1
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Keuenhof KS, Kohler V, Broeskamp F, Panagaki D, Speese SD, Büttner S, Höög JL. Nuclear envelope budding and its cellular functions. Nucleus 2023; 14:2178184. [PMID: 36814098 PMCID: PMC9980700 DOI: 10.1080/19491034.2023.2178184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
The nuclear pore complex (NPC) has long been assumed to be the sole route across the nuclear envelope, and under normal homeostatic conditions it is indeed the main mechanism of nucleo-cytoplasmic transport. However, it has also been known that e.g. herpesviruses cross the nuclear envelope utilizing a pathway entitled nuclear egress or envelopment/de-envelopment. Despite this, a thread of observations suggests that mechanisms similar to viral egress may be transiently used also in healthy cells. It has since been proposed that mechanisms like nuclear envelope budding (NEB) can facilitate the transport of RNA granules, aggregated proteins, inner nuclear membrane proteins, and mis-assembled NPCs. Herein, we will summarize the known roles of NEB as a physiological and intrinsic cellular feature and highlight the many unanswered questions surrounding these intriguing nuclear events.
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Affiliation(s)
| | - Verena Kohler
- Institute of Molecular Biosciences, University of Graz, Austria
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Filomena Broeskamp
- Department for Chemistry and Molecular biology, University of Gothenburg, Sweden
| | - Dimitra Panagaki
- Department for Chemistry and Molecular biology, University of Gothenburg, Sweden
| | - Sean D. Speese
- Knight Cancer Early Detection Advanced Research Center, Oregon Health and Science University, 2720 S Moody Ave, Portland, OR, 97201, USA
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Sweden
| | - Johanna L. Höög
- Department for Chemistry and Molecular biology, University of Gothenburg, Sweden
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2
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Stankunas E, Köhler A. The interplay of nuclear pores and lipids. Curr Opin Cell Biol 2023; 85:102251. [PMID: 37804774 DOI: 10.1016/j.ceb.2023.102251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/24/2023] [Accepted: 09/07/2023] [Indexed: 10/09/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the bidirectional transport of cargo across the nuclear envelope (NE). NPCs are also membrane remodeling machines with a capacity to curve and fuse the membranes of the NE. However, little is known about the interplay of NPCs and lipids at a mechanistic level. A full understanding of NPC structure and function needs to encompass how the NPC shapes membranes and is itself shaped by lipids. Here we attempt to connect recent findings in NPC research with the broader field of membrane biochemistry to illustrate how an interplay between NPCs and lipids may facilitate the conformational plasticity of NPCs and the generation of a unique pore membrane topology. We highlight the need to better understand the NPC's lipid environment and outline experimental avenues towards that goal.
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Affiliation(s)
- Edvinas Stankunas
- Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Alwin Köhler
- Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9/3, 1030 Vienna, Austria.
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3
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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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4
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Kuiper EFE, Prophet SM, Schlieker C. Coordinating nucleoporin condensation and nuclear pore complex assembly. FEBS Lett 2023; 597:2534-2545. [PMID: 37620293 DOI: 10.1002/1873-3468.14725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/24/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023]
Abstract
The nuclear pore complex (NPC) is among the most elaborate protein complexes in eukaryotes. While ribosomes and proteasomes are known to require dedicated assembly machinery, our understanding of NPC assembly is at a relatively early stage. Defects in NPC assembly or homeostasis are tied to movement disorders, including dystonia and amyotrophic lateral sclerosis (ALS), as well as aging, requiring a better understanding of these processes to enable therapeutic intervention. Here, we discuss recent progress in the understanding of NPC assembly and highlight how related defects in human disorders can shed light on NPC biogenesis. We propose that the condensation of phenylalanine-glycine repeat nucleoporins needs to be carefully controlled during NPC assembly to prevent aberrant condensation, aggregation, or amyloid formation.
