1
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Lin J, Sumara I. Cytoplasmic nucleoporin assemblage: the cellular artwork in physiology and disease. Nucleus 2024; 15:2387534. [PMID: 39135336 PMCID: PMC11323873 DOI: 10.1080/19491034.2024.2387534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/16/2024] Open
Abstract
Nucleoporins, essential proteins building the nuclear pore, are pivotal for ensuring nucleocytoplasmic transport. While traditionally confined to the nuclear envelope, emerging evidence indicates their presence in various cytoplasmic structures, suggesting potential non-transport-related roles. This review consolidates findings on cytoplasmic nucleoporin assemblies across different states, including normal physiological conditions, stress, and pathology, exploring their structural organization, formation dynamics, and functional implications. We summarize the current knowledge and the latest concepts on the regulation of nucleoporin homeostasis, aiming to enhance our understanding of their unexpected roles in physiological and pathological processes.
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Affiliation(s)
- Junyan Lin
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
| | - Izabela Sumara
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology (IGBMC), Illkirch, France
- Centre National de la Recherche Scientifique UMR 7104, Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale U964, Strasbourg, France
- Université de Strasbourg, Strasbourg, France
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2
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Nageshan RK, Krogan N, Cooper JP. Parallel genetic screens identify nuclear envelope homeostasis as a key determinant of telomere entanglement resolution in fission yeast. G3 (BETHESDA, MD.) 2024; 14:jkae078. [PMID: 38657142 PMCID: PMC11228871 DOI: 10.1093/g3journal/jkae078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
In fission yeast lacking the telomere binding protein, Taz1, replication forks stall at telomeres, triggering deleterious downstream events. Strand invasion from one taz1Δ telomeric stalled fork to another on a separate (nonsister) chromosome leads to telomere entanglements, which are resolved in mitosis at 32°C; however, entanglement resolution fails at ≤20°C, leading to cold-specific lethality. Previously, we found that loss of the mitotic function of Rif1, a conserved DNA replication and repair factor, suppresses cold sensitivity by promoting resolution of entanglements without affecting entanglement formation. To understand the underlying pathways of mitotic entanglement resolution, we performed a series of genome-wide synthetic genetic array screens to generate a comprehensive list of genetic interactors of taz1Δ and rif1Δ. We modified a previously described screening method to ensure that the queried cells were kept in log phase growth. In addition to recapitulating previously identified genetic interactions, we find that loss of genes encoding components of the nuclear pore complex (NPC) promotes telomere disentanglement and suppresses taz1Δ cold sensitivity. We attribute this to more rapid anaphase midregion nuclear envelope (NE) breakdown in the absence of these NPC components. Loss of genes involved in lipid metabolism reverses the ability of rif1+ deletion to suppress taz1Δ cold sensitivity, again pinpointing NE modulation. A rif1+ separation-of-function mutant that specifically loses Rif1's mitotic functions yields similar genetic interactions. Genes promoting membrane fluidity were enriched in a parallel taz1+ synthetic lethal screen at permissive temperature, cementing the idea that the cold specificity of taz1Δ lethality stems from altered NE homeostasis.
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Affiliation(s)
- Rishi Kumar Nageshan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave, Aurora, CO 80045, USA
- Former address: Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, NCI, NIH, Bethesda, MD 20892, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, 308D, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Julia Promisel Cooper
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, 12801 E. 17th Ave, Aurora, CO 80045, USA
- Former address: Telomere Biology Laboratory, Laboratory of Biochemistry and Molecular Biology, NCI, NIH, Bethesda, MD 20892, USA
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3
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Penzo A, Palancade B. Puzzling out nuclear pore complex assembly. FEBS Lett 2023; 597:2705-2727. [PMID: 37548888 DOI: 10.1002/1873-3468.14713] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Nuclear pore complexes (NPCs) are sophisticated multiprotein assemblies embedded within the nuclear envelope and controlling the exchanges of molecules between the cytoplasm and the nucleus. In this review, we summarize the mechanisms by which these elaborate complexes are built from their subunits, the nucleoporins, based on our ever-growing knowledge of NPC structural organization and on the recent identification of additional features of this process. We present the constraints faced during the production of nucleoporins, their gathering into oligomeric complexes, and the formation of NPCs within nuclear envelopes, and review the cellular strategies at play, from co-translational assembly to the enrolment of a panel of cofactors. Remarkably, the study of NPCs can inform our perception of the biogenesis of multiprotein complexes in general - and vice versa.
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Affiliation(s)
- Arianna Penzo
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
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4
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Veldsink AC, Gallardo P, Lusk CP, Veenhoff LM. Changing the guard-nuclear pore complex quality control. FEBS Lett 2023; 597:2739-2749. [PMID: 37715940 DOI: 10.1002/1873-3468.14739] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/18/2023]
Abstract
The integrity of the nuclear envelope depends on the function of nuclear pore complexes (NPCs), transport channels that control macromolecular traffic between the nucleus and cytosol. The central importance of NPCs suggests the existence of quality control (QC) mechanisms that oversee their assembly and function. In this perspective, we emphasize the challenges associated with NPC assembly and the need for QC mechanisms that operate at various stages of an NPC's life. This includes cytosolic preassembly QC that helps enforce key nucleoporin-nucleoporin interactions and their ultimate stoichiometry in the NPC in addition to mechanisms that monitor aberrant fusion of the inner and outer nuclear membranes. Furthermore, we discuss whether and how these QC mechanisms may operate to sense faulty mature NPCs to facilitate their repair or removal. The so far uncovered mechanisms for NPC QC provide fertile ground for future research that not only benefits a better understanding of the vital role that NPCs play in cellular physiology but also how loss of NPC function and/or these QC mechanisms might be an input to aging and disease.
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Affiliation(s)
- Annemiek C Veldsink
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - Paola Gallardo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, CT, New Haven, USA
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, Groningen, 9713 AV, The Netherlands
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5
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Amm I, Weberruss M, Hellwig A, Schwarz J, Tatarek-Nossol M, Lüchtenborg C, Kallas M, Brügger B, Hurt E, Antonin W. Distinct domains in Ndc1 mediate its interaction with the Nup84 complex and the nuclear membrane. J Cell Biol 2023; 222:e202210059. [PMID: 37154843 PMCID: PMC10165475 DOI: 10.1083/jcb.202210059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 01/31/2023] [Accepted: 03/17/2023] [Indexed: 05/10/2023] Open
Abstract
Nuclear pore complexes (NPCs) are embedded in the nuclear envelope and built from ∼30 different nucleoporins (Nups) in multiple copies, few are integral membrane proteins. One of these transmembrane nucleoporins, Ndc1, is thought to function in NPC assembly at the fused inner and outer nuclear membranes. Here, we show a direct interaction of Ndc1's transmembrane domain with Nup120 and Nup133, members of the pore membrane coating Y-complex. We identify an amphipathic helix in Ndc1's C-terminal domain binding highly curved liposomes. Upon overexpression, this amphipathic motif is toxic and dramatically alters the intracellular membrane organization in yeast. Ndc1's amphipathic motif functionally interacts with related motifs in the C-terminus of the nucleoporins Nup53 and Nup59, important for pore membrane binding and interconnecting NPC modules. The essential function of Ndc1 can be suppressed by deleting the amphipathic helix from Nup53. Our data indicate that nuclear membrane and presumably NPC biogenesis depends on a balanced ratio between amphipathic motifs in diverse nucleoporins.
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Affiliation(s)
- Ingo Amm
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marion Weberruss
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Andrea Hellwig
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), University of Heidelberg, Heidelberg, Germany
| | - Johannes Schwarz
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Christian Lüchtenborg
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Martina Kallas
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
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6
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Borah S, Dhanasekaran K, Kumar S. The LEM-ESCRT toolkit: Repair and maintenance of the nucleus. Front Cell Dev Biol 2022; 10:989217. [PMID: 36172278 PMCID: PMC9512039 DOI: 10.3389/fcell.2022.989217] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/24/2022] [Indexed: 12/04/2022] Open
Abstract
The eukaryotic genome is enclosed in a nuclear envelope that protects it from potentially damaging cellular activities and physically segregates transcription and translation.Transport across the NE is highly regulated and occurs primarily via the macromolecular nuclear pore complexes.Loss of nuclear compartmentalization due to defects in NPC function and NE integrity are tied to neurological and ageing disorders like Alzheimer’s, viral pathogenesis, immune disorders, and cancer progression.Recent work implicates inner-nuclear membrane proteins of the conserved LEM domain family and the ESCRT machinery in NE reformation during cell division and NE repair upon rupture in migrating cancer cells, and generating seals over defective NPCs. In this review, we discuss the recent in-roads made into defining the molecular mechanisms and biochemical networks engaged by LEM and many other integral inner nuclear membrane proteins to preserve the nuclear barrier.
