1
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Cruz-León S, Majtner T, Hoffmann PC, Kreysing JP, Kehl S, Tuijtel MW, Schaefer SL, Geißler K, Beck M, Turoňová B, Hummer G. High-confidence 3D template matching for cryo-electron tomography. Nat Commun 2024; 15:3992. [PMID: 38734767 PMCID: PMC11088655 DOI: 10.1038/s41467-024-47839-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/12/2024] [Indexed: 05/13/2024] Open
Abstract
Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures of macromolecules. However, their applicability remains limited in terms of both the abundance and size of the molecular targets. Here we show that the performance of TM is greatly improved by using template-specific search parameter optimization and by including higher-resolution information. We establish a TM pipeline with systematically tuned parameters for the automated, objective and comprehensive identification of structures with confidence 10 to 100-fold above the noise level. We demonstrate high-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, fatty acid synthases, lipid membranes and microtubules, and individual subunits inside crowded eukaryotic cells. We provide software tools for the generic implementation of our method that is broadly applicable towards realizing visual proteomics.
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Affiliation(s)
- Sergio Cruz-León
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Tomáš Majtner
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Patrick C Hoffmann
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Sebastian Kehl
- Max Planck Computing and Data Facility, Gießenbachstraße 2, 85748, Garching, Germany
| | - Maarten W Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Stefan L Schaefer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Katharina Geißler
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biochemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
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2
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Ibáñez de Opakua A, Pantoja CF, Cima-Omori MS, Dienemann C, Zweckstetter M. Impact of distinct FG nucleoporin repeats on Nup98 self-association. Nat Commun 2024; 15:3797. [PMID: 38714656 PMCID: PMC11076500 DOI: 10.1038/s41467-024-48194-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 04/24/2024] [Indexed: 05/10/2024] Open
Abstract
Nucleoporins rich in phenylalanine/glycine (FG) residues form the permeability barrier within the nuclear pore complex and are implicated in several pathological cellular processes, including oncogenic fusion condensates. The self-association of FG-repeat proteins and interactions between FG-repeats play a critical role in these activities by forming hydrogel-like structures. Here we show that mutation of specific FG repeats of Nup98 can strongly decrease the protein's self-association capabilities. We further present a cryo-electron microscopy structure of a Nup98 peptide fibril with higher stability per residue compared with previous Nup98 fibril structures. The high-resolution structure reveals zipper-like hydrophobic patches which contain a GLFG motif and are less compatible for binding to nuclear transport receptors. The identified distinct molecular properties of different regions of the nucleoporin may contribute to spatial variations in the self-association of FG-repeats, potentially influencing transport processes through the nuclear pore.
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Affiliation(s)
- Alain Ibáñez de Opakua
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, Göttingen, Germany
| | - Christian F Pantoja
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, Göttingen, Germany
| | - Maria-Sol Cima-Omori
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Am Fassberg 11, Göttingen, Germany.
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3
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Gallusser B, Maltese G, Di Caprio G, Vadakkan TJ, Sanyal A, Somerville E, Sahasrabudhe M, O’Connor J, Weigert M, Kirchhausen T. Deep neural network automated segmentation of cellular structures in volume electron microscopy. J Cell Biol 2023; 222:e202208005. [PMID: 36469001 PMCID: PMC9728137 DOI: 10.1083/jcb.202208005] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/03/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Volume electron microscopy is an important imaging modality in contemporary cell biology. Identification of intracellular structures is a laborious process limiting the effective use of this potentially powerful tool. We resolved this bottleneck with automated segmentation of intracellular substructures in electron microscopy (ASEM), a new pipeline to train a convolutional neural network to detect structures of a wide range in size and complexity. We obtained dedicated models for each structure based on a small number of sparsely annotated ground truth images from only one or two cells. Model generalization was improved with a rapid, computationally effective strategy to refine a trained model by including a few additional annotations. We identified mitochondria, Golgi apparatus, endoplasmic reticulum, nuclear pore complexes, caveolae, clathrin-coated pits, and vesicles imaged by focused ion beam scanning electron microscopy. We uncovered a wide range of membrane-nuclear pore diameters within a single cell and derived morphological metrics from clathrin-coated pits and vesicles, consistent with the classical constant-growth assembly model.
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Affiliation(s)
- Benjamin Gallusser
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Giorgio Maltese
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
| | - Giuseppe Di Caprio
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Tegy John Vadakkan
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
| | - Anwesha Sanyal
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Elliott Somerville
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
| | - Mihir Sahasrabudhe
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Université Paris-Saclay, CentraleSupélec, Mathématiques et Informatique pour la Complexité et les Systèmes, Gif-sur-Yvette, France
| | - Justin O’Connor
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Martin Weigert
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Tom Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Department of Cell Biology, Harvard Medical School, Boston, MA
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4
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Tai L, Zhu Y, Ren H, Huang X, Zhang C, Sun F. 8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI. Protein Cell 2022; 13:760-777. [PMID: 35015240 PMCID: PMC9233733 DOI: 10.1007/s13238-021-00895-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 11/27/2022] Open
Abstract
The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the outer rings containing nuclear ring (NR) and cytoplasmic ring (CR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the outer rings, including the Y complexes and flanking components. In this most comprehensive and accurate model of outer rings to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. In addition to two copies of Y complexes, each asymmetric subunit in CR contains five copies of Nup358, two copies of the Nup214 complex, two copies of Nup205 and one copy of newly identified Nup93, while that in NR contains one copy of Nup205, one copy of ELYS and one copy of Nup93. These in-depth structural features represent a great advance in understanding the assembly of NPCs.
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Affiliation(s)
- Linhua Tai
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China
| | - He Ren
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaojun Huang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China.
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
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5
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Gunkel P, Iino H, Krull S, Cordes VC. ZC3HC1 Is a Novel Inherent Component of the Nuclear Basket, Resident in a State of Reciprocal Dependence with TPR. Cells 2021; 10:1937. [PMID: 34440706 PMCID: PMC8393659 DOI: 10.3390/cells10081937] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022] Open
Abstract
The nuclear basket (NB) scaffold, a fibrillar structure anchored to the nuclear pore complex (NPC), is regarded as constructed of polypeptides of the coiled-coil dominated protein TPR to which other proteins can bind without contributing to the NB's structural integrity. Here we report vertebrate protein ZC3HC1 as a novel inherent constituent of the NB, common at the nuclear envelopes (NE) of proliferating and non-dividing, terminally differentiated cells of different morphogenetic origin. Formerly described as a protein of other functions, we instead present the NB component ZC3HC1 as a protein required for enabling distinct amounts of TPR to occur NB-appended, with such ZC3HC1-dependency applying to about half the total amount of TPR at the NEs of different somatic cell types. Furthermore, pointing to an NB structure more complex than previously anticipated, we discuss how ZC3HC1 and the ZC3HC1-dependent TPR polypeptides could enlarge the NB's functional repertoire.
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Affiliation(s)
| | | | | | - Volker C. Cordes
- Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany; (P.G.); (H.I.); (S.K.)
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6
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Heydarian H, Joosten M, Przybylski A, Schueder F, Jungmann R, Werkhoven BV, Keller-Findeisen J, Ries J, Stallinga S, Bates M, Rieger B. 3D particle averaging and detection of macromolecular symmetry in localization microscopy. Nat Commun 2021; 12:2847. [PMID: 33990554 PMCID: PMC8121824 DOI: 10.1038/s41467-021-22006-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/22/2021] [Indexed: 11/20/2022] Open
Abstract
Single molecule localization microscopy offers in principle resolution down to the molecular level, but in practice this is limited primarily by incomplete fluorescent labeling of the structure. This missing information can be completed by merging information from many structurally identical particles. In this work, we present an approach for 3D single particle analysis in localization microscopy which hugely increases signal-to-noise ratio and resolution and enables determining the symmetry groups of macromolecular complexes. Our method does not require a structural template, and handles anisotropic localization uncertainties. We demonstrate 3D reconstructions of DNA-origami tetrahedrons, Nup96 and Nup107 subcomplexes of the nuclear pore complex acquired using multiple single molecule localization microscopy techniques, with their structural symmetry deducted from the data.
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Affiliation(s)
- Hamidreza Heydarian
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Maarten Joosten
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Adrian Przybylski
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Florian Schueder
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ralf Jungmann
- Department of Physics and Center for Nanoscience, Ludwig Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Jan Keller-Findeisen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Sjoerd Stallinga
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Mark Bates
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bernd Rieger
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands.
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7
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Kittisopikul M, Shimi T, Tatli M, Tran JR, Zheng Y, Medalia O, Jaqaman K, Adam SA, Goldman RD. Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins. J Cell Biol 2021; 220:e202007082. [PMID: 33570570 PMCID: PMC7883741 DOI: 10.1083/jcb.202007082] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/15/2020] [Accepted: 01/05/2021] [Indexed: 12/29/2022] Open
Abstract
Nuclear lamin isoforms form fibrous meshworks associated with nuclear pore complexes (NPCs). Using datasets prepared from subpixel and segmentation analyses of 3D-structured illumination microscopy images of WT and lamin isoform knockout mouse embryo fibroblasts, we determined with high precision the spatial association of NPCs with specific lamin isoform fibers. These relationships are retained in the enlarged lamin meshworks of Lmna-/- and Lmnb1-/- fibroblast nuclei. Cryo-ET observations reveal that the lamin filaments composing the fibers contact the nucleoplasmic ring of NPCs. Knockdown of the ring-associated nucleoporin ELYS induces NPC clusters that exclude lamin A/C fibers but include LB1 and LB2 fibers. Knockdown of the nucleoporin TPR or NUP153 alters the arrangement of lamin fibers and NPCs. Evidence that the number of NPCs is regulated by specific lamin isoforms is presented. Overall the results demonstrate that lamin isoforms and nucleoporins act together to maintain the normal organization of lamin meshworks and NPCs within the nuclear envelope.