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Affiliation(s)
- E F Elsiena Kuiper
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Sarah M Prophet
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Christian Schlieker
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
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5
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Sontag EM, Morales-Polanco F, Chen JH, McDermott G, Dolan PT, Gestaut D, Le Gros MA, Larabell C, Frydman J. Nuclear and cytoplasmic spatial protein quality control is coordinated by nuclear-vacuolar junctions and perinuclear ESCRT. Nat Cell Biol 2023; 25:699-713. [PMID: 37081164 DOI: 10.1038/s41556-023-01128-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/14/2023] [Indexed: 04/22/2023]
Abstract
Effective protein quality control (PQC), essential for cellular health, relies on spatial sequestration of misfolded proteins into defined inclusions. Here we reveal the coordination of nuclear and cytoplasmic spatial PQC. Cytoplasmic misfolded proteins concentrate in a cytoplasmic juxtanuclear quality control compartment, while nuclear misfolded proteins sequester into an intranuclear quality control compartment (INQ). Particle tracking reveals that INQ and the juxtanuclear quality control compartment converge to face each other across the nuclear envelope at a site proximal to the nuclear-vacuolar junction marked by perinuclear ESCRT-II/III protein Chm7. Strikingly, convergence at nuclear-vacuolar junction contacts facilitates VPS4-dependent vacuolar clearance of misfolded cytoplasmic and nuclear proteins, the latter entailing extrusion of nuclear INQ into the vacuole. Finding that nuclear-vacuolar contact sites are cellular hubs of spatial PQC to facilitate vacuolar clearance of nuclear and cytoplasmic inclusions highlights the role of cellular architecture in proteostasis maintenance.
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Affiliation(s)
- Emily M Sontag
- Department of Biology, Stanford University, Stanford, CA, USA.
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.
| | | | - Jian-Hua Chen
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gerry McDermott
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Patrick T Dolan
- Department of Biology, Stanford University, Stanford, CA, USA
- Quantitative Virology and Evolution Unit, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Daniel Gestaut
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Mark A Le Gros
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Carolyn Larabell
- Department of Anatomy, School of Medicine, University of California San Francisco, San Francisco, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA.
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6
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Tai L, Yin G, Sun F, Zhu Y. Cryo-electron microscopy reveals the structure of the nuclear pore complex. J Mol Biol 2023; 435:168051. [PMID: 36933820 DOI: 10.1016/j.jmb.2023.168051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
The nuclear pore complex (NPC) is a giant protein assembly that penetrates the double layers of the nuclear membrane. The overall structure of the NPC has approximately eightfold symmetry and is formed by approximately 30 nucleoporins. The great size and complexity of the NPC have hindered the study of its structure for many years until recent breakthroughs were achieved by integrating the latest high-resolution cryo-electron microscopy (cryo-EM), the emerging artificial intelligence-based modeling and all other available structural information from crystallography and mass spectrometry. Here, we review our latest knowledge of the NPC architecture and the history of its structural study from in vitro to in situ with progressively improved resolutions by cryo-EM, with a particular focus on the latest subnanometer-resolution structural studies. The future directions for structural studies of NPCs are also discussed.
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Affiliation(s)
- Linhua Tai
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Yin
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong 510005, China.
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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7
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McGoldrick P, Lau A, You Z, Durcan TM, Robertson J. Loss of C9orf72 perturbs the Ran-GTPase gradient and nucleocytoplasmic transport, generating compositionally diverse Importin β-1 granules. Cell Rep 2023; 42:112134. [PMID: 36821445 DOI: 10.1016/j.celrep.2023.112134] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/05/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
A hexanucleotide (GGGGCC)n repeat expansion in C9orf72 causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), eliciting toxic effects through generation of RNA foci, dipeptide repeat proteins, and/or loss of C9orf72 protein. Defects in nucleocytoplasmic transport (NCT) have been implicated as a pathogenic mechanism underlying repeat expansion toxicity. Here, we show that loss of C9orf72 disrupts the Ran-GTPase gradient and NCT in vitro and in vivo. NCT disruption in vivo is enhanced by the presence of compositionally different types of cytoplasmic Importin β-1 granule that exhibit neuronal subtype-specific properties. We show that the abundance of Importin β-1 granules is increased in the context of C9orf72 deficiency, disrupting interactions with nuclear pore complex proteins. These granules appear to associate with the nuclear envelope and are co-immunoreactive for G3BP1 and K63-ubiquitin. These findings link loss of C9orf72 protein to gain-of-function mechanisms and defects in NCT.