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Affiliation(s)
- Sapan Borah
- National Institute of Immunohaematology, Mumbai, Maharashtra, India
- *Correspondence: Sapan Borah, ; Karthigeyan Dhanasekaran, ; Santosh Kumar,
| | - Karthigeyan Dhanasekaran
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
- *Correspondence: Sapan Borah, ; Karthigeyan Dhanasekaran, ; Santosh Kumar,
| | - Santosh Kumar
- National Centre for Cell Science, Pune, Maharashtra, India
- *Correspondence: Sapan Borah, ; Karthigeyan Dhanasekaran, ; Santosh Kumar,
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7
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Kralt A, Wojtynek M, Fischer JS, Agote-Aran A, Mancini R, Dultz E, Noor E, Uliana F, Tatarek-Nossol M, Antonin W, Onischenko E, Medalia O, Weis K. An amphipathic helix in Brl1 is required for nuclear pore complex biogenesis in S. cerevisiae. eLife 2022; 11:78385. [PMID: 36000978 PMCID: PMC9402233 DOI: 10.7554/elife.78385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/03/2022] [Indexed: 12/28/2022] Open
Abstract
The nuclear pore complex (NPC) is the central portal for macromolecular exchange between the nucleus and cytoplasm. In all eukaryotes, NPCs assemble into an intact nuclear envelope (NE) during interphase, but the process of NPC biogenesis remains poorly characterized. Furthermore, little is known about how NPC assembly leads to the fusion of the outer and inner NE, and no factors have been identified that could trigger this event. Here, we characterize the transmembrane protein Brl1 as an NPC assembly factor required for NE fusion in budding yeast. Brl1 preferentially associates with NPC assembly intermediates and its depletion halts NPC biogenesis, leading to NE herniations that contain inner and outer ring nucleoporins but lack the cytoplasmic export platform. Furthermore, we identify an essential amphipathic helix in the luminal domain of Brl1 that mediates interactions with lipid bilayers. Mutations in this amphipathic helix lead to NPC assembly defects, and cryo-electron tomography analyses reveal multilayered herniations of the inner nuclear membrane with NPC-like structures at the neck, indicating a failure in NE fusion. Taken together, our results identify a role for Brl1 in NPC assembly and suggest a function of its amphipathic helix in mediating the fusion of the inner and outer nuclear membranes.
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Affiliation(s)
- Annemarie Kralt
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Wojtynek
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland.,Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Jonas S Fischer
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Arantxa Agote-Aran
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Roberta Mancini
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elisa Dultz
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Federico Uliana
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Evgeny Onischenko
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zürich, Switzerland
| | - Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
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8
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Dultz E, Wojtynek M, Medalia O, Onischenko E. The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth. Cells 2022; 11:1456. [PMID: 35563762 PMCID: PMC9100368 DOI: 10.3390/cells11091456] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/01/2023] Open
Abstract
Nuclear pore complexes (NPCs) are the only transport channels that cross the nuclear envelope. Constructed from ~500-1000 nucleoporin proteins each, they are among the largest macromolecular assemblies in eukaryotic cells. Thanks to advances in structural analysis approaches, the construction principles and architecture of the NPC have recently been revealed at submolecular resolution. Although the overall structure and inventory of nucleoporins are conserved, NPCs exhibit significant compositional and functional plasticity even within single cells and surprising variability in their assembly pathways. Once assembled, NPCs remain seemingly unexchangeable in post-mitotic cells. There are a number of as yet unresolved questions about how the versatility of NPC assembly and composition is established, how cells monitor the functional state of NPCs or how they could be renewed. Here, we review current progress in our understanding of the key aspects of NPC architecture and lifecycle.
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Affiliation(s)
- Elisa Dultz
- Institute of Biochemistry, Department of Biology, ETHZ Zurich, 8093 Zurich, Switzerland;
| | - Matthias Wojtynek
- Institute of Biochemistry, Department of Biology, ETHZ Zurich, 8093 Zurich, Switzerland;
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland;
| | - Evgeny Onischenko
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway
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9
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Vitale J, Khan A, Neuner A, Schiebel E. A perinuclear α-helix with amphipathic features in Brl1 promotes NPC assembly. Mol Biol Cell 2022; 33:ar35. [PMID: 35293775 PMCID: PMC9282021 DOI: 10.1091/mbc.e21-12-0616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
How nuclear pore complexes (NPC) assemble in the intact nuclear envelope (NE) is only rudimentarily understood. Nucleoporins accumulate at the inner NE (INM), deform this membrane towards the outer nuclear membrane (ONM) and eventually INM and ONM fuse by an unclear mechanism. In budding yeast, the integral membrane protein Brl1 that transiently associates with NPC assembly intermediates is involved in INM/ONM fusion during NPC assembly but leaving the molecular mechanism open. AlphaFold predictions indicate that Brl1-like proteins carry as common motifs an α-helix with amphipathic features (AαH) and a disulfide-stabilized anti-parallel helix bundle (DAH) in the perinuclear space. Mutants with defective AαH (brl1F391E, brl1F391P, brl1L402E) impair the essential function of BRL1. Overexpression of brl1F391E promotes formation of INM and ONM enclosed petal-like structures that carry nucleoporins at their base suggesting that they are derived from an NPC assembly attempt with failed INM/ONM fusion. Accordingly, brl1F391E expression triggers mis-localisation of Nup159 and Nup42 and to a lesser extent Nsp1 that localize on the cytoplasmic face of the NPC. The DAH also contributes to the function of Brl1 and AαH has functions independent of DAH. We propose that AαH and DAH in Brl1 promote INM/ONM fusion during NPC assembly.
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Affiliation(s)
- Jlenia Vitale
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Allianz, Universität Heidelberg, 69120 Heidelberg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), Universität Heidelberg, 69120 Heidelberg, Germany
| | - Azqa Khan
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Allianz, Universität Heidelberg, 69120 Heidelberg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), Universität Heidelberg, 69120 Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Allianz, Universität Heidelberg, 69120 Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Deutsches Krebsforschungszentrum (DKFZ)-ZMBH Allianz, Universität Heidelberg, 69120 Heidelberg, Germany
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10
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Characterization and Role of Sterols in Saccharomyces cerevisiae during White Wine Alcoholic Fermentation. FERMENTATION 2022. [DOI: 10.3390/fermentation8020090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Responsible for plasma membrane structure maintenance in eukaryotic organisms, sterols are essential for yeast development. The role of two sterol sources in Saccharomyces cerevisiae during wine fermentation is highlighted in this review: ergosterol (yeast sterol produced by yeast cells under aerobic conditions) and phytosterols (plant sterols imported by yeast cells from grape musts in the absence of oxygen). These compounds are responsible for the maintenance of yeast cell viability during white wine fermentation under stress conditions, such as ethanol stress and sterol starvation, to avoid sluggish and stuck fermentations.
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11
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Deolal P, Jamir I, Mishra K. Uip4p modulates nuclear pore complex function in Saccharomyces cerevisiae. Nucleus 2022; 13:79-93. [PMID: 35171083 PMCID: PMC8855845 DOI: 10.1080/19491034.2022.2034286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A double membrane bilayer perforated by nuclear pore complexes (NPCs) governs the shape of the nucleus, the prominent distinguishing organelle of a eukaryotic cell. Despite the absence of lamins in yeasts, the nuclear morphology is stably maintained and shape changes occur in a regulated fashion. In a quest to identify factors that contribute to regulation of nuclear shape and function in Saccharomyces cerevisiae, we used a fluorescence imaging based approach. Here we report the identification of a novel protein, Uip4p, that is required for regulation of nuclear morphology. Loss of Uip4 compromises NPC function and loss of nuclear envelope (NE) integrity. Our localization studies show that Uip4 localizes to the NE and endoplasmic reticulum (ER) network. Furthermore, we demonstrate that the localization and expression of Uip4 is regulated during growth, which is crucial for NPC distribution.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Imlitoshi Jamir
- Department of Biotechnology, School of Engineering and Technology, Nagaland University, Dimapur, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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12
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Zhang W, Khan A, Vitale J, Neuner A, Rink K, Lüchtenborg C, Brügger B, Söllner TH, Schiebel E. A short perinuclear amphipathic α-helix in Apq12 promotes nuclear pore complex biogenesis. Open Biol 2021; 11:210250. [PMID: 34814743 PMCID: PMC8611336 DOI: 10.1098/rsob.210250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The integral membrane protein Apq12 is an important nuclear envelope (NE)/endoplasmic reticulum (ER) modulator that cooperates with the nuclear pore complex (NPC) biogenesis factors Brl1 and Brr6. How Apq12 executes these functions is unknown. Here, we identified a short amphipathic α-helix (AαH) in Apq12 that links the two transmembrane domains in the perinuclear space and has liposome-binding properties. Cells expressing an APQ12 (apq12-ah) version in which AαH is disrupted show NPC biogenesis and NE integrity defects, without impacting Apq12-ah topology or NE/ER localization. Overexpression of APQ12 but not apq12-ah triggers striking over-proliferation of the outer nuclear membrane (ONM)/ER and promotes accumulation of phosphatidic acid (PA) at the NE. Apq12 and Apq12-ah both associate with NPC biogenesis intermediates and removal of AαH increases both Brl1 levels and the interaction between Brl1 and Brr6. We conclude that the short amphipathic α-helix of Apq12 regulates the function of Brl1 and Brr6 and promotes PA accumulation at the NE possibly during NPC biogenesis.
