1
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Keeley O, Coyne AN. Nuclear and degradative functions of the ESCRT-III pathway: implications for neurodegenerative disease. Nucleus 2024; 15:2349085. [PMID: 38700207 PMCID: PMC11073439 DOI: 10.1080/19491034.2024.2349085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
The ESCRT machinery plays a pivotal role in membrane-remodeling events across multiple cellular processes including nuclear envelope repair and reformation, nuclear pore complex surveillance, endolysosomal trafficking, and neuronal pruning. Alterations in ESCRT-III functionality have been associated with neurodegenerative diseases including Frontotemporal Dementia (FTD), Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Disease (AD). In addition, mutations in specific ESCRT-III proteins have been identified in FTD/ALS. Thus, understanding how disruptions in the fundamental functions of this pathway and its individual protein components in the human central nervous system (CNS) may offer valuable insights into mechanisms underlying neurodegenerative disease pathogenesis and identification of potential therapeutic targets. In this review, we discuss ESCRT components, dynamics, and functions, with a focus on the ESCRT-III pathway. In addition, we explore the implications of altered ESCRT-III function for neurodegeneration with a primary emphasis on nuclear surveillance and endolysosomal trafficking within the CNS.
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Affiliation(s)
- Olivia Keeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyssa N. Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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2
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Butterfield ER, Obado SO, Scutts SR, Zhang W, Chait BT, Rout MP, Field MC. A lineage-specific protein network at the trypanosome nuclear envelope. Nucleus 2024; 15:2310452. [PMID: 38605598 PMCID: PMC11018031 DOI: 10.1080/19491034.2024.2310452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024] Open
Abstract
The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
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Affiliation(s)
| | - Samson O. Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Simon R. Scutts
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
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3
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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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4
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Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. The molecular architecture of the nuclear basket. Cell 2024:S0092-8674(24)00780-3. [PMID: 39127037 DOI: 10.1016/j.cell.2024.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/24/2024] [Accepted: 07/12/2024] [Indexed: 08/12/2024]
Abstract
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of nucleoporins (Nups) in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.
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Affiliation(s)
- Digvijay Singh
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neelesh Soni
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Farhaz Shaikh
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Madeleine Duquette
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sergey Suslov
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kelly Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P.R. China
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA; Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain; Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Elizabeth Villa
- School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.
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5
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Skowicki M, Tarvirdipour S, Kraus M, Schoenenberger CA, Palivan CG. Nanoassemblies designed for efficient nuclear targeting. Adv Drug Deliv Rev 2024; 211:115354. [PMID: 38857762 DOI: 10.1016/j.addr.2024.115354] [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: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
One of the key aspects of coping efficiently with complex pathological conditions is delivering the desired therapeutic compounds with precision in both space and time. Therefore, the focus on nuclear-targeted delivery systems has emerged as a promising strategy with high potential, particularly in gene therapy and cancer treatment. Here, we explore the design of supramolecular nanoassemblies as vehicles to deliver specific compounds to the nucleus, with the special focus on polymer and peptide-based carriers that expose nuclear localization signals. Such nanoassemblies aim at maximizing the concentration of genetic and therapeutic agents within the nucleus, thereby optimizing treatment outcomes while minimizing off-target effects. A complex scenario of conditions, including cellular uptake, endosomal escape, and nuclear translocation, requires fine tuning of the nanocarriers' properties. First, we introduce the principles of nuclear import and the role of nuclear pore complexes that reveal strategies for targeting nanosystems to the nucleus. Then, we provide an overview of cargoes that rely on nuclear localization for optimal activity as their integrity and accumulation are crucial parameters to consider when designing a suitable delivery system. Considering that they are in their early stages of research, we present various cargo-loaded peptide- and polymer nanoassemblies that promote nuclear targeting, emphasizing their potential to enhance therapeutic response. Finally, we briefly discuss further advancements for more precise and effective nuclear delivery.
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Affiliation(s)
- Michal Skowicki
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Shabnam Tarvirdipour
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Manuel Kraus
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
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6
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Smits DJ, Dekker J, Douben H, Schot R, Magee H, Bakhtiari S, Koehler K, Huebner A, Schuelke M, Darvish H, Vosoogh S, Tafakhori A, Jameie M, Taghiabadi E, Wilson Y, Shah M, van Slegtenhorst MA, Medici-van den Herik EG, van Ham TJ, Kruer MC, Mancini GMS. Biallelic NDC1 variants that interfere with ALADIN binding are associated with neuropathy and triple A-like syndrome. HGG ADVANCES 2024; 5:100327. [PMID: 39003500 DOI: 10.1016/j.xhgg.2024.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/15/2024] Open
Abstract
Nuclear pore complexes (NPCs) regulate nucleocytoplasmic transport and are anchored in the nuclear envelope by the transmembrane nucleoporin NDC1. NDC1 is essential for post-mitotic NPC assembly and the recruitment of ALADIN to the nuclear envelope. While no human disorder has been associated to one of the three transmembrane nucleoporins, biallelic variants in AAAS, encoding ALADIN, cause triple A syndrome (Allgrove syndrome). Triple A syndrome, characterized by alacrima, achalasia, and adrenal insufficiency, often includes progressive demyelinating polyneuropathy and other neurological complaints. In this report, diagnostic exome and/or RNA sequencing was performed in seven individuals from four unrelated consanguineous families with AAAS-negative triple A syndrome. Molecular and clinical studies followed to elucidate the pathogenic mechanism. The affected individuals presented with intellectual disability, motor impairment, severe demyelinating with secondary axonal polyneuropathy, alacrima, and achalasia. None of the affected individuals has adrenal insufficiency. All individuals presented with biallelic NDC1 in-frame deletions or missense variants that affect amino acids and protein domains required for ALADIN binding. No other significant variants associated with the phenotypic features were reported. Skin fibroblasts derived from affected individuals show decreased recruitment of ALADIN to the NE and decreased post-mitotic NPC insertion, confirming pathogenicity of the variants. Taken together, our results implicate biallelic NDC1 variants in the pathogenesis of polyneuropathy and a triple A-like disorder without adrenal insufficiency, by interfering with physiological NDC1 functions, including the recruitment of ALADIN to the NPC.
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Affiliation(s)
- Daphne J Smits
- Department of Clinical Genetics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands.
| | - Jordy Dekker
- Department of Clinical Genetics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Hannie Douben
- Department of Clinical Genetics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Rachel Schot
- Department of Clinical Genetics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Helen Magee
- Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Somayeh Bakhtiari
- Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Katrin Koehler
- Department of Pediatrics, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Angela Huebner
- Department of Pediatrics, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Markus Schuelke
- Department of Neuropediatrics and NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Hossein Darvish
- Neuroscience Research Center, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Shohreh Vosoogh
- Clinical Research Development Unit (CRDU), Sayad Shirazi Hospital, Golestan University of Medical Sciences, Gorgan, Iran
| | - Abbas Tafakhori
- Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Melika Jameie
- Iranian Center of Neurological Research, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Taghiabadi
- Skin and Stem Cell Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Yana Wilson
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Cerebral Palsy Alliance Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Margit Shah
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospitals Network, Westmead, NSW, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marjon A van Slegtenhorst
- Department of Clinical Genetics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Evita G Medici-van den Herik
- Department of Neurology, Section of Child Neurology, Erasmus University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
| | - Michael C Kruer
- Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ 85016, USA; Departments of Child Health, Neurology, Cellular & Molecular Medicine and Program in Genetics, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, USA
| | - Grazia M S Mancini
- Department of Clinical Genetics, Erasmus University Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands
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7
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Liao Y, Andronov L, Liu X, Lin J, Guerber L, Lu L, Agote-Arán A, Pangou E, Ran L, Kleiss C, Qu M, Schmucker S, Cirillo L, Zhang Z, Riveline D, Gotta M, Klaholz BP, Sumara I. UBAP2L ensures homeostasis of nuclear pore complexes at the intact nuclear envelope. J Cell Biol 2024; 223:e202310006. [PMID: 38652117 PMCID: PMC11040503 DOI: 10.1083/jcb.202310006] [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: 10/03/2023] [Revised: 02/15/2024] [Accepted: 03/12/2024] [Indexed: 04/25/2024] Open
Abstract
Assembly of macromolecular complexes at correct cellular sites is crucial for cell function. Nuclear pore complexes (NPCs) are large cylindrical assemblies with eightfold rotational symmetry, built through hierarchical binding of nucleoporins (Nups) forming distinct subcomplexes. Here, we uncover a role of ubiquitin-associated protein 2-like (UBAP2L) in the assembly and stability of properly organized and functional NPCs at the intact nuclear envelope (NE) in human cells. UBAP2L localizes to the nuclear pores and facilitates the formation of the Y-complex, an essential scaffold component of the NPC, and its localization to the NE. UBAP2L promotes the interaction of the Y-complex with POM121 and Nup153, the critical upstream factors in a well-defined sequential order of Nups assembly onto NE during interphase. Timely localization of the cytoplasmic Nup transport factor fragile X-related protein 1 (FXR1) to the NE and its interaction with the Y-complex are likewise dependent on UBAP2L. Thus, this NPC biogenesis mechanism integrates the cytoplasmic and the nuclear NPC assembly signals and ensures efficient nuclear transport, adaptation to nutrient stress, and cellular proliferative capacity, highlighting the importance of NPC homeostasis at the intact NE.