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Affiliation(s)
- Philip McGoldrick
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada.
| | - Agnes Lau
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Zhipeng You
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Thomas M Durcan
- The Neuro's Early Drug Discovery Unit (EDDU), McGill University, 3801 University Street, Montreal, QC H3A 2B4, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada; Department of Laboratory Medicine and Pathobiology, 27 King's College Circle, Toronto, ON M5S 1A1, Canada.
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8
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Chaperoning the nuclear envelope. Nat Cell Biol 2022; 24:1563-1564. [PMID: 36302972 DOI: 10.1038/s41556-022-01013-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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9
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Atypical nuclear envelope condensates linked to neurological disorders reveal nucleoporin-directed chaperone activities. Nat Cell Biol 2022; 24:1630-1641. [PMID: 36302970 PMCID: PMC10041656 DOI: 10.1038/s41556-022-01001-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/26/2022] [Indexed: 01/18/2023]
Abstract
DYT1 dystonia is a debilitating neurological movement disorder arising from mutation in the AAA+ ATPase TorsinA. The hallmark of Torsin dysfunction is nuclear envelope blebbing resulting from defects in nuclear pore complex biogenesis. Whether blebs actively contribute to disease manifestation is unknown. We report that FG-nucleoporins in the bleb lumen form aberrant condensates and contribute to DYT1 dystonia by provoking two proteotoxic insults. Short-lived ubiquitylated proteins that are normally rapidly degraded partition into the bleb lumen and become stabilized. In addition, blebs selectively sequester a specific HSP40-HSP70 chaperone network that is modulated by the bleb component MLF2. MLF2 suppresses the ectopic accumulation of FG-nucleoporins and modulates the selective properties and size of condensates in vitro. Our study identifies dual mechanisms of proteotoxicity in the context of condensate formation and establishes FG-nucleoporin-directed activities for a nuclear chaperone network.
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10
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Mannino PJ, Lusk CP. Quality control mechanisms that protect nuclear envelope identity and function. J Biophys Biochem Cytol 2022; 221:213424. [PMID: 36036741 PMCID: PMC9442147 DOI: 10.1083/jcb.202205123] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/22/2022] Open
Abstract
The nuclear envelope (NE) is a specialization of the endoplasmic reticulum with distinct biochemistry that defines inner and outer membranes connected at a pore membrane that houses nuclear pore complexes (NPCs). Quality control mechanisms that maintain the physical integrity and biochemical identity of these membranes are critical to ensure that the NE acts as a selective barrier that also contributes to genome stability and metabolism. As the proteome of the NE is highly integrated, it is challenging to turn over by conventional ubiquitin-proteasome and autophagy mechanisms. Further, removal of entire sections of the NE requires elaborate membrane remodeling that is poorly understood. Nonetheless, recent work has made inroads into discovering specializations of cellular degradative machineries tailored to meeting the unique challenges imposed by the NE. In addition, cells have evolved mechanisms to surveil and repair the NE barrier to protect against the deleterious effects of a breach in NE integrity, in the form of either a ruptured NE or a dysfunctional NPC. Here, we synthesize the most recent work exploring NE quality control mechanisms across eukaryotes.
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11
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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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12
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The Nuclear Pore Complex: Birth, Life, and Death of a Cellular Behemoth. Cells 2022; 11:cells11091456. [PMID: 35563762 PMCID: PMC9100368 DOI: 10.3390/cells11091456] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [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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13
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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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14
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Booth A, Marklew CJ, Ciani B, Beales PA. The influence of phosphatidylserine localisation and lipid phase on membrane remodelling by the ESCRT-II/ESCRT-III complex. Faraday Discuss 2021; 232:188-202. [PMID: 34590635 DOI: 10.1039/d0fd00042f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The endosomal sorting complex required for transport (ESCRT) organises in supramolecular structures on the surface of lipid bilayers to drive membrane invagination and scission of intraluminal vesicles (ILVs), a process also controlled by membrane mechanics. However, ESCRT association with the membrane is also mediated by electrostatic interactions with anionic phospholipids. Phospholipid distribution within natural biomembranes is inhomogeneous due to, for example, the formation of lipid rafts and curvature-driven lipid sorting. Here, we have used phase-separated giant unilamellar vesicles (GUVs) to investigate the link between phosphatidylserine (PS)-rich lipid domains and ESCRT activity. We employ GUVs composed of phase separating lipid mixtures, where unsaturated DOPS and saturated DPPS lipids are incorporated individually or simultaneously to enhance PS localisation in liquid disordered (Ld) and/or liquid ordered (Lo) domains, respectively. PS partitioning between the coexisting phases is confirmed by a fluorescent Annexin V probe. Ultimately, we find that ILV generation promoted by ESCRTs is significantly enhanced when PS lipids localise within Ld domains. However, the ILVs that form are rich in Lo lipids. We interpret this surprising observation as preferential recruitment of the Lo phase beneath the ESCRT complex due to its increased rigidity, where the Ld phase is favoured in the neck of the resultant buds to facilitate the high membrane curvature in these regions of the membrane during the ILV formation process. Ld domains offer lower resistance to membrane bending, demonstrating a mechanism by which the composition and mechanics of membranes can be coupled to regulate the location and efficiency of ESCRT activity.