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Affiliation(s)
- Wanlu Zhang
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Azqa Khan
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Jlenia Vitale
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Kerstin Rink
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Christian Lüchtenborg
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Britta Brügger
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Thomas H. Söllner
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
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13
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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14
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Jacquemyn J, Foroozandeh J, Vints K, Swerts J, Verstreken P, Gounko NV, Gallego SF, Goodchild R. Torsin and NEP1R1-CTDNEP1 phosphatase affect interphase nuclear pore complex insertion by lipid-dependent and lipid-independent mechanisms. EMBO J 2021; 40:e106914. [PMID: 34313336 PMCID: PMC8408595 DOI: 10.15252/embj.2020106914] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/30/2021] [Accepted: 06/28/2021] [Indexed: 12/25/2022] Open
Abstract
The interphase nuclear envelope (NE) is extensively remodeled during nuclear pore complex (NPC) insertion. How this remodeling occurs and why it requires Torsin ATPases, which also regulate lipid metabolism, remains poorly understood. Here, we show that Drosophila Torsin (dTorsin) affects lipid metabolism via the NEP1R1‐CTDNEP1 phosphatase and the Lipin phosphatidic acid (PA) phosphatase. This includes that Torsins remove NEP1R1‐CTDNEP1 from the NE in fly and mouse cells, leading to subsequent Lipin exclusion from the nucleus. NEP1R1‐CTDNEP1 downregulation also restores nuclear pore membrane fusion in post‐mitotic dTorsinKO fat body cells. However, dTorsin‐associated nuclear pore defects do not correlate with lipidomic abnormalities and are not resolved by silencing of Lipin. Further testing confirmed that membrane fusion continues in cells with hyperactivated Lipin. It also led to the surprising finding that excessive PA metabolism inhibits recruitment of the inner ring complex Nup35 subunit, resulting in elongated channel‐like structures in place of mature nuclear pores. We conclude that the NEP1R1‐CTDNEP1 phosphatase affects interphase NPC biogenesis by lipid‐dependent and lipid‐independent mechanisms, explaining some of the pleiotropic effects of Torsins.
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Affiliation(s)
- Julie Jacquemyn
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Joyce Foroozandeh
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
| | - Jef Swerts
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Natalia V Gounko
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
| | - Sandra F Gallego
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Rose Goodchild
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.,Department of Neurosciences, KU Leuven, Leuven, Belgium
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15
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Panagaki D, Croft JT, Keuenhof K, Larsson Berglund L, Andersson S, Kohler V, Büttner S, Tamás MJ, Nyström T, Neutze R, Höög JL. Nuclear envelope budding is a response to cellular stress. Proc Natl Acad Sci U S A 2021; 118:e2020997118. [PMID: 34290138 PMCID: PMC8325156 DOI: 10.1073/pnas.2020997118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nuclear envelope budding (NEB) is a recently discovered alternative pathway for nucleocytoplasmic communication distinct from the movement of material through the nuclear pore complex. Through quantitative electron microscopy and tomography, we demonstrate how NEB is evolutionarily conserved from early protists to human cells. In the yeast Saccharomyces cerevisiae, NEB events occur with higher frequency during heat shock, upon exposure to arsenite or hydrogen peroxide, and when the proteasome is inhibited. Yeast cells treated with azetidine-2-carboxylic acid, a proline analog that induces protein misfolding, display the most dramatic increase in NEB, suggesting a causal link to protein quality control. This link was further supported by both localization of ubiquitin and Hsp104 to protein aggregates and NEB events, and the evolution of these structures during heat shock. We hypothesize that NEB is part of normal cellular physiology in a vast range of species and that in S. cerevisiae NEB comprises a stress response aiding the transport of protein aggregates across the nuclear envelope.
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Affiliation(s)
- Dimitra Panagaki
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jacob T Croft
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Katharina Keuenhof
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Lisa Larsson Berglund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Stefanie Andersson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Verena Kohler
- Department of Molecular Bioscienses, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Sabrina Büttner
- Department of Molecular Bioscienses, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Markus J Tamás
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Thomas Nyström
- Department of Microbiology and Immunology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden;
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16
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Deolal P, Mishra K. Regulation of diverse nuclear shapes: pathways working independently, together. Commun Integr Biol 2021; 14:158-175. [PMID: 34262635 PMCID: PMC8259725 DOI: 10.1080/19420889.2021.1939942] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
Membrane-bound organelles provide physical and functional compartmentalization of biological processes in eukaryotic cells. The characteristic shape and internal organization of these organelles is determined by a combination of multiple internal and external factors. The maintenance of the shape of nucleus, which houses the genetic material within a double membrane bilayer, is crucial for a seamless spatio-temporal control over nuclear and cellular functions. Dynamic morphological changes in the shape of nucleus facilitate various biological processes. Chromatin packaging, nuclear and cytosolic protein organization, and nuclear membrane lipid homeostasis are critical determinants of overall nuclear morphology. As such, a multitude of molecular players and pathways act together to regulate the nuclear shape. Here, we review the known mechanisms governing nuclear shape in various unicellular and multicellular organisms, including the non-spherical nuclei and non-lamin-related structural determinants. The review also touches upon cellular consequences of aberrant nuclear morphologies.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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17
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Thaller DJ, Tong D, Marklew CJ, Ader NR, Mannino PJ, Borah S, King MC, Ciani B, Lusk CP. Direct binding of ESCRT protein Chm7 to phosphatidic acid-rich membranes at nuclear envelope herniations. J Cell Biol 2021; 220:e202004222. [PMID: 33464310 PMCID: PMC7816628 DOI: 10.1083/jcb.202004222] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/04/2020] [Accepted: 12/11/2020] [Indexed: 12/03/2022] Open
Abstract
Mechanisms that control nuclear membrane remodeling are essential to maintain the integrity of the nucleus but remain to be fully defined. Here, we identify a phosphatidic acid (PA)-binding capacity in the nuclear envelope (NE)-specific ESCRT, Chm7, in budding yeast. Chm7's interaction with PA-rich membranes is mediated through a conserved hydrophobic stretch of amino acids, which confers recruitment to the NE in a manner that is independent of but required for Chm7's interaction with the LAP2-emerin-MAN1 (LEM) domain protein Heh1 (LEM2). Consistent with the functional importance of PA binding, mutation of this region abrogates recruitment of Chm7 to membranes and abolishes Chm7 function in the context of NE herniations that form during defective nuclear pore complex (NPC) biogenesis. In fact, we show that a PA sensor specifically accumulates within these NE herniations. We suggest that local control of PA metabolism is important for ensuring productive NE remodeling and that its dysregulation may contribute to pathologies associated with defective NPC assembly.