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Affiliation(s)
- Yongrong Liao
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Leonid Andronov
- 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
- Department of Integrated Structural Biology, Centre for Integrative Biology, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Xiaotian Liu
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Junyan Lin
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Lucile Guerber
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Linjie Lu
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Arantxa Agote-Arán
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Evanthia Pangou
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Li Ran
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Charlotte Kleiss
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Mengdi Qu
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Stephane Schmucker
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Luca Cirillo
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Zhirong Zhang
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Daniel Riveline
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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
| | - Monica Gotta
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Bruno P. Klaholz
- 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
- Department of Integrated Structural Biology, Centre for Integrative Biology, Institute of Genetics and Molecular and Cellular Biology, Illkirch, France
| | - Izabela Sumara
- Department of Development and Stem Cells, Institute of Genetics and Molecular and Cellular Biology, 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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8
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Guo Y, Tao T, Wu T, Hou J, Lin W. Nucleoporin Nup98 is an essential factor for ipo4 dependent protein import. J Cell Biochem 2024; 125:e30573. [PMID: 38780165 DOI: 10.1002/jcb.30573] [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: 11/16/2023] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Nucleocytoplasmic transport of macromolecules is essential in eukaryotic cells. In this process, the karyopherins play a central role when they transport cargoes across the nuclear pore complex. Importin 4 belongs to the karyopherin β family. Many studies have focused on finding substrates for importin 4, but no direct mechanism studies of its precise transport function have been reported. Therefore, this paper mainly aimed to study the mechanism of nucleoporins in mediating nuclear import and export of importin 4. To address this question, we constructed shRNAs targeting Nup358, Nup153, Nup98, and Nup50. We found that depletion of Nup98 resulted in a shift in the subcellular localization of importin 4 from the cytoplasm to the nucleus. Mutational analysis demonstrated that Nup98 physically and functionally interacts with importin 4 through its N-terminal phenylalanine-glycine (FG) repeat region. Mutation of nine of these FG motifs to SG motifs significantly attenuated the binding of Nup98 to importin 4, and we further confirmed the essential role of the six FG motifs in amino acids 121-360 of Nup98 in binding with importin 4. In vitro transport assay also confirmed that VDR, the substrate of importin 4, could not be transported into the nucleus after Nup98 knockdown. Overall, our results showed that Nup98 is required for efficient importin 4-mediated transport. This is the first study to reveal the mechanism of importin 4 in transporting substrates into the nucleus.
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Affiliation(s)
- Yingying Guo
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiame, Fujian, China
| | - Tao Tao
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiame, Fujian, China
| | - Ting Wu
- Department of Basic Medicine, School of Medicine, Cancer Research Center, Xiamen University, Xiamen, Fujian, China
| | - Jingjing Hou
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiame, Fujian, China
- Department of Gastrointestinal Surgery, School of Medicine, Zhongshan Hospital of Xiamen University, Xiamen University, Xiamen, Fujian, China
| | - Wenbo Lin
- State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiame, Fujian, China
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9
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Tang Y, Yang X, Huang A, Seong K, Ye M, Li M, Zhao Q, Krasileva K, Gu Y. Proxiome assembly of the plant nuclear pore reveals an essential hub for gene expression regulation. NATURE PLANTS 2024; 10:1005-1017. [PMID: 38773271 DOI: 10.1038/s41477-024-01698-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/11/2024] [Indexed: 05/23/2024]
Abstract
The nuclear pore complex (NPC) is vital for nucleocytoplasmic communication. Recent evidence emphasizes its extensive association with proteins of diverse functions, suggesting roles beyond cargo transport. Yet, our understanding of NPC's composition and functionality at this extended level remains limited. Here, through proximity-labelling proteomics, we uncover both local and global NPC-associated proteome in Arabidopsis, comprising over 500 unique proteins, predominantly associated with NPC's peripheral extension structures. Compositional analysis of these proteins revealed that the NPC concentrates chromatin remodellers, transcriptional regulators and mRNA processing machineries in the nucleoplasmic region while recruiting translation regulatory machinery on the cytoplasmic side, achieving a remarkable orchestration of the genetic information flow by coupling RNA transcription, maturation, transport and translation regulation. Further biochemical and structural modelling analyses reveal that extensive interactions with nucleoporins, along with phase separation mediated by substantial intrinsically disordered proteins, may drive the formation of the unexpectedly large nuclear pore proteome assembly.
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Affiliation(s)
- Yu Tang
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, Shandong, China
| | - Xiangyun Yang
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, Shandong, China
| | - Aobo Huang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Mao Ye
- Institute of Advanced Agricultural Sciences, Peking University, Weifang, Shandong, China
| | - Mengting Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qiao Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Ksenia Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
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10
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Feng Q, Saladin M, Wu C, Cao E, Zheng W, Zhang A, Bhardwaj P, Li X, Shen Q, Kapinos LE, Mariappan M, Lusk CP, Xiong Y, Lim RYH, Lin C. Channel width modulates the permeability of DNA origami based nuclear pore mimics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593438. [PMID: 38766144 PMCID: PMC11100828 DOI: 10.1101/2024.05.09.593438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Nucleoporins (nups) in the central channel of nuclear pore complexes (NPCs) form a selective barrier that suppresses the diffusion of most macromolecules while enabling rapid transport of nuclear transport receptors (NTRs) with bound cargos. The complex molecular interactions between nups and NTRs have been thought to underlie the gatekeeping function of the NPC. Recent studies have shown considerable variation in NPC diameter but how altering NPC diameter might impact the selective barrier properties remains unclear. Here, we build DNA nanopores with programmable diameters and nup arrangement to mimic NPCs of different diameters. We use hepatitis B virus (HBV) capsids as a model for large-size cargos. We find that Nup62 proteins form a dynamic cross-channel meshwork impermeable to HBV capsids when grafted on the interior of 60-nm wide nanopores but not in 79-nm pores, where Nup62 cluster locally. Furthermore, importing substantially changes the dynamics of Nup62 assemblies and facilitates the passage of HBV capsids through NPC mimics containing Nup62 and Nup153. Our study shows the transport channel width is critical to the permeability of nup barriers and underscores the role of NTRs in dynamically remodeling nup assemblies and mediating the nuclear entry of viruses.
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Affiliation(s)
- Qingzhou Feng
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Chunxiang Wu
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Eason Cao
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | - Wei Zheng
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Amy Zhang
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Xia Li
- Department of Cell Biology, Yale School of Medicine, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biophysics and Biochemistry, Yale University, USA
| | | | - Malaiyalam Mariappan
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
| | | | - Yong Xiong
- Department of Biophysics and Biochemistry, Yale University, USA
| | - Roderick Y. H. Lim
- Biozentrum, University of Basel, Switzerland
- Swiss Nanoscience Institute, University of Basel, Switzerland
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, USA
- Nanobiology Institute, Yale University, USA
- Department of Biomedical Engineering, Yale University, USA
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11
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James C, Möller U, Spillner C, König S, Dybkov O, Urlaub H, Lenz C, Kehlenbach RH. Phosphorylation of ELYS promotes its interaction with VAPB at decondensing chromosomes during mitosis. EMBO Rep 2024; 25:2391-2417. [PMID: 38605278 PMCID: PMC11094025 DOI: 10.1038/s44319-024-00125-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
ELYS is a nucleoporin that localizes to the nuclear side of the nuclear pore complex (NPC) in interphase cells. In mitosis, it serves as an assembly platform that interacts with chromatin and then with nucleoporin subcomplexes to initiate post-mitotic NPC assembly. Here we identify ELYS as a major binding partner of the membrane protein VAPB during mitosis. In mitosis, ELYS becomes phosphorylated at many sites, including a predicted FFAT (two phenylalanines in an acidic tract) motif, which mediates interaction with the MSP (major sperm protein)-domain of VAPB. Binding assays using recombinant proteins or cell lysates and co-immunoprecipitation experiments show that VAPB binds the FFAT motif of ELYS in a phosphorylation-dependent manner. In anaphase, the two proteins co-localize to the non-core region of the newly forming nuclear envelope. Depletion of VAPB results in prolonged mitosis, slow progression from meta- to anaphase and in chromosome segregation defects. Together, our results suggest a role of VAPB in mitosis upon recruitment to or release from ELYS at the non-core region of the chromatin in a phosphorylation-dependent manner.
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Affiliation(s)
- Christina James
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Ulrike Möller
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Christiane Spillner
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Sabine König
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christof Lenz
- Bioanalytics Group, Institute of Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
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12
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Han Y, Sha H, Yang Y, Yu Z, Zhou L, Wang Y, Yang F, Qiu L, Zhang Y, Zhou J. Mutations in the NUP93, NUP107 and NUP160 genes cause steroid-resistant nephrotic syndrome in Chinese children. Ital J Pediatr 2024; 50:81. [PMID: 38650033 PMCID: PMC11036785 DOI: 10.1186/s13052-024-01656-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 04/07/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The variants of nucleoporins are extremely rare in hereditary steroid-resistant nephrotic syndrome (SRNS). Most of the patients carrying such variants progress to end stage kidney disease (ESKD) in their childhood. More clinical and genetic data from these patients are needed to characterize their genotype-phenotype relationships and elucidate the role of nucleoporins in SRNS. METHODS Four patients of SRNS carrying biallelic variants in the NUP93, NUP107 and NUP160 genes were presented. The clinical and molecular genetic characteristics of these patients were summarized, and relevant literature was reviewed. RESULTS All four patients in this study were female and initially presented with SRNS. The median age at the onset of the disease was 5.08 years, ranging from 1 to 10.5 years. Among the four patients, three progressed to ESKD at a median age of 7 years, ranging from 1.5 to 10.5 years, while one patient reached stage 3 chronic kidney disease (CKD3). Kidney biopsies revealed focal segmental glomerulosclerosis in three patients. Biallelic variants were detected in NUP93 in one patient, NUP107 in two patients, as well as NUP160 in one patient respectively. Among these variants, five yielded single amino acid substitutions, one led to nonsense mutation causing premature termination of NUP107 translation, one caused a single nucleotide deletion resulting in frameshift and truncation of NUP107. Furthermore, one splicing donor mutation was observed in NUP160. None of these variants had been reported previously. CONCLUSION This report indicates that biallelic variants in NUP93, NUP107 and NUP160 can cause severe early-onset SRNS, which rapidly progresses to ESKD. Moreover, these findings expand the spectrum of phenotypes and genotypes and highlight the importance of next-generation sequencing in elucidating the molecular basis of SRNS and allowing rational treatment for affected individuals.
