1
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Preuß B, Frank A, Terjung B, Spengler U, Berg C, Klein R. Autoantibodies to beta tubulin in autoimmune liver diseases-Relation to pANCA and clinical relevance. Clin Exp Immunol 2024; 216:146-158. [PMID: 37823420 PMCID: PMC11036111 DOI: 10.1093/cei/uxad114] [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: 06/26/2023] [Revised: 08/30/2023] [Accepted: 10/10/2023] [Indexed: 10/13/2023] Open
Abstract
There was evidence that perinuclear antineutrophil cytoplasmic antibodies (pANCA) in autoimmune liver diseases react with human beta-tubulin-5 (TBB5). Here, we reevaluate the specificity and clinical relevance of anti-TBB5 antibodies. Patients with untreated autoimmune hepatitis (AIH; n = 53), AIH under immunosuppressive therapy (AIH-IS; n = 125), primary sclerosing cholangitis (PSC; n = 40), primary biliary cholangitis (PBC; n = 250), nonautoimmune liver diseases (n = 158), inflammatory bowel diseases (IBD; n = 30), and healthy individuals (n = 62) were tested by enzyme-linked immunosorbent assay for IgG- and IgA-antibodies against recombinant human TBB5. pANCA were detected by immunofluorescence test. Sera were absorbed with TBB5 coupled to cyanogen bromide-activated sepharose. Prevalence and reactivity of IgG anti-TBB5 were significantly higher in patients with untreated AIH (68%; arbitrary units [AU] median: 369) than in PSC (28%; AU median: 84, P < 0.001), other liver diseases (14%; AU median: 185, P < 0.0001), IBD (3%; AU median: 111, P < 0.0001), and healthy controls (3%; AU median: 135; P < 0.0001). Anti-TBB5 did not correlate with pANCA, and immunoprecipitation with TBB5 did not abolish pANCA reactivity. In untreated AIH, anti-TBB5-reactivity was significantly higher than in AIH-IS. Transaminases decreased under IS preferentially in anti-TBB5-negative patients. There was no correlation between anti-TBB5-reactivity and histological stages. IgA-anti-TBB5 was mainly found in alcohol-associated liver disease (ALD; 39%). Our data do not support TBB5 as an autoantigenic target of pANCA. However, IgG-anti-TBB5 showed high specificity for (untreated) AIH. While they did not correlate with histological and laboratory parameters, their presence may indicate a poor response to IS.
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Affiliation(s)
- Beate Preuß
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University of Tuebingen, Tuebingen, Germany
| | - Amelie Frank
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University of Tuebingen, Tuebingen, Germany
| | - Birgit Terjung
- Department of Gastroenterology, GFO Kliniken Bonn, St. Josef Hospital, Bonn, Germany
| | - Ulrich Spengler
- Department of Gastroenterology and Hepatology, Nephrology, Infectious Diseases, Endocrinology and Diabetology, University of Bonn, Bonn, Germany
| | - Christoph Berg
- Department of Gastroenterology and Infectiology, University of Tuebingen, Tuebingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University of Tuebingen, Tuebingen, Germany
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2
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Mendes A, Heil HS, Coelho S, Leterrier C, Henriques R. Mapping molecular complexes with super-resolution microscopy and single-particle analysis. Open Biol 2022; 12:220079. [PMID: 35892200 PMCID: PMC9326279 DOI: 10.1098/rsob.220079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding the structure of supramolecular complexes provides insight into their functional capabilities and how they can be modulated in the context of disease. Super-resolution microscopy (SRM) excels in performing this task by resolving ultrastructural details at the nanoscale with molecular specificity. However, technical limitations, such as underlabelling, preclude its ability to provide complete structures. Single-particle analysis (SPA) overcomes this limitation by combining information from multiple images of identical structures and producing an averaged model, effectively enhancing the resolution and coverage of image reconstructions. This review highlights important studies using SRM-SPA, demonstrating how it broadens our knowledge by elucidating features of key biological structures with unprecedented detail.
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Affiliation(s)
| | | | - Simao Coelho
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras, Portugal,MRC Laboratory for Molecular Cell Biology, University College London, London, UK
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3
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Mauro MS, Celma G, Zimyanin V, Magaj MM, Gibson KH, Redemann S, Bahmanyar S. Ndc1 drives nuclear pore complex assembly independent of membrane biogenesis to promote nuclear formation and growth. eLife 2022; 11:75513. [PMID: 35852146 PMCID: PMC9296133 DOI: 10.7554/elife.75513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/15/2022] [Indexed: 01/19/2023] Open
Abstract
The nuclear envelope (NE) assembles and grows from bilayer lipids produced at the endoplasmic reticulum (ER). How ER membrane incorporation coordinates with assembly of nuclear pore complexes (NPCs) to generate a functional NE is not well understood. Here, we use the stereotypical first division of the early C. elegans embryo to test the role of the membrane-associated nucleoporin Ndc1 in coupling NPC assembly to NE formation and growth. 3D-EM tomography of reforming and expanded NEs establishes that Ndc1 determines NPC density. Loss of ndc1 results in faster turnover of the outer scaffold nucleoporin Nup160 at the NE, providing an explanation for how Ndc1 controls NPC number. NE formation fails in the absence of both Ndc1 and the inner ring component Nup53, suggesting partially redundant roles in NPC assembly. Importantly, upregulation of membrane synthesis restored the slow rate of nuclear growth resulting from loss of ndc1 but not from loss of nup53. Thus, membrane biogenesis can be decoupled from Ndc1-mediated NPC assembly to promote nuclear growth. Together, our data suggest that Ndc1 functions in parallel with Nup53 and membrane biogenesis to control NPC density and nuclear size.