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Affiliation(s)
- Andrew Booth
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Christopher J Marklew
- Department of Chemistry, Centre for Membrane Interactions and Dynamics, University of Sheffield, Sheffield S3 7HF, UK
| | - Barbara Ciani
- Department of Chemistry, Centre for Membrane Interactions and Dynamics, University of Sheffield, Sheffield S3 7HF, UK
| | - Paul A Beales
- School of Chemistry, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. .,Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK
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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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Abstract
The nuclear envelope (NE) is continuous with the endoplasmic reticulum (ER), yet the NE carries out many functions distinct from those of bulk ER. This functional specialization depends on a unique protein composition that defines NE identity and must be both established and actively maintained. The NE undergoes extensive remodeling in interphase and mitosis, so mechanisms that seal NE holes and protect its unique composition are critical for maintaining its functions. New evidence shows that closure of NE holes relies on regulated de novo lipid synthesis, providing a link between lipid metabolism and generating and maintaining NE identity. Here, we review regulation of the lipid bilayers of the NE and suggest ways to generate lipid asymmetry across the NE despite its direct continuity with the ER. We also discuss the elusive mechanism of membrane fusion during nuclear pore complex (NPC) biogenesis. We propose a model in which NPC biogenesis is carefully controlled to ensure that a permeability barrier has been established before membrane fusion, thereby avoiding a major threat to compartmentalization.
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Affiliation(s)
- Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520
| | - Christian Schlieker
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520.,Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
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17
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Borah S, Thaller DJ, Hakhverdyan Z, Rodriguez EC, Isenhour AW, Rout MP, King MC, Lusk CP. Heh2/Man1 may be an evolutionarily conserved sensor of NPC assembly state. Mol Biol Cell 2021; 32:1359-1373. [PMID: 34010011 PMCID: PMC8694041 DOI: 10.1091/mbc.e20-09-0584] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Integral membrane proteins of the Lap2-emerin-MAN1 (LEM) family have emerged as important components of the inner nuclear membrane (INM) required for the functional and physical integrity of the nuclear envelope. However, like many INM proteins, there is limited understanding of the biochemical interaction networks that enable LEM protein function. Here, we show that Heh2/Man1 can interact with major scaffold components of the nuclear pore complex (NPC), specifically the inner ring complex (IRC), in evolutionarily distant yeasts. Although an N-terminal domain is required for Heh2 targeting to the INM, we demonstrate that more stable interactions with the NPC are mediated by a C-terminal winged helix (WH) domain, thus decoupling INM targeting and NPC binding. Inhibiting Heh2's interactions with the NPC by deletion of the Heh2 WH domain leads to NPC clustering. Interestingly, Heh2's association with NPCs can also be disrupted by knocking out several outer ring nucleoporins. Thus, Heh2's interaction with NPCs depends on the structural integrity of both major NPC scaffold complexes. We propose a model in which Heh2 acts as a sensor of NPC assembly state, which may be important for NPC quality control mechanisms and the segregation of NPCs during cell division.