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Affiliation(s)
- Yanxinli Han
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei province, 430030, China
| | - Hongyu Sha
- Department of Pharmacy, Yantai Yuhuangding Hospital, Yantai, Shandong Province, 264000, China
| | - Yuan Yang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei province, 430030, China
| | - Zhuowei Yu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei province, 430030, China
| | - Lanqi Zhou
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei province, 430030, China
| | - Yi Wang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei province, 430030, China
| | - Fengjie Yang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei province, 430030, China
| | - Liru Qiu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei province, 430030, China
| | - Yu Zhang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei province, 430030, China
| | - Jianhua Zhou
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei province, 430030, China.
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13
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Shakhi PK, Bijeesh MM, Hareesh J, Joseph T, Nandakumar P, K. Varier G. Size-dependent steady state saturation limit in biomolecular transport through nuclear membranes. PLoS One 2024; 19:e0297738. [PMID: 38626108 PMCID: PMC11020410 DOI: 10.1371/journal.pone.0297738] [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: 10/02/2023] [Accepted: 01/11/2024] [Indexed: 04/18/2024] Open
Abstract
The nucleus preserves the genomic DNA of eukaryotic organisms and maintains the integrity of the cell by regulating the transport of molecules across the nuclear membrane. It is hitherto assumed that small molecules having a size below the passive permeability limit are allowed to diffuse freely to the nucleus while the transport of larger molecules is regulated via an active mechanism involving energy. Here we report on the kinetics of nuclear import and export of dextran molecules having a size below the passive permeability limit. The studies carried out using time-lapse confocal fluorescence microscopy show a clear deviation from the passive diffusion model. In particular, it is observed that the steady-state concentration of dextran molecules inside the nucleus is consistently less than the concentration outside, in contradiction to the predictions of the passive diffusion model. Detailed analysis and modeling of the transport show that the nuclear export rates significantly differ from the import rates, and the difference in rates is dependent on the size of the molecules. The nuclear export rates are further confirmed by an independent experimental study where we observe the diffusion of dextran molecules from the nucleus directly. Our experiments and transport model would suggest that the nucleus actively rejects exogenous macromolecules even below the passive permeability limit. This result can have a significant impact on biomedical research, especially in areas related to targeted drug delivery and gene therapy.
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Affiliation(s)
- P. K. Shakhi
- Department of Physics, BITS Pilani K. K. Birla Goa Campus, Goa, India
| | - M. M. Bijeesh
- Department of Physics, BITS Pilani K. K. Birla Goa Campus, Goa, India
| | - J. Hareesh
- Department of Physics, BITS Pilani K. K. Birla Goa Campus, Goa, India
| | - Toby Joseph
- Department of Physics, BITS Pilani K. K. Birla Goa Campus, Goa, India
| | - P. Nandakumar
- Department of Physics, BITS Pilani K. K. Birla Goa Campus, Goa, India
| | - Geetha K. Varier
- Department of Physics, BITS Pilani K. K. Birla Goa Campus, Goa, India
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14
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Ikeda T, Yamazaki K, Okumura F, Kamura T, Nakatsukasa K. Role of the San1 ubiquitin ligase in the heat stress-induced degradation of nonnative Nup1 in the nuclear pore complex. Genetics 2024; 226:iyae017. [PMID: 38302116 DOI: 10.1093/genetics/iyae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 11/21/2022] [Accepted: 01/23/2024] [Indexed: 02/03/2024] Open
Abstract
The nuclear pore complex (NPC) mediates the selective exchange of macromolecules between the nucleus and the cytoplasm. Neurodegenerative diseases such as amyotrophic lateral sclerosis are characterized by mislocalization of nucleoporins (Nups), transport receptors, and Ras-related nuclear proteins into nucleoplasmic or cytosolic aggregates, underscoring the importance of precise assembly of the NPC. The assembly state of large protein complexes is strictly monitored by the protein quality control system. The ubiquitin-proteasome system may eliminate aberrant, misfolded, and/or orphan components; however, the involvement of the ubiquitin-proteasome system in the degradation of nonnative Nups in the NPC remains unclear. Here, we show that in Saccharomyces cerevisiae, although Nup1 (the FG-Nup component of the central core of the NPC) was stable, C-terminally green fluorescent protein-tagged Nup1, which had been incorporated into the NPC, was degraded by the proteasome especially under heat stress conditions. The degradation was dependent on the San1 ubiquitin ligase and Cdc48/p97, as well as its cofactor Doa1. We also demonstrate that San1 weakly but certainly contributes to the degradation of nontagged endogenous Nup1 in cells defective in NPC biogenesis by the deletion of NUP120. In addition, the overexpression of SAN1 exacerbated the growth defect phenotype of nup120Δ cells, which may be caused by excess degradation of defective Nups due to the deletion of NUP120. These biochemical and genetic data suggest that San1 is involved in the degradation of nonnative Nups generated by genetic mutation or when NPC biogenesis is impaired.
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Affiliation(s)
- Takanari Ikeda
- Graduate School of Science, Nagoya City University, Nagoya, Aichi 467-8501, Japan
| | - Kenji Yamazaki
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Fumihiko Okumura
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, Fukuoka 813-8529, Japan
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Kunio Nakatsukasa
- Graduate School of Science, Nagoya City University, Nagoya, Aichi 467-8501, Japan
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15
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Singh D, Soni N, Hutchings J, Echeverria I, Shaikh F, Duquette M, Suslov S, Li Z, van Eeuwen T, Molloy K, Shi Y, Wang J, Guo Q, Chait BT, Fernandez-Martinez J, Rout MP, Sali A, Villa E. The Molecular Architecture of the Nuclear Basket. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587068. [PMID: 38586009 PMCID: PMC10996695 DOI: 10.1101/2024.03.27.587068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The nuclear pore complex (NPC) is the sole mediator of nucleocytoplasmic transport. Despite great advances in understanding its conserved core architecture, the peripheral regions can exhibit considerable variation within and between species. One such structure is the cage-like nuclear basket. Despite its crucial roles in mRNA surveillance and chromatin organization, an architectural understanding has remained elusive. Using in-cell cryo-electron tomography and subtomogram analysis, we explored the NPC's structural variations and the nuclear basket across fungi (yeast; S. cerevisiae), mammals (mouse; M. musculus), and protozoa (T. gondii). Using integrative structural modeling, we computed a model of the basket in yeast and mammals that revealed how a hub of Nups in the nuclear ring binds to basket-forming Mlp/Tpr proteins: the coiled-coil domains of Mlp/Tpr form the struts of the basket, while their unstructured termini constitute the basket distal densities, which potentially serve as a docking site for mRNA preprocessing before nucleocytoplasmic transport.
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Affiliation(s)
- Digvijay Singh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Neelesh Soni
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Hutchings
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Farhaz Shaikh
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Madeleine Duquette
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergey Suslov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kelly Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Javier Fernandez-Martinez
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, 48940 Leioa, Spain
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
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16
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Bender SWB, Dreisler MW, Zhang M, Kæstel-Hansen J, Hatzakis NS. SEMORE: SEgmentation and MORphological fingErprinting by machine learning automates super-resolution data analysis. Nat Commun 2024; 15:1763. [PMID: 38409214 PMCID: PMC10897458 DOI: 10.1038/s41467-024-46106-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/13/2024] [Indexed: 02/28/2024] Open
Abstract
The morphology of protein assemblies impacts their behaviour and contributes to beneficial and aberrant cellular responses. While single-molecule localization microscopy provides the required spatial resolution to investigate these assemblies, the lack of universal robust analytical tools to extract and quantify underlying structures limits this powerful technique. Here we present SEMORE, a semi-automatic machine learning framework for universal, system- and input-dependent, analysis of super-resolution data. SEMORE implements a multi-layered density-based clustering module to dissect biological assemblies and a morphology fingerprinting module for quantification by multiple geometric and kinetics-based descriptors. We demonstrate SEMORE on simulations and diverse raw super-resolution data: time-resolved insulin aggregates, and published data of dSTORM imaging of nuclear pore complexes, fibroblast growth receptor 1, sptPALM of Syntaxin 1a and dynamic live-cell PALM of ryanodine receptors. SEMORE extracts and quantifies all protein assemblies, their temporal morphology evolution and provides quantitative insights, e.g. classification of heterogeneous insulin aggregation pathways and NPC geometry in minutes. SEMORE is a general analysis platform for super-resolution data, and being a time-aware framework can also support the rise of 4D super-resolution data.
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Affiliation(s)
- Steen W B Bender
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Marcus W Dreisler
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Min Zhang
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Kæstel-Hansen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
| | - Nikos S Hatzakis
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Center for 4D cellular dynamics, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Optimised Oligo Escape and Control of Disease, University of Copenhagen, Copenhagen, Denmark.