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Affiliation(s)
- Michael Sean Mauro
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew HavenUnited States
| | - Gunta Celma
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew HavenUnited States
| | - Vitaly Zimyanin
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States,Department of Molecular Physiology and Biological Physics, University of Virginia, School of MedicineCharlottesvilleUnited States
| | - Magdalena M Magaj
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States,Department of Molecular Physiology and Biological Physics, University of Virginia, School of MedicineCharlottesvilleUnited States
| | - Kimberley H Gibson
- Center for Cellular and Molecular Imaging: Electron Microscopy, Department of Cell Biology, Yale School of MedicineNew HavenUnited States
| | - Stefanie Redemann
- Center for Membrane and Cell Physiology, University of VirginiaCharlottesvilleUnited States,Department of Molecular Physiology and Biological Physics, University of Virginia, School of MedicineCharlottesvilleUnited States,Department of Cell Biology, University of VirginiaCharlottesvilleUnited States
| | - Shirin Bahmanyar
- Department of Molecular, Cellular and Developmental Biology, Yale UniversityNew HavenUnited States
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4
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Zhang Y, Li S, Zeng C, Huang G, Zhu X, Wang Q, Wang K, Zhou Q, Yan C, Zhang W, Yang G, Liu M, Tao Q, Lei J, Shi Y. Molecular architecture of the luminal ring of the Xenopus laevis nuclear pore complex. Cell Res 2020; 30:532-540. [PMID: 32367042 PMCID: PMC7264284 DOI: 10.1038/s41422-020-0320-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 12/23/2022] Open
Abstract
The nuclear pore complex (NPC) mediates the flow of substances between the nucleus and cytoplasm in eukaryotic cells. Here we report the cryo-electron tomography (cryo-ET) structure of the luminal ring (LR) of the NPC from Xenopus laevis oocyte. The observed key structural features of the LR are independently confirmed by single-particle cryo-electron microscopy (cryo-EM) analysis. The LR comprises eight butterfly-shaped subunits, each containing two symmetric wings. Each wing consists of four elongated, tubular protomers. Within the LR subunit, the eight protomers form a Finger domain, which directly contacts the fusion between the inner and outer nuclear membranes and a Grid domain, which serves as a rigid base for the Finger domain. Two neighboring LR subunits interact with each other through the lateral edges of their wings to constitute a Bumper domain, which displays two major conformations and appears to cushion neighboring NPCs. Our study reveals previously unknown features of the LR and potentially explains the elastic property of the NPC.
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Affiliation(s)
- Yanqing Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Sai Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Chao Zeng
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Gaoxingyu Huang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xuechen Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Qifan Wang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Kunpeng Wang
- Tsinghua Computing Facility & Department of Computer Science, Tsinghua University, Beijing, 100084, China
| | - Qiang Zhou
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wusheng Zhang
- Tsinghua Computing Facility & Department of Computer Science, Tsinghua University, Beijing, 100084, China
| | - Guangwen Yang
- Tsinghua Computing Facility & Department of Computer Science, Tsinghua University, Beijing, 100084, China
| | - Minhao Liu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qinghua Tao
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yigong Shi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China.
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, 310024, China.
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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5
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Abstract
The nuclear pore complex (NPC) serves as the sole bidirectional gateway of macromolecules in and out of the nucleus. Owing to its size and complexity (∼1,000 protein subunits, ∼110 MDa in humans), the NPC has remained one of the foremost challenges for structure determination. Structural studies have now provided atomic-resolution crystal structures of most nucleoporins. The acquisition of these structures, combined with biochemical reconstitution experiments, cross-linking mass spectrometry, and cryo-electron tomography, has facilitated the determination of the near-atomic overall architecture of the symmetric core of the human, fungal, and algal NPCs. Here, we discuss the insights gained from these new advances and outstanding issues regarding NPC structure and function. The powerful combination of bottom-up and top-down approaches toward determining the structure of the NPC offers a paradigm for uncovering the architectures of other complex biological machines to near-atomic resolution.
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Affiliation(s)
- Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
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6
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van Nieuwenhuijze A, Burton O, Lemaitre P, Denton AE, Cascalho A, Goodchild RE, Malengier-Devlies B, Cauwe B, Linterman MA, Humblet-Baron S, Liston A. Mice Deficient in Nucleoporin Nup210 Develop Peripheral T Cell Alterations. Front Immunol 2018; 9:2234. [PMID: 30323813 PMCID: PMC6173157 DOI: 10.3389/fimmu.2018.02234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 09/07/2018] [Indexed: 12/15/2022] Open
Abstract
The nucleopore is an essential structure of the eukaryotic cell, regulating passage between the nucleus and cytoplasm. While individual functions of core nucleopore proteins have been identified, the role of other components, such as Nup210, are poorly defined. Here, through the use of an unbiased ENU mutagenesis screen for mutations effecting the peripheral T cell compartment, we identified a Nup210 mutation in a mouse strain with altered CD4/CD8 T cell ratios. Through the generation of Nup210 knockout mice we identified Nup210 as having a T cell-intrinsic function in the peripheral homeostasis of T cells. Remarkably, despite the deep evolutionary conservation of this key nucleopore complex member, no other major phenotypes developed, with viable and healthy knockout mice. These results identify Nup210 as an important nucleopore complex component for peripheral T cells, and raise further questions of why this nucleopore component shows deep evolutionary conservation despite seemingly redundant functions in most cell types.
