151
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Sakiyama Y, Panatala R, Lim RYH. Structural dynamics of the nuclear pore complex. Semin Cell Dev Biol 2017; 68:27-33. [PMID: 28579449 DOI: 10.1016/j.semcdb.2017.05.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 05/29/2017] [Indexed: 11/18/2022]
Abstract
Nuclear pore complexes (NPCs) are the sole conduits that facilitate macromolecular exchange between the nucleus and cytosol. Recent advancements have led to a more highly resolved NPC structure. However, our understanding of the NPC modus operandi that facilitates transport selectivity, and speed, of diverse cargoes remains incomplete. For the most part, assorted cargo-complexes of different sizes traverse the NPC central channel in milliseconds, yet little is known about the nanoscopic movements of its barrier-forming Phe-Gly nucleoporins (FG Nups) and related sub-structures at transport-relevant time and length scales. Here, we discuss how dynamic FG Nup behavior may confer NPCs with an effective permeability barrier according to the functional needs of the cell. Moreover, we postulate that structural flexibility might resonate throughout the NPC framework from the cytoplasmic filaments to the nuclear basket.
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Affiliation(s)
- Yusuke Sakiyama
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Radhakrishnan Panatala
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland.
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152
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Chase AR, Laudermilch E, Schlieker C. Torsin ATPases: Harnessing Dynamic Instability for Function. Front Mol Biosci 2017; 4:29. [PMID: 28553638 PMCID: PMC5425593 DOI: 10.3389/fmolb.2017.00029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022] Open
Abstract
Torsins are essential, disease-relevant AAA+ (ATPases associated with various cellular activities) proteins residing in the endoplasmic reticulum and perinuclear space, where they are implicated in a variety of cellular functions. Recently, new structural and functional details about Torsins have emerged that will have a profound influence on unraveling the precise mechanistic details of their yet-unknown mode of action in the cell. While Torsins are phylogenetically related to Clp/HSP100 proteins, they exhibit comparatively weak ATPase activities, which are tightly controlled by virtue of an active site complementation through accessory cofactors. This control mechanism is offset by a TorsinA mutation implicated in the severe movement disorder DYT1 dystonia, suggesting a critical role for the functional Torsin-cofactor interplay in vivo. Notably, TorsinA lacks aromatic pore loops that are both conserved and critical for the processive unfolding activity of Clp/HSP100 proteins. Based on these distinctive yet defining features, we discuss how the apparent dynamic nature of the Torsin-cofactor system can inform emerging models and hypotheses for Torsin complex formation and function. Specifically, we propose that the dynamic assembly and disassembly of the Torsin/cofactor system is a critical property that is required for Torsins' functional roles in nuclear trafficking and nuclear pore complex assembly or homeostasis that merit further exploration. Insights obtained from these future studies will be a valuable addition to our understanding of disease etiology of DYT1 dystonia.
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Affiliation(s)
- Anna R Chase
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT, USA
| | - Ethan Laudermilch
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT, USA
| | - Christian Schlieker
- Department of Molecular Biophysics and Biochemistry, Yale UniversityNew Haven, CT, USA.,Department of Cell Biology, Yale School of MedicineNew Haven, CT, USA
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153
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Functional implication of the common evolutionary origin of nuclear pore complex and endomembrane management systems. Semin Cell Dev Biol 2017; 68:10-17. [PMID: 28473267 DOI: 10.1016/j.semcdb.2017.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 11/24/2022]
Abstract
Nuclear pore complexes (NPCs) are the sole gateway between the cytoplasm and the nucleus serving both as stringent permeability barrier and active transporters between the two compartments of eukaryotic cells. Complete mechanistic understanding of how these two functions are implemented within one and the same transport machine has not been attained to date. Based on several lines of structural evidence, a hypothesis was proposed postulating that NPCs shares common evolutionary origin with other intracellular systems responsible for active management of endomembranes. In this review we attempt to summarize the evidence supporting this hypothesis. The structural data obtained so far is evaluated and supplemented with the analysis of the functional evidence. Based on this analysis, a model is proposed which integrates the knowledge from the field of NPC function with that obtained from other endomembrane management systems in an attempt to shed new light on the mechanism of the NPC active transport.