- Novo Nordisk Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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17
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Fu L, Weiskopf EN, Akkermans O, Swanson NA, Cheng S, Schwartz TU, Görlich D. HIV-1 capsids enter the FG phase of nuclear pores like a transport receptor. Nature 2024; 626:843-851. [PMID: 38267583 PMCID: PMC10881386 DOI: 10.1038/s41586-023-06966-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024]
Abstract
HIV-1 infection requires nuclear entry of the viral genome. Previous evidence suggests that this entry proceeds through nuclear pore complexes (NPCs), with the 120 × 60 nm capsid squeezing through an approximately 60-nm-wide central channel1 and crossing the permeability barrier of the NPC. This barrier can be described as an FG phase2 that is assembled from cohesively interacting phenylalanine-glycine (FG) repeats3 and is selectively permeable to cargo captured by nuclear transport receptors (NTRs). Here we show that HIV-1 capsid assemblies can target NPCs efficiently in an NTR-independent manner and bind directly to several types of FG repeats, including barrier-forming cohesive repeats. Like NTRs, the capsid readily partitions into an in vitro assembled cohesive FG phase that can serve as an NPC mimic and excludes much smaller inert probes such as mCherry. Indeed, entry of the capsid protein into such an FG phase is greatly enhanced by capsid assembly, which also allows the encapsulated clients to enter. Thus, our data indicate that the HIV-1 capsid behaves like an NTR, with its interior serving as a cargo container. Because capsid-coating with trans-acting NTRs would increase the diameter by 10 nm or more, we suggest that such a 'self-translocating' capsid undermines the size restrictions imposed by the NPC scaffold, thereby bypassing an otherwise effective barrier to viral infection.
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Affiliation(s)
- Liran Fu
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Erika N Weiskopf
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Onno Akkermans
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas A Swanson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Shiya Cheng
- Department of Meiosis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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18
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Beck M, Covino R, Hänelt I, Müller-McNicoll M. Understanding the cell: Future views of structural biology. Cell 2024; 187:545-562. [PMID: 38306981 DOI: 10.1016/j.cell.2023.12.017] [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: 10/04/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 02/04/2024]
Abstract
Determining the structure and mechanisms of all individual functional modules of cells at high molecular detail has often been seen as equal to understanding how cells work. Recent technical advances have led to a flush of high-resolution structures of various macromolecular machines, but despite this wealth of detailed information, our understanding of cellular function remains incomplete. Here, we discuss present-day limitations of structural biology and highlight novel technologies that may enable us to analyze molecular functions directly inside cells. We predict that the progression toward structural cell biology will involve a shift toward conceptualizing a 4D virtual reality of cells using digital twins. These will capture cellular segments in a highly enriched molecular detail, include dynamic changes, and facilitate simulations of molecular processes, leading to novel and experimentally testable predictions. Transferring biological questions into algorithms that learn from the existing wealth of data and explore novel solutions may ultimately unveil how cells work.
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Affiliation(s)
- Martin Beck
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany; Goethe University Frankfurt, Frankfurt, Germany.
| | - Roberto Covino
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
| | - Inga Hänelt
- Goethe University Frankfurt, Frankfurt, Germany.
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19
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Khalil B, Linsenmeier M, Smith CL, Shorter J, Rossoll W. Nuclear-import receptors as gatekeepers of pathological phase transitions in ALS/FTD. Mol Neurodegener 2024; 19:8. [PMID: 38254150 PMCID: PMC10804745 DOI: 10.1186/s13024-023-00698-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative disorders on a disease spectrum that are characterized by the cytoplasmic mislocalization and aberrant phase transitions of prion-like RNA-binding proteins (RBPs). The common accumulation of TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), and other nuclear RBPs in detergent-insoluble aggregates in the cytoplasm of degenerating neurons in ALS/FTD is connected to nuclear pore dysfunction and other defects in the nucleocytoplasmic transport machinery. Recent advances suggest that beyond their canonical role in the nuclear import of protein cargoes, nuclear-import receptors (NIRs) can prevent and reverse aberrant phase transitions of TDP-43, FUS, and related prion-like RBPs and restore their nuclear localization and function. Here, we showcase the NIR family and how they recognize cargo, drive nuclear import, and chaperone prion-like RBPs linked to ALS/FTD. We also discuss the promise of enhancing NIR levels and developing potentiated NIR variants as therapeutic strategies for ALS/FTD and related neurodegenerative proteinopathies.
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Affiliation(s)
- Bilal Khalil
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - Miriam Linsenmeier
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A
| | - Courtney L Smith
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
- Mayo Clinic Graduate School of Biomedical Sciences, Neuroscience Track, Mayo Clinic, Jacksonville, FL, 32224, U.S.A
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, U.S.A..
| | - Wilfried Rossoll
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, U.S.A..
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20
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Yang X, Ji C, Liu X, Wei Z, Pang Q, Zhang A. Arabidopsis nucleoporin NUP96 mediates plant salt tolerance by modulating the transcription of salt-responsive genes. PLANTA 2023; 259:34. [PMID: 38160450 DOI: 10.1007/s00425-023-04312-y] [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: 07/03/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
MAIN CONCLUSION Physiological and molecular tests show that NUP96 plays an important role in the plant response to salt stress, resulting from the reprogramming of transcriptomic profiles, which are likely to be mediated by the influence on the nuclear/cytosol shuttling of the key regulators of salt tolerance. As a key component of the nuclear pore complex (NPC), nucleoporin 96 (NUP96) is critical for modulating plant development and interactions with environmental factors, but whether NUP96 is involved in the salt response is still unknown. Here, we analyzed the role of Arabidopsis NUP96 under salt stress. The loss-of-function mutant nup96 exhibited salt sensitivity in terms of rosette growth and root elongation, and showed attenuated capacity in maintaining ion and ROS homeostasis, which could be compensated for by the overexpression of NUP96. RNA sequencing revealed that many salt-responsive genes were misregulated after NUP96 mutation, and especially NUP96 is required for the expression of a large portion of salt-induced genes. This is likely correlated with the activity in facilitating nuclear/cytosol transport of the underlying regulators in salt tolerance such as the transcription factor ATAP2, targeted by eight downregulated genes in nup96 under salt stress. Our results illustrate that NUP96 plays an important role in the salt response, probably by regulating the nucleocytoplasmic shuttling of key mRNAs or proteins associated with plant salt responsiveness.
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Affiliation(s)
- Xiaomin Yang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Chengcheng Ji
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Xinxin Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Zhaoxin Wei
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
| | - Qiuying Pang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Aiqin Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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21
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Baum B, Spang A. On the origin of the nucleus: a hypothesis. Microbiol Mol Biol Rev 2023; 87:e0018621. [PMID: 38018971 PMCID: PMC10732040 DOI: 10.1128/mmbr.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
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Affiliation(s)
- Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
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22
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Behrens RT, Sherer NM. Retroviral hijacking of host transport pathways for genome nuclear export. mBio 2023; 14:e0007023. [PMID: 37909783 PMCID: PMC10746203 DOI: 10.1128/mbio.00070-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Recent advances in the study of virus-cell interactions have improved our understanding of how viruses that replicate their genomes in the nucleus (e.g., retroviruses, hepadnaviruses, herpesviruses, and a subset of RNA viruses) hijack cellular pathways to export these genomes to the cytoplasm where they access virion egress pathways. These findings shed light on novel aspects of viral life cycles relevant to the development of new antiviral strategies and can yield new tractable, virus-based tools for exposing additional secrets of the cell. The goal of this review is to summarize defined and emerging modes of virus-host interactions that drive the transit of viral genomes out of the nucleus across the nuclear envelope barrier, with an emphasis on retroviruses that are most extensively studied. In this context, we prioritize discussion of recent progress in understanding the trafficking and function of the human immunodeficiency virus type 1 Rev protein, exemplifying a relatively refined example of stepwise, cooperativity-driven viral subversion of multi-subunit host transport receptor complexes.
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Affiliation(s)
- Ryan T. Behrens
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, USA
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23
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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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24
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Barrientos ECR, Otto TA, Mouton SN, Steen A, Veenhoff LM. A survey of the specificity and mechanism of 1,6 hexanediol-induced disruption of nuclear transport. Nucleus 2023; 14:2240139. [PMID: 37498221 PMCID: PMC10376917 DOI: 10.1080/19491034.2023.2240139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023] Open
Abstract
Selective transport through the nuclear pore complex (NPC) depends on the dynamic binding of FG-repeat containing nucleoporins, the FG-nups, with each other and with Karyopherins (Kaps). Here, we assessed the specificity and mechanism by which the aliphatic alcohol 1,6-hexanediol (1,6HD) disrupts the permeability barrier of NPCs in live baker's yeast cells. After a 10-minute exposure to 5% 1,6HD, no notable changes were observed in cell growth, cytosolic pH and ATP levels, or the appearance of organelles. However, effects on the cytoskeleton and Hsp104 were noted. 1,6HD clearly affected the NPC permeability barrier, allowing passive nuclear entry of a 177kDa reporter protein that is normally confined to the cytosol. Moreover, multiple Kaps were displaced from NPCs, and the displacement of Kap122-GFP correlated with the observed passive permeability changes. 1,6HD thus temporarily permeates NPCs, and in line with Kap-centric models, the mechanism includes the release of numerous Kaps from the NPCs.