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Affiliation(s)
- Annemarie van Nieuwenhuijze
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Oliver Burton
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Pierre Lemaitre
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Alice E Denton
- Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Ana Cascalho
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Neurosciences, University of Leuven, Leuven, Belgium
| | - Rose E Goodchild
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Neurosciences, University of Leuven, Leuven, Belgium
| | - Bert Malengier-Devlies
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Bénédicte Cauwe
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | | | - Stephanie Humblet-Baron
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
| | - Adrian Liston
- VIB Centre for Brain & Disease Research, VIB, Leuven, Belgium.,Department of Microbiology and Immunology University of Leuven, Leuven, Belgium
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7
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Zhang W, Neuner A, Rüthnick D, Sachsenheimer T, Lüchtenborg C, Brügger B, Schiebel E. Brr6 and Brl1 locate to nuclear pore complex assembly sites to promote their biogenesis. J Cell Biol 2018; 217:877-894. [PMID: 29439116 PMCID: PMC5839787 DOI: 10.1083/jcb.201706024] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 11/21/2017] [Accepted: 01/10/2018] [Indexed: 12/30/2022] Open
Abstract
The conserved paralogous Brr6 and Brl1 promote NPC biogenesis in an unclear manner. Here, Zhang et al. show that both transmembrane proteins transiently associate with NPC assembly intermediates and directly promote NPC biogenesis. The paralogous Brr6 and Brl1 are conserved integral membrane proteins of the nuclear envelope (NE) with an unclear role in nuclear pore complex (NPC) biogenesis. Here, we analyzed double-degron mutants of Brr6/Brl1 to understand this function. Depletion of Brr6 and Brl1 caused defects in NPC biogenesis, whereas the already assembled NPCs remained unaffected. This NPC biogenesis defect was not accompanied by a change in lipid composition. However, Brl1 interacted with Ndc1 and Nup188 by immunoprecipitation, and with transmembrane and outer and inner ring NPC components by split yellow fluorescent protein analysis, indicating a direct role in NPC biogenesis. Consistently, we found that Brr6 and Brl1 associated with a subpopulation of NPCs and emerging NPC assembly sites. Moreover, BRL1 overexpression affected NE morphology without a change in lipid composition and completely suppressed the nuclear pore biogenesis defect of nup116Δ and gle2Δ cells. We propose that Brr6 and Brl1 transiently associate with NPC assembly sites where they promote NPC biogenesis.
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Affiliation(s)
- Wanlu Zhang
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Diana Rüthnick
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | | | | | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
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8
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Beck M, Hurt E. The nuclear pore complex: understanding its function through structural insight. Nat Rev Mol Cell Biol 2016; 18:73-89. [PMID: 27999437 DOI: 10.1038/nrm.2016.147] [Citation(s) in RCA: 422] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. They are large macromolecular assemblies with a complex composition and diverse functions. Apart from facilitating nucleocytoplasmic transport, NPCs are involved in chromatin organization, the regulation of gene expression and DNA repair. Understanding the molecular mechanisms underlying these functions has been hampered by a lack of structural knowledge about the NPC. The recent convergence of crystallographic and biochemical in vitro analysis of nucleoporins (NUPs), the components of the NPC, with cryo-electron microscopic imaging of the entire NPC in situ has provided first pseudo-atomic view of its central core and revealed that an unexpected network of short linear motifs is an important spatial organization principle. These breakthroughs have transformed the way we understand NPC structure, and they provide an important base for functional investigations, including the elucidation of the molecular mechanisms underlying clinically manifested mutations of the nucleocytoplasmic transport system.
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Affiliation(s)
- Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg D-69117, Germany
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, INF328, Heidelberg D-69120, Germany
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9
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Soheilypour M, Peyro M, Jahed Z, Mofrad MRK. On the Nuclear Pore Complex and Its Roles in Nucleo-Cytoskeletal Coupling and Mechanobiology. Cell Mol Bioeng 2016. [DOI: 10.1007/s12195-016-0443-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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10
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Korfali N, Florens L, Schirmer EC. Isolation, Proteomic Analysis, and Microscopy Confirmation of the Liver Nuclear Envelope Proteome. Methods Mol Biol 2016; 1411:3-44. [PMID: 27147032 DOI: 10.1007/978-1-4939-3530-7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nuclei can be relatively easily extracted from homogenized liver due to the softness of the tissue and crudely separated from other cellular organelles by low-speed centrifugation due to the comparatively large size of nuclei. However, further purification is complicated by nuclear envelope continuity with the endoplasmic reticulum, invaginations containing mitochondria, and connections to the cytoskeleton. Subsequent purification to nuclear envelopes is additionally confounded by connections of inner nuclear membrane proteins to chromatin. For these reasons, it is necessary to confirm proteomic identification of nuclear envelope proteins by testing targeting of individual proteins. The proteomic identification of nuclear envelope fractions is affected by the tendencies of transmembrane proteins to have extreme isoelectric points, strongly hydrophobic peptides, posttranslational modifications, and a propensity to aggregate, thus making proteolysis inefficient. To circumvent these problems, we have developed a MudPIT approach that uses multiple extractions and sequential proteolysis to increase identifications. Here we describe methods for isolating nuclear envelopes, determining their proteome by MudPIT, and confirming their targeting to the nuclear periphery by microscopy.