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154
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Duclos C, Lavoie C, Denault JB. Caspases rule the intracellular trafficking cartel. FEBS J 2017; 284:1394-1420. [PMID: 28371378 DOI: 10.1111/febs.14071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 03/17/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022]
Abstract
During apoptosis, caspases feast on several hundreds of cellular proteins to orchestrate rapid cellular demise. Indeed, caspases are known to get a taste of every cellular process in one way or another, activating some, but most often shutting them down. Thus, it is not surprising that caspases proteolyze proteins involved in intracellular trafficking with particularly devastating consequences for this important process. This review article focuses on how caspases target the machinery responsible for smuggling goods within and outside the cell.
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Affiliation(s)
- Catherine Duclos
- Institut de Pharmacologie de Sherbrooke, Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC, Canada
| | - Christine Lavoie
- Institut de Pharmacologie de Sherbrooke, Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC, Canada
| | - Jean-Bernard Denault
- Institut de Pharmacologie de Sherbrooke, Department of Pharmacology-Physiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC, Canada
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155
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Abstract
Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.
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Affiliation(s)
- Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; ,
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; , .,Howard Hughes Medical Institute, Pasadena, California 91125
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156
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Lord CL, Ospovat O, Wente SR. Nup100 regulates Saccharomyces cerevisiae replicative life span by mediating the nuclear export of specific tRNAs. RNA (NEW YORK, N.Y.) 2017; 23:365-377. [PMID: 27932586 PMCID: PMC5311497 DOI: 10.1261/rna.057612.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/29/2016] [Indexed: 06/06/2023]
Abstract
Nuclear pore complexes (NPCs), which are composed of nucleoporins (Nups) and regulate transport between the nucleus and cytoplasm, significantly impact the replicative life span (RLS) of Saccharomyces cerevisiae We previously reported that deletion of the nonessential gene NUP100 increases RLS, although the molecular basis for this effect was unknown. In this study, we find that nuclear tRNA accumulation contributes to increased longevity in nup100Δ cells. Fluorescence in situ hybridization (FISH) experiments demonstrate that several specific tRNAs accumulate in the nuclei of nup100Δ mutants. Protein levels of the transcription factor Gcn4 are increased when NUP100 is deleted, and GCN4 is required for the elevated life spans of nup100Δ mutants, similar to other previously described tRNA export and ribosomal mutants. Northern blots indicate that tRNA splicing and aminoacylation are not significantly affected in nup100Δ cells, suggesting that Nup100 is largely required for nuclear export of mature, processed tRNAs. Distinct tRNAs accumulate in the nuclei of nup100Δ and msn5Δ mutants, while Los1-GFP nucleocytoplasmic shuttling is unaffected by Nup100. Thus, we conclude that Nup100 regulates tRNA export in a manner distinct from Los1 or Msn5. Together, these experiments reveal a novel Nup100 role in the tRNA life cycle that impacts the S. cerevisiae life span.
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Affiliation(s)
- Christopher L Lord
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240, USA
| | - Ophir Ospovat
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240, USA
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37240, USA
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157
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Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. Structure 2017; 25:434-445. [PMID: 28162953 DOI: 10.1016/j.str.2017.01.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/06/2017] [Accepted: 01/19/2017] [Indexed: 02/06/2023]
Abstract
The membrane ring that equatorially circumscribes the nuclear pore complex (NPC) in the perinuclear lumen of the nuclear envelope is composed largely of Pom152 in yeast and its ortholog Nup210 (or Gp210) in vertebrates. Here, we have used a combination of negative-stain electron microscopy, nuclear magnetic resonance, and small-angle X-ray scattering methods to determine an integrative structure of the ∼120 kDa luminal domain of Pom152. Our structural analysis reveals that the luminal domain is formed by a flexible string-of-pearls arrangement of nine repetitive cadherin-like Ig-like domains, indicating an evolutionary connection between NPCs and the cell adhesion machinery. The 16 copies of Pom152 known to be present in the yeast NPC are long enough to form the observed membrane ring, suggesting how interactions between Pom152 molecules help establish and maintain the NPC architecture.
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158
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Kennedy MB. Biochemistry and neuroscience: the twain need to meet. Curr Opin Neurobiol 2017; 43:79-86. [PMID: 28160757 DOI: 10.1016/j.conb.2017.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/12/2017] [Accepted: 01/12/2017] [Indexed: 10/20/2022]
Abstract
Neuroscience has come to mean the study of electrophysiology of neurons and synapses, micro and macro-scale neuroanatomy, and the functional organization of brain areas. The molecular axis of the field, as reflected in textbooks, often includes only descriptions of the structure and function of individual channels and receptor proteins, and the extracellular signals that guide development and repair. Studies of cytosolic 'molecular machines', large assemblies of proteins that orchestrate regulation of neuronal functions, have been neglected. However, a complete understanding of brain function that will enable new strategies for treatment of the most intractable neural disorders will require that in vitro biochemical studies of molecular machines be reintegrated into the field of neuroscience.