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Affiliation(s)
- Mark Kittisopikul
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Takeshi Shimi
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
- Cell Biology Center and World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Meltem Tatli
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Joseph Riley Tran
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Khuloud Jaqaman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Stephen A. Adam
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Robert D. Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
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8
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Zila V, Margiotta E, Turoňová B, Müller TG, Zimmerli CE, Mattei S, Allegretti M, Börner K, Rada J, Müller B, Lusic M, Kräusslich HG, Beck M. Cone-shaped HIV-1 capsids are transported through intact nuclear pores. Cell 2021; 184:1032-1046.e18. [PMID: 33571428 PMCID: PMC7895898 DOI: 10.1016/j.cell.2021.01.025] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/20/2020] [Accepted: 01/19/2021] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus (HIV-1) remains a major health threat. Viral capsid uncoating and nuclear import of the viral genome are critical for productive infection. The size of the HIV-1 capsid is generally believed to exceed the diameter of the nuclear pore complex (NPC), indicating that capsid uncoating has to occur prior to nuclear import. Here, we combined correlative light and electron microscopy with subtomogram averaging to capture the structural status of reverse transcription-competent HIV-1 complexes in infected T cells. We demonstrated that the diameter of the NPC in cellulo is sufficient for the import of apparently intact, cone-shaped capsids. Subsequent to nuclear import, we detected disrupted and empty capsid fragments, indicating that uncoating of the replication complex occurs by breaking the capsid open, and not by disassembly into individual subunits. Our data directly visualize a key step in HIV-1 replication and enhance our mechanistic understanding of the viral life cycle.
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Affiliation(s)
- Vojtech Zila
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Erica Margiotta
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Beata Turoňová
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Thorsten G Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Christian E Zimmerli
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Simone Mattei
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland; European Molecular Biology Laboratory, Imaging Center, 69117 Heidelberg, Germany
| | - Matteo Allegretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Kathleen Börner
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research, partner site Heidelberg, 69120 Heidelberg, Germany
| | - Jona Rada
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany
| | - Marina Lusic
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research, partner site Heidelberg, 69120 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University of Heidelberg, 69120 Heidelberg, Germany; German Center for Infection Research, partner site Heidelberg, 69120 Heidelberg, Germany.
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany; Max Planck Institute of Biophysics, Department of Molecular Sociology, 60438 Frankfurt, Germany.
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9
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Abstract
While the static structure of the nuclear pore complex (NPC) continues to be refined with cryo-EM and x-ray crystallography, in vivo conformational changes of the NPC remain under-explored. We developed sensors that report on the orientation of NPC components by rigidly conjugating mEGFP to different NPC proteins. Our studies show conformational changes to select domains of nucleoporins (Nups) within the inner ring (Nup54, Nup58, Nup62) when transport through the NPC is perturbed and no conformational changes to Nups elsewhere in the NPC. Our results suggest that select components of the NPC are flexible and undergo conformational changes upon engaging with cargo.
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Affiliation(s)
- Joan Pulupa
- Laboratory of Cellular Biophysics, Rockefeller UniversityNew YorkUnited States
| | - Harriet Prior
- Laboratory of Cellular Biophysics, Rockefeller UniversityNew YorkUnited States
| | - Daniel S Johnson
- Department of Physics and Astronomy, Hofstra UniversityHempsteadUnited States
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, Rockefeller UniversityNew YorkUnited States
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10
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Nino DF, Djayakarsana D, Milstein JN. FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy. PLoS Comput Biol 2020; 16:e1008479. [PMID: 33290385 PMCID: PMC7748281 DOI: 10.1371/journal.pcbi.1008479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/18/2020] [Accepted: 10/30/2020] [Indexed: 12/03/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) is a powerful tool for studying intracellular structure and macromolecular organization at the nanoscale. The increasingly massive pointillistic data sets generated by SMLM require the development of new and highly efficient quantification tools. Here we present FOCAL3D, an accurate, flexible and exceedingly fast (scaling linearly with the number of localizations) density-based algorithm for quantifying spatial clustering in large 3D SMLM data sets. Unlike DBSCAN, which is perhaps the most commonly employed density-based clustering algorithm, an optimum set of parameters for FOCAL3D may be objectively determined. We initially validate the performance of FOCAL3D on simulated datasets at varying noise levels and for a range of cluster sizes. These simulated datasets are used to illustrate the parametric insensitivity of the algorithm, in contrast to DBSCAN, and clustering metrics such as the F1 and Silhouette score indicate that FOCAL3D is highly accurate, even in the presence of significant background noise and mixed populations of variable sized clusters, once optimized. We then apply FOCAL3D to 3D astigmatic dSTORM images of the nuclear pore complex (NPC) in human osteosaracoma cells, illustrating both the validity of the parameter optimization and the ability of the algorithm to accurately cluster complex, heterogeneous 3D clusters in a biological dataset. FOCAL3D is provided as an open source software package written in Python. We have developed an accurate, highly-efficient and flexible algorithm for quantifying spatial clustering in large, 3-dimensional single-molecule localization microscopy (SMLM) datasets. Our method, FOCAL3D, is provided as an open-source software package written in Python. FOCAL3D scales linearly with the number of localizations and the algorithmic parameters may be systematically optimized so that the resulting analysis is insensitive to variation over a range of parameter choices. We initially validate the performance and parametric insensitivity of FOCAL3D on simulated datasets, then apply the algorithm to 3-dimensional, astigmatic dSTORM images of the nuclear pore complex in human osteosarcoma cells.
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Affiliation(s)
- Daniel F. Nino
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Daniel Djayakarsana
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Joshua N. Milstein
- Department of Physics, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
- * E-mail:
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11
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Sakamoto Y, Sakamoto T. Toward an understanding of nuclear substructures beyond their classical functions. J Plant Res 2020; 133:447-448. [PMID: 32519078 DOI: 10.1007/s10265-020-01209-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Yuki Sakamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1‑1 Machikaneyama‑cho, Toyonaka, Osaka, 560-0043, Japan
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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12
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Giampetruzzi A, Danielson EW, Gumina V, Jeon M, Boopathy S, Brown RH, Ratti A, Landers JE, Fallini C. Modulation of actin polymerization affects nucleocytoplasmic transport in multiple forms of amyotrophic lateral sclerosis. Nat Commun 2019; 10:3827. [PMID: 31444357 PMCID: PMC6707192 DOI: 10.1038/s41467-019-11837-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 08/01/2019] [Indexed: 12/30/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease of unknown etiology. Although defects in nucleocytoplasmic transport (NCT) may be central to the pathogenesis of ALS and other neurodegenerative diseases, the molecular mechanisms modulating the nuclear pore function are still largely unknown. Here we show that genetic and pharmacological modulation of actin polymerization disrupts nuclear pore integrity, nuclear import, and downstream pathways such as mRNA post-transcriptional regulation. Importantly, we demonstrate that modulation of actin homeostasis can rescue nuclear pore instability and dysfunction caused by mutant PFN1 as well as by C9ORF72 repeat expansion, the most common mutation in ALS patients. Collectively, our data link NCT defects to ALS-associated cellular pathology and propose the regulation of actin homeostasis as a novel therapeutic strategy for ALS and other neurodegenerative diseases.
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Affiliation(s)
- Anthony Giampetruzzi
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Eric W Danielson
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Valentina Gumina
- Istituto Auxologico Italiano, IRCCS, Department of Neurology - Stroke Unit and Laboratory of Neuroscience, Milan, Italy
| | - Maryangel Jeon
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Sivakumar Boopathy
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Antonia Ratti
- Istituto Auxologico Italiano, IRCCS, Department of Neurology - Stroke Unit and Laboratory of Neuroscience, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Claudia Fallini
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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13
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Gopal S, Chiappini C, Armstrong JPK, Chen Q, Serio A, Hsu CC, Meinert C, Klein TJ, Hutmacher DW, Rothery S, Stevens MM. Immunogold FIB-SEM: Combining Volumetric Ultrastructure Visualization with 3D Biomolecular Analysis to Dissect Cell-Environment Interactions. Adv Mater 2019; 31:e1900488. [PMID: 31197896 PMCID: PMC6778054 DOI: 10.1002/adma.201900488] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/20/2019] [Indexed: 05/03/2023]
Abstract
Volumetric imaging techniques capable of correlating structural and functional information with nanoscale resolution are necessary to broaden the insight into cellular processes within complex biological systems. The recent emergence of focused ion beam scanning electron microscopy (FIB-SEM) has provided unparalleled insight through the volumetric investigation of ultrastructure; however, it does not provide biomolecular information at equivalent resolution. Here, immunogold FIB-SEM, which combines antigen labeling with in situ FIB-SEM imaging, is developed in order to spatially map ultrastructural and biomolecular information simultaneously. This method is applied to investigate two different cell-material systems: the localization of histone epigenetic modifications in neural stem cells cultured on microstructured substrates and the distribution of nuclear pore complexes in myoblasts differentiated on a soft hydrogel surface. Immunogold FIB-SEM offers the potential for broad applicability to correlate structure and function with nanoscale resolution when addressing questions across cell biology, biomaterials, and regenerative medicine.