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Affiliation(s)
- Nadia Korfali
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Laurence Florens
- The Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO, 64110, USA.
| | - Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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11
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RECEPTORES NUCLEARES: DEL NÚCLEO AL CITOPLASMA. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2015. [DOI: 10.1016/j.recqb.2015.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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12
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Worman HJ, Schirmer EC. Nuclear membrane diversity: underlying tissue-specific pathologies in disease? Curr Opin Cell Biol 2015; 34:101-12. [PMID: 26115475 PMCID: PMC4522394 DOI: 10.1016/j.ceb.2015.06.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 06/05/2015] [Accepted: 06/10/2015] [Indexed: 11/16/2022]
Abstract
Human 'laminopathy' diseases result from mutations in genes encoding nuclear lamins or nuclear envelope (NE) transmembrane proteins (NETs). These diseases present a seeming paradox: the mutated proteins are widely expressed yet pathology is limited to specific tissues. New findings suggest tissue-specific pathologies arise because these widely expressed proteins act in various complexes that include tissue-specific components. Diverse mechanisms to achieve NE tissue-specificity include tissue-specific regulation of the expression, mRNA splicing, signaling, NE-localization and interactions of potentially hundreds of tissue-specific NETs. New findings suggest these NETs underlie tissue-specific NE roles in cytoskeletal mechanics, cell-cycle regulation, signaling, gene expression and genome organization. This view of the NE as 'specialized' in each cell type is important to understand the tissue-specific pathology of NE-linked diseases.
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Affiliation(s)
- Howard J Worman
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, USA
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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13
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Gomez-Cavazos JS, Hetzer MW. The nucleoporin gp210/Nup210 controls muscle differentiation by regulating nuclear envelope/ER homeostasis. ACTA ACUST UNITED AC 2015; 208:671-81. [PMID: 25778917 PMCID: PMC4362455 DOI: 10.1083/jcb.201410047] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The luminal domain of Nup210 that lacks NPC sorting signals is sufficient for myogenesis, which suggests that Nup210 may operate within the nuclear envelope/ER lumen during differentiation. Previously, we identified the nucleoporin gp210/Nup210 as a critical regulator of muscle and neuronal differentiation, but how this nucleoporin exerts its function and whether it modulates nuclear pore complex (NPC) activity remain unknown. Here, we show that gp210/Nup210 mediates muscle cell differentiation in vitro via its conserved N-terminal domain that extends into the perinuclear space. Removal of the C-terminal domain, which partially mislocalizes gp210/Nup210 away from NPCs, efficiently rescues the differentiation defect caused by the knockdown of endogenous gp210/Nup210. Unexpectedly, a gp210/Nup210 mutant lacking the NPC-targeting transmembrane and C-terminal domains is sufficient for C2C12 myoblast differentiation. We demonstrate that the endoplasmic reticulum (ER) stress-specific caspase cascade is exacerbated during Nup210 depletion and that blocking ER stress-mediated apoptosis rescues differentiation of Nup210-deficient cells. Our results suggest that the role of gp210/Nup210 in cell differentiation is mediated by its large luminal domain, which can act independently of NPC association and appears to play a pivotal role in the maintenance of nuclear envelope/ER homeostasis.
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Affiliation(s)
- J Sebastian Gomez-Cavazos
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037 Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
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14
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Bcl-2 family in inter-organelle modulation of calcium signaling; roles in bioenergetics and cell survival. J Bioenerg Biomembr 2014; 46:1-15. [PMID: 24078116 DOI: 10.1007/s10863-013-9527-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/27/2013] [Indexed: 01/01/2023]
Abstract
Bcl-2 family proteins, known for their apoptosis functioning at the mitochondria, have been shown to localize to other cellular compartments to mediate calcium (Ca2+) signals. Since the proper supply of Ca2+ in cells serves as an important mechanism for cellular survival and bioenergetics, we propose an integrating role for Bcl-2 family proteins in modulating Ca2+ signaling. The endoplasmic reticulum (ER) is the main Ca2+ storage for the cell and Bcl-2 family proteins competitively regulate its Ca2+ concentration. Bcl-2 family proteins also regulate the flux of Ca2+ from the ER by physically interacting with inositol 1,4,5-trisphosphate receptors (IP3Rs) to mediate their opening. Type 1 IP3Rs reside at the bulk ER to coordinate cytosolic Ca2+ signals, while type 3 IP3Rs reside at mitochondria-associated ER membrane (MAM) to facilitate mitochondrial Ca2+ uptake. In healthy cells, mitochondrial Ca2+ drives pyruvate into the citric acid (TCA) cycle to facilitate ATP production, while a continuous accumulation of Ca2+ can trigger the release of cytochrome c, thus initiating apoptosis. Since multiple organelles and Bcl-2 family proteins are involved in Ca2+ signaling, we aim to clarify the role that Bcl-2 family proteins play in facilitating Ca2+ signaling and how mitochondrial Ca2+ is relevant in both bioenergetics and apoptosis. We also explore how these insights could be useful in controlling bioenergetics in apoptosis-resistant cell lines.