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Affiliation(s)
- David J. Thaller
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Danqing Tong
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Christopher J. Marklew
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Brook Hill, Sheffield, UK
| | - Nicholas R. Ader
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | | | - Sapan Borah
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Megan C. King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Barbara Ciani
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Brook Hill, Sheffield, UK
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
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18
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Maturation Kinetics of a Multiprotein Complex Revealed by Metabolic Labeling. Cell 2020; 183:1785-1800.e26. [DOI: 10.1016/j.cell.2020.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 09/21/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022]
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19
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Burla R, La Torre M, Maccaroni K, Verni F, Giunta S, Saggio I. Interplay of the nuclear envelope with chromatin in physiology and pathology. Nucleus 2020; 11:205-218. [PMID: 32835589 PMCID: PMC7529417 DOI: 10.1080/19491034.2020.1806661] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
The nuclear envelope compartmentalizes chromatin in eukaryotic cells. The main nuclear envelope components are lamins that associate with a panoply of factors, including the LEM domain proteins. The nuclear envelope of mammalian cells opens up during cell division. It is reassembled and associated with chromatin at the end of mitosis when telomeres tether to the nuclear periphery. Lamins, LEM domain proteins, and DNA binding factors, as BAF, contribute to the reorganization of chromatin. In this context, an emerging role is that of the ESCRT complex, a machinery operating in multiple membrane assembly pathways, including nuclear envelope reformation. Research in this area is unraveling how, mechanistically, ESCRTs link to nuclear envelope associated factors as LEM domain proteins. Importantly, ESCRTs work also during interphase for repairing nuclear envelope ruptures. Altogether the advances in this field are giving new clues for the interpretation of diseases implicating nuclear envelope fragility, as laminopathies and cancer. ABBREVIATIONS na, not analyzed; ko, knockout; kd, knockdown; NE, nuclear envelope; LEM, LAP2-emerin-MAN1 (LEM)-domain containing proteins; LINC, linker of nucleoskeleton and cytoskeleton complexes; Cyt, cytoplasm; Chr, chromatin; MB, midbody; End, endosomes; Tel, telomeres; INM, inner nuclear membrane; NP, nucleoplasm; NPC, Nuclear Pore Complex; ER, Endoplasmic Reticulum; SPB, spindle pole body.
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Affiliation(s)
- Romina Burla
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
| | - Mattia La Torre
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Klizia Maccaroni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Fiammetta Verni
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Simona Giunta
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- Rockefeller University, New York, NY, USA
| | - Isabella Saggio
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
- CNR Institute of Molecular Biology and Pathology, Italy
- Institute of Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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20
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Allegretti M, Zimmerli CE, Rantos V, Wilfling F, Ronchi P, Fung HKH, Lee CW, Hagen W, Turoňová B, Karius K, Börmel M, Zhang X, Müller CW, Schwab Y, Mahamid J, Pfander B, Kosinski J, Beck M. In-cell architecture of the nuclear pore and snapshots of its turnover. Nature 2020; 586:796-800. [PMID: 32879490 DOI: 10.1038/s41586-020-2670-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 06/01/2020] [Indexed: 12/25/2022]
Abstract
Nuclear pore complexes (NPCs) fuse the inner and outer membranes of the nuclear envelope. They comprise hundreds of nucleoporins (Nups) that assemble into multiple subcomplexes and form large central channels for nucleocytoplasmic exchange1,2. How this architecture facilitates messenger RNA export, NPC biogenesis and turnover remains poorly understood. Here we combine in situ structural biology and integrative modelling with correlative light and electron microscopy and molecular perturbation to structurally analyse NPCs in intact Saccharomyces cerevisiae cells within the context of nuclear envelope remodelling. We find an in situ conformation and configuration of the Nup subcomplexes that was unexpected from the results of previous in vitro analyses. The configuration of the Nup159 complex appears critical to spatially accommodate its function as an mRNA export platform, and as a mediator of NPC turnover. The omega-shaped nuclear envelope herniae that accumulate in nup116Δ cells3 conceal partially assembled NPCs lacking multiple subcomplexes, including the Nup159 complex. Under conditions of starvation, herniae of a second type are formed that cytoplasmically expose NPCs. These results point to a model of NPC turnover in which NPC-containing vesicles bud off from the nuclear envelope before degradation by the autophagy machinery. Our study emphasizes the importance of investigating the structure-function relationship of macromolecular complexes in their cellular context.
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Affiliation(s)
- Matteo Allegretti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian E Zimmerli
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Vasileios Rantos
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory, Hamburg, Germany
| | | | - Paolo Ronchi
- Electron Microscopy Core Facility (EMCF), European Molecular Biology Laboratory, Heidelberg, Germany
| | - Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Chia-Wei Lee
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wim Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Beata Turoňová
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kai Karius
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory, Hamburg, Germany
| | - Mandy Börmel
- Electron Microscopy Core Facility (EMCF), European Molecular Biology Laboratory, Heidelberg, Germany
| | - Xiaojie Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yannick Schwab
- Electron Microscopy Core Facility (EMCF), European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Boris Pfander
- Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory, Hamburg, Germany.
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany.
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21
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Expósito-Serrano M, Sánchez-Molina A, Gallardo P, Salas-Pino S, Daga RR. Selective Nuclear Pore Complex Removal Drives Nuclear Envelope Division in Fission Yeast. Curr Biol 2020; 30:3212-3222.e2. [DOI: 10.1016/j.cub.2020.05.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/24/2020] [Accepted: 05/20/2020] [Indexed: 01/09/2023]
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22
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Hirano Y, Kinugasa Y, Osakada H, Shindo T, Kubota Y, Shibata S, Haraguchi T, Hiraoka Y. Lem2 and Lnp1 maintain the membrane boundary between the nuclear envelope and endoplasmic reticulum. Commun Biol 2020; 3:276. [PMID: 32483293 PMCID: PMC7264229 DOI: 10.1038/s42003-020-0999-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/11/2020] [Indexed: 01/09/2023] Open
Abstract
The nuclear envelope (NE) continues to the endoplasmic reticulum (ER). Proper partitioning of NE and ER is crucial for cellular activity, but the key factors maintaining the boundary between NE and ER remain to be elucidated. Here we show that the conserved membrane proteins Lem2 and Lnp1 cooperatively play a crucial role in maintaining the NE-ER membrane boundary in fission yeast Schizosaccharomyces pombe. Cells lacking both Lem2 and Lnp1 caused severe growth defects associated with aberrant expansion of the NE/ER membranes, abnormal leakage of nuclear proteins, and abnormal formation of vacuolar-like structures in the nucleus. Overexpression of the ER membrane protein Apq12 rescued the growth defect associated with membrane disorder caused by the loss of Lem2 and Lnp1. Genetic analysis showed that Apq12 had overlapping functions with Lnp1. We propose that a membrane protein network with Lem2 and Lnp1 acts as a critical factor to maintain the NE-ER boundary.
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Affiliation(s)
- Yasuhiro Hirano
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan.
| | - Yasuha Kinugasa
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, 734-8553, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
| | - Tomoko Shindo
- Electron Microscope Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Yoshino Kubota
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, 565-0871, Japan.
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe, 651-2492, Japan.
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23
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Martín‐Expósito M, Gas M, Mohamad N, Nuño‐Cabanes C, Tejada‐Colón A, Pascual‐García P, de la Fuente L, Chaves‐Arquero B, Merran J, Corden J, Conesa A, Pérez‐Cañadillas JM, Bravo J, Rodríguez‐Navarro S. Mip6 binds directly to the Mex67 UBA domain to maintain low levels of Msn2/4 stress-dependent mRNAs. EMBO Rep 2019; 20:e47964. [PMID: 31680439 PMCID: PMC6893359 DOI: 10.15252/embr.201947964] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 08/30/2019] [Accepted: 09/11/2019] [Indexed: 11/09/2022] Open
Abstract
RNA-binding proteins (RBPs) participate in all steps of gene expression, underscoring their potential as regulators of RNA homeostasis. We structurally and functionally characterize Mip6, a four-RNA recognition motif (RRM)-containing RBP, as a functional and physical interactor of the export factor Mex67. Mip6-RRM4 directly interacts with the ubiquitin-associated (UBA) domain of Mex67 through a loop containing tryptophan 442. Mip6 shuttles between the nucleus and the cytoplasm in a Mex67-dependent manner and concentrates in cytoplasmic foci under stress. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation experiments show preferential binding of Mip6 to mRNAs regulated by the stress-response Msn2/4 transcription factors. Consistent with this binding, MIP6 deletion affects their export and expression levels. Additionally, Mip6 interacts physically and/or functionally with proteins with a role in mRNA metabolism and transcription such as Rrp6, Xrn1, Sgf73, and Rpb1. These results reveal a novel role for Mip6 in the homeostasis of Msn2/4-dependent transcripts through its direct interaction with the Mex67 UBA domain.