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Affiliation(s)
- Sahana Gopal
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
- Department of Medicine, Imperial College London, London, W12 0NN, UK
| | - Ciro Chiappini
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - James P K Armstrong
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Qu Chen
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Andrea Serio
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Chia-Chen Hsu
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Christoph Meinert
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
| | - Travis J Klein
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
- Australian Research Council Industrial Transformation Training Centre, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
| | - Dietmar W Hutmacher
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
- Australian Research Council Industrial Transformation Training Centre, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
| | - Stephen Rothery
- Facility for Light Microscopy, Imperial College London, London, SW7 2AZ, UK
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
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14
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Kobayashi W, Takizawa Y, Aihara M, Negishi L, Ishii H, Kurumizaka H. Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding. Commun Biol 2019; 2:163. [PMID: 31069272 PMCID: PMC6499780 DOI: 10.1038/s42003-019-0385-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
The nuclear pore complex embedded within the nuclear envelope is the essential architecture for trafficking macromolecules, such as proteins and RNAs, between the cytoplasm and nucleus. The nuclear pore complex assembly occurs on chromatin in the post-mitotic phase of the cell cycle. ELYS (MEL-28/AHCTF1) binds to the nucleosome, which is the basic chromatin unit, and promotes assembly of the complex around the chromosomes in cells. Here we show that the Arg-Arg-Lys (RRK) stretch of the C-terminal ELYS region plays an essential role in the nucleosome binding. The cryo-EM structure and the crosslinking mass spectrometry reveal that the ELYS C-terminal region directly binds to the acidic patch of the nucleosome. These results provide mechanistic insight into the ELYS-nucleosome interaction, which promotes the post-mitotic nuclear pore complex formation around chromosomes in cells.
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Affiliation(s)
- Wataru Kobayashi
- 1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
- 2Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Yoshimasa Takizawa
- 1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
| | - Maya Aihara
- 2Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Lumi Negishi
- 1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
| | - Hajime Ishii
- 2Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
| | - Hitoshi Kurumizaka
- 1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan
- 2Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan
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15
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Lim JSY, Wright GD, Burke B, Xie W. A user-interactive algorithm quantifying nuclear pore complex distribution within the nuclear lamina network in single molecular localization microscopic image. Methods 2019; 157:42-46. [PMID: 30268406 DOI: 10.1016/j.ymeth.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/04/2018] [Accepted: 09/25/2018] [Indexed: 11/17/2022] Open
Abstract
For decades, components of the mammalian nuclear envelope (NE), such as the nuclear lamina and nuclear pore complexes (NPCs), have been largely resistant to quantitative cell biological analysis using conventional fluorescence microscopy. This is in part due to their sub diffraction limit dimensions. Super-resolution microscopy, a major advancement in cell biology research, has now made possible the acquisition of images in which nuclear lamin networks and single NPCs can be resolved in intact mammalian somatic cells. In particular, single molecule localization microscopy is able to generate data sets that are accurate enough to allow detailed quantitative analysis. Here we describe an algorithm that will identify the centroid of single NPCs and will determine their localization relative to the distribution of lamin protein filaments. Using this algorithm, a percentage of NPCs localized within the nuclear lamin network was accurately calculated, that could be compared between cells expressing different lamin complements. With modifications tweaked according to user specified sample images, this algorithm serves as a semi-automatic and fast computational tool to quantify and compare the localization and distribution of two or more cellular components at the nanometre scale.
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Affiliation(s)
- John S Y Lim
- Institute of Medical Biology, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore; Skin Research Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Graham D Wright
- Institute of Medical Biology, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore; Skin Research Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Brian Burke
- Institute of Medical Biology, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore
| | - Wei Xie
- Institute of Medical Biology, Agency for Science, Technology and Research, 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore.
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16
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Mosalaganti S, Kosinski J, Albert S, Schaffer M, Strenkert D, Salomé PA, Merchant SS, Plitzko JM, Baumeister W, Engel BD, Beck M. In situ architecture of the algal nuclear pore complex. Nat Commun 2018; 9:2361. [PMID: 29915221 PMCID: PMC6006428 DOI: 10.1038/s41467-018-04739-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/23/2018] [Indexed: 12/19/2022] Open
Abstract
Nuclear pore complexes (NPCs) span the nuclear envelope and mediate nucleocytoplasmic exchange. They are a hallmark of eukaryotes and deeply rooted in the evolutionary origin of cellular compartmentalization. NPCs have an elaborate architecture that has been well studied in vertebrates. Whether this architecture is unique or varies significantly in other eukaryotic kingdoms remains unknown, predominantly due to missing in situ structural data. Here, we report the architecture of the algal NPC from the early branching eukaryote Chlamydomonas reinhardtii and compare it to the human NPC. We find that the inner ring of the Chlamydomonas NPC has an unexpectedly large diameter, and the outer rings exhibit an asymmetric oligomeric state that has not been observed or predicted previously. Our study provides evidence that the NPC is subject to substantial structural variation between species. The divergent and conserved features of NPC architecture provide insights into the evolution of the nucleocytoplasmic transport machinery.
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Affiliation(s)
- Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory, Center for Structural Systems Biology (CSSB), Notkestrasse 85, 22607, Hamburg, Germany
| | - Sahradha Albert
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Daniela Strenkert
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Patrice A Salomé
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Sabeeha S Merchant
- Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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17
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Abstract
The eukaryotic nucleus is enclosed by the nuclear envelope, which is perforated by the nuclear pores, the gateways of macromolecular exchange between the nucleoplasm and cytoplasm. The nucleoplasm is organized in a complex three-dimensional fashion that changes over time and in response to stimuli. Within the cell, the nucleus must be viewed as an organelle (albeit a gigantic one) that is a recipient of cytoplasmic forces and capable of morphological and positional dynamics. The most dramatic reorganization of this organelle occurs during mitosis and meiosis. Although many of these aspects are less well understood for the nuclei of plants than for those of animals or fungi, several recent discoveries have begun to place our understanding of plant nuclei firmly into this broader cell-biological context.
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Affiliation(s)
- Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210;
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom;
| | | | - David E Evans
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom;
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18
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Affiliation(s)
- Michael P. Rout
- The Rockefeller University, New York, New York, United States of America
| | - Samson O. Obado
- The Rockefeller University, New York, New York, United States of America
| | | | - Mark C. Field
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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19
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Sagulenko E, Nouwens A, Webb RI, Green K, Yee B, Morgan G, Leis A, Lee KC, Butler MK, Chia N, Pham UTP, Lindgreen S, Catchpole R, Poole AM, Fuerst JA. Nuclear Pore-Like Structures in a Compartmentalized Bacterium. PLoS One 2017; 12:e0169432. [PMID: 28146565 PMCID: PMC5287468 DOI: 10.1371/journal.pone.0169432] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/02/2016] [Indexed: 01/02/2023] Open
Abstract
Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.
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Affiliation(s)
- Evgeny Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard I. Webb
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Kathryn Green
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin Yee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Garry Morgan
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Leis
- CSIRO - Livestock Industries, Australian Animal Health Laboratory, Biosecurity Microscopy Facility (ABMF), Geelong, Victoria, Australia
| | - Kuo-Chang Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Margaret K. Butler
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Chia
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Uyen Thi Phuong Pham
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Stinus Lindgreen
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ryan Catchpole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Anthony M. Poole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Allan Wilson Centre, University of Canterbury, Christchurch, New Zealand
- Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John A. Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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20
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Sakiyama Y, Mazur A, Kapinos LE, Lim RYH. Spatiotemporal dynamics of the nuclear pore complex transport barrier resolved by high-speed atomic force microscopy. Nat Nanotechnol 2016; 11:719-23. [PMID: 27136131 DOI: 10.1038/nnano.2016.62] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 03/15/2016] [Indexed: 05/27/2023]
Abstract
Nuclear pore complexes (NPCs) are biological nanomachines that mediate the bidirectional traffic of macromolecules between the cytoplasm and nucleus in eukaryotic cells. This process involves numerous intrinsically disordered, barrier-forming proteins known as phenylalanine-glycine nucleoporins (FG Nups) that are tethered inside each pore. The selective barrier mechanism has so far remained unresolved because the FG Nups have eluded direct structural analysis within NPCs. Here, high-speed atomic force microscopy is used to visualize the nanoscopic spatiotemporal dynamics of FG Nups inside Xenopus laevis oocyte NPCs at timescales of ∼100 ms. Our results show that the cytoplasmic orifice is circumscribed by highly flexible, dynamically fluctuating FG Nups that rapidly elongate and retract, consistent with the diffusive motion of tethered polypeptide chains. On this basis, intermingling FG Nups exhibit transient entanglements in the central channel, but do not cohere into a tightly crosslinked meshwork. Therefore, the basic functional form of the NPC barrier is comprised of highly dynamic FG Nups that manifest as a central plug or transporter when averaged in space and time.