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15
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Abstract
Mutations in genes encoding nuclear envelope proteins cause a wide range of inherited diseases, many of which are neurological. We review the genetic causes and what little is known about pathogenesis of these nuclear envelopathies that primarily affect striated muscle, peripheral nerve and the central nervous system. We conclude by providing examples of experimental therapeutic approaches to these rare but important neuromuscular diseases.
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Affiliation(s)
- Howard J. Worman
- />Department of Medicine and Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032 USA
| | - William T. Dauer
- />Department of Neurology and Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109 USA
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16
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Löschberger A, Franke C, Krohne G, van de Linde S, Sauer M. Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution. J Cell Sci 2014; 127:4351-5. [PMID: 25146397 DOI: 10.1242/jcs.156620] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Here, we combine super-resolution fluorescence localization microscopy with scanning electron microscopy to map the position of proteins of nuclear pore complexes in isolated Xenopus laevis oocyte nuclear envelopes with molecular resolution in both imaging modes. We use the periodic molecular structure of the nuclear pore complex to superimpose direct stochastic optical reconstruction microscopy images with a precision of <20 nm on electron micrographs. The correlative images demonstrate quantitative molecular labeling and localization of nuclear pore complex proteins by standard immunocytochemistry with primary and secondary antibodies and reveal that the nuclear pore complex is composed of eight gp210 (also known as NUP210) protein homodimers. In addition, we find subpopulations of nuclear pore complexes with ninefold symmetry, which are found occasionally among the more typical eightfold symmetrical structures.
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Affiliation(s)
- Anna Löschberger
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Christian Franke
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Georg Krohne
- Department of Electron Microscopy, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Sebastian van de Linde
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilian University Würzburg, Am Hubland, 97074 Würzburg, Germany
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17
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Wong X, Luperchio TR, Reddy KL. NET gains and losses: the role of changing nuclear envelope proteomes in genome regulation. Curr Opin Cell Biol 2014; 28:105-20. [PMID: 24886773 DOI: 10.1016/j.ceb.2014.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 03/21/2014] [Accepted: 04/11/2014] [Indexed: 01/13/2023]
Abstract
In recent years, our view of the nucleus has changed considerably with an increased awareness of the roles dynamic higher order chromatin structure and nuclear organization play in nuclear function. More recently, proteomics approaches have identified differential expression of nuclear lamina and nuclear envelope transmembrane (NET) proteins. Many NETs have been implicated in a range of developmental disorders as well as cell-type specific biological processes, including genome organization and nuclear morphology. While further studies are needed, it is clear that the differential nuclear envelope proteome contributes to cell-type specific nuclear identity and functions. This review discusses the importance of proteome diversity at the nuclear periphery and highlights the putative roles of NET proteins, with a focus on nuclear architecture.
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Affiliation(s)
- Xianrong Wong
- Johns Hopkins University, School of Medicine, Department of Biological Chemistry and Center for Epigenetics, 855N. Wolfe St., Rangos 574, Baltimore, MD 21044, United States
| | - Teresa R Luperchio
- Johns Hopkins University, School of Medicine, Department of Biological Chemistry and Center for Epigenetics, 855N. Wolfe St., Rangos 574, Baltimore, MD 21044, United States
| | - Karen L Reddy
- Johns Hopkins University, School of Medicine, Department of Biological Chemistry and Center for Epigenetics, 855N. Wolfe St., Rangos 574, Baltimore, MD 21044, United States.
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18
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Eisenhardt N, Redolfi J, Antonin W. Interaction of Nup53 with Ndc1 and Nup155 is required for nuclear pore complex assembly. J Cell Sci 2013; 127:908-21. [PMID: 24363447 DOI: 10.1242/jcs.141739] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nuclear pore complexes (NPCs) are the gateways for nucleocytoplasmic exchange. The ordered assembly of these huge complexes from several hundred individual components into an intricate protein interaction network which deforms the two membranes of the nuclear envelope into a pore is only rudimentarily understood. Here, we show that the interaction between Nup53 and the integral pore membrane protein Ndc1 is essential for vertebrate NPC assembly. The Ndc1 binding site on Nup53 overlaps with a region that induces membrane bending and is specifically required to modulate this activity, suggesting that the membrane-deforming capability of Nup53 is adjusted during the NPC assembly process. We further demonstrate that the interaction of Nup53 and Nup155 has a crucial role in NPC formation as the main determinant of recruitment of Nup155 to the assembling pore. Overall, our results pinpoint the diversity of interaction modes accomplished by Nup53, highlighting this protein as an essential link between the pore membrane and the NPC, and as a crucial factor in the formation of the pore membrane.