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Affiliation(s)
- Elizabeth C Riquelme Barrientos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Tegan A Otto
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Groningen, The Netherlands
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25
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Yang Y, Guo L, Chen L, Gong B, Jia D, Sun Q. Nuclear transport proteins: structure, function, and disease relevance. Signal Transduct Target Ther 2023; 8:425. [PMID: 37945593 PMCID: PMC10636164 DOI: 10.1038/s41392-023-01649-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 11/12/2023] Open
Abstract
Proper subcellular localization is crucial for the functioning of biomacromolecules, including proteins and RNAs. Nuclear transport is a fundamental cellular process that regulates the localization of many macromolecules within the nuclear or cytoplasmic compartments. In humans, approximately 60 proteins are involved in nuclear transport, including nucleoporins that form membrane-embedded nuclear pore complexes, karyopherins that transport cargoes through these complexes, and Ran system proteins that ensure directed and rapid transport. Many of these nuclear transport proteins play additional and essential roles in mitosis, biomolecular condensation, and gene transcription. Dysregulation of nuclear transport is linked to major human diseases such as cancer, neurodegenerative diseases, and viral infections. Selinexor (KPT-330), an inhibitor targeting the nuclear export factor XPO1 (also known as CRM1), was approved in 2019 to treat two types of blood cancers, and dozens of clinical trials of are ongoing. This review summarizes approximately three decades of research data in this field but focuses on the structure and function of individual nuclear transport proteins from recent studies, providing a cutting-edge and holistic view on the role of nuclear transport proteins in health and disease. In-depth knowledge of this rapidly evolving field has the potential to bring new insights into fundamental biology, pathogenic mechanisms, and therapeutic approaches.
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Affiliation(s)
- Yang Yang
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lu Guo
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Chen
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bo Gong
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.
| | - Qingxiang Sun
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, China.
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26
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Nikolić S, Oasa S, Krmpot AJ, Terenius L, Belić MR, Rigler R, Vukojević V. Mapping the Direction of Nucleocytoplasmic Transport of Glucocorticoid Receptor (GR) in Live Cells Using Two-Foci Cross-Correlation in Massively Parallel Fluorescence Correlation Spectroscopy (mpFCS). Anal Chem 2023; 95:15171-15179. [PMID: 37782779 PMCID: PMC10585663 DOI: 10.1021/acs.analchem.3c01427] [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: 04/02/2023] [Accepted: 09/15/2023] [Indexed: 10/04/2023]
Abstract
Nucleocytoplasmic transport of transcription factors is vital for normal cellular function, and its breakdown is a major contributing factor in many diseases. The glucocorticoid receptor (GR) is an evolutionarily conserved, ligand-dependent transcription factor that regulates homeostasis and response to stress and is an important target for therapeutics in inflammation and cancer. In unstimulated cells, the GR resides in the cytoplasm bound to other molecules in a large multiprotein complex. Upon stimulation with endogenous or synthetic ligands, GR translocation to the cell nucleus occurs, where the GR regulates the transcription of numerous genes by direct binding to glucocorticoid response elements or by physically associating with other transcription factors. While much is known about molecular mechanisms underlying GR function, the spatial organization of directionality of GR nucleocytoplasmic transport remains less well characterized, and it is not well understood how the bidirectional nucleocytoplasmic flow of GR is coordinated in stimulated cells. Here, we use two-foci cross-correlation in a massively parallel fluorescence correlation spectroscopy (mpFCS) system to map in live cells the directionality of GR translocation at different positions along the nuclear envelope. We show theoretically and experimentally that cross-correlation of signals from two nearby observation volume elements (OVEs) in an mpFCS setup presents a sharp peak when the OVEs are positioned along the trajectory of molecular motion and that the time position of the peak corresponds to the average time of flight of the molecule between the two OVEs. Hence, the direction and velocity of nucleocytoplasmic transport can be determined simultaneously at several locations along the nuclear envelope. We reveal that under ligand-induced GR translocation, nucleocytoplasmic import/export of GR proceeds simultaneously but at different locations in the cell nucleus. Our data show that mpFCS can characterize in detail the heterogeneity of directional nucleocytoplasmic transport in a live cell and may be invaluable for studies aiming to understand how the bidirectional flow of macromolecules through the nuclear pore complex (NPC) is coordinated to avoid intranuclear transcription factor accretion/abatement.
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Affiliation(s)
- Stanko
N. Nikolić
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
- Institute
of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
- Division
of Arts and Sciences, Texas A&M University
at Qatar, Doha, Qatar
| | - Sho Oasa
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
| | - Aleksandar J. Krmpot
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
- Institute
of Physics Belgrade, University of Belgrade, 11080 Belgrade, Serbia
- Division
of Arts and Sciences, Texas A&M University
at Qatar, Doha, Qatar
| | - Lars Terenius
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
| | - Milivoj R. Belić
- Division
of Arts and Sciences, Texas A&M University
at Qatar, Doha, Qatar
| | - Rudolf Rigler
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
| | - Vladana Vukojević
- Department
of Clinical Neuroscience (CNS), Center for Molecular Medicine (CMM), Karolinska Institute, 17176 Stockholm, Sweden
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27
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Desgraupes S, Etienne L, Arhel NJ. RANBP2 evolution and human disease. FEBS Lett 2023; 597:2519-2533. [PMID: 37795679 DOI: 10.1002/1873-3468.14749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023]
Abstract
Ran-binding protein 2 (RANBP2)/Nup358 is a nucleoporin and a key component of the nuclear pore complex. Through its multiple functions (e.g., SUMOylation, regulation of nucleocytoplasmic transport) and subcellular localizations (e.g., at the nuclear envelope, kinetochores, annulate lamellae), it is involved in many cellular processes. RANBP2 dysregulation or mutation leads to the development of human pathologies, such as acute necrotizing encephalopathy 1, cancer, neurodegenerative diseases, and it is also involved in viral infections. The chromosomal region containing the RANBP2 gene is highly dynamic, with high structural variation and recombination events that led to the appearance of a gene family called RANBP2 and GCC2 Protein Domains (RGPD), with multiple gene loss/duplication events during ape evolution. Although RGPD homoplasy and maintenance during evolution suggest they might confer an advantage to their hosts, their functions are still unknown and understudied. In this review, we discuss the appearance and importance of RANBP2 in metazoans and its function-related pathologies, caused by an alteration of its expression levels (through promotor activity, post-transcriptional, or post-translational modifications), its localization, or genetic mutations.
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Affiliation(s)
- Sophie Desgraupes
- Institut de Recherche en Infectiologie de Montpellier (IRIM), University of Montpellier, France
| | - Lucie Etienne
- Centre International de Recherche en Infectiologie (CIRI), Inserm U1111, UCBL1, CNRS UMR 5308, ENS de Lyon, Université de Lyon, France
| | - Nathalie J Arhel
- Institut de Recherche en Infectiologie de Montpellier (IRIM), University of Montpellier, France
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28
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Cristi AC, Rapuri S, Coyne AN. Nuclear pore complex and nucleocytoplasmic transport disruption in neurodegeneration. FEBS Lett 2023; 597:2546-2566. [PMID: 37657945 PMCID: PMC10612469 DOI: 10.1002/1873-3468.14729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/29/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Nuclear pore complexes (NPCs) play a critical role in maintaining the equilibrium between the nucleus and cytoplasm, enabling bidirectional transport across the nuclear envelope, and are essential for proper nuclear organization and gene regulation. Perturbations in the regulatory mechanisms governing NPCs and nuclear envelope homeostasis have been implicated in the pathogenesis of several neurodegenerative diseases. The ESCRT-III pathway emerges as a critical player in the surveillance and preservation of well-assembled, functional NPCs, as well as nuclear envelope sealing. Recent studies have provided insights into the involvement of nuclear ESCRT-III in the selective reduction of specific nucleoporins associated with neurodegenerative pathologies. Thus, maintaining quality control of the nuclear envelope and NPCs represents a pivotal element in the pathological cascade leading to neurodegenerative diseases. This review describes the constituents of the nuclear-cytoplasmic transport machinery, encompassing the nuclear envelope, NPC, and ESCRT proteins, and how their structural and functional alterations contribute to the development of neurodegenerative diseases.
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Affiliation(s)
- América Chandía Cristi
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Sampath Rapuri
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
| | - Alyssa N Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore MD 21205, USA
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29
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Nobari P, Doye V, Boumendil C. Metazoan nuclear pore complexes in gene regulation and genome stability. DNA Repair (Amst) 2023; 130:103565. [PMID: 37696111 DOI: 10.1016/j.dnarep.2023.103565] [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: 05/11/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
The nuclear pore complexes (NPCs), one of the hallmarks of eukaryotic nuclei, allow selective transport of macromolecules between the cytoplasm and the nucleus. Besides this canonical function, an increasing number of additional roles have been attributed to the NPCs and their constituents, the nucleoporins. Here we review recent insights into the mechanisms by which NPCs and nucleoporins affect transcription and DNA repair in metazoans. In the first part, we discuss how gene expression can be affected by the localization of genome-nucleoporin interactions at pores or "off-pores", by the role of nucleoporins in chromatin organization at different scales, or by the physical properties of nucleoporins. In the second part, we review the contribution of NPCs to genome stability, including transport-dependent and -independent functions and the role of positioning at NPCs in the repair of heterochromatic breaks and the regulation of replication stress.