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Grants
- BFU2014-57636 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- BFU2015-71978 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- SAF2015-67077-R Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- SAF2017-89901-R Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- CTQ2018-84371 Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- PGC2018-099872-B-I00 Ministerio de Ciencia, Innovación y Universidades (Ministry of Science, Innovation and Universities)
- PROM/2012/061 Generalitat Valenciana (Regional Government of Valencia)
- PROMETEO 2016/093 Generalitat Valenciana (Regional Government of Valencia)
- ACOMP2014/061 Generalitat Valenciana (Regional Government of Valencia)
- B2017/BMD-3770 Comunidad de Madrid (Madrid Autonomous Community)
- Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO)
- Comunidad de Madrid (Madrid Autonomous Community)
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Affiliation(s)
- Manuel Martín‐Expósito
- Gene Expression and RNA Metabolism LaboratoryInstituto de Biomedicina de Valencia (CSIC)ValenciaSpain
- Gene Expression and RNA Metabolism LaboratoryCentro de Investigación Príncipe Felipe (CIPF)ValenciaSpain
| | - Maria‐Eugenia Gas
- Gene Expression and RNA Metabolism LaboratoryCentro de Investigación Príncipe Felipe (CIPF)ValenciaSpain
| | - Nada Mohamad
- Signal Transduction LaboratoryInstituto de Biomedicina de Valencia (CSIC)ValenciaSpain
| | - Carme Nuño‐Cabanes
- Gene Expression and RNA Metabolism LaboratoryInstituto de Biomedicina de Valencia (CSIC)ValenciaSpain
- Gene Expression and RNA Metabolism LaboratoryCentro de Investigación Príncipe Felipe (CIPF)ValenciaSpain
| | - Ana Tejada‐Colón
- Gene Expression and RNA Metabolism LaboratoryInstituto de Biomedicina de Valencia (CSIC)ValenciaSpain
| | - Pau Pascual‐García
- Gene Expression and RNA Metabolism LaboratoryCentro de Investigación Príncipe Felipe (CIPF)ValenciaSpain
- Present address:
Department of Cell and Developmental BiologyEpigenetics InstitutePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lorena de la Fuente
- Genomics of Gene Expression LaboratoryCentro de Investigación Príncipe Felipe (CIPF)ValenciaSpain
| | - Belén Chaves‐Arquero
- Department of Biological Physical ChemistryInstitute of Physical‐Chemistry “Rocasolano” (CSIC)MadridSpain
| | - Jonathan Merran
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Jeffry Corden
- Department of Molecular Biology and GeneticsJohns Hopkins University School of MedicineBaltimoreMDUSA
| | - Ana Conesa
- Genetics InstituteUniversity of FloridaGainesvilleFLUSA
- Microbiology and Cell Science DepartmentInstitute for Food and Agricultural ResearchUniversity of FloridaGainesvilleFLUSA
| | | | - Jerónimo Bravo
- Signal Transduction LaboratoryInstituto de Biomedicina de Valencia (CSIC)ValenciaSpain
| | - Susana Rodríguez‐Navarro
- Gene Expression and RNA Metabolism LaboratoryInstituto de Biomedicina de Valencia (CSIC)ValenciaSpain
- Gene Expression and RNA Metabolism LaboratoryCentro de Investigación Príncipe Felipe (CIPF)ValenciaSpain
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24
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Rempel IL, Crane MM, Thaller DJ, Mishra A, Jansen DP, Janssens G, Popken P, Akşit A, Kaeberlein M, van der Giessen E, Steen A, Onck PR, Lusk CP, Veenhoff LM. Age-dependent deterioration of nuclear pore assembly in mitotic cells decreases transport dynamics. eLife 2019; 8:48186. [PMID: 31157618 PMCID: PMC6579512 DOI: 10.7554/elife.48186] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/02/2019] [Indexed: 12/28/2022] Open
Abstract
Nuclear transport is facilitated by the Nuclear Pore Complex (NPC) and is essential for life in eukaryotes. The NPC is a long-lived and exceptionally large structure. We asked whether NPC quality control is compromised in aging mitotic cells. Our images of single yeast cells during aging, show that the abundance of several NPC components and NPC assembly factors decreases. Additionally, the single-cell life histories reveal that cells that better maintain those components are longer lived. The presence of herniations at the nuclear envelope of aged cells suggests that misassembled NPCs are accumulated in aged cells. Aged cells show decreased dynamics of transcription factor shuttling and increased nuclear compartmentalization. These functional changes are likely caused by the presence of misassembled NPCs, as we find that two NPC assembly mutants show similar transport phenotypes as aged cells. We conclude that NPC interphase assembly is a major challenge for aging mitotic cells.
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Affiliation(s)
- Irina L Rempel
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Matthew M Crane
- Department of Pathology, University of Washington, Seattle, United States
| | - David J Thaller
- Department of Cell Biology, Yale School of Medicine, New Haven, United States
| | - Ankur Mishra
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Daniel Pm Jansen
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Georges Janssens
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Petra Popken
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Arman Akşit
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, United States
| | - Erik van der Giessen
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, United States
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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25
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Thaller DJ, Allegretti M, Borah S, Ronchi P, Beck M, Lusk CP. An ESCRT-LEM protein surveillance system is poised to directly monitor the nuclear envelope and nuclear transport system. eLife 2019; 8:e45284. [PMID: 30942170 PMCID: PMC6461442 DOI: 10.7554/elife.45284] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022] Open
Abstract
The integrity of the nuclear membranes coupled to the selective barrier of nuclear pore complexes (NPCs) are essential for the segregation of nucleoplasm and cytoplasm. Mechanical membrane disruption or perturbation to NPC assembly triggers an ESCRT-dependent surveillance system that seals nuclear pores: how these pores are sensed and sealed is ill defined. Using a budding yeast model, we show that the ESCRT Chm7 and the integral inner nuclear membrane (INM) protein Heh1 are spatially segregated by nuclear transport, with Chm7 being actively exported by Xpo1/Crm1. Thus, the exposure of the INM triggers surveillance with Heh1 locally activating Chm7. Sites of Chm7 hyperactivation show fenestrated sheets at the INM and potential membrane delivery at sites of nuclear envelope herniation. Our data suggest that perturbation to the nuclear envelope barrier would lead to local nuclear membrane remodeling to promote membrane sealing. Our findings have implications for disease mechanisms linked to NPC assembly and nuclear envelope integrity.
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Affiliation(s)
- David J Thaller
- Department of Cell BiologyYale School of MedicineNew HavenUnited States
| | - Matteo Allegretti
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryMeyerhofstrasseGermany
| | - Sapan Borah
- Department of Cell BiologyYale School of MedicineNew HavenUnited States
| | - Paolo Ronchi
- Electron Microscopy Core FacilityEuropean Molecular Biology LaboratoryMeyerhofstrasseGermany
| | - Martin Beck
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryMeyerhofstrasseGermany
| | - C Patrick Lusk
- Department of Cell BiologyYale School of MedicineNew HavenUnited States
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26
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de Bruyn Kops A, Burke JE, Guthrie C. Brr6 plays a role in gene recruitment and transcriptional regulation at the nuclear envelope. Mol Biol Cell 2018; 29:2578-2590. [PMID: 30133335 PMCID: PMC6254580 DOI: 10.1091/mbc.e18-04-0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Correlation between transcriptional regulation and positioning of genes at the nuclear envelope is well established in eukaryotes, but the mechanisms involved are not well understood. We show that brr6-1, a mutant of the essential yeast envelope transmembrane protein Brr6p, impairs normal positioning and expression of the PAB1 and FUR4-GAL1,10,7 loci. Similarly, expression of a dominant negative nucleoplasmic Brr6 fragment in wild-type cells reproduced many of the brr6-1 effects. Histone chromatin immunoprecipitation (ChIP) experiments showed decreased acetylation at the key histone H4K16 residue in the FUR4-GAL1,10,7 region in brr6-1. Importantly, blocking deacetylation significantly suppressed selected brr6-1 phenotypes. ChIPseq with FLAG-tagged Brr6 fragments showed enrichment at FUR4 and several other genes that showed striking changes in brr6-1 RNAseq data. These associations depended on a Brr6 putative zinc finger domain. Importantly, artificially tethering the GAL1 locus to the envelope suppressed the brr6-1 effects on GAL1 and FUR4 expression and increased H4K16 acetylation between GAL1 and FUR4 in the mutant. Together these results argue that Brr6 interacts with chromatin, helping to maintain normal chromatin architecture and transcriptional regulation of certain loci at the nuclear envelope.
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Affiliation(s)
- Anne de Bruyn Kops
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
| | - Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
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27
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Identification of the Novel Nup188-brr7 Allele in a Screen for Cold-Sensitive mRNA Export Mutants in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2018; 8:2991-3003. [PMID: 30021831 PMCID: PMC6118305 DOI: 10.1534/g3.118.200447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The maturation and export of mRNA from the nucleus through the nuclear pore complex is critical for maintaining an appropriate proteome in all eukaryotic cells. Here we summarize a previously unpublished screen in S. cerevisiae that utilized an established dT50 in situ hybridization assay to identify cold-sensitive mutants that accumulated bulk poly A RNA in the nucleus. The screen identified seven mutants in six complementation groups, including the brr6-1 strain that we described previously. In addition to brr6-1, we identified novel alleles of the key transport gene GLE1 and NUP188, a component of the Nic96 nucleoporin complex. Notably, we show that the nup188-brr7 allele causes defects in select protein import pathways as well as mRNA export. Given recent structural and functional evidence linking the Nic96 complex to transport components, this mutant may be particularly useful to the transport community.
