length regulation.
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Affiliation(s)
- T Legal
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - M Tong
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - C Black
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - M Valente Paterno
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
| | - J Gaertig
- Department of Cellular Biology, University of Georgia, Athens, GA, United States of America
| | - K H Bui
- Department of Anatomy and Cell Biology, Faculty of Medicine and Health Sciences, McGill University, Québec, Canada
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48
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Integrated multimodality microscope for accurate and efficient target-guided cryo-lamellae preparation. Nat Methods 2023; 20:268-275. [PMID: 36646896 PMCID: PMC9911353 DOI: 10.1038/s41592-022-01749-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023]
Abstract
Cryo-electron tomography (cryo-ET) is a revolutionary technique for resolving the structure of subcellular organelles and macromolecular complexes in their cellular context. However, the application of the cryo-ET is hampered by the sample preparation step. Performing cryo-focused ion beam milling at an arbitrary position on the sample is inefficient, and the target of interest is not guaranteed to be preserved when thinning the cell from several micrometers to less than 300 nm thick. Here, we report a cryogenic correlated light, ion and electron microscopy (cryo-CLIEM) technique that is capable of preparing cryo-lamellae under the guidance of three-dimensional confocal imaging. Moreover, we demonstrate a workflow to preselect and preserve nanoscale target regions inside the finished cryo-lamellae. By successfully preparing cryo-lamellae that contain a single centriole or contact sites between subcellular organelles, we show that this approach is generally applicable, and shall help in innovating more applications of cryo-ET.
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49
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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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50
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Bieber A, Capitanio C, Erdmann PS, Fiedler F, Beck F, Lee CW, Li D, Hummer G, Schulman BA, Baumeister W, Wilfling F. In situ structural analysis reveals membrane shape transitions during autophagosome formation. Proc Natl Acad Sci U S A 2022; 119:e2209823119. [PMID: 36122245 PMCID: PMC9522377 DOI: 10.1073/pnas.2209823119] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
Autophagosomes are unique organelles that form de novo as double-membrane vesicles engulfing cytosolic material for destruction. Their biogenesis involves membrane transformations of distinctly shaped intermediates whose ultrastructure is poorly understood. Here, we combine cell biology, correlative cryo-electron tomography (cryo-ET), and extensive data analysis to reveal the step-by-step structural progression of autophagosome biogenesis at high resolution directly within yeast cells. The analysis uncovers an unexpectedly thin intermembrane distance that is dilated at the phagophore rim. Mapping of individual autophagic structures onto a timeline based on geometric features reveals a dynamical change of membrane shape and curvature in growing phagophores. Moreover, our tomograms show the organelle interactome of growing autophagosomes, highlighting a polar organization of contact sites between the phagophore and organelles, such as the vacuole and the endoplasmic reticulum (ER). Collectively, these findings have important implications for the contribution of different membrane sources during autophagy and for the forces shaping and driving phagophores toward closure without a templating cargo.
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Affiliation(s)
- Anna Bieber
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Cristina Capitanio
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Philipp S. Erdmann
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Human Technopole, 20157 Milan, Italy
| | - Fabian Fiedler
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, 60438 Frankfurt a. M., Germany
| | - Florian Beck
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- CryoEM Technology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Chia-Wei Lee
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Delong Li
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, 60438 Frankfurt a. M., Germany
| | - Gerhard Hummer
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt a. M., Germany
- Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt a. M., Germany
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
| | - Florian Wilfling
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, 60438 Frankfurt a. M., Germany
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