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Affiliation(s)
- Parisa Nobari
- IGH, Université de Montpellier, CNRS, Montpellier, France
| | - Valérie Doye
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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30
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Gandhimathi R, Pinotsi D, Köhler M, Mansfeld J, Ashiono C, Kleele T, Pawar S, Kutay U. Super-resolution microscopy reveals focal organization of ER-associated Y-complexes in mitosis. EMBO Rep 2023; 24:e56766. [PMID: 37469276 PMCID: PMC10481662 DOI: 10.15252/embr.202356766] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023] Open
Abstract
During mitotic entry of vertebrate cells, nuclear pore complexes (NPCs) are rapidly disintegrated. NPC disassembly is initiated by hyperphosphorylation of linker nucleoporins (Nups), which leads to the dissociation of FG repeat Nups and relaxation of the nuclear permeability barrier. However, less is known about disintegration of the huge nuclear and cytoplasmic rings, which are formed by annular assemblies of Y-complexes that are dissociated from NPCs as intact units. Surprisingly, we observe that Y-complex Nups display slower dissociation kinetics compared with other Nups during in vitro NPC disassembly, indicating a mechanistic difference in the disintegration of Y-based rings. Intriguingly, biochemical experiments reveal that a fraction of Y-complexes remains associated with mitotic ER membranes, supporting recent microscopic observations. Visualization of mitotic Y-complexes by super-resolution microscopy demonstrates that they form two classes of higher order assemblies: large clusters at kinetochores and small, focal ER-associated assemblies. These, however, lack features qualifying them as persisting ring-shaped subassemblies previously proposed to serve as structural templates for NPC reassembly during mitotic exit, which helps to refine current models of nuclear reassembly.
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Affiliation(s)
- Rojapriyadharshini Gandhimathi
- Department of Biology, Institute of BiochemistryETH ZurichZurichSwitzerland
- Molecular Life Sciences Ph.D. ProgramZurichSwitzerland
| | | | - Mario Köhler
- Department of Biology, Institute of BiochemistryETH ZurichZurichSwitzerland
| | - Jörg Mansfeld
- Department of Biology, Institute of BiochemistryETH ZurichZurichSwitzerland
- The Institute of Cancer ResearchLondonUK
| | - Caroline Ashiono
- Department of Biology, Institute of BiochemistryETH ZurichZurichSwitzerland
| | - Tatjana Kleele
- Department of Biology, Institute of BiochemistryETH ZurichZurichSwitzerland
| | - Sumit Pawar
- Department of Biology, Institute of BiochemistryETH ZurichZurichSwitzerland
- Present address:
Myllia BiotechnologyViennaAustria
| | - Ulrike Kutay
- Department of Biology, Institute of BiochemistryETH ZurichZurichSwitzerland
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31
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Lee S, Carrasquillo Rodríguez JW, Merta H, Bahmanyar S. A membrane-sensing mechanism links lipid metabolism to protein degradation at the nuclear envelope. J Cell Biol 2023; 222:e202304026. [PMID: 37382667 PMCID: PMC10309186 DOI: 10.1083/jcb.202304026] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023] Open
Abstract
Lipid composition determines organelle identity; however, whether the lipid composition of the inner nuclear membrane (INM) domain of the ER contributes to its identity is not known. Here, we show that the INM lipid environment of animal cells is under local control by CTDNEP1, the master regulator of the phosphatidic acid phosphatase lipin 1. Loss of CTDNEP1 reduces association of an INM-specific diacylglycerol (DAG) biosensor and results in a decreased percentage of polyunsaturated containing DAG species. Alterations in DAG metabolism impact the levels of the resident INM protein Sun2, which is under local proteasomal regulation. We identify a lipid-binding amphipathic helix (AH) in the nucleoplasmic domain of Sun2 that prefers membrane packing defects. INM dissociation of the Sun2 AH is linked to its proteasomal degradation. We suggest that direct lipid-protein interactions contribute to sculpting the INM proteome and that INM identity is adaptable to lipid metabolism, which has broad implications on disease mechanisms associated with the nuclear envelope.
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Affiliation(s)
- Shoken Lee
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | | | - Holly Merta
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Shirin Bahmanyar
- Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT, USA
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32
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Brickner JH. The nuclear pore complex as a platform for epigenetic regulation. J Cell Biol 2023; 222:e202307078. [PMID: 37603083 PMCID: PMC10439725 DOI: 10.1083/jcb.202307078] [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] [Indexed: 08/22/2023] Open
Abstract
The nuclear pore complex (NPC) both mediates exchange of proteins and RNA between the nucleus and the cytoplasm and physically interacts with chromatin to regulate transcription. In this issue of JCB, Kumar et al. (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202207060) provide new insight into the molecular basis for NPC-mediated epigenetic silencing through loading of the replication processivity factor PCNA.
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Affiliation(s)
- Jason H. Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
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33
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Wang W, Jakobi A, Wu YL, Ries J, Stallinga S, Rieger B. Particle fusion of super-resolution data reveals the unit structure of Nup96 in Nuclear Pore Complex. Sci Rep 2023; 13:13327. [PMID: 37587192 PMCID: PMC10432550 DOI: 10.1038/s41598-023-39829-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
Single molecule localization microscopy offers resolution nearly down to the molecular level with specific molecular labelling, and is thereby a promising tool for structural biology. In practice, however, the actual value to this field is limited primarily by incomplete fluorescent labelling of the structure. This missing information can be completed by merging information from many structurally identical particles in a particle fusion approach similar to cryo-EM single-particle analysis. In this paper, we present a data analysis of particle fusion results of fluorescently labelled Nup96 nucleoporins in the Nuclear Pore Complex to show that Nup96 occurs in a spatial arrangement of two rings of 8 units with two Nup96 copies per unit giving a total of 32 Nup96 copies per pore. We use Artificial Intelligence assisted modeling in Alphafold to extend the existing cryo-EM model of Nup96 to accurately pinpoint the positions of the fluorescent labels and show the accuracy of the match between fluorescent and cryo-EM data to be better than 3 nm in-plane and 5 nm out-of-plane.
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Affiliation(s)
- Wenxiu Wang
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Arjen Jakobi
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Yu-Le Wu
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jonas Ries
- Department of Chromosome Biology, University of Vienna, Max-Perutz Labs, Center for Molecular Biology, Vienna, Austria
| | - Sjoerd Stallinga
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands.
| | - Bernd Rieger
- Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands.
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34
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Li S, Zhang K, Wen J, Zeng Y, Deng Y, Hu Q, Weng Q. Molecular Mechanism of Male Sterility Induced by 60Co γ-Rays on Plutella xylostella (Linnaeus). Molecules 2023; 28:5727. [PMID: 37570697 PMCID: PMC10420029 DOI: 10.3390/molecules28155727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/19/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Plutella xylostella (Linnaeus) is one of the notorious pests causing substantial loses to numerous cruciferous vegetables across many nations. The sterile insect technique (SIT) is a safe and effective pest control method, which does not pollute the environment and does not produce drug resistance. We used proteomics technology and bioinformatics analysis to investigate the molecular mechanisms responsible for the effects of different doses of radiation treatment on the reproductive ability of male P. xylostella. A total of 606 differentially expressed proteins (DEPs) were identified in the 200 Gy/CK group, 1843 DEPs were identified in the 400 Gy/CK group, and 2057 DEPs were identified in the 400 Gy/200 Gy group. The results showed that after 200 Gy irradiation, the testes resisted radiation damage by increasing energy supply, amino acid metabolism and transport, and protein synthesis, while transcription-related pathways were inhibited. After 400 Gy irradiation, the mitochondria and DNA in the testis tissue of P. xylostella were damaged, which caused cell autophagy and apoptosis, affected the normal life activities of sperm cells, and greatly weakened sperm motility and insemination ability. Meanwhile, Western blotting showed that irradiation affects tyrosine phosphorylation levels, which gradually decrease with increasing irradiation dose.
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Affiliation(s)
- Shifan Li
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Ke Zhang
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Jiaqi Wen
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Yuhao Zeng
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Yukun Deng
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
| | - Qiongbo Hu
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
| | - Qunfang Weng
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China; (S.L.); (K.Z.); (J.W.); (Y.Z.); (Y.D.)
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
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35
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Nkombo Nkoula S, Velez-Aguilera G, Ossareh-Nazari B, Van Hove L, Ayuso C, Legros V, Chevreux G, Thomas L, Seydoux G, Askjaer P, Pintard L. Mechanisms of nuclear pore complex disassembly by the mitotic Polo-like kinase 1 (PLK-1) in C. elegans embryos. SCIENCE ADVANCES 2023; 9:eadf7826. [PMID: 37467327 PMCID: PMC10355831 DOI: 10.1126/sciadv.adf7826] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023]
Abstract
The nuclear envelope, which protects and organizes the genome, is dismantled during mitosis. In the Caenorhabditis elegans zygote, nuclear envelope breakdown (NEBD) of the parental pronuclei is spatially and temporally regulated during mitosis to promote the unification of the maternal and paternal genomes. Nuclear pore complex (NPC) disassembly is a decisive step of NEBD, essential for nuclear permeabilization. By combining live imaging, biochemistry, and phosphoproteomics, we show that NPC disassembly is a stepwise process that involves Polo-like kinase 1 (PLK-1)-dependent and -independent steps. PLK-1 targets multiple NPC subcomplexes, including the cytoplasmic filaments, central channel, and inner ring. PLK-1 is recruited to and phosphorylates intrinsically disordered regions (IDRs) of several multivalent linker nucleoporins. Notably, although the phosphosites are not conserved between human and C. elegans nucleoporins, they are located in IDRs in both species. Our results suggest that targeting IDRs of multivalent linker nucleoporins is an evolutionarily conserved driver of NPC disassembly during mitosis.