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28
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Fantastic nuclear envelope herniations and where to find them. Biochem Soc Trans 2018; 46:877-889. [PMID: 30026368 DOI: 10.1042/bst20170442] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 12/19/2022]
Abstract
Morphological abnormalities of the bounding membranes of the nucleus have long been associated with human diseases from cancer to premature aging to neurodegeneration. Studies over the past few decades support that there are both cell intrinsic and extrinsic factors (e.g. mechanical force) that can lead to nuclear envelope 'herniations', a broad catch-all term that reveals little about the underlying molecular mechanisms that contribute to these morphological defects. While there are many genetic perturbations that could ultimately change nuclear shape, here, we focus on a subset of nuclear envelope herniations that likely arise as a consequence of disrupting physiological nuclear membrane remodeling pathways required to maintain nuclear envelope homeostasis. For example, stalling of the interphase nuclear pore complex (NPC) biogenesis pathway and/or triggering of NPC quality control mechanisms can lead to herniations in budding yeast, which are remarkably similar to those observed in human disease models of early-onset dystonia. By also examining the provenance of nuclear envelope herniations associated with emerging nuclear autophagy and nuclear egress pathways, we will provide a framework to help understand the molecular pathways that contribute to nuclear deformation.
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29
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30
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Otsuka S, Ellenberg J. Mechanisms of nuclear pore complex assembly - two different ways of building one molecular machine. FEBS Lett 2018; 592:475-488. [PMID: 29119545 PMCID: PMC6220763 DOI: 10.1002/1873-3468.12905] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 12/16/2022]
Abstract
The nuclear pore complex (NPC) mediates all macromolecular transport across the nuclear envelope. In higher eukaryotes that have an open mitosis, NPCs assemble at two points in the cell cycle: during nuclear assembly in late mitosis and during nuclear growth in interphase. How the NPC, the largest nonpolymeric protein complex in eukaryotic cells, self-assembles inside cells remained unclear. Recent studies have started to uncover the assembly process, and evidence has been accumulating that postmitotic and interphase NPC assembly use fundamentally different mechanisms; the duration, structural intermediates, and regulation by molecular players are different and different types of membrane deformation are involved. In this Review, we summarize the current understanding of these two modes of NPC assembly and discuss the structural and regulatory steps that might drive the assembly processes. We furthermore integrate understanding of NPC assembly with the mechanisms for rapid nuclear growth in embryos and, finally, speculate on the evolutionary origin of the NPC implied by the presence of two distinct assembly mechanisms.
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Affiliation(s)
- Shotaro Otsuka
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Jan Ellenberg
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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31
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Yang HJ, Iwamoto M, Hiraoka Y, Haraguchi T. Function of nuclear membrane proteins in shaping the nuclear envelope integrity during closed mitosis. J Biochem 2017; 161:471-477. [PMID: 28398483 DOI: 10.1093/jb/mvx020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/28/2017] [Indexed: 11/13/2022] Open
Abstract
The nuclear envelope (NE) not only protects the genome from being directly accessed by detrimental agents but also regulates genome organization. Breaches in NE integrity threaten genome stability and impede cellular function. Nonetheless, the NE constantly remodels, and NE integrity is endangered in dividing or differentiating cells. Specifically, in unicellular eukaryotes undergoing closed mitosis, the NE expands instead of breaking down during chromosome segregation. The newly assembling nuclear pore complexes (NPCs) penetrate the existing NE in interphase. A peculiar example of NE remodelling during nuclear differentiation in Tetrahymena involves formation of the redundant NE and clustered NPCs. Even under these conditions, the NE remains intact. Many recent studies on unicellular organisms have revealed that nuclear membrane proteins, such as LEM-domain proteins, play a role in maintaining NE integrity. This review summarizes and discusses how nuclear membrane proteins participate in NE integrity.
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Affiliation(s)
- Hui-Ju Yang
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Masaaki Iwamoto
- Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advance ICT Research Institute Kobe, National Institute of Information and Communications Technology, 588-2 Iwaoka, Iwaoka-cho, Nishi-ku, Kobe 651-2492, Japan
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32
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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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33
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Abstract
As a compartment border, the nuclear envelope (NE) needs to serve as both a protective membrane shell for the genome and a versatile communication interface between the nucleus and the cytoplasm. Despite its important structural role in sheltering the genome, the NE is a dynamic and highly adaptable boundary that changes composition during differentiation, deforms in response to mechanical challenges, can be repaired upon rupture and even rapidly disassembles and reforms during open mitosis. NE remodelling is fundamentally involved in cell growth, division and differentiation, and if perturbed can lead to devastating diseases such as muscular dystrophies or premature ageing.
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34
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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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35
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Webster BM, Thaller DJ, Jäger J, Ochmann SE, Borah S, Lusk CP. Chm7 and Heh1 collaborate to link nuclear pore complex quality control with nuclear envelope sealing. EMBO J 2016; 35:2447-2467. [PMID: 27733427 DOI: 10.15252/embj.201694574] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 11/09/2022] Open
Abstract
The integrity of the nuclear envelope barrier relies on membrane remodeling by the ESCRTs, which seal nuclear envelope holes and contribute to the quality control of nuclear pore complexes (NPCs); whether these processes are mechanistically related remains poorly defined. Here, we show that the ESCRT-II/III chimera, Chm7, is recruited to a nuclear envelope subdomain that expands upon inhibition of NPC assembly and is required for the formation of the storage of improperly assembled NPCs (SINC) compartment. Recruitment to sites of NPC assembly is mediated by its ESCRT-II domain and the LAP2-emerin-MAN1 (LEM) family of integral inner nuclear membrane proteins, Heh1 and Heh2. We establish direct binding between Heh2 and the "open" forms of both Chm7 and the ESCRT-III, Snf7, and between Chm7 and Snf7. Interestingly, Chm7 is required for the viability of yeast strains where double membrane seals have been observed over defective NPCs; deletion of CHM7 in these strains leads to a loss of nuclear compartmentalization suggesting that the sealing of defective NPCs and nuclear envelope ruptures could proceed through similar mechanisms.
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Affiliation(s)
- Brant M Webster
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - David J Thaller
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Jens Jäger
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Sarah E Ochmann
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Sapan Borah
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
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36
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Otsuka S, Bui KH, Schorb M, Hossain MJ, Politi AZ, Koch B, Eltsov M, Beck M, Ellenberg J. Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope. eLife 2016; 5. [PMID: 27630123 PMCID: PMC5065316 DOI: 10.7554/elife.19071] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/13/2016] [Indexed: 01/01/2023] Open
Abstract
The nuclear pore complex (NPC) mediates nucleocytoplasmic transport through the nuclear envelope. How the NPC assembles into this double membrane boundary has remained enigmatic. Here, we captured temporally staged assembly intermediates by correlating live cell imaging with high-resolution electron tomography and super-resolution microscopy. Intermediates were dome-shaped evaginations of the inner nuclear membrane (INM), that grew in diameter and depth until they fused with the flat outer nuclear membrane. Live and super-resolved fluorescence microscopy revealed the molecular maturation of the intermediates, which initially contained the nuclear and cytoplasmic ring component Nup107, and only later the cytoplasmic filament component Nup358. EM particle averaging showed that the evagination base was surrounded by an 8-fold rotationally symmetric ring structure from the beginning and that a growing mushroom-shaped density was continuously associated with the deforming membrane. Quantitative structural analysis revealed that interphase NPC assembly proceeds by an asymmetric inside-out extrusion of the INM.