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Affiliation(s)
- Nathalie Eisenhardt
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstr. 39, 72076 Tübingen, Germany
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19
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Osorio DS, Gomes ER. The contemporary nucleus: A trip down memory lane. Biol Cell 2013; 105:430-41. [DOI: 10.1111/boc.201300009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 06/21/2013] [Indexed: 01/12/2023]
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20
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Poring over pores: nuclear pore complex insertion into the nuclear envelope. Trends Biochem Sci 2013; 38:292-301. [DOI: 10.1016/j.tibs.2013.04.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 03/29/2013] [Accepted: 04/02/2013] [Indexed: 11/18/2022]
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21
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Tamura K, Hara-Nishimura I. The molecular architecture of the plant nuclear pore complex. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:823-32. [PMID: 22987840 DOI: 10.1093/jxb/ers258] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The nucleus contains the cell's genetic material, which directs cellular activity via gene regulation. The physical barrier of the nuclear envelope needs to be permeable to a variety of macromolecules and signals. The most prominent gateways for the transport of macromolecules are the nuclear pore complexes (NPCs). The NPC is the largest multiprotein complex in the cell, and is composed of multiple copies of ~30 different proteins called nucleoporins. Although much progress has been made in dissecting the NPC structure in vertebrates and yeast, the molecular architecture and physiological function of nucleoporins in plants remain poorly understood. In this review, we summarize the current knowledge regarding the plant NPC proteome and address structural and functional aspects of plant nucleoporins, which support the fundamental cellular machinery.
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Affiliation(s)
- Kentaro Tamura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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22
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Gomez-Cavazos JS, Hetzer MW. Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins. Curr Opin Cell Biol 2012; 24:775-83. [PMID: 22995343 DOI: 10.1016/j.ceb.2012.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/07/2012] [Accepted: 08/20/2012] [Indexed: 11/29/2022]
Abstract
The Nuclear Envelope (NE) contains over 100 different proteins that associate with nuclear components such as chromatin, the lamina and the transcription machinery. Mutations in genes encoding NE proteins have been shown to result in tissue-specific defects and disease, suggesting cell-type specific differences in NE composition and function. Consistent with these observations, recent studies have revealed unexpected functions for numerous NE associated proteins during cell differentiation and development. Here we review the latest insights into the roles played by the NE in cell differentiation, development, disease and aging, focusing primarily on inner nuclear membrane (INM) proteins and nuclear pore components.
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Affiliation(s)
- J Sebastian Gomez-Cavazos
- Salk Institute for Biological Studies, Molecular and Cell Biology Laboratory, 10010N. Torrey Pines Road, La Jolla, 92037 CA, United States
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23
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Löschberger A, van de Linde S, Dabauvalle MC, Rieger B, Heilemann M, Krohne G, Sauer M. Super-resolution imaging visualizes the eightfold symmetry of gp210 proteins around the nuclear pore complex and resolves the central channel with nanometer resolution. J Cell Sci 2012; 125:570-5. [PMID: 22389396 DOI: 10.1242/jcs.098822] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
One of the most complex molecular machines of cells is the nuclear pore complex (NPC), which controls all trafficking of molecules in and out of the nucleus. Because of their importance for cellular processes such as gene expression and cytoskeleton organization, the structure of NPCs has been studied extensively during the last few decades, mainly by electron microscopy. We have used super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM) to investigate the structure of NPCs in isolated Xenopus laevis oocyte nuclear envelopes, with a lateral resolution of ~15 nm. By generating accumulated super-resolved images of hundreds of NPCs we determined the diameter of the central NPC channel to be 41 ± 7 nm and demonstrate that the integral membrane protein gp210 is distributed in an eightfold radial symmetry. Two-color dSTORM experiments emphasize the highly symmetric NPCs as ideal model structures to control the quality of corrections to chromatic aberration and to test the capability and reliability of super-resolution imaging methods.
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Affiliation(s)
- Anna Löschberger
- Department of Biotechnology and Biophysics, Biozentrum, Julius Maximilians University Würzburg, Am Hubland, 97074 Würzburg, Germany
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24
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Nguyen KT, Holloway MP, Altura RA. The CRM1 nuclear export protein in normal development and disease. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 3:137-151. [PMID: 22773955 PMCID: PMC3388738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/16/2012] [Indexed: 06/01/2023]
Abstract
CRM1 (Chromosomal Maintenance 1, also known as Exportin 1) is the major mammalian export protein that facilitates the transport of large macromolecules including RNA and protein across the nuclear membrane to the cytoplasm. The gene encoding CRM1 was originally identified in yeast as required to maintain higher order chromosome structure. In mammalian cells, CRM1 was found to bind several nuclear pore proteins hence its role in nuclear-cytosolic transport was discovered. In addition to nuclear-cytosolic transport, CRM1 also plays a role in centrosome duplication and spindle assembly, especially in response to DNA damage. The crystal structure of CRM1 suggests a complex protein that binds the Ran protein bound to GTP, allowing for a conformational change that facilitates binding to different cargo proteins through a nuclear export signal (NES). Included in the cadre of cargo are multiple tumor suppressor and oncoproteins as p53, BRCA1, Survivin, NPM, and APC, which function in the nucleus to regulate transcription or aid in chromosomal assembly and movement. An imbalance in the cytosolic level of these proteins has been observed in cancer cells, resulting in either inactivation (tumor suppressor) or an excess of anti-apoptotic activity (oncoprotein). Thus, the concept of inhibiting CRM1 has been explored as a potential therapeutic intervention. Indeed, inhibition of CRM1 by a variety of small molecules that interfere with cargo-NES binding results in cancer cell death. Whether all of these proteins together are responsible for this phenotype or whether specific proteins are required for this effect is unclear at this time.