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Affiliation(s)
- Sylvia Nkombo Nkoula
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Programme Équipe Labellisée Ligue contre le Cancer, Paris, France
| | - Griselda Velez-Aguilera
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Programme Équipe Labellisée Ligue contre le Cancer, Paris, France
| | - Batool Ossareh-Nazari
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Programme Équipe Labellisée Ligue contre le Cancer, Paris, France
| | - Lucie Van Hove
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Programme Équipe Labellisée Ligue contre le Cancer, Paris, France
| | - Cristina Ayuso
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Véronique Legros
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Guillaume Chevreux
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Laura Thomas
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Géraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Lionel Pintard
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Programme Équipe Labellisée Ligue contre le Cancer, Paris, France
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36
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Huang P, Hu YD, Liu YJ, Li JP, Zhang YH. An Analysis Regarding the Association Between the Nuclear Pore Complex (NPC) and Hepatocellular Carcinoma (HCC). J Hepatocell Carcinoma 2023; 10:959-978. [PMID: 37377841 PMCID: PMC10292625 DOI: 10.2147/jhc.s417501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Background The nuclear pore complex (NPC) is the main mediator of nuclear and cytoplasmic communication, and delaying or blocking nuclear RNA export and protein shuttling can inhibit cell proliferation and induce apoptosis. Although NPC is a research hotspot in structural biology, relevant studies in hepatocellular carcinoma are scarce, especially in terms of translation into clinical practice. Methods This study used a bioinformatics approach combining validation experiments to investigate the biological mechanisms that may be related with NPC. A series of experiments performed to explore the function of the Targeting protein for Xenopus kinesin-like protein 2 (TPX2) in HCC. Results Patients with HCC can be divided into two NPC clusters. Patients with high NPC levels (C1) had a shorter survival time than those with low NPC levels (C2) and are characterised by high levels of proliferative signals. We demonstrated that TPX2 regulates HCC growth and inhibits apoptosis in an NPC-dependent manner and contributes to the maintenance of HCC stemness. We developed the NPCScore to predict the prognosis and degree of differentiation in HCC patients. Conclusion NPC plays an important role in the malignant proliferation of HCC. Assessing NPC expression patterns could help enhance our understanding of tumor cell proliferation and could guide more effective chemotherapeutic strategies.
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Affiliation(s)
- Pan Huang
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
| | - Yi-dou Hu
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
| | - Yuan-jie Liu
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
| | - Jie-pin Li
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
- No. 1 Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, People’s Republic of China
- Key Laboratory of Tumor System Biology of Traditional Chinese Medicine, Nanjing, Jiangsu, 210029, People’s Republic of China
| | - Yong-hua Zhang
- Department of Oncology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang, Jiangsu, 215600, People’s Republic of China
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37
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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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38
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Li Z, Chen S, Zhao L, Huang G, Xu H, Yang X, Wang P, Gao N, Sui SF. Nuclear export of pre-60S particles through the nuclear pore complex. Nature 2023:10.1038/s41586-023-06128-y. [PMID: 37258668 DOI: 10.1038/s41586-023-06128-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm1-3. The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the export of these gigantic ribonucleoproteins requires numerous export factors4,5. Here we report the cryo-electron microscopy structure of native pre-60S particles trapped in the channel of yeast NPCs. In addition to known assembly factors, multiple factors with export functions are also included in the structure. These factors in general bind to either the flexible regions or subunit interface of the pre-60S particle, and virtually form many anchor sites for NPC binding. Through interactions with phenylalanine-glycine (FG) repeats from various nucleoporins of NPC, these factors collectively facilitate the passage of the pre-60S particle through the central FG repeat network of the NPC. Moreover, in silico analysis of the axial and radial distribution of pre-60S particles within the NPC shows that a single NPC can take up to four pre-60S particles simultaneously, and pre-60S particles are enriched in the inner ring regions close to the wall of the NPC with the solvent-exposed surface facing the centre of the nuclear pore. Our data suggest a translocation model for the export of pre-60S particles through the NPC.
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Affiliation(s)
- Zongqiang Li
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Shuaijiabin Chen
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Liang Zhao
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Guoqiang Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huiqin Xu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xiaoyun Yang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Peiyi Wang
- Cryo-EM Center, Southern University of Science and Technology, Shenzhen, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Sen-Fang Sui
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
- Cryo-EM Center, Southern University of Science and Technology, Shenzhen, China.
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39
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Thomas L, Taleb Ismail B, Askjaer P, Seydoux G. Nucleoporin foci are stress-sensitive condensates dispensable for C. elegans nuclear pore assembly. EMBO J 2023:e112987. [PMID: 37254647 DOI: 10.15252/embj.2022112987] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Nucleoporins (Nups) assemble nuclear pores that form the permeability barrier between nucleoplasm and cytoplasm. Nucleoporins also localize in cytoplasmic foci proposed to function as pore pre-assembly intermediates. Here, we characterize the composition and incidence of cytoplasmic Nup foci in an intact animal, C. elegans. We find that, in young non-stressed animals, Nup foci only appear in developing sperm, oocytes and embryos, tissues that express high levels of nucleoporins. The foci are condensates of highly cohesive FG repeat-containing nucleoporins (FG-Nups), which are maintained near their solubility limit in the cytoplasm by posttranslational modifications and chaperone activity. Only a minor fraction of FG-Nup molecules concentrate in Nup foci, which dissolve during M phase and are dispensable for nuclear pore assembly. Nucleoporin condensation is enhanced by stress and advancing age, and overexpression of a single FG-Nup in post-mitotic neurons is sufficient to induce ectopic condensation and organismal paralysis. We speculate that Nup foci are non-essential and potentially toxic condensates whose assembly is actively suppressed in healthy cells.
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Affiliation(s)
- Laura Thomas
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Basma Taleb Ismail
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Geraldine Seydoux
- HHMI and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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40
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Cowburn D, Rout M. Improving the hole picture: towards a consensus on the mechanism of nuclear transport. Biochem Soc Trans 2023; 51:871-886. [PMID: 37099395 PMCID: PMC10212546 DOI: 10.1042/bst20220494] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/27/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the exchange of materials between the nucleoplasm and cytoplasm, playing a key role in the separation of nucleic acids and proteins into their required compartments. The static structure of the NPC is relatively well defined by recent cryo-EM and other studies. The functional roles of dynamic components in the pore of the NPC, phenylalanyl-glycyl (FG) repeat rich nucleoporins, is less clear because of our limited understanding of highly dynamic protein systems. These proteins form a 'restrained concentrate' which interacts with and concentrates nuclear transport factors (NTRs) to provide facilitated nucleocytoplasmic transport of cargoes. Very rapid on- and off-rates among FG repeats and NTRs supports extremely fast facilitated transport, close to the rate of macromolecular diffusion in cytoplasm, while complexes without specific interactions are entropically excluded, though details on several aspects of the transport mechanism and FG repeat behaviors remain to be resolved. However, as discussed here, new technical approaches combined with more advanced modeling methods will likely provide an improved dynamic description of NPC transport, potentially at the atomic level in the near future. Such advances are likely to be of major benefit in comprehending the roles the malfunctioning NPC plays in cancer, ageing, viral diseases, and neurodegeneration.
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Affiliation(s)
- David Cowburn
- Departments of Biochemistry and Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, U.S.A
| | - Michael Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, U.S.A
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41
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Li Y, Zhu J, Yu Z, Li H, Jin X. The role of Lamin B2 in human diseases. Gene 2023; 870:147423. [PMID: 37044185 DOI: 10.1016/j.gene.2023.147423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
Lamin B2 (LMNB2), on the inner side of the nuclear envelope, constitutes the nuclear skeleton by connecting with other nuclear proteins. LMNB2 is involved in a wide range of nuclear functions, including DNA replication and stability, regulation of chromatin, and nuclear stiffness. Moreover, LMNB2 regulates several cellular processes, such as tissue development, cell cycle, cellular proliferation and apoptosis, chromatin localization and stability, and DNA methylation. Besides, the influence of abnormal expression and mutations of LMNB2 has been gradually discovered in cancers and laminopathies. Therefore, this review summarizes the recent advances of LMNB2-associated biological roles in physiological or pathological conditions, with a particular emphasis on cancers and laminopathies, as well as the potential mechanism of LMNB2 in related cancers.
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Affiliation(s)
- Yuxuan Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Zongdong Yu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hong Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
| | - Xiaofeng Jin
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
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42
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Vial A, Costa L, Dosset P, Rosso P, Boutières G, Faklaris O, Haschke H, Milhiet PE, Doucet CM. Structure and mechanics of the human nuclear pore complex basket using correlative AFM-fluorescence superresolution microscopy. NANOSCALE 2023; 15:5756-5770. [PMID: 36786384 DOI: 10.1039/d2nr06034e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Nuclear pore complexes (NPCs) are the only gateways between the nucleus and cytoplasm in eukaryotic cells. They restrict free diffusion to molecules below 5 nm while facilitating the active transport of selected cargoes, sometimes as large as the pore itself. This versatility implies an important pore plasticity. Recently, cryo-EM and AI-based protein modeling of human NPC revealed with acute precision how most constituents are arranged. But the basket, a fish trap-like structure capping the nucleoplasmic side of the pore, remains poorly resolved. Here by atomic force microscopy (AFM) coupled to single molecule localization microscopy (SMLM) we revealed that the basket is very soft and explores a large conformational landscape: apart from its canonical basket shape, it dives into the central pore channel or opens, with filaments reaching to the pore sides. Our observations highlight how this structure can adapt and let morphologically diverse cargoes shuttle through NPCs.