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Affiliation(s)
- Yusuke Sakiyama
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Adam Mazur
- Research IT, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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21
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Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL, Wan W, Bui KH, Hagen WJ, Briggs JAG, Glavy JS, Hurt E, Beck M. Molecular architecture of the inner ring scaffold of the human nuclear pore complex. Science 2016; 352:363-365. [PMID: 27081072 PMCID: PMC8926079 DOI: 10.1126/science.aaf0643] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/19/2016] [Indexed: 07/21/2023]
Abstract
Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar.
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Affiliation(s)
- Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Alexander von Appen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Roman Teimer
- Biochemistry Center of Heidelberg University, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Amanda L. DiGuilio
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 507 River Street, Hoboken, NJ 07030, USA
| | - William Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Wim J.H. Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - John A. G. Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Joseph S. Glavy
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 507 River Street, Hoboken, NJ 07030, USA
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
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22
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Iwamoto M, Koujin T, Osakada H, Mori C, Kojidani T, Matsuda A, Asakawa H, Hiraoka Y, Haraguchi T. Biased assembly of the nuclear pore complex is required for somatic and germline nuclear differentiation in Tetrahymena. J Cell Sci 2015; 128:1812-23. [PMID: 25788697 PMCID: PMC4432229 DOI: 10.1242/jcs.167353] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/07/2015] [Indexed: 12/18/2022] Open
Abstract
Ciliates have two functionally distinct nuclei, a somatic macronucleus (MAC) and a germline micronucleus (MIC) that develop from daughter nuclei of the last postzygotic division (PZD) during the sexual process of conjugation. Understanding this nuclear dimorphism is a central issue in ciliate biology. We show, by live-cell imaging of Tetrahymena, that biased assembly of the nuclear pore complex (NPC) occurs immediately after the last PZD, which generates anterior-posterior polarized nuclei: MAC-specific NPCs assemble in anterior presumptive MACs but not in posterior presumptive MICs. MAC-specific NPC assembly in the anterior nuclei occurs much earlier than transport of Twi1p, which is required for MAC genome rearrangement. Correlative light-electron microscopy shows that addition of new nuclear envelope (NE) precursors occurs through the formation of domains of redundant NE, where the outer double membrane contains the newly assembled NPCs. Nocodazole inhibition of the second PZD results in assembly of MAC-specific NPCs in the division-failed zygotic nuclei, leading to failure of MIC differentiation. Our findings demonstrate that NPC type switching has a crucial role in the establishment of nuclear differentiation in ciliates.
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Affiliation(s)
- Masaaki Iwamoto
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Takako Koujin
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan
| | - Tomoko Kojidani
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Japan Women's University, Tokyo 112-8681, Japan
| | - Atsushi Matsuda
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Haruhiko Asakawa
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yasushi Hiraoka
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Tokuko Haraguchi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe 651-2492, Japan Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
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Kuvichkin V. Holes in the Nuclear Membrane as an Illustration of Gaps in the Understanding of the Biology by Biologists. J Membr Biol 2015; 248:741-4. [PMID: 25758231 DOI: 10.1007/s00232-015-9786-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 02/24/2015] [Indexed: 11/25/2022]
Abstract
At the moment, the conditions are in place to describe how to construct nuclear pores and how they work, missing only real understanding of process. The DNA-RNA-protein paradigm proposed by Crick 53 years ago (Symp Soc Exp Biol 12:138-163, 1958; Nature 227:561-563, 1970) severely hampers our understanding of nuclear pore structure and assembly because the problem lies outside paradigm. DNA in this scheme only plays the role of information storage from which information is transferred to RNA, then from RNA to proteins after which proteins perform all of the functions in the cell. Although it is known that DNA is able to build nucleosomes in vivo, many in vitro structures types of origami (Rothemund, Nature 440:297-302, 2006), the DNA is considered to be exotic as structural material for cells. The structural role of RNA is difficult to ignore, in connections with their participation in structures of ribosomes, ribonucleoproteins, and ribozymes, but imagine that DNA performs an important structural role in the cell is impossible in opinion of many authors. So, when there was a problem in explaining the origin of the nuclear pore, all efforts of biologists were directed to proteins such as nucleoporins, especially when taking into account that there are 30 nucleoporins and only one DNA. Here, I try to explain the typical mistakes of the old approach to such a complex problem as nuclear pore structure and assembly.
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Affiliation(s)
- Vasily Kuvichkin
- Institute of Cell Biophysics, Russian Academy of Sciences, 3, Institutskaya, 142290, Pushchino, Moscow Region, Russia,
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Bestembayeva A, Kramer A, Labokha AA, Osmanović D, Liashkovich I, Orlova EV, Ford IJ, Charras G, Fassati A, Hoogenboom BW. Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes. Nat Nanotechnol 2015; 10:60-64. [PMID: 25420031 PMCID: PMC4286247 DOI: 10.1038/nnano.2014.262] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 10/13/2014] [Indexed: 05/17/2023]
Abstract
The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ∼5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins, and is therefore not well understood. Here, we show that stiffness topography with sharp atomic force microscopy tips can generate nanoscale cross-sections of the NPC. The cross-sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel.
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Affiliation(s)
- Aizhan Bestembayeva
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Armin Kramer
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Institute of Physiology II, University of Münster, Robert-Koch Strasse 27b, 48149 Münster, Germany
| | - Aksana A. Labokha
- Wohl Virion Centre, Division of Infection & Immunity, MRC Centre for Medical Molecular Virology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Dino Osmanović
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Ivan Liashkovich
- Institute of Physiology II, University of Münster, Robert-Koch Strasse 27b, 48149 Münster, Germany
| | - Elena V. Orlova
- Department of Biological Sciences, Birkbeck College, Institute of Structural and Molecular Biology, Malet Street, London WC1E 7HX, United Kingdom
| | - Ian J. Ford
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Guillaume Charras
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Ariberto Fassati
- Wohl Virion Centre, Division of Infection & Immunity, MRC Centre for Medical Molecular Virology, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Correspondence and requests for materials should be addressed to A.F. () and B.W.H. ()
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, United Kingdom
- Correspondence and requests for materials should be addressed to A.F. () and B.W.H. ()
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25
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Souza RRD, Oliveira VCD, Curi TCP, Maldonado DC. Effects of ovariectomy on the secretory apparatus in the right atrial cardiomyocytes of middle-aged mice. Clinics (Sao Paulo) 2014; 69:554-8. [PMID: 25141115 PMCID: PMC4129560 DOI: 10.6061/clinics/2014(08)09] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 02/28/2014] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE The aim of the present study was to evaluate the effects of ovariectomy on the secretory apparatus of natriuretic peptides in right atrial cardiomyocytes. METHODS Nine-month-old mice underwent bilateral ovariectomy or sham surgery. The blood exam of the ovariectomized mice showed results consistent with castrated females. Systolic blood pressure was measured after ovariectomy (9 mo of age) and at the moment of sacrifice (12 mo of age). Fragments of the right atrium were collected and prepared for electron microscopy examination. The following variables were quantified: the quantitative density and area of the natriuretic peptide granules, the relative volume of euchromatin in the nucleus, the number of pores per 10 μm of the nuclear membrane and the relative volumes of the mitochondria and Golgi complex. RESULTS The cardiomyocytes obtained from ovariectomized mice indicated that the quantitative density and the area of secretory granules of natriuretic peptides were significantly lower compared with the sham-operated mice. Furthermore, there was a decrease in the relative volume of euchromatin, a lower density of nuclear pores, and lower relative volumes of the mitochondria and Golgi complex in the ovariectomized mice compared with the sham-operated mice. These findings suggest a pool with a low turnover rate, i.e., low synthesis and elimination of natriuretic peptides. CONCLUSION A lack of estrogen caused hypotrophy of the secretory apparatus in right atrial cardiomyocytes that could explain the weak synthesis of natriuretic peptides in mice. Furthermore, one of the mechanisms of blood pressure control was lost, which may explain, in part, the elevated blood pressure in ovariectomized mice.
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Affiliation(s)
- Romeu R de Souza
- ICB-USP and Department of Biology, Department of Anatomy, São Judas Tadeu University, São Paulo, SP, Brazil
| | | | | | - Diogo C Maldonado
- Department of Anatomy, Federal University of São Paulo, Department of Morphology and Genetics and Nove de Julho University, São Paulo, SP, Brazil
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26
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Goodwin EC, Motamedi N, Lipovsky A, Fernández-Busnadiego R, DiMaio D. Expression of DNAJB12 or DNAJB14 causes coordinate invasion of the nucleus by membranes associated with a novel nuclear pore structure. PLoS One 2014; 9:e94322. [PMID: 24732912 PMCID: PMC3986390 DOI: 10.1371/journal.pone.0094322] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/15/2014] [Indexed: 11/18/2022] Open
Abstract
DNAJB12 and DNAJB14 are transmembrane proteins in the endoplasmic reticulum (ER) that serve as co-chaperones for Hsc70/Hsp70 heat shock proteins. We demonstrate that over-expression of DNAJB12 or DNAJB14 causes the formation of elaborate membranous structures within cell nuclei, which we designate DJANGOS for DNAJ-associated nuclear globular structures. DJANGOS contain DNAJB12, DNAJB14, Hsc70 and markers of the ER lumen and ER and nuclear membranes. Strikingly, they are evenly distributed underneath the nuclear envelope and are of uniform size in any one nucleus. DJANGOS are composed primarily of single-walled membrane tubes and sheets that connect to the nuclear envelope via a unique configuration of membranes, in which the nuclear pore complex appears anchored exclusively to the outer nuclear membrane, allowing both the inner and outer nuclear membranes to flow past the circumference of the nuclear pore complex into the nucleus. DJANGOS break down rapidly during cell division and reform synchronously in the daughter cell nuclei, demonstrating that they are dynamic structures that undergo coordinate formation and dissolution. Genetic studies showed that the chaperone activity of DNAJ/Hsc70 is required for the formation of DJANGOS. Further analysis of these structures will provide insight into nuclear pore formation and function, activities of molecular chaperones, and mechanisms that maintain membrane identity.