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Affiliation(s)
- Sapan Borah
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | - David J Thaller
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | | | - Elisa C Rodriguez
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | - Anthony W Isenhour
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | | | - Megan C King
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
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18
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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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19
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One Ring to Rule them All? Structural and Functional Diversity in the Nuclear Pore Complex. Trends Biochem Sci 2021; 46:595-607. [PMID: 33563541 DOI: 10.1016/j.tibs.2021.01.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 02/07/2023]
Abstract
The nuclear pore complex (NPC) is the massive protein assembly that regulates the transport of macromolecules between the nucleus and the cytoplasm. Recent breakthroughs have provided major insights into the structure of the NPC in different eukaryotes, revealing a previously unsuspected diversity of NPC architectures. In parallel, the NPC has been shown to be a key player in regulating essential nuclear processes such as chromatin organization, gene expression, and DNA repair. However, our knowledge of the NPC structure has not been able to address the molecular mechanisms underlying its regulatory roles. We discuss potential explanations, including the coexistence of alternative NPC architectures with specific functional roles.
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20
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Schuller AP, Wojtynek M, Mankus D, Tatli M, Kronenberg-Tenga R, Regmi SG, Dip PV, Lytton-Jean AKR, Brignole EJ, Dasso M, Weis K, Medalia O, Schwartz TU. The cellular environment shapes the nuclear pore complex architecture. Nature 2021; 598:667-671. [PMID: 34646014 PMCID: PMC8550940 DOI: 10.1038/s41586-021-03985-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/01/2021] [Indexed: 12/04/2022]
Abstract
Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE)1-3. These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel4-6. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture.
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Affiliation(s)
- Anthony P. Schuller
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Matthias Wojtynek
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland ,grid.5801.c0000 0001 2156 2780Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - David Mankus
- grid.116068.80000 0001 2341 2786Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Meltem Tatli
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Rafael Kronenberg-Tenga
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Saroj G. Regmi
- grid.94365.3d0000 0001 2297 5165Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD USA
| | - Phat V. Dip
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786MIT.nano, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Abigail K. R. Lytton-Jean
- grid.116068.80000 0001 2341 2786Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Edward J. Brignole
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786MIT.nano, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Mary Dasso
- grid.94365.3d0000 0001 2297 5165Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD USA
| | - Karsten Weis
- grid.5801.c0000 0001 2156 2780Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ohad Medalia
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Thomas U. Schwartz
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA
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21
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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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22
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Lord CL, Wente SR. Nuclear envelope-vacuole contacts mitigate nuclear pore complex assembly stress. J Cell Biol 2020; 219:211463. [PMID: 33053148 PMCID: PMC7563749 DOI: 10.1083/jcb.202001165] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 08/10/2020] [Accepted: 09/23/2020] [Indexed: 01/04/2023] Open
Abstract
The intricacy of nuclear pore complex (NPC) biogenesis imposes risks of failure that can cause defects in nuclear transport and nuclear envelope (NE) morphology; however, cellular mechanisms used to alleviate NPC assembly stress are not well defined. In the budding yeast Saccharomyces cerevisiae, we demonstrate that NVJ1- and MDM1-enriched NE-vacuole contacts increase when NPC assembly is compromised in several nup mutants, including nup116ΔGLFG cells. These interorganelle nucleus-vacuole junctions (NVJs) cooperate with lipid droplets to maintain viability and enhance NPC formation in assembly mutants. Additionally, NVJs function with ATG1 to remodel the NE and promote vacuole-dependent degradation of specific nucleoporins in nup116ΔGLFG cells. Importantly, NVJs significantly improve the physiology of NPC assembly mutants, despite having only negligible effects when NPC biogenesis is unperturbed. These results therefore define how NE-vacuole interorganelle contacts coordinate responses to mitigate deleterious cellular effects caused by disrupted NPC assembly.
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23
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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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24
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Gross AS, Graef M. Stress eating: Autophagy targets nuclear pore complexes. J Cell Biol 2020; 219:e202006007. [PMID: 32584933 PMCID: PMC7337487 DOI: 10.1083/jcb.202006007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Lee et al. (2020. Nat. Cell Biol.https://doi.org/10.1038/s41556-019-0459-2) and, in this issue, Tomioka et al. (2020. J. Cell Biol.https://doi.org/10.1083/jcb.201910063) describe the targeted degradation of nuclear pore complexes (NPCs) by selective autophagy, providing insight into the mechanisms of turnover for individual nucleoporins and entire NPCs.