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Affiliation(s)
- Kevin T Nguyen
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, Hasbro Children's Hospital and The Warren Alpert Medical School at Brown University Providence, Rhode Island, USA
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25
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Ma Y, Yuan X, Wyatt WR, Pomerening JR. Expression of constitutively active CDK1 stabilizes APC-Cdh1 substrates and potentiates premature spindle assembly and checkpoint function in G1 cells. PLoS One 2012; 7:e33835. [PMID: 22479455 PMCID: PMC3315497 DOI: 10.1371/journal.pone.0033835] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 02/17/2012] [Indexed: 01/13/2023] Open
Abstract
Mitotic progression in eukaryotic cells depends upon the activation of cyclin-dependent kinase 1 (CDK1), followed by its inactivation through the anaphase-promoting complex (APC)/cyclosome-mediated degradation of M-phase cyclins. Previous work revealed that expression of a constitutively active CDK1 (CDK1AF) in HeLa cells permitted their division, but yielded G1 daughter cells that underwent premature S-phase and early mitotic events. While CDK1AF was found to impede the sustained activity of APC-Cdh1, it was unknown if this defect improperly stabilized mitotic substrates and contributed to the occurrence of these premature M phases. Here, we show that CDK1AF expression in HeLa cells improperly stabilized APC-Cdh1 substrates in G1-phase daughter cells, including mitotic kinases and the APC adaptor, Cdc20. Division of CDK1AF-expressing cells produced G1 daughters with an accelerated S-phase onset, interrupted by the formation of premature bipolar spindles capable of spindle assembly checkpoint function. Further characterization of these phenotypes induced by CDK1AF expression revealed that this early spindle formation depended upon premature CDK1 and Aurora B activities, and their inhibition induced rapid spindle disassembly. Following its normal M-phase degradation, we found that the absence of Wee1 in these prematurely cycling daughter cells permitted the endogenous CDK1 to contribute to these premature mitotic events, since expression of a non-degradable Wee1 reduced the number of cells that exhibited premature cyclin B1oscillations. Lastly, we discovered that Cdh1-ablated cells could not be forced into a premature M phase, despite cyclin B1 overexpression and proteasome inhibition. Together, these results demonstrate that expression of constitutively active CDK1AF hampers the destruction of critical APC-Cdh1 targets, and that this type of condition could prevent newly divided cells from properly maintaining a prolonged interphase state. We propose that this more subtle type of defect in activity of the APC-driven negative-feedback loop may have implications for triggering genome instability and tumorigenesis.
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Affiliation(s)
- Yan Ma
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Xi Yuan
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - William R. Wyatt
- Department of Statistics, Indiana University, Bloomington, Indiana, United States of America
| | - Joseph R. Pomerening
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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26
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Clever M, Funakoshi T, Mimura Y, Takagi M, Imamoto N. The nucleoporin ELYS/Mel28 regulates nuclear envelope subdomain formation in HeLa cells. Nucleus 2012; 3:187-99. [PMID: 22555603 PMCID: PMC3383574 DOI: 10.4161/nucl.19595] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In open mitosis the nuclear envelope (NE) reassembles at the end of each mitosis. This process involves the reformation of the nuclear pore complex (NPC), the inner and outer nuclear membranes, and the nuclear lamina. In human cells cell cycle-dependent NE subdomains exist, characterized as A-type lamin-rich/NPC-free or B-type lamin-rich/NPC-rich, which are initially formed as core or noncore regions on mitotic chromosomes, respectively. Although postmitotic NE formation has been extensively studied, little is known about the coordination of NPC and NE assembly. Here, we report that the nucleoporin ELYS/Mel28, which is crucial for postmitotic NPC formation, is essential for recruiting the lamin B receptor (LBR) to the chromosomal noncore region. Furthermore, ELYS/Mel28 is responsible for focusing of A-type lamin-binding proteins like emerin, Lap2α and the barrier-to-autointegration factor (BAF) at the chromosomal core region. ELYS/Mel28 biochemically interacts with the LBR in a phosphorylation-dependent manner. Recruitment of the LBR depends on the nucleoporin Nup107, which interacts with ELYS/Mel28 but not on nucleoporin Pom121, suggesting that the specific molecular interactions with ELYS/Mel28 are involved in the NE assembly at the noncore region. The depletion of the LBR affected neither the behavior of emerin nor Lap2α indicating that the recruitment of the LBR to mitotic chromosomes is not involved in formation of the core region. The depletion of ELYS/Mel28 also accelerates the entry into cytokinesis after recruitment of emerin to chromosomes. Our data show that ELYS/Mel28 plays a role in NE subdomain formation in late mitosis.