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Affiliation(s)
- Edward C. Goodwin
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Nasim Motamedi
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Alex Lipovsky
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | | | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Cancer Center, New Haven, Connecticut, United States of America
- * E-mail:
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Kim J, Izadyar A, Shen M, Ishimatsu R, Amemiya S. Ion permeability of the nuclear pore complex and ion-induced macromolecular permeation as studied by scanning electrochemical and fluorescence microscopy. Anal Chem 2014; 86:2090-8. [PMID: 24460147 PMCID: PMC3955255 DOI: 10.1021/ac403607s] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/25/2014] [Indexed: 12/20/2022]
Abstract
Efficient delivery of therapeutic macromolecules and nanomaterials into the nucleus is imperative for gene therapy and nanomedicine. Nucleocytoplasmic molecular transport, however, is tightly regulated by the nuclear pore complex (NPC) with the hydrophobic transport barriers based on phenylalanine and glycine repeats. Herein, we apply scanning electrochemical microscopy (SECM) to quantitatively study the permeability of the NPCs to small probe ions with a wide range of hydrophobicity as a measure of their hydrophobic interactions with the transport barriers. Amperometric detection of the redox-inactive probe ions is enabled by using the ion-selective SECM tips based on the micropipet- or nanopipet-supported interfaces between two immiscible electrolyte solutions. The remarkably high ion permeability of the NPCs is successfully measured by SECM and theoretically analyzed. This analysis demonstrates that the ion permeability of the NPCs is determined by the dimensions and density of the nanopores without a significant effect of the transport barriers on the transported ions. Importantly, the weak ion-barrier interactions become significant at sufficiently high concentrations of extremely hydrophobic ions, i.e., tetraphenylarsonium and perfluorobutylsulfonate, to permeabilize the NPCs to naturally impermeable macromolecules. Dependence of ion-induced permeabilization of the NPC on the pathway and mode of macromolecular transport is studied by using fluorescence microscopy to obtain deeper insights into the gating mechanism of the NPC as the basis of a new transport model.
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Affiliation(s)
| | | | | | | | - Shigeru Amemiya
- Department of Chemistry, University
of Pittsburgh, 219 Parkman
Avenue, Pittsburgh, Pennsylvania 15260, United States
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28
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Abstract
The nucleus contains the cell's genetic material, which directs cellular activity via gene regulation. The physical barrier of the nuclear envelope needs to be permeable to a variety of macromolecules and signals. The most prominent gateways for the transport of macromolecules are the nuclear pore complexes (NPCs). The NPC is the largest multiprotein complex in the cell, and is composed of multiple copies of ~30 different proteins called nucleoporins. Although much progress has been made in dissecting the NPC structure in vertebrates and yeast, the molecular architecture and physiological function of nucleoporins in plants remain poorly understood. In this review, we summarize the current knowledge regarding the plant NPC proteome and address structural and functional aspects of plant nucleoporins, which support the fundamental cellular machinery.
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Affiliation(s)
- Kentaro Tamura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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29
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Liashkovich I, Meyring A, Oberleithner H, Shahin V. Structural organization of the nuclear pore permeability barrier. J Control Release 2012; 160:601-8. [PMID: 22386519 DOI: 10.1016/j.jconrel.2012.02.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/13/2012] [Accepted: 02/17/2012] [Indexed: 12/26/2022]
Abstract
The efficiency of gene therapy in non-dividing cells is particularly poor due to restricted nuclear delivery rates of exogenously applied macromolecules across the nuclear pore complexes (NPCs). Therefore, improved intranuclear delivery of transgenes requires an ability to modulate the barrier function of the NPC. Despite a large body of experimental evidence accumulated to date, the contribution of individual NPC proteins (nucleoporins) to the formation of the NPC permeability barrier as well as their structural organization within the NPC remains under debate. In the present study, we revisit the view on the spatial arrangement of the Phe-Gly rich domains (FG-domains) of a subset of nucleoporins known as FG-nucleoporins. They are generally believed to be the key constituents of the NPC permeability barrier. Comparison of the binding pattern of a transport receptor importin β fragment, that binds specifically to FG-domains, with the binding pattern of wheat germ agglutinin that binds elsewhere in the NPC, reveals that FG-domains tend to cluster in the very center of the NPC. Furthermore, a controlled sequential release of the barrier-forming nucleoporins results in a gradual breakdown of the NPC permeability barrier. The breakdown is initiated by a dissociation of Nup62 from the NPC. This is accompanied by an increased passive diffusion of small molecules across the NPC. Subsequent dissociation of Nup98 and possibly other nucleoporins results in a collapse of the barrier for larger molecules. We therefore conclude that FG-nucleoporins do not contribute equally to the maintenance of the NPC permeability barrier exclusion limit. This implies that a controlled release of nucleoporins that contribute most to the formation and maintenance of the NPC barrier can facilitate access of therapeutic macromolecules into the nucleus.
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Affiliation(s)
- Ivan Liashkovich
- Institute of Physiology II, WWU Münster, Robert-Koch-Straße 27b, 48149 Münster, Germany.
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30
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Goulbourne CN, Malhas AN, Vaux DJ. The induction of a nucleoplasmic reticulum by prelamin A accumulation requires CTP:phosphocholine cytidylyltransferase-α. J Cell Sci 2011; 124:4253-66. [PMID: 22223883 PMCID: PMC3258109 DOI: 10.1242/jcs.091009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2011] [Indexed: 12/24/2022] Open
Abstract
Farnesylated prelamin A accumulates when the final endoproteolytic maturation of the protein fails to occur and causes a dysmorphic nuclear phenotype; however, the morphology and mechanisms of biogenesis of these changes remain unclear. We show here that acute prelamin A accumulation after reduction in the activity of the ZMPSTE24 endoprotease by short interfering RNA knockdown, results in the generation of a complex nucleoplasmic reticulum that depends for its formation on the enzyme CTP:phosphocholine-cytidylyltransferase-α (CCT-α, also known as choline-phosphate cytidylyltransferase A). This structure can form during interphase, confirming that it is independent of mitosis and therefore not a consequence of disordered nuclear envelope assembly. Serial-section dual-axis electron tomography reveals that these invaginations can take two forms: one in which the inner nuclear membrane infolds alone with an inter membrane space interior, and the other in which an invagination of both nuclear membranes occurs, enclosing a cytoplasmic core. Both types of invagination can co-exist in one nucleus and both are frequently studded with nuclear pore complexes (NPC), which reduces NPC abundance on the nuclear surface.
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Affiliation(s)
- Chris N. Goulbourne
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Ashraf N. Malhas
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - David J. Vaux
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
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31
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Au S, Panté N. Nuclear transport of baculovirus: revealing the nuclear pore complex passage. J Struct Biol 2011; 177:90-8. [PMID: 22100338 DOI: 10.1016/j.jsb.2011.11.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/02/2011] [Accepted: 11/05/2011] [Indexed: 12/26/2022]
Abstract
Baculoviruses are one of the largest viruses that replicate in the nucleus of their host cells. During an infection the capsid, containing the DNA viral genome, is released into the cytoplasm and delivers the genome into the nucleus by a mechanism that is largely unknown. Here, we used capsids of the baculovirus Autographa californica multiple nucleopolyhedrovirus in combination with electron microscopy and discovered this capsid crosses the NPC and enters into the nucleus intact, where it releases its genome. To better illustrate the existence of this capsid through the NPC in its native conformation, we reconstructed the nuclear import event using electron tomography. In addition, using different experimental conditions, we were able to visualize the intact capsid interacting with NPC cytoplasmic filaments, as an initial docking site, and midway through the NPC. Our data suggests the NPC central channel undergoes large-scale rearrangements to allow translocation of the intact 250-nm long baculovirus capsid. We discuss our results in the light of the hypothetical models of NPC function.