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Affiliation(s)
| | - Martin Graef
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster for Aging and Age-Associated Diseases, University of Cologne, Cologne, Germany
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25
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Lusk CP, Ader NR. CHMPions of repair: Emerging perspectives on sensing and repairing the nuclear envelope barrier. Curr Opin Cell Biol 2020; 64:25-33. [PMID: 32105978 PMCID: PMC7371540 DOI: 10.1016/j.ceb.2020.01.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/20/2022]
Abstract
Understanding how the integrity of the nuclear membranes is protected against internal and external stresses is an emergent challenge. Work reviewed here investigated the mechanisms by which losses of nuclear-cytoplasmic compartmentalization are sensed and ameliorated. Fundamental to these is spatial control over interactions between the endosomal sorting complexes required for transport machinery and LAP2-emerin-MAN1 family inner nuclear membrane proteins, which together promote nuclear envelope sealing in interphase and at the end of mitosis. We suggest that the size of the nuclear envelope hole dictates the mechanism of its repair, with larger holes requiring barrier-to-autointegration factor and the potential triggering of a postmitotic nuclear envelope reassembly pathway in interphase. We also consider why these mechanisms fail at ruptured micronuclei. Together, this work re-emphasizes the need to understand how membrane flow and local lipid metabolism help ensure that the nuclear envelope is refractory to mechanical rupture yet fluid enough to allow its essential dynamics.
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Affiliation(s)
- C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, 295 Congress Avenue, New Haven, CT, 06520, USA.
| | - Nicholas R Ader
- Department of Cell Biology, Yale School of Medicine, 295 Congress Avenue, New Haven, CT, 06520, USA
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26
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Rampello AJ, Laudermilch E, Vishnoi N, Prophet SM, Shao L, Zhao C, Lusk CP, Schlieker C. Torsin ATPase deficiency leads to defects in nuclear pore biogenesis and sequestration of MLF2. J Cell Biol 2020; 219:151708. [PMID: 32342107 PMCID: PMC7265317 DOI: 10.1083/jcb.201910185] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/11/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022] Open
Abstract
Nuclear envelope herniations (blebs) containing FG-nucleoporins and ubiquitin are the phenotypic hallmark of Torsin ATPase manipulation. Both the dynamics of blebbing and the connection to nuclear pore biogenesis remain poorly understood. We employ a proteomics-based approach to identify myeloid leukemia factor 2 (MLF2) as a luminal component of the bleb. Using an MLF2-based live-cell imaging platform, we demonstrate that nuclear envelope blebbing occurs rapidly and synchronously immediately after nuclear envelope reformation during mitosis. Bleb formation is independent of ubiquitin conjugation within the bleb, but strictly dependent on POM121, a transmembrane nucleoporin essential for interphase nuclear pore biogenesis. Nup358, a late marker for interphase nuclear pore complex (NPC) biogenesis, is underrepresented relative to FG-nucleoporins in nuclear envelopes of Torsin-deficient cells. The kinetics of bleb formation, its dependence on POM121, and a reduction of mature NPCs in Torsin-deficient cells lead us to conclude that the hallmark phenotype of Torsin manipulation represents aberrant NPC intermediates.