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Affiliation(s)
- Mary B Kennedy
- Division of Biology and Biochemical Engineering, Mail Code 216-76, California Institute of Technology, Pasadena, CA 91125, United States.
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159
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Raices M, D'Angelo MA. Nuclear pore complexes and regulation of gene expression. Curr Opin Cell Biol 2017; 46:26-32. [PMID: 28088069 DOI: 10.1016/j.ceb.2016.12.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/09/2016] [Accepted: 12/21/2016] [Indexed: 12/31/2022]
Abstract
Nuclear pore complexes (NPCs), are large multiprotein channels that penetrate the nuclear envelope connecting the nucleus to the cytoplasm. Accumulating evidence shows that besides their main role in regulating the exchange of molecules between these two compartments, NPCs and their components also play important transport-independent roles, including gene expression regulation, chromatin organization, DNA repair, RNA processing and quality control, and cell cycle control. Here, we will describe the recent findings about the role of these structures in the regulation of gene expression.
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Affiliation(s)
- Marcela Raices
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, 10901 N. Torrey Pines Road, La Jolla, 92037 CA, United States
| | - Maximiliano A D'Angelo
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, 10901 N. Torrey Pines Road, La Jolla, 92037 CA, United States.
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160
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Cellular Reorganization during Mitotic Entry. Trends Cell Biol 2017; 27:26-41. [DOI: 10.1016/j.tcb.2016.07.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/14/2016] [Accepted: 07/18/2016] [Indexed: 12/27/2022]
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161
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Beck M, Hurt E. The nuclear pore complex: understanding its function through structural insight. Nat Rev Mol Cell Biol 2016; 18:73-89. [PMID: 27999437 DOI: 10.1038/nrm.2016.147] [Citation(s) in RCA: 423] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. They are large macromolecular assemblies with a complex composition and diverse functions. Apart from facilitating nucleocytoplasmic transport, NPCs are involved in chromatin organization, the regulation of gene expression and DNA repair. Understanding the molecular mechanisms underlying these functions has been hampered by a lack of structural knowledge about the NPC. The recent convergence of crystallographic and biochemical in vitro analysis of nucleoporins (NUPs), the components of the NPC, with cryo-electron microscopic imaging of the entire NPC in situ has provided first pseudo-atomic view of its central core and revealed that an unexpected network of short linear motifs is an important spatial organization principle. These breakthroughs have transformed the way we understand NPC structure, and they provide an important base for functional investigations, including the elucidation of the molecular mechanisms underlying clinically manifested mutations of the nucleocytoplasmic transport system.
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Affiliation(s)
- Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg D-69117, Germany
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, INF328, Heidelberg D-69120, Germany
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162
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Orlov I, Myasnikov AG, Andronov L, Natchiar SK, Khatter H, Beinsteiner B, Ménétret JF, Hazemann I, Mohideen K, Tazibt K, Tabaroni R, Kratzat H, Djabeur N, Bruxelles T, Raivoniaina F, Pompeo LD, Torchy M, Billas I, Urzhumtsev A, Klaholz BP. The integrative role of cryo electron microscopy in molecular and cellular structural biology. Biol Cell 2016; 109:81-93. [PMID: 27730650 DOI: 10.1111/boc.201600042] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 01/10/2023]
Abstract
After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo-EM) is now heading off at unprecedented speed towards high-resolution analysis of biological objects of various sizes. This 'revolution in resolution' is happening largely thanks to new developments of new-generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo-EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo-EM in synergy with other methods such as X-ray crystallography, fluorescence imaging or focussed-ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi-scale and multi-resolution approaches allow integrating molecular and cellular levels when applied to purified or in situ macromolecular complexes, thus illustrating the trend of the field towards cellular structural biology.