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Affiliation(s)
- Anthony Vial
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Luca Costa
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Patrice Dosset
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Pietro Rosso
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Gaëlle Boutières
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Orestis Faklaris
- MRI, Biocampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | | | | | - Christine M Doucet
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
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43
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Rosenkranz AA, Slastnikova TA. Prospects of Using Protein Engineering for Selective Drug Delivery into a Specific Compartment of Target Cells. Pharmaceutics 2023; 15:pharmaceutics15030987. [PMID: 36986848 PMCID: PMC10055131 DOI: 10.3390/pharmaceutics15030987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
A large number of proteins are successfully used to treat various diseases. These include natural polypeptide hormones, their synthetic analogues, antibodies, antibody mimetics, enzymes, and other drugs based on them. Many of them are demanded in clinical settings and commercially successful, mainly for cancer treatment. The targets for most of the aforementioned drugs are located at the cell surface. Meanwhile, the vast majority of therapeutic targets, which are usually regulatory macromolecules, are located inside the cell. Traditional low molecular weight drugs freely penetrate all cells, causing side effects in non-target cells. In addition, it is often difficult to elaborate a small molecule that can specifically affect protein interactions. Modern technologies make it possible to obtain proteins capable of interacting with almost any target. However, proteins, like other macromolecules, cannot, as a rule, freely penetrate into the desired cellular compartment. Recent studies allow us to design multifunctional proteins that solve these problems. This review considers the scope of application of such artificial constructs for the targeted delivery of both protein-based and traditional low molecular weight drugs, the obstacles met on the way of their transport to the specified intracellular compartment of the target cells after their systemic bloodstream administration, and the means to overcome those difficulties.
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Affiliation(s)
- Andrey A Rosenkranz
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
| | - Tatiana A Slastnikova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
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44
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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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45
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Tuning between Nuclear Organization and Functionality in Health and Disease. Cells 2023; 12:cells12050706. [PMID: 36899842 PMCID: PMC10000962 DOI: 10.3390/cells12050706] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/08/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
The organization of eukaryotic genome in the nucleus, a double-membraned organelle separated from the cytoplasm, is highly complex and dynamic. The functional architecture of the nucleus is confined by the layers of internal and cytoplasmic elements, including chromatin organization, nuclear envelope associated proteome and transport, nuclear-cytoskeletal contacts, and the mechano-regulatory signaling cascades. The size and morphology of the nucleus could impose a significant impact on nuclear mechanics, chromatin organization, gene expression, cell functionality and disease development. The maintenance of nuclear organization during genetic or physical perturbation is crucial for the viability and lifespan of the cell. Abnormal nuclear envelope morphologies, such as invagination and blebbing, have functional implications in several human disorders, including cancer, accelerated aging, thyroid disorders, and different types of neuro-muscular diseases. Despite the evident interplay between nuclear structure and nuclear function, our knowledge about the underlying molecular mechanisms for regulation of nuclear morphology and cell functionality during health and illness is rather poor. This review highlights the essential nuclear, cellular, and extracellular components that govern the organization of nuclei and functional consequences associated with nuclear morphometric aberrations. Finally, we discuss the recent developments with diagnostic and therapeutic implications targeting nuclear morphology in health and disease.
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Nkoula SN, Velez-Aguilera G, Ossareh-Nazari B, Hove LV, Ayuso C, Legros V, Chevreux G, Thomas L, Seydoux G, Askjaer P, Pintard L. Mechanisms of Nuclear Pore Complex disassembly by the mitotic Polo-Like Kinase 1 (PLK-1) in C. elegans embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.528438. [PMID: 36865292 PMCID: PMC9980100 DOI: 10.1101/2023.02.21.528438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The nuclear envelope, which protects and organizes the interphase genome, is dismantled during mitosis. In the C. elegans zygote, nuclear envelope breakdown (NEBD) of the parental pronuclei is spatially and temporally regulated during mitosis to promote the unification of the parental genomes. During NEBD, Nuclear Pore Complex (NPC) disassembly is critical for rupturing the nuclear permeability barrier and removing the NPCs from the membranes near the centrosomes and between the juxtaposed pronuclei. By combining live imaging, biochemistry, and phosphoproteomics, we characterized NPC disassembly and unveiled the exact role of the mitotic kinase PLK-1 in this process. We show that PLK-1 disassembles the NPC by targeting multiple NPC sub-complexes, including the cytoplasmic filaments, the central channel, and the inner ring. Notably, PLK-1 is recruited to and phosphorylates intrinsically disordered regions of several multivalent linker nucleoporins, a mechanism that appears to be an evolutionarily conserved driver of NPC disassembly during mitosis. (149/150 words). One-Sentence Summary PLK-1 targets intrinsically disordered regions of multiple multivalent nucleoporins to dismantle the nuclear pore complexes in the C. elegans zygote.
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47
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Ng SC, Biswas A, Huyton T, Schünemann J, Reber S, Görlich D. Barrier properties of Nup98 FG phases ruled by FG motif identity and inter-FG spacer length. Nat Commun 2023; 14:747. [PMID: 36765044 PMCID: PMC9918544 DOI: 10.1038/s41467-023-36331-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
Nup98 FG repeat domains comprise hydrophobic FG motifs linked through uncharged spacers. FG motifs capture nuclear transport receptors (NTRs) during nuclear pore complex (NPC) passage, confer inter-repeat cohesion, and condense the domains into a selective phase with NPC-typical barrier properties. We show that shortening inter-FG spacers enhances cohesion, increases phase density, and tightens such barrier - all consistent with a sieve-like phase. Phase separation tolerates mutating the Nup98-typical GLFG motifs, provided domain-hydrophobicity remains preserved. NTR-entry, however, is sensitive to (certain) deviations from canonical FG motifs, suggesting co-evolutionary adaptation. Unexpectedly, we observed that arginines promote FG-phase-entry apparently also by hydrophobic interactions/ hydrogen-bonding and not just through cation-π interactions. Although incompatible with NTR·cargo complexes, a YG phase displays remarkable transport selectivity, particularly for engineered GFPNTR-variants. GLFG to FSFG mutations make the FG phase hypercohesive, precluding NTR-entry. Extending spacers relaxes this hypercohesion. Thus, antagonism between cohesion and NTR·FG interactions is key to transport selectivity.
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Affiliation(s)
- Sheung Chun Ng
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Abin Biswas
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Biological Optomechanics, Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Simone Reber
- Quantitative Biology, IRI Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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48
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King GA, Wettstein R, Varberg JM, Chetlapalli K, Walsh ME, Gillet LC, Hernández-Armenta C, Beltrao P, Aebersold R, Jaspersen SL, Matos J, Ünal E. Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. J Cell Biol 2023; 222:e202204039. [PMID: 36515990 PMCID: PMC9754704 DOI: 10.1083/jcb.202204039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/12/2022] [Accepted: 11/05/2022] [Indexed: 12/15/2022] Open
Abstract
Nuclear pore complexes (NPCs) are large proteinaceous assemblies that mediate nuclear compartmentalization. NPCs undergo large-scale structural rearrangements during mitosis in metazoans and some fungi. However, our understanding of NPC remodeling beyond mitosis remains limited. Using time-lapse fluorescence microscopy, we discovered that NPCs undergo two mechanistically separable remodeling events during budding yeast meiosis in which parts or all of the nuclear basket transiently dissociate from the NPC core during meiosis I and II, respectively. Meiosis I detachment, observed for Nup60 and Nup2, is driven by Polo kinase-mediated phosphorylation of Nup60 at its interface with the Y-complex. Subsequent reattachment of Nup60-Nup2 to the NPC core is facilitated by a lipid-binding amphipathic helix in Nup60. Preventing Nup60-Nup2 reattachment causes misorganization of the entire nuclear basket in gametes. Strikingly, meiotic nuclear basket remodeling also occurs in the distantly related fission yeast, Schizosaccharomyces pombe. Our study reveals a conserved and developmentally programmed aspect of NPC plasticity, providing key mechanistic insights into the nuclear basket organization.
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Affiliation(s)
- Grant A. King
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Rahel Wettstein
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | | | - Madison E. Walsh
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Ludovic C.J. Gillet
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Claudia Hernández-Armenta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Sue L. Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS
| | - Joao Matos
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
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49
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Huang G, Zeng C, Shi Y. Structure of the nuclear pore complex goes atomic. Curr Opin Struct Biol 2023; 78:102523. [PMID: 36641895 DOI: 10.1016/j.sbi.2022.102523] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 01/14/2023]
Abstract
The nuclear pore complex (NPC) is a supra-molecular assembly that mediates substance and information flow across the nuclear envelope (NE). Due to its extraordinary size and complexity, the NPC remains one of the most challenging tasks in structural elucidation at atomic resolution. Recent breakthroughs in cryo-electron microscopy (cryo-EM) reconstruction, Machine Learning empowered structure prediction and biochemical reconstitution have combined to yield molecular models of the NPC at unprecedented accuracy. Furthermore, in cellulo cryo-electron tomography (cryo-ET) structures reveal substantial structural dynamics of the NPC. These advances shed light on the organizational principles and functions of the NPC.
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Affiliation(s)
- Gaoxingyu Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China.
| | - Chao Zeng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China.
| | - Yigong Shi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024, China; Beijing Advanced Innovation Center for Structural Biology & Advanced Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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50
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Nuclear envelope assembly and dynamics during development. Semin Cell Dev Biol 2023; 133:96-106. [PMID: 35249812 DOI: 10.1016/j.semcdb.2022.02.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 01/22/2023]
Abstract
The nuclear envelope (NE) protects but also organizes the eukaryotic genome. In this review we will discuss recent literature on how the NE disassembles and reassembles, how it varies in surface area and protein composition and how this translates into chromatin organization and gene expression in the context of animal development.
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