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Affiliation(s)
- Anthony J Rampello
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Ethan Laudermilch
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Nidhi Vishnoi
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Sarah M Prophet
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Lin Shao
- Department of Neuroscience, Yale School of Medicine, New Haven, CT
| | - Chenguang Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - C Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Christian Schlieker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.,Department of Cell Biology, Yale School of Medicine, New Haven, CT
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27
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The Role of Torsin AAA+ Proteins in Preserving Nuclear Envelope Integrity and Safeguarding Against Disease. Biomolecules 2020; 10:biom10030468. [PMID: 32204310 PMCID: PMC7175109 DOI: 10.3390/biom10030468] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/17/2022] Open
Abstract
Torsin ATPases are members of the AAA+ (ATPases associated with various cellular activities) superfamily of proteins, which participate in essential cellular processes. While AAA+ proteins are ubiquitously expressed and demonstrate distinct subcellular localizations, Torsins are the only AAA+ to reside within the nuclear envelope (NE) and endoplasmic reticulum (ER) network. Moreover, due to the absence of integral catalytic features, Torsins require the NE- and ER-specific regulatory cofactors, lamina-associated polypeptide 1 (LAP1) and luminal domain like LAP1 (LULL1), to efficiently trigger their atypical mode of ATP hydrolysis. Despite their implication in an ever-growing list of diverse processes, the specific contributions of Torsin/cofactor assemblies in maintaining normal cellular physiology remain largely enigmatic. Resolving gaps in the functional and mechanistic principles of Torsins and their cofactors are of considerable medical importance, as aberrant Torsin behavior is the principal cause of the movement disorder DYT1 early-onset dystonia. In this review, we examine recent findings regarding the phenotypic consequences of compromised Torsin and cofactor activities. In particular, we focus on the molecular features underlying NE defects and the contributions of Torsins to nuclear pore complex biogenesis, as well as the growing implications of Torsins in cellular lipid metabolism. Additionally, we discuss how understanding Torsins may facilitate the study of essential but poorly understood processes at the NE and ER, and aid in the development of therapeutic strategies for dystonia.
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28
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Lee CW, Wilfling F, Ronchi P, Allegretti M, Mosalaganti S, Jentsch S, Beck M, Pfander B. Selective autophagy degrades nuclear pore complexes. Nat Cell Biol 2020; 22:159-166. [DOI: 10.1038/s41556-019-0459-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 12/17/2019] [Indexed: 01/02/2023]
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29
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Rempel IL, Steen A, Veenhoff LM. Poor old pores-The challenge of making and maintaining nuclear pore complexes in aging. FEBS J 2020; 287:1058-1075. [PMID: 31912972 PMCID: PMC7154712 DOI: 10.1111/febs.15205] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/20/2019] [Accepted: 01/06/2020] [Indexed: 12/11/2022]
Abstract
The nuclear pore complex (NPC) is the sole gateway to the nuclear interior, and its function is essential to all eukaryotic life. Controlling the functionality of NPCs is a tremendous challenge for cells. Firstly, NPCs are large structures, and their complex assembly does occasionally go awry. Secondly, once assembled, some components of the NPC persist for an extremely long time and, as a result, are susceptible to accumulate damage. Lastly, a significant proportion of the NPC is composed of intrinsically disordered proteins that are prone to aggregation. In this review, we summarize how the quality of NPCs is guarded in young cells and discuss the current knowledge on the fate of NPCs during normal aging in different tissues and organisms. We discuss the extent to which current data supports a hypothesis that NPCs are poorly maintained during aging of nondividing cells, while in dividing cells the main challenge is related to the assembly of new NPCs. Our survey of current knowledge points toward NPC quality control as an important node in aging of both dividing and nondividing cells. Here, the loss of protein homeostasis during aging is central and the NPC appears to both be impacted by, and to drive, this process.
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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, The Netherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, The Netherlands
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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: 47] [Impact Index Per Article: 9.4] [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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31
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Booth A, Marklew CJ, Ciani B, Beales PA. In Vitro Membrane Remodeling by ESCRT is Regulated by Negative Feedback from Membrane Tension. iScience 2019; 15:173-184. [PMID: 31060000 PMCID: PMC6503128 DOI: 10.1016/j.isci.2019.04.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/08/2019] [Accepted: 04/17/2019] [Indexed: 01/08/2023] Open
Abstract
Artificial cells can shed new light on the molecular basis for life and hold potential for new chemical technologies. Inspired by how nature dynamically regulates its membrane compartments, we aim to repurpose the endosomal sorting complex required for transport (ESCRT) to generate complex membrane architectures as suitable scaffolds for artificial cells. Purified ESCRT-III components perform topological transformations on giant unilamellar vesicles to create complex “vesicles-within-a-vesicle” architectures resembling the compartmentalization in eukaryotic cells. Thus far, the proposed mechanisms for this activity are based on how assembly and disassembly of ESCRT-III on the membrane drives deformation. Here we demonstrate the existence of a negative feedback mechanism from membrane mechanics that regulates ESCRT-III remodeling activity. Intraluminal vesicle (ILV) formation removes excess membrane area, increasing tension, which in turn suppresses downstream ILV formation. This mechanism for in vitro regulation of ESCRT-III activity may also have important implications for its in vivo functions. ESCRT proteins are used to create compartmentalized artificial cell architectures In vitro ESCRT activity is weakly dependent on the stoichiometry of Vps20 or Vps24 ESCRT function is strongly regulated by membrane tension Membrane tension provides a negative feedback mechanism to attenuate remodeling
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Affiliation(s)
- Andrew Booth
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Christopher J Marklew
- Department of Chemistry and Centre for Membrane Interactions and Dynamics, University of Sheffield, Sheffield S3 7HF, UK
| | - Barbara Ciani
- Department of Chemistry and Centre for Membrane Interactions and Dynamics, University of Sheffield, Sheffield S3 7HF, UK.