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Affiliation(s)
- Igor Orlov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexander G Myasnikov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Heena Khatter
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Brice Beinsteiner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Jean-François Ménétret
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Kareem Mohideen
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Karima Tazibt
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Rachel Tabaroni
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Hanna Kratzat
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Nadia Djabeur
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Tatiana Bruxelles
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Finaritra Raivoniaina
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Lorenza di Pompeo
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Morgan Torchy
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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163
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Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell 2016; 167:1215-1228.e25. [PMID: 27839866 DOI: 10.1016/j.cell.2016.10.028] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/20/2016] [Accepted: 10/14/2016] [Indexed: 12/28/2022]
Abstract
The last steps in mRNA export and remodeling are performed by the Nup82 complex, a large conserved assembly at the cytoplasmic face of the nuclear pore complex (NPC). By integrating diverse structural data, we have determined the molecular architecture of the native Nup82 complex at subnanometer precision. The complex consists of two compositionally identical multiprotein subunits that adopt different configurations. The Nup82 complex fits into the NPC through the outer ring Nup84 complex. Our map shows that this entire 14-MDa Nup82-Nup84 complex assembly positions the cytoplasmic mRNA export factor docking sites and messenger ribonucleoprotein (mRNP) remodeling machinery right over the NPC's central channel rather than on distal cytoplasmic filaments, as previously supposed. We suggest that this configuration efficiently captures and remodels exporting mRNP particles immediately upon reaching the cytoplasmic side of the NPC.
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Affiliation(s)
| | - Seung Joong Kim
- Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Paula Upla
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Riccardo Pellarin
- Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, 75015 Paris, France
| | - Michael Gagnon
- Département de Biochimie et Médecine Moléculaire, University of Montréal, Montréal, QC H3C3J7, Canada
| | - Ilan E Chemmama
- Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Ilona Nudelman
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Rosemary Williams
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - William J Rice
- Simons Electron Microscopy Center at New York Structural Biology Center, New York, NY 10027, USA
| | - David L Stokes
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, University of Montréal, Montréal, QC H3C3J7, Canada
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
| | - Andrej Sali
- Departments of Bioengineering and Therapeutic Sciences and Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
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164
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Laudermilch E, Tsai PL, Graham M, Turner E, Zhao C, Schlieker C. Dissecting Torsin/cofactor function at the nuclear envelope: a genetic study. Mol Biol Cell 2016; 27:3964-3971. [PMID: 27798237 PMCID: PMC5156537 DOI: 10.1091/mbc.e16-07-0511] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/18/2016] [Accepted: 10/20/2016] [Indexed: 01/12/2023] Open
Abstract
Torsins are essential, disease-relevant ATPases, but their function is unknown. Monitoring of nuclear envelope morphology after deletion of multiple Torsins or their cofactors reveals a robust inner nuclear membrane–blebbing phenotype in HeLa cells. Nucleoporins and ubiquitin are defining molecular components of these omega-shaped blebs. The human genome encodes four Torsin ATPases, the functions of which are poorly understood. In this study, we use CRISPR/Cas9 engineering to delete all four Torsin ATPases individually and in combination. Using nuclear envelope (NE) blebbing as a phenotypic measure, we establish a direct correlation between the number of inactivated Torsin alleles and the occurrence of omega-shaped herniations within the lumen of the NE. A similar, although not identical, redundancy is observed for LAP1 and LULL1, which serve as regulatory cofactors for a subset of Torsin ATPases. Unexpectedly, deletion of Tor2A in a TorA/B/3A-deficient background results in a stark increase of bleb formation, even though Tor2A does not respond to LAP1/LULL1 stimulation. The robustness of the observed phenotype in Torsin-deficient cells enables a structural analysis via electron microscopy tomography and a compositional analysis via immunogold labeling. Ubiquitin and nucleoporins were identified as distinctively localizing components of the omega-shaped bleb structure. These findings suggest a functional link between the Torsin/cofactor system and NE/nuclear pore complex biogenesis or homeostasis and establish a Torsin-deficient cell line as a valuable experimental platform with which to decipher Torsin function.