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Affiliation(s)
- Shotaro Otsuka
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Khanh Huy Bui
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Schorb
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - M Julius Hossain
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Antonio Z Politi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Birgit Koch
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail Eltsov
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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37
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Meseroll RA, Cohen-Fix O. The Malleable Nature of the Budding Yeast Nuclear Envelope: Flares, Fusion, and Fenestrations. J Cell Physiol 2016; 231:2353-60. [PMID: 26909870 DOI: 10.1002/jcp.25355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 02/19/2016] [Indexed: 11/10/2022]
Abstract
In eukaryotes, the nuclear envelope (NE) physically separates nuclear components and activities from rest of the cell. The NE also provides rigidity to the nucleus and contributes to chromosome organization. At the same time, the NE is highly dynamic; it must change shape and rearrange its components during development and throughout the cell cycle, and its morphology can be altered in response to mutation and disease. Here we focus on the NE of budding yeast, Saccharomyces cerevisiae, which has several unique features: it remains intact throughout the cell cycle, expands symmetrically during interphase, elongates during mitosis and, expands asymmetrically during mitotic delay. Moreover, its NE is safely breached during mating and when large structures, such as nuclear pore complexes and the spindle pole body, are embedded into its double membrane. The budding yeast NE lacks lamins and yet the nucleus is capable of maintaining a spherical shape throughout interphase. Despite these eccentricities, studies of the budding yeast NE have uncovered interesting, and likely conserved, processes that contribute to NE dynamics. In particular, we discuss the processes that drive and enable NE expansion and the dramatic changes in the NE that lead to extensions and fenestrations. J. Cell. Physiol. 231: 2353-2360, 2016. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Rebecca A Meseroll
- The Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Orna Cohen-Fix
- The Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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38
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Evidence for a Nonendosomal Function of the Saccharomyces cerevisiae ESCRT-III-Like Protein Chm7. Genetics 2015; 201:1439-52. [PMID: 26510789 DOI: 10.1534/genetics.115.178939] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/15/2015] [Indexed: 11/18/2022] Open
Abstract
Endosomal sorting complex required for transport (ESCRT) proteins are involved in a number of cellular processes, such as endosomal protein sorting, HIV budding, cytokinesis, plasma membrane repair, and resealing of the nuclear envelope during mitosis. Here we explored the function of a noncanonical member of the ESCRT-III protein family, the Saccharomyces cerevisiae ortholog of human CHMP7. Very little is known about this protein. In silico analysis predicted that Chm7 (yeast ORF YJL049w) is a fusion of an ESCRT-II and ESCRT-III-like domain, which would suggest a role in endosomal protein sorting. However, our data argue against a role of Chm7 in endosomal protein sorting. The turnover of the endocytic cargo protein Ste6 and the vacuolar protein sorting of carboxypeptidase S (CPS) were not affected by CHM7 deletion, and Chm7 also responded very differently to a loss in Vps4 function compared to a canonical ESCRT-III protein. Our data indicate that the Chm7 function could be connected to the endoplasmic reticulum (ER). In line with a function at the ER, we observed a strong negative genetic interaction between the deletion of a gene function (APQ12) implicated in nuclear pore complex assembly and messenger RNA (mRNA) export and the CHM7 deletion. The patterns of genetic interactions between the APQ12 deletion and deletions of ESCRT-III genes, two-hybrid interactions, and the specific localization of mCherry fusion proteins are consistent with the notion that Chm7 performs a novel function at the ER as part of an alternative ESCRT-III complex.
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39
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Yeast Integral Membrane Proteins Apq12, Brl1, and Brr6 Form a Complex Important for Regulation of Membrane Homeostasis and Nuclear Pore Complex Biogenesis. EUKARYOTIC CELL 2015; 14:1217-27. [PMID: 26432634 DOI: 10.1128/ec.00101-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/01/2015] [Indexed: 11/20/2022]
Abstract
Proper functioning of intracellular membranes is critical for many cellular processes. A key feature of membranes is their ability to adapt to changes in environmental conditions by adjusting their composition so as to maintain constant biophysical properties, including fluidity and flexibility. Similar changes in the biophysical properties of membranes likely occur when intracellular processes, such as vesicle formation and fusion, require dramatic changes in membrane curvature. Similar modifications must also be made when nuclear pore complexes (NPCs) are constructed within the existing nuclear membrane, as occurs during interphase in all eukaryotes. Here we report on the role of the essential nuclear envelope/endoplasmic reticulum (NE/ER) protein Brl1 in regulating the membrane composition of the NE/ER. We show that Brl1 and two other proteins characterized previously-Brr6, which is closely related to Brl1, and Apq12-function together and are required for lipid homeostasis. All three transmembrane proteins are localized to the NE and can be coprecipitated. As has been shown for mutations affecting Brr6 and Apq12, mutations in Brl1 lead to defects in lipid metabolism, increased sensitivity to drugs that inhibit enzymes involved in lipid synthesis, and strong genetic interactions with mutations affecting lipid metabolism. Mutations affecting Brl1 or Brr6 or the absence of Apq12 leads to hyperfluid membranes, because mutant cells are hypersensitive to agents that increase membrane fluidity. We suggest that the defects in nuclear pore complex biogenesis and mRNA export seen in these mutants are consequences of defects in maintaining the biophysical properties of the NE.
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40
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Webster BM, Lusk CP. Border Safety: Quality Control at the Nuclear Envelope. Trends Cell Biol 2015; 26:29-39. [PMID: 26437591 DOI: 10.1016/j.tcb.2015.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/27/2015] [Accepted: 08/07/2015] [Indexed: 10/23/2022]
Abstract
The unique biochemical identity of the nuclear envelope confers its capacity to establish a barrier that protects the nuclear compartment and directly contributes to nuclear function. Recent work uncovered quality control mechanisms employing the endosomal sorting complexes required for transport (ESCRT) machinery and a new arm of endoplasmic reticulum-associated protein degradation (ERAD) to counteract the unfolding, damage, or misassembly of nuclear envelope proteins and ensure the integrity of the nuclear envelope membranes. Moreover, cells have the capacity to recognize and triage defective nuclear pore complexes to prevent their inheritance and preserve the longevity of progeny. These mechanisms serve to highlight the diverse strategies used by cells to maintain nuclear compartmentalization; we suggest they mitigate the progression and severity of diseases associated with nuclear envelope malfunction such as the laminopathies.
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41
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Abstract
The endosomal sorting complexes required for transport (ESCRT) are best known for their role in sorting ubiquitylated membrane proteins into endosomes. The most ancient component of the ESCRT machinery is ESCRT-III, which is capable of oligomerizing into a helical filament that drives the invagination and scission of membranes aided by the AAA ATPase, Vps4, in several additional subcellular contexts. Our recent study broadens the work of ESCRT-III by identifying its role in a quality control pathway at the nuclear envelope (NE) that ensures the normal biogenesis of nuclear pore complexes (NPCs). Here, we will elaborate on how we envision this mechanism to progress and incorporate ESCRT-III into an emerging model of nuclear pore formation. Moreover, we speculate there are additional roles for the ESCRT-III machinery at the NE that broadly function to ensure its integrity and the maintenance of the nuclear compartment.
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Key Words
- ERAD, ER-Associated Degradation
- ESCRT, Endosomal Sorting Complexes Required for Transport
- INM, Inner Nuclear Membrane
- LEM, Lap2, Emerin, MAN1
- MVB, Multivesicular Body
- NE, Nuclear Envelope
- NLS, Nuclear Localization Signal
- NPC, Nuclear Pore Complex
- ONM, Outer Nuclear Membrane
- SINC, Storage of Improperly assembled Nuclear pore Complexes
- endosomal sorting complex required for transport
- membrane curvature
- nuclear envelope
- nuclear pore complex
- quality control
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Webster BM, Colombi P, Jäger J, Lusk CP. Surveillance of nuclear pore complex assembly by ESCRT-III/Vps4. Cell 2015; 159:388-401. [PMID: 25303532 DOI: 10.1016/j.cell.2014.09.012] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/07/2014] [Accepted: 09/04/2014] [Indexed: 12/19/2022]
Abstract
The maintenance of nuclear compartmentalization by the nuclear envelope and nuclear pore complexes (NPCs) is essential for cell function; loss of compartmentalization is associated with cancers, laminopathies, and aging. We uncovered a pathway that surveils NPC assembly intermediates to promote the formation of functional NPCs. Surveillance is mediated by Heh2, a member of the LEM (Lap2-emerin-MAN1) family of integral inner nuclear membrane proteins, which binds to an early NPC assembly intermediate, but not to mature NPCs. Heh2 recruits the endosomal sorting complex required for transport (ESCRT)-III subunit Snf7 and the AAA-ATPase Vps4 to destabilize and clear defective NPC assembly intermediates. When surveillance or clearance is compromised, malformed NPCs accumulate in a storage of improperly assembled nuclear pore complexes compartment, or SINC. The SINC is retained in old mothers to prevent loss of daughter lifespan, highlighting a continuum of mechanisms to ensure nuclear compartmentalization.
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Affiliation(s)
- Brant M Webster
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Paolo Colombi
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jens Jäger
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA.
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Smoyer CJ, Jaspersen SL. Breaking down the wall: the nuclear envelope during mitosis. Curr Opin Cell Biol 2013; 26:1-9. [PMID: 24529240 DOI: 10.1016/j.ceb.2013.08.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/13/2013] [Accepted: 08/13/2013] [Indexed: 11/28/2022]
Abstract
A defining feature of eukaryotic cells is the nucleus, which houses the genome inside the nuclear envelope (NE): a double lipid bilayer that separates the nuclear and cytoplasmic materials. Although the NE is commonly viewed as a barrier that is overcome only by embedded nuclear pore complexes (NPCs) that facilitate nuclear-cytoplasmic trafficking, recent work in a wide range of eukaryotes reveals that the NE is a dynamic organelle that is modified each time the cell divides to ultimately establish two functional daughter nuclei. Here, we review how studies of divergent mitotic strategies have helped elucidate common properties of NE biology that allow it to function throughout the cell cycle.