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Affiliation(s)
- Shelly Au
- Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
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Abstract
One very striking feature of T-cell recognition is the formation of an immunological synapse between a T cell and a cell that it is recognizing. Formation of this complex structure correlates with cytotoxicity in the case of killer (largely CD8(+)) T-cell activity, or robust cytokine release and proliferation in the case of the much longer lived synapses formed by helper (CD4(+)) T cells. Here we have used electron microscopy and 3D tomography to characterize the synapses of antigen-specific CD4(+) T cells recognizing B cells and dendritic cells at different time points. We show that there are at least four distinct stages in synapse formation, proceeding over several hours, including an initial stage involving invasive T-cell pseudopodia that penetrate deeply into the antigen-presenting cell, almost to the nuclear envelope. This must involve considerable force and may serve to widen the search for potential ligands on the surface of the cell being recognized. We also show that centrioles and the Golgi complex are always located immediately beneath the synapse and that centrioles are significantly shifted toward the late contact zone with either B lymphocytes or bone marrow-derived dendritic cells such as antigen-presenting cells, and that there are dynamic, stage-dependent changes in the organization of microtubules beneath the synapse. These data reinforce and extend previous data on cytotoxic T cells that one of the principal functions of the immunological synapse is to facilitate cytokine secretion into the synaptic cleft, as well as provide important insights into the overall dynamics of this phenomenon.
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Affiliation(s)
- Hironori Ueda
- The Howard Hughes Medical Institute and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5323; and
| | - Mary K. Morphew
- Laboratory for 3D Structure of Cells and Molecules, Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347
| | - J. Richard McIntosh
- Laboratory for 3D Structure of Cells and Molecules, Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347
| | - Mark M. Davis
- The Howard Hughes Medical Institute and
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5323; and
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Yahav T, Maimon T, Grossman E, Dahan I, Medalia O. Cryo-electron tomography: gaining insight into cellular processes by structural approaches. Curr Opin Struct Biol 2011; 21:670-7. [PMID: 21813274 DOI: 10.1016/j.sbi.2011.07.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 06/23/2011] [Accepted: 07/11/2011] [Indexed: 11/18/2022]
Abstract
Visualization of cellular processes at a resolution of the individual protein should involve integrative and complementary approaches that can eventually draw realistic functional and cellular landscapes. Electron tomography of vitrified but otherwise unaltered cells emerges as a central method for three-dimensional reconstruction of cellular architecture at a resolution of 2-6 nm. While a combination of correlative light-based microscopy with cryo-electron tomography (cryo-ET) provides medium-resolution insight into pivotal cellular processes, fitting high-resolution structural approaches, for example, X-ray crystallography, into reconstructed macromolecular assemblies provides unprecedented information on native protein assemblies. Thus, cryo-ET bridges the resolution gap between cellular and structural biology. In this article, we focus on the study of eukaryotic cells and macromolecular complexes in a close-to-life-state. We discuss recent developments and structural findings enabling major strides to be made in understanding complex physiological functions.
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Affiliation(s)
- Tal Yahav
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Abstract
Sustained activity-dependent synaptic modifications require protein synthesis. Although proteins can be synthesized locally in dendrites, long-term changes also require nuclear signaling. Amyloid-beta protein precursor intracellular domain-associated protein-1 (AIDA-1), an abundant component of the biochemical postsynaptic density fraction, contains a nuclear localization sequence, making it a plausible candidate for synapse-to-nucleus signaling. We used immunohistochemistry to study the regional, cellular, and subcellular distribution of AIDA-1. Immunostaining was prominent in the hippocampus, cerebral cortex, and neostriatum. Along with diffuse staining of neuropil, fluorescence microscopy revealed immunostaining of excitatory synapses throughout the forebrain, and immunoreactive puncta within and directly outside the nucleus. Presynaptic staining was conspicuous in hippocampal mossy fibers. Electron microscopic analysis of material processed for postembedding immunogold revealed AIDA-1 label within postsynaptic densities in both hippocampus and cortex. Together with previous work, these data suggest that AIDA-1 serves as a direct signaling link between synapses and the nucleus in adult rat brain.
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Affiliation(s)
- Amanda L Jacob
- Curriculum in Neurobiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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35
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Cavicchia JC, Guembe G, Fóscolo M. Nuclear pores in luteal cells during pregnancy and after parturition and pup removal in the rat. A freeze-fracture study. BIOCELL 2010; 34:81-89. [PMID: 20925197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In a previous paper we described a pronounced increase of apoptotic nuclei in rat corpus luteum of pregnancy whose programmed chromatin degeneration was induced by the progesterone antagonist mifepristone. Those observations encouraged us to study the apoptotic nuclear membrane during pregnancy and after parturition and pup removal, by using a freeze-fracture technique which allows us to observe 'en face' the nuclear envelop and also permits nuclear pore counting. This study was complemented with the TUNEL assay (TdT-mediated dUTP nick-end labelling). Changes in nuclear pores during pregnancy begin with an intense reduction in number but still showing an even distribution on the nuclear membrane, never forming aggregations sharply separated from pore-free areas, which are characteristic of other apoptotic models. Electron microscopy of thin-sections shows, coincidently with findings in the freeze-fracture replicas, a moderately irregular aggregation of marginal heterochromatin condensations. After nuclear fragmentation and micronuclear formation, pores behave in the usual manner in other apoptotic models, i.e., mainly showing migrations of nuclear pores toward the chromatin-free areas. The present results support the hypothesis that nuclear pore complexes are dynamic structures, which permit their migration toward nuclear membrane areas devoid of chromatin aggregations that might block the nucleocytoplasmic transport in such areas.
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Affiliation(s)
- Juan Carlos Cavicchia
- Instituto de Histología y Embriología "Dr. Mario H. Burgos" (IHEM), CONICET, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Argentina.
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36
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Ben-Harush K, Maimon T, Patla I, Villa E, Medalia O. Visualizing cellular processes at the molecular level by cryo-electron tomography. J Cell Sci 2010; 123:7-12. [PMID: 20016061 DOI: 10.1242/jcs.060111] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The cellular landscape rapidly changes throughout the biological processes that transpire within a cell. For example, the cytoskeleton is remodeled within fractions of a second. Therefore, reliable structural analysis of the cell requires approaches that allow for instantaneous arrest of functional states of a given process while offering the best possible preservation of the delicate cellular structure. Electron tomography of vitrified but otherwise unaltered cells (cryo-ET) has proven to be the method of choice for three-dimensional (3D) reconstruction of cellular architecture at a resolution of 4-6 nm. Through the use of cryo-ET, the 3D organization of macromolecular complexes and organelles can be studied in their native environment in the cell. In this Commentary, we focus on the application of cryo-ET to study eukaryotic cells - in particular, the cytoskeletal-driven processes that are involved in cell movements, filopodia protrusion and viral entry. Finally, we demonstrate the potential of cryo-ET to determine structures of macromolecular complexes in situ, such as the nuclear pore complex.
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37
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Meier I, Brkljacic J. Adding pieces to the puzzling plant nuclear envelope. Curr Opin Plant Biol 2009; 12:752-9. [PMID: 19875325 DOI: 10.1016/j.pbi.2009.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 08/19/2009] [Accepted: 09/22/2009] [Indexed: 05/10/2023]
Abstract
The nuclear envelope (NE) and the nuclear pores are important structures that both separate and selectively connect the nucleoplasm and the cytoplasm. NE and nuclear pore research in plants have recently seen an elevated level of interest. This is based both on new findings demonstrating the importance of nucleocytoplasmic trafficking for several signal transduction events, and on increasing evidence that NE and nuclear pore components play important roles during plant cell division. Here, we review the most recent reports in the field and compare them to the more advanced knowledge about yeast and animal model systems. They deal with the refined ultrastructure of the NE and NPC, with the discovery of novel NE components, and, importantly, with novel roles and fates of NE-associated and NPC-associated proteins during plant mitosis and cytokinesis.
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Affiliation(s)
- Iris Meier
- Department of Molecular Genetics and Plant Biotechnology Center, The Ohio State University, Columbus, OH 43210, USA.
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Meier I, Brkljacic J. Adding pieces to the puzzling plant nuclear envelope. Curr Opin Plant Biol 2009; 12:752-759. [PMID: 19875325 DOI: 10.1016/j.pbi.2008.09.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 08/19/2009] [Accepted: 09/22/2009] [Indexed: 05/26/2023]
Abstract
The nuclear envelope (NE) and the nuclear pores are important structures that both separate and selectively connect the nucleoplasm and the cytoplasm. NE and nuclear pore research in plants have recently seen an elevated level of interest. This is based both on new findings demonstrating the importance of nucleocytoplasmic trafficking for several signal transduction events, and on increasing evidence that NE and nuclear pore components play important roles during plant cell division. Here, we review the most recent reports in the field and compare them to the more advanced knowledge about yeast and animal model systems. They deal with the refined ultrastructure of the NE and NPC, with the discovery of novel NE components, and, importantly, with novel roles and fates of NE-associated and NPC-associated proteins during plant mitosis and cytokinesis.
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Affiliation(s)
- Iris Meier
- Department of Molecular Genetics and Plant Biotechnology Center, The Ohio State University, Columbus, OH 43210, USA.