| | - Paul A Beales
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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32
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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: 73] [Impact Index Per Article: 14.6] [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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33
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Chalfant M, Barber KW, Borah S, Thaller D, Lusk CP. Expression of TorsinA in a heterologous yeast system reveals interactions with lumenal domains of LINC and nuclear pore complex components. Mol Biol Cell 2019; 30:530-541. [PMID: 30625036 PMCID: PMC6589686 DOI: 10.1091/mbc.e18-09-0585] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
DYT1 dystonia is caused by an in-frame deletion of a glutamic acid codon in the gene encoding the AAA+ ATPase TorsinA (TorA). TorA localizes within the lumen of the nuclear envelope/endoplasmic reticulum and binds to a membrane-spanning cofactor, lamina associated polypeptide 1 (LAP1) or lumenal domain like LAP1 (LULL1), to form an ATPase; the substrate(s) of TorA remains ill-defined. Here we use budding yeast, which lack Torsins, to interrogate TorA function. We show that TorA accumulates at nuclear envelope-embedded spindle pole bodies (SPBs) in a way that requires its oligomerization and the SUN (Sad1 and UNc-84)-domain protein, Mps3. We further show that TorA physically interacts with human SUN1/2 within this system, supporting the physiological relevance of these interactions. Consistent with the idea that TorA acts on a SPB substrate, its binding to SPBs is modulated by the ATPase-stimulating activity of LAP1. TorA and TorA-ΔE reduce the fitness of cells expressing mps3 alleles, whereas TorA alone inhibits growth of cells lacking Pom152, a component of the nuclear pore complex. This genetic specificity is mirrored biochemically as TorA, but not TorA-ΔE, binds Pom152. Thus, TorA–nucleoporin interactions might be abrogated by TorA-ΔE, suggesting new experimental avenues to interrogate the molecular basis behind nuclear envelope herniations seen in mammalian cells lacking TorA function.
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Affiliation(s)
| | - Karl W. Barber
- Department of Cellular and Molecular Physiology, Yale School of Medicine, Yale University, New Haven, CT 06520
- Systems Biology Institute, Yale University, West Haven, CT 06477
| | - Sapan Borah
- Department of Cell Biology, Yale University, New Haven, CT 06520
| | - David Thaller
- Department of Cell Biology, Yale University, New Haven, CT 06520
| | - C. Patrick Lusk
- Department of Cell Biology, Yale University, New Haven, CT 06520
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34
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Blank spots on the map: some current questions on nuclear organization and genome architecture. Histochem Cell Biol 2018; 150:579-592. [PMID: 30238154 DOI: 10.1007/s00418-018-1726-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
The past decades have provided remarkable insights into how the eukaryotic cell nucleus and the genome within it are organized. The combined use of imaging, biochemistry and molecular biology approaches has revealed several basic principles of nuclear architecture and function, including the existence of chromatin domains of various sizes, the presence of a large number of non-membranous intranuclear bodies, non-random positioning of genes and chromosomes in 3D space, and a prominent role of the nuclear lamina in organizing genomes. Despite this tremendous progress in elucidating the biological properties of the cell nucleus, many questions remain. Here, we highlight some of the key open areas of investigation in the field of nuclear organization and genome architecture with a particular focus on the mechanisms and principles of higher-order genome organization, the emerging role of liquid phase separation in cellular organization, and the functional role of the nuclear lamina in physiological processes.
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