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Affiliation(s)
- Christine J Smoyer
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, United States.
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Poring over pores: nuclear pore complex insertion into the nuclear envelope. Trends Biochem Sci 2013; 38:292-301. [DOI: 10.1016/j.tibs.2013.04.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/29/2013] [Accepted: 04/02/2013] [Indexed: 11/18/2022]
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Wolyniak MJ. Improved student linkage of Mendelian and molecular genetic concepts through a yeast-based laboratory module. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:163-172. [PMID: 23408554 DOI: 10.1002/bmb.20679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 11/11/2012] [Indexed: 06/01/2023]
Abstract
A study of modern genetics requires students to successfully unite the principles of Mendelian genetics with the functions of DNA. Traditional means of teaching genetics are often successful in teaching Mendelian and molecular ideas but not in allowing students to see how the two subjects relate. The laboratory module presented here attempts to present classical and molecular genetic concepts together as an inquiry-based exploration appropriate for high school or introductory undergraduate students. Using the non-essential APQ12 gene in the budding yeast Saccharomyces cerevisiae, students perform PCR, selective growth, and sporulation experiments to establish the ploidy and APQ12 zygosity of a series of unknown strains. Each experiment contributes data to characterize the unknown strains, but complete characterization is not possible without assimilating the data from all of the experiments. The module allows students to consider concepts normally introduced and emphasized in Mendelian genetics and explore them using molecular and experimental tools. Comparison of pre-module and post-module assessment surveys show an increase in student ability to link Mendelian concepts to experimental procedures relying on DNA analysis. The development of modules such as these provides students of all backgrounds with the tools to engage the complexities and issues that constitute modern principles of inheritance.
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Affiliation(s)
- Michael J Wolyniak
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA 23943, USA.
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46
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Genetic analysis of Mps3 SUN domain mutants in Saccharomyces cerevisiae reveals an interaction with the SUN-like protein Slp1. G3-GENES GENOMES GENETICS 2012; 2:1703-18. [PMID: 23275891 PMCID: PMC3516490 DOI: 10.1534/g3.112.004614] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 10/26/2012] [Indexed: 01/16/2023]
Abstract
In virtually all eukaryotic cells, protein bridges formed by the conserved inner nuclear membrane SUN (for Sad1-UNC-84) domain-containing proteins and their outer nuclear membrane binding partners span the nuclear envelope (NE) to connect the nucleoplasm and cytoplasm. These linkages are important for chromosome movements within the nucleus during meiotic prophase and are essential for nuclear migration and centrosome attachment to the NE. In Saccharomyces cerevisiae, MPS3 encodes the sole SUN protein. Deletion of MPS3 or the conserved SUN domain is lethal in three different genetic backgrounds. Mutations in the SUN domain result in defects in duplication of the spindle pole body, the yeast centrosome-equivalent organelle. A genome-wide screen for mutants that exhibited synthetic fitness defects in combination with mps3 SUN domain mutants yielded a large number of hits in components of the spindle apparatus and the spindle checkpoint. Mutants in lipid metabolic processes and membrane organization also exacerbated the growth defects of mps3 SUN domain mutants, pointing to a role for Mps3 in nuclear membrane organization. Deletion of SLP1 or YER140W/EMP65 (for ER membrane protein of 65 kDa) aggravated growth of mps3 SUN domain mutants. Slp1 and Emp65 form an ER-membrane associated protein complex that is not required directly for spindle pole body duplication or spindle assembly. Rather, Slp1 is involved in Mps3 localization to the NE.
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47
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Zhang D, Oliferenko S. Remodeling the nuclear membrane during closed mitosis. Curr Opin Cell Biol 2012; 25:142-8. [PMID: 23040820 DOI: 10.1016/j.ceb.2012.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 09/06/2012] [Accepted: 09/10/2012] [Indexed: 11/28/2022]
Abstract
The mitotic spindle assembly and chromosome segregation in eukaryotes must be coordinated with the nuclear envelope (NE) remodeling. In a so-called 'open' mitosis the envelope of the mother nucleus is dismantled allowing the cytoplasmic spindle microtubules to capture the chromosomes. Alternatively, cells undergoing 'closed' mitosis assemble the intranuclear spindle and divide the nucleus without ever losing the nucleocytoplasmic compartmentalization. Here we focus on the mechanisms underlying mitotic NE dynamics in unicellular eukaryotes undergoing a closed nuclear division, paying specific attention to the emerging roles of the lipid biosynthesis machinery in this process. We argue that lessons learned in these organisms may be generally relevant to understanding the NE remodeling and the evolution of mitotic mechanisms throughout the eukaryotic domain.
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Affiliation(s)
- Dan Zhang
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore
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48
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Abstract
Take a look at a textbook illustration of a cell and you will immediately be able to locate the nucleus, which is often drawn as a spherical or ovoid shaped structure. But not all cells have such nuclei. In fact, some disease states are diagnosed by the presence of nuclei that have an abnormal shape or size. What defines nuclear shape and nuclear size, and how does nuclear geometry affect nuclear function? While the answer to the latter question remains largely unknown, significant progress has been made towards understanding the former. In this review, we provide an overview of the factors and forces that affect nuclear shape and size, discuss the relationship between ER structure and nuclear morphology, and speculate on the possible connection between nuclear size and its shape. We also note the many interesting questions that remain to be explored.
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Affiliation(s)
- Alison D. Walters
- The Laboratory of Cell and Molecular Biology, NIDDK, NIH, Bethesda, Maryland 20892
| | - Ananth Bommakanti
- The Laboratory of Cell and Molecular Biology, NIDDK, NIH, Bethesda, Maryland 20892
| | - Orna Cohen-Fix
- The Laboratory of Cell and Molecular Biology, NIDDK, NIH, Bethesda, Maryland 20892
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49
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Abstract
Exchange of macromolecules between the nucleus and cytoplasm is a key regulatory event in the expression of a cell's genome. This exchange requires a dedicated transport system: (1) nuclear pore complexes (NPCs), embedded in the nuclear envelope and composed of proteins termed nucleoporins (or "Nups"), and (2) nuclear transport factors that recognize the cargoes to be transported and ferry them across the NPCs. This transport is regulated at multiple levels, and the NPC itself also plays a key regulatory role in gene expression by influencing nuclear architecture and acting as a point of control for various nuclear processes. Here we summarize how the yeast Saccharomyces has been used extensively as a model system to understand the fundamental and highly conserved features of this transport system, revealing the structure and function of the NPC; the NPC's role in the regulation of gene expression; and the interactions of transport factors with their cargoes, regulatory factors, and specific nucleoporins.
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Integrity and function of the Saccharomyces cerevisiae spindle pole body depends on connections between the membrane proteins Ndc1, Rtn1, and Yop1. Genetics 2012; 192:441-55. [PMID: 22798490 DOI: 10.1534/genetics.112.141465] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The nuclear envelope in Saccharomyces cerevisiae harbors two essential macromolecular protein assemblies: the nuclear pore complexes (NPCs) that enable nucleocytoplasmic transport, and the spindle pole bodies (SPBs) that mediate chromosome segregation. Previously, based on metazoan and budding yeast studies, we reported that reticulons and Yop1/DP1 play a role in the early steps of de novo NPC assembly. Here, we examined if Rtn1 and Yop1 are required for SPB function in S. cerevisiae. Electron microscopy of rtn1Δ yop1Δ cells revealed lobular abnormalities in SPB structure. Using an assay that monitors lateral expansion of the SPB central layer, we found that rtn1Δ yop1Δ SPBs had decreased connections to the NE compared to wild type, suggesting that SPBs are less stable in the NE. Furthermore, large budded rtn1Δ yop1Δ cells exhibited a high incidence of short mitotic spindles, which were frequently misoriented with respect to the mother-daughter axis. This correlated with cytoplasmic microtubule defects. We found that overexpression of the SPB insertion factors NDC1, MPS2, or BBP1 rescued the SPB defects observed in rtn1Δ yop1Δ cells. However, only overexpression of NDC1, which is also required for NPC biogenesis, rescued both the SPB and NPC associated defects. Rtn1 and Yop1 also physically interacted with Ndc1 and other NPC membrane proteins. We propose that NPC and SPB biogenesis are altered in cells lacking Rtn1 and Yop1 due to competition between these complexes for Ndc1, an essential common component of both NPCs and SPBs.
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