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Frenkiel-Krispin D, Maco B, Aebi U, Medalia O. Structural analysis of a metazoan nuclear pore complex reveals a fused concentric ring architecture. J Mol Biol 2009; 395:578-86. [PMID: 19913035 DOI: 10.1016/j.jmb.2009.11.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 10/26/2009] [Accepted: 11/05/2009] [Indexed: 12/22/2022]
Abstract
The sole gateway for molecular exchange between the cytoplasm and the nucleus is the nuclear pore complex (NPC). This large supramolecular assembly mediates transport of cargo into and out of the nucleus and fuse the inner and outer nuclear membranes to form an aqueous translocation channel. The NPC is composed of eight proteinaceous asymmetric units forming a pseudo-8-fold symmetric passage. Due to its shear size, complexity, and plastic nature, dissecting the high-resolution three-dimensional structure of the NPC in its hydrated state is a formidable challenge. Toward this goal, we applied cryo-electron tomography to spread nuclear envelopes from Xenopus oocytes. To compensate for perturbations of the 8-fold symmetry of individual NPCs, we performed symmetry-independent asymmetric unit averaging of three-dimensional tomographic NPC volumes to eventually yield a refined model at 6.4 nm resolution. This approach revealed novel structural features, particularly in the spoke-ring complex and luminal domains. Fused concentric ring architecture of the spoke-ring complex was found along the translocation channel. Additionally, a comparison of the refined Xenopus model to that of its Dictyostelium homologue yielded similar pore diameters at the level of the three canonical rings, although the Xenopus NPC was found to be 30% taller than the Dictyostelium pore. This discrepancy is attributed primarily to the relatively low homology and different organization of some nucleoporins in the Dictyostelium genome as compared to that of vertebrates. Nevertheless, the experimental conditions impose a preferred axial orientation of the NPCs within spread Xenopus oocyte nuclear envelopes. This may at least in part explain the increased height of the reconstructed vertebrate NPCs compared to those obtained from tomographic reconstruction of intact Dictyostelium nuclei.
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40
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Kuvichkin VV. Investigation of Ternary Complexes: DNA–Phosphatidylcholine Liposomes–Mg2+ by Freeze-Fracture Method and Their Role in the Formation of Some Cell Structures. J Membr Biol 2009; 231:29-34. [PMID: 19809848 DOI: 10.1007/s00232-009-9201-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 09/03/2009] [Indexed: 11/27/2022]
Affiliation(s)
- Vasily V Kuvichkin
- Department of Mechanisms Reception of the Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Moscow region, Russia.
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41
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Peters R. Functionalization of a nanopore: the nuclear pore complex paradigm. Biochim Biophys Acta 2009; 1793:1533-9. [PMID: 19596381 PMCID: PMC2756448 DOI: 10.1016/j.bbamcr.2009.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 06/26/2009] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
Abstract
Biological cells maintain a myriad of nanopores which, although relying on the same basic small-hole principle, serve a large variety of functions. Here we consider how the nuclear pore complex (NPC), a large nanopore mediating the traffic between genetic material and protein synthesizing apparatus, is functionalized to carry out a set of transport functions. A major parameter of NPC functionalization is a lining of it external and internal surfaces with so-called phenylalanine glycine (FG) proteins. FG proteins integrate a multitude of transport factor binding sites into intrinsically disordered domains. This surprising finding has given rise to a number of transport models assigning direct gating functions to FG proteins. However, recent data suggest that the properties of FG proteins cannot be properly assessed by considering only the purified, transport-factor-stripped NPC. At physiological conditions transport factors may shape FG proteins in a way allotting an essential role to surface diffusion, reconciling tight binding with efficient transport. Thus, NPC studies are revealing both general traits and novel aspects of nanopore functionalization. In addition, they inspire artificial molecule sorters for proteomic and pharmaceutical applications.
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Affiliation(s)
- Reiner Peters
- The Rockefeller University, Laboratory for mass spectrometry and gaseous ion chemistry, 1230 York Avenue, New York, NY 10065, USA.
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42
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Abstract
The nuclear envelope (NE) is a fundamental structure of eukaryotic cells with a dual role: it separates two distinct compartments, and enables communication between them via nuclear pore complexes (NPCs). Little is known about NPCs and NE structural organization in plants. We investigated the structure of NPCs from both sides of the NE in tobacco BY-2 cells. We detected structural differences between the NPCs of dividing and quiescent nuclei. Importantly, we also traced the organizational pattern of the NPCs, and observed non-random NPC distribution over the nuclear surface. Lastly, we observed an organized filamentous protein structure that underlies the inner nuclear membrane, and interconnects NPCs. The results are discussed within the context of the current understanding of NE structure and function in higher eukaryotes.
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Affiliation(s)
- Jindriska Fiserova
- Department of Biological and Biomedical Sciences, Durham University, South Road, Durham DH13LE, UK
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43
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Wild P, Senn C, Manera CL, Sutter E, Schraner EM, Tobler K, Ackermann M, Ziegler U, Lucas MS, Kaech A. Exploring the nuclear envelope of herpes simplex virus 1-infected cells by high-resolution microscopy. J Virol 2009; 83:408-19. [PMID: 18922868 PMCID: PMC2612326 DOI: 10.1128/jvi.01568-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Accepted: 10/06/2008] [Indexed: 01/11/2023] Open
Abstract
Herpesviruses are composed of capsid, tegument, and envelope. Capsids assemble in the nucleus and exit the nucleus by budding at the inner nuclear membrane, acquiring tegument and the envelope. This study focuses on the changes of the nuclear envelope during herpes simplex virus 1 (HSV-1) infection in HeLa and Vero cells by employing preparation techniques at ambient and low temperatures for high-resolution scanning and transmission electron microscopy and confocal laser scanning microscopy. Cryo-field emission scanning electron microscopy of freeze-fractured cells showed for the first time budding of capsids at the nuclear envelope at the third dimension with high activity at 10 h and low activity at 15 h of incubation. The mean number of pores was significantly lower, and the mean interpore distance and the mean interpore area were significantly larger than those for mock-infected cells 15 h after inoculation. Forty-five percent of nuclear pores in HSV-1-infected cells were dilated to more than 140 nm. Nuclear material containing capsids protrude through them into the cytoplasm. Examination of in situ preparations after dry fracturing revealed significant enlargements of the nuclear pore diameter and of the nuclear pore central channel in HSV-1-infected cells compared to mock-infected cells. The demonstration of nucleoporins by confocal microscopy also revealed fewer pores but focal enhancement of fluorescence signals in HSV-1-infected cells, whereas Western blots showed no loss of nucleoporins from cells. The data suggest that infection with HSV-1 alters the number, size, and architecture of nuclear pores without a loss of nucleoporins from altered nuclear pore complexes.
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Affiliation(s)
- Peter Wild
- Electron Microscopy, Institute of Virology, Winterthurerstrasse 266a, CH-8057 Zürich, Switzerland.
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Kramer A, Liashkovich I, Oberleithner H, Ludwig S, Mazur I, Shahin V. Apoptosis leads to a degradation of vital components of active nuclear transport and a dissociation of the nuclear lamina. Proc Natl Acad Sci U S A 2008; 105:11236-41. [PMID: 18678902 PMCID: PMC2516273 DOI: 10.1073/pnas.0801967105] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Indexed: 02/05/2023] Open
Abstract
Apoptosis, a physiologically critical process, is characterized by a destruction of the cell after sequential degradation of key cellular components. Here, we set out to explore the fate of the physiologically indispensable nuclear envelope (NE) in this process. The NE mediates the critical nucleocytoplasmic transport through nuclear pore complexes (NPCs). In addition, the NE is involved in gene expression and contributes significantly to the overall structure and mechanical stability of the cell nucleus through the nuclear lamina, which underlies the entire nucleoplasmic face of the NE and thereby interconnects the NPCs, the NE, and the genomic material. Using the nano-imaging and mechanical probing approach atomic force microscopy (AFM) and biochemical methods, we unveiled the fate of the NE during apoptosis. The doomed NE sustains a degradation of both the mediators of the critical selective nucleocytoplasmic transport, namely NPC cytoplasmic filaments and basket, and the nuclear lamina. These observations are paralleled by marked softening and destabilization of the NE and the detection of vesicle-like nuclear fragments. We conclude that destruction of the cell nucleus during apoptosis proceeds in a strategic fashion. Degradation of NPC cytoplasmic filaments and basket shuts down the critical selective nucleocytoplasmic cross-talk. Degradation of the nuclear lamina disrupts the pivotal connection between the NE and the chromatin, breaks up the overall nuclear architecture, and softens the NE, thereby enabling the formation of nuclear fragments at later stages of apoptosis.