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Affiliation(s)
- Ethan Laudermilch
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Pei-Ling Tsai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Morven Graham
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | - Elizabeth Turner
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Chenguang Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Christian Schlieker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 .,Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
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165
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Garcia A, Rodriguez Matas JF, Raimondi MT. Modeling of the mechano-chemical behaviour of the nuclear pore complex: current research and perspectives. Integr Biol (Camb) 2016; 8:1011-1021. [PMID: 27713975 PMCID: PMC5166569 DOI: 10.1039/c6ib00153j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 09/19/2016] [Indexed: 12/30/2022]
Abstract
Recent evidence suggests that mechanical deformation of the cell nucleus regulates the nuclear import of the transcriptional activators of genes involved in primary physiological cell responses such as stem cell differentiation. In addition, this nuclear mechanosensing response is de-regulated in pathological states, such as cancer and neurodegeneration. One hypothesis that could greatly advance the field is that the deformation of the nuclear envelope activates nuclear pore complexes through a direct mechanical link. The understanding of this possible mechanism for nuclear pore complex stretch-activation entails studying the mechanical connection of this complex to the nuclear envelope at the nanoscale. The nanomechanics of the nuclear pore complex is thus emerging as a novel research field, bridging nanoscience with nanotechnology. This review examines the frontier of research methodologies that are potentially useful for building a computational model of this interaction. This includes, for example, electron tomography to assess the geometrical features of the nuclear pore complex and nanoindentation to estimate its mechanical properties and that of the nuclear envelope. In order to summarize the state-of-the-art and perspectives in the field of NPC nanomechanics, this review covers highly interdisciplinary experimental and theoretical research methodologies pertaining to the fields of physics, chemistry, biology, materials and mechanics.
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Affiliation(s)
- Alberto Garcia
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza L. da Vinci, 32, 20133 Milan, Italy.
| | - Jose F Rodriguez Matas
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza L. da Vinci, 32, 20133 Milan, Italy.
| | - Manuela T Raimondi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza L. da Vinci, 32, 20133 Milan, Italy.
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166
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Beck M, Baumeister W. Cryo-Electron Tomography: Can it Reveal the Molecular Sociology of Cells in Atomic Detail? Trends Cell Biol 2016; 26:825-837. [PMID: 27671779 DOI: 10.1016/j.tcb.2016.08.006] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
Traditionally, macromolecular structure determination is performed ex situ, that is, with purified materials. But, there are strong incentives to develop approaches to study them in situ in their native functional context. In recent years, cryo-electron tomography (cryo-ET) has emerged as a powerful method for visualizing the molecular organization of unperturbed cellular landscapes with the potential to attain near-atomic resolution. Here, we review recent work on several macromolecular assemblies, demonstrating the power of in situ studies. We also highlight technical challenges and discuss ways to meet them.
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Affiliation(s)
- Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried (Planegg), Germany.
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167
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Hurley JH, Nogales E. Next-generation electron microscopy in autophagy research. Curr Opin Struct Biol 2016; 41:211-216. [PMID: 27614295 DOI: 10.1016/j.sbi.2016.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/25/2016] [Accepted: 08/25/2016] [Indexed: 12/24/2022]
Abstract
Autophagy is the process whereby cytosol, organelles, and inclusions are taken up in a double-membrane vesicle known as the autophagosome, and transported to the lysosome for destruction and recycling. Electron microscopy (EM) led to the discovery of autophagy in the 1950s and has been a central part of its characterization ever since. New capabilities in single particle EM studies of the autophagy machinery are beginning to provide exciting insights into the mechanisms of autophagosome initiation, growth, and substrate targeting. These include EM structures at various resolutions of part of the Atg1 protein kinase complex and all of the class III phosphatidylinositol 3-phosphate complex I that initiate autophagy; the mTORC1 complex that regulates autophagy initiation; the Ape1 particle, a major substrate for selective autophagy in yeast; and p62, a mammalian selective autophagy adaptor. Equally exciting are the prospects for increased resolution and insight into autophagosome formation in cells from advances in cryo-EM tomography and focused ion beam-scanning electron microscopy (FIB-SEM). This review considers recent accomplishments, prospects for progress, and remaining obstacles that still need to be overcome.
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Affiliation(s)
- James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.
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168
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Apelt L, Knockenhauer KE, Leksa NC, Benlasfer N, Schwartz TU, Stelzl U. Systematic Protein-Protein Interaction Analysis Reveals Intersubcomplex Contacts in the Nuclear Pore Complex. Mol Cell Proteomics 2016; 15:2594-606. [PMID: 27194810 PMCID: PMC4974338 DOI: 10.1074/mcp.m115.054627] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 05/17/2016] [Indexed: 11/06/2022] Open
Abstract
The nuclear pore complex (NPC) enables transport across the nuclear envelope. It is one of the largest multiprotein assemblies in the cell, built from about 30 proteins called nucleoporins (Nups), organized into distinct subcomplexes. Structure determination of the NPC is a major research goal. The assembled ∼40-112 MDa NPC can be visualized by cryoelectron tomography (cryo-ET), while Nup subcomplexes are studied crystallographically. Docking the crystal structures into the cryo-ET maps is difficult because of limited resolution. Further, intersubcomplex contacts are not well characterized. Here, we systematically investigated direct interactions between Nups. In a comprehensive, structure-based, yeast two-hybrid interaction matrix screen, we mapped protein-protein interactions in yeast and human. Benchmarking against crystallographic and coaffinity purification data from the literature demonstrated the high coverage and accuracy of the data set. Novel intersubcomplex interactions were validated biophysically in microscale thermophoresis experiments and in intact cells through protein fragment complementation. These intersubcomplex interaction data provide direct experimental evidence toward possible structural arrangements of architectural elements within the assembled NPC, or they may point to assembly intermediates. Our data favors an assembly model in which major architectural elements of the NPC, notably the Y-complex, exist in different structural contexts within the scaffold.