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Affiliation(s)
- A. Kramer
- *Institute of Physiology II, Westfälische Wilhelms-Universität Münster, Robert-Koch-Strasse 27b, 48149 Münster, Germany; and
| | - I. Liashkovich
- *Institute of Physiology II, Westfälische Wilhelms-Universität Münster, Robert-Koch-Strasse 27b, 48149 Münster, Germany; and
| | - H. Oberleithner
- *Institute of Physiology II, Westfälische Wilhelms-Universität Münster, Robert-Koch-Strasse 27b, 48149 Münster, Germany; and
| | - S. Ludwig
- Molecular Virology, Zentrums für Molekularbiologie der Entzündung, Westfälische Wilhelms-Universität Münster, Von-Esmach-Strasse 56, 48149 Münster, Germany
| | - I. Mazur
- Molecular Virology, Zentrums für Molekularbiologie der Entzündung, Westfälische Wilhelms-Universität Münster, Von-Esmach-Strasse 56, 48149 Münster, Germany
| | - V. Shahin
- *Institute of Physiology II, Westfälische Wilhelms-Universität Münster, Robert-Koch-Strasse 27b, 48149 Münster, Germany; and
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45
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Krishnan VV, Lau EY, Yamada J, Denning DP, Patel SS, Colvin ME, Rexach MF. Intramolecular cohesion of coils mediated by phenylalanine--glycine motifs in the natively unfolded domain of a nucleoporin. PLoS Comput Biol 2008; 4:e1000145. [PMID: 18688269 PMCID: PMC2475668 DOI: 10.1371/journal.pcbi.1000145] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 06/26/2008] [Indexed: 01/23/2023] Open
Abstract
The nuclear pore complex (NPC) provides the sole aqueous conduit for macromolecular exchange between the nucleus and the cytoplasm of cells. Its diffusion conduit contains a size-selective gate formed by a family of NPC proteins that feature large, natively unfolded domains with phenylalanine–glycine repeats (FG domains). These domains of nucleoporins play key roles in establishing the NPC permeability barrier, but little is known about their dynamic structure. Here we used molecular modeling and biophysical techniques to characterize the dynamic ensemble of structures of a representative FG domain from the yeast nucleoporin Nup116. The results showed that its FG motifs function as intramolecular cohesion elements that impart order to the FG domain and compact its ensemble of structures into native premolten globular configurations. At the NPC, the FG motifs of nucleoporins may exert this cohesive effect intermolecularly as well as intramolecularly to form a malleable yet cohesive quaternary structure composed of highly flexible polypeptide chains. Dynamic shifts in the equilibrium or competition between intra- and intermolecular FG motif interactions could facilitate the rapid and reversible structural transitions at the NPC conduit needed to accommodate passing karyopherin–cargo complexes of various shapes and sizes while simultaneously maintaining a size-selective gate against protein diffusion. The nuclear pore complex is a molecular filter that gates macromolecular exchange between the cytoplasm and the nucleoplasm of cells. It contains a size-selective diffusion barrier at its center composed of proteins named FG nucleoporins. These nucleoporins feature large, structurally disordered domains that are highly decorated with phenylalanine–glycine (FG) sequence motifs. The dynamic structure of these disordered FG domains excludes them from classical structural biology analyses such as X-ray crystallography; thus, new approaches are needed to characterize their shape. Here computational and biophysical approaches were used to elucidate the ensemble of structures adopted by the FG domain of a nucleoporin. The analyses showed that the FG motifs function as intramolecular cohesion elements that compact the shape of the FG domain, forcing it to adopt loosely knit globular configurations that are constantly reconfiguring. Within the nuclear pore complex, dozens of these nucleoporin FG domains may stack as loosely knit globules forming a porous sieve that gates molecular diffusion by size exclusion.
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Affiliation(s)
- V. V. Krishnan
- Department of Applied Science, University of California Davis, Davis, California, United States of America
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry, California State University Fresno, Fresno, California, United States of America
| | - Edmond Y. Lau
- Chemistry, Materials, Earth and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Justin Yamada
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Daniel P. Denning
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Samir S. Patel
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael E. Colvin
- Center for Computational Biology, School of Natural Sciences, University of California Merced, Merced, California, United States of America
| | - Michael F. Rexach
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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46
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Wolf C, Mofrad MRK. On the octagonal structure of the nuclear pore complex: insights from coarse-grained models. Biophys J 2008; 95:2073-85. [PMID: 18487299 PMCID: PMC2483776 DOI: 10.1529/biophysj.108.130336] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 04/24/2008] [Indexed: 11/18/2022] Open
Abstract
The basic structure of the nuclear pore complex (NPC), conserved across almost all organisms from yeast to humans, persists in featuring an octagonal symmetry involving the nucleoporins that constitute the NPC ring. In this article, we seek to understand and evaluate the potential biomechanical reasons for this eightfold symmetry. Our analytical investigation shows that the eightfold symmetry maximizes the bending stiffness of each of the eight NPC spokes while our computational analyses identify the most likely deformation modes, frequencies, and associated kinetic energies of the NPC. These modes have energies close to other published findings using membrane analysis of the nuclear membrane pore opening, and deformation states in agreement with experimental observations. A better understanding of NPC mechanics is essential for characterizing the nucleocytoplasmic transport, which has a central importance in cell biology.
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Affiliation(s)
- Christopher Wolf
- Molecular Cell Biomechanics Laboratory, Department of Bioengineering, University of California, Berkeley, California 94720, USA
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47
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Guffanti E, Kittur N, Brodt ZN, Polotsky AJ, Kuokkanen SM, Heller DS, Young SL, Santoro N, Meier UT. Nuclear pore complex proteins mark the implantation window in human endometrium. J Cell Sci 2008; 121:2037-45. [PMID: 18505792 PMCID: PMC2657873 DOI: 10.1242/jcs.030437] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nucleolar channel systems (NCSs) are membranous organelles appearing transiently in the epithelial cell nuclei of postovulatory human endometrium. Their characterization and use as markers for a healthy receptive endometrium have been limited because they are only identifiable by electron microscopy. Here we describe the light microscopic detection of NCSs using immunofluorescence. Specifically, the monoclonal nuclear pore complex antibody 414 shows that NCSs are present in about half of all human endometrial epithelial cells but not in any other cell type, tissue or species. Most nuclei contain only a single NCS of uniform 1 microm diameter indicating a tightly controlled organelle. The composition of NCSs is as unique as their structure; they contain only a subset each of the proteins of nuclear pore complexes, inner nuclear membrane, nuclear lamina and endoplasmic reticulum. Validation of our robust NCS detection method on 95 endometrial biopsies defines a 6-day window, days 19-24 (+/-1) of an idealized 28 day cycle, wherein NCSs occur. Therefore, NCSs precede and overlap with the implantation window and serve as potential markers of uterine receptivity. The immunodetection assay, combined with the hitherto underappreciated prevalence of NCSs, now enables simple screening and further molecular and functional dissection.
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Affiliation(s)
- Elisa Guffanti
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Nupur Kittur
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Z. Nilly Brodt
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Alex J. Polotsky
- Department of Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Satu M. Kuokkanen
- Department of Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Debra S. Heller
- Department of Pathology, UMDNJ – New Jersey Medical School, Newark, NJ 07101, USA
| | - Steven L. Young
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Nanette Santoro
- Department of Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - U. Thomas Meier
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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48
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Gubanova NV, Kiseleva EV. [Dynamics of the annulate lamellae in Drosophila syncytial embryos]. Tsitologiia 2008; 50:681-691. [PMID: 18822788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In eukaryotic cells, mitotic events are controlled by evolutionarily conserved cyclin-dependent kinases (cdk): these kinases phosphorylate cell proteins, which causes structural reorganization of the entire cell. Our recent studies of Drosophila syncytial embryos have demonstrated that cdk1 activity is a key factor that controls nuclear pore complex assembly/disassembly and affects the structure of cytoplasmic pores in the annulate. In this paper, we report a comparative analysis of these cytoplasmic organelles throughout the cell-cycle and throughout the development of Drosophila syncytial embryos. Based on the results obtained, it was presupposed that distribution of annulate lamellae containing cytoplasmic pores could reflect the inactivation of the mitotic kinase cdk1 in Drosophila syncytial embryos.
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49
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Beshr SM. Ultrastructural studies on Icerya Seychellarum seychellarum (Westwood) ovaries (Hemipotera: Margarodidae). Commun Agric Appl Biol Sci 2008; 73:509-520. [PMID: 19226791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The paired ovaries of the scale insect Icerya seychellarum are composed of Large number of telotrophic ovarioles that are devoid of terminal filaments. Each ovariole is subdivided into an apical tropharium (= trophic chamber) and the vitellarium. The tropharium contains 7 trophocytes, while a single oocyte develops in the vitellarium. The tubular paired accessory glands are also been distinguished. This investigation clearly points out the cytotogical features of the ovaries as well as the accessory glands.
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Affiliation(s)
- Sahar M Beshr
- Plant Protection Institute, A.R.C., Sabahia, Alexandria, Egypt
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50
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Abstract
The nuclear pore complex (NPC) is both the major conduit for nucleocytoplasmic trafficking and a platform for organizing macromolecules at the nuclear envelope. We report that yeast Esc1, a non-NPC nuclear envelope protein, is required both for proper assembly of the nuclear basket, a structure extending into the nucleus from the NPC, and for normal NPC localization of the Ulp1 SUMO protease. In esc1Delta cells, Ulp1 and nuclear basket components Nup60 and Mlp1 no longer distribute broadly around the nuclear periphery, but co-localize in a small number of dense-staining perinuclear foci. Loss of Esc1 (or Nup60) alters SUMO conjugate accumulation and enhances ulp1 mutant defects. Similar to previous findings with Mlp1, both Esc1 and Ulp1 help retain unspliced pre-mRNAs in the nucleus. Therefore, these proteins are essential for proper nuclear basket function, which includes mRNA surveillance and regulation of SUMO protein dynamics. The results raise the possibility that NPC-localized protein desumoylation may be a key regulatory event preventing inappropriate pre-mRNA export.
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Affiliation(s)
- Alaron Lewis
- Departments of Cell Biology, Yale University, New Haven, CT 06520, USA
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