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Affiliation(s)
- Luise Apelt
- From the ‡Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | | | - Nina C Leksa
- §Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge
| | - Nouhad Benlasfer
- From the ‡Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany
| | - Thomas U Schwartz
- §Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge
| | - Ulrich Stelzl
- From the ‡Otto-Warburg Laboratory, Max-Planck Institute for Molecular Genetics (MPIMG), Berlin, Germany; ¶Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Graz, Austria
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169
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Ben-Yishay R, Ashkenazy AJ, Shav-Tal Y. Dynamic Encounters of Genes and Transcripts with the Nuclear Pore. Trends Genet 2016; 32:419-431. [DOI: 10.1016/j.tig.2016.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 04/20/2016] [Indexed: 01/04/2023]
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170
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Hoelz A, Glavy JS, Beck M. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up. Nat Struct Mol Biol 2016; 23:624-30. [PMID: 27273515 DOI: 10.1038/nsmb.3244] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/13/2016] [Indexed: 01/16/2023]
Abstract
Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, owing to its sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom-up approaches rely on biochemical interaction studies and crystal-structure determination of NPC components, top-down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, thereby bridging the resolution gap from the higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function.
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Affiliation(s)
- André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Joseph S Glavy
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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171
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Soheilypour M, Peyro M, Jahed Z, Mofrad MRK. On the Nuclear Pore Complex and Its Roles in Nucleo-Cytoskeletal Coupling and Mechanobiology. Cell Mol Bioeng 2016. [DOI: 10.1007/s12195-016-0443-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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172
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173
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Jahed Z, Soheilypour M, Peyro M, Mofrad MRK. The LINC and NPC relationship – it's complicated! J Cell Sci 2016; 129:3219-29. [DOI: 10.1242/jcs.184184] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT
The genetic information of eukaryotic cells is enclosed within a double-layered nuclear envelope, which comprises an inner and outer nuclear membrane. Several transmembrane proteins locate to the nuclear envelope; however, only two integral protein complexes span the nuclear envelope and connect the inside of the nucleus to the cytoplasm. The nuclear pore complex (NPC) acts as a gateway for molecular exchange between the interior of the nucleus and the cytoplasm, whereas so-called LINC complexes physically link the nucleoskeleton and the cytoskeleton. In this Commentary, we will discuss recent studies that have established direct functional associations between these two complexes. The assembly of NPCs and their even distribution throughout the nuclear envelope is dependent on components of the LINC complex. Additionally, LINC complex formation is dependent on the successful localization of inner nuclear membrane components of LINC complexes and their transport through the NPC. Furthermore, the architecture of the nuclear envelope depends on both protein complexes. Finally, we will present recent evidence showing that LINC complexes can affect nucleo-cytoplasmic transport through the NPC, further highlighting the importance of understanding the associations of these essential complexes at the nuclear envelope.
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Affiliation(s)
- Zeinab Jahed
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Mohammad Soheilypour
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Mohaddeseh Peyro
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
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174
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Weberruss M, Antonin W. Perforating the nuclear boundary – how nuclear pore complexes assemble. J Cell Sci 2016; 129:4439-4447. [DOI: 10.1242/jcs.194753] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
ABSTRACT
The nucleus is enclosed by the nuclear envelope, a double membrane which creates a selective barrier between the cytoplasm and the nuclear interior. Its barrier and transport characteristics are determined by nuclear pore complexes (NPCs) that are embedded within the nuclear envelope, and control molecular exchange between the cytoplasm and nucleoplasm. In this Commentary, we discuss the biogenesis of these huge protein assemblies from approximately one thousand individual proteins. We will summarize current knowledge about distinct assembly modes in animal cells that are characteristic for different cell cycle phases and their regulation.
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Affiliation(s)
- Marion Weberruss
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
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