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Affiliation(s)
- Michaela Clever
- Cellular Dynamics Laboratory; Riken Advanced Science Institute; Saitama, Japan
| | - Tomoko Funakoshi
- Cellular Dynamics Laboratory; Riken Advanced Science Institute; Saitama, Japan
- Live-Cell Molecular Imaging Research Team; Riken Advanced Science Institute; Saitama, Japan
| | - Yasuhiro Mimura
- Cellular Dynamics Laboratory; Riken Advanced Science Institute; Saitama, Japan
| | - Masatoshi Takagi
- Cellular Dynamics Laboratory; Riken Advanced Science Institute; Saitama, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory; Riken Advanced Science Institute; Saitama, Japan
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27
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Malik P, Tabarraei A, Kehlenbach RH, Korfali N, Iwasawa R, Graham SV, Schirmer EC. Herpes simplex virus ICP27 protein directly interacts with the nuclear pore complex through Nup62, inhibiting host nucleocytoplasmic transport pathways. J Biol Chem 2012; 287:12277-92. [PMID: 22334672 PMCID: PMC3320978 DOI: 10.1074/jbc.m111.331777] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The herpes simplex virus ICP27 protein is important for the expression and nuclear export of viral mRNAs. Although several binding sites have been mapped along the ICP27 sequence for various RNA and protein partners, including the transport receptor TAP of the host cell nuclear transport machinery, several aspects of ICP27 trafficking through the nuclear pore complex remain unclear. We investigated if ICP27 could interact directly with the nuclear pore complex itself, finding that ICP27 directly binds the core nucleoporin Nup62. This is confirmed through co-immunoprecipitation and in vitro binding assays with purified components. Mapping with ICP27 deletion and point mutants further shows that the interaction requires sequences in both the N and C termini of ICP27. Expression of wild type ICP27 protein inhibited both classical, importin α/β-dependent and transportin-dependent nuclear import. In contrast, an ICP27 point mutant that does not interact with Nup62 had no such inhibitory effect. We suggest that ICP27 association with Nup62 provides additional binding sites at the nuclear pore for ICP27 shuttling, thus supporting ICP27-mediated transport. We propose that ICP27 competes with some host cell transport receptors for binding, resulting in inhibition of those host transport pathways.
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Affiliation(s)
- Poonam Malik
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, Scotland, United Kingdom.
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28
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Waldmann I, Spillner C, Kehlenbach RH. The nucleoporin-like protein NLP1 (hCG1) promotes CRM1-dependent nuclear protein export. J Cell Sci 2012; 125:144-54. [PMID: 22250199 DOI: 10.1242/jcs.090316] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Translocation of transport complexes across the nuclear envelope is mediated by nucleoporins, proteins of the nuclear pore complex that contain phenylalanine-glycine (FG) repeats as a characteristic binding motif for transport receptors. CRM1 (exportin 1), the major export receptor, forms trimeric complexes with RanGTP and proteins containing nuclear export sequences (NESs). We analyzed the role of the nucleoporin-like protein 1, NLP1 (also known as hCG1 and NUPL2) in CRM1-dependent nuclear transport. NLP1, which contains many FG repeats, localizes to the nuclear envelope and could also be mobile within the nucleus. It promotes the formation of complexes containing CRM1 and RanGTP, with or without NES-containing cargo proteins, that can be dissociated by RanBP1 and/or the cytoplasmic nucleoporin Nup214. The FG repeats of NLP1 do not play a major role in CRM1 binding. Overexpression of NLP1 promotes CRM1-dependent export of certain cargos, whereas its depletion by small interfering RNAs leads to reduced export rates. Thus, NLP1 functions as an accessory factor in CRM1-dependent nuclear protein export.
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Affiliation(s)
- Inga Waldmann
- Department of Biochemistry I, Faculty of Medicine, Georg-August-University of Göttingen, Göttingen, Germany
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29
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Wälde S, Thakar K, Hutten S, Spillner C, Nath A, Rothbauer U, Wiemann S, Kehlenbach RH. The nucleoporin Nup358/RanBP2 promotes nuclear import in a cargo- and transport receptor-specific manner. Traffic 2011; 13:218-33. [PMID: 21995724 DOI: 10.1111/j.1600-0854.2011.01302.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 10/11/2011] [Accepted: 10/11/2011] [Indexed: 12/31/2022]
Abstract
In vertebrates, the nuclear pore complex (NPC), the gate for transport of macromolecules between the nucleus and the cytoplasm, consists of approximately 30 different nucleoporins (Nups). The Nup and SUMO E3-ligase Nup358/RanBP2 are the major components of the cytoplasmic filaments of the NPC. In this study, we perform a structure-function analysis of Nup358 and describe its role in nuclear import of specific proteins. In a screen for nuclear proteins that accumulate in the cytoplasm upon Nup358 depletion, we identified proteins that were able to interact with Nup358 in a receptor-independent manner. These included the importin α/β-cargo DBC-1 (deleted in breast cancer 1) and DMAP-1 (DNA methyltransferase 1 associated protein 1). Strikingly, a short N-terminal fragment of Nup358 was sufficient to promote import of DBC-1, whereas DMAP-1 required a larger portion of Nup358 for stimulated import. Neither the interaction of RanGAP with Nup358 nor its SUMO-E3 ligase activity was required for nuclear import of all tested cargos. Together, Nup358 functions as a cargo- and receptor-specific assembly platform, increasing the efficiency of nuclear import of proteins through various mechanisms.
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Affiliation(s)
- Sarah Wälde
- Department of Biochemistry I, Faculty of Medicine, Georg-August-University of Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
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30
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Shaulov L, Gruber R, Cohen I, Harel A. A dominant-negative form of POM121 binds chromatin and disrupts the two separate modes of nuclear pore assembly. J Cell Sci 2011; 124:3822-34. [PMID: 22100917 DOI: 10.1242/jcs.086660] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Nuclear pore complexes (NPCs) are formed during two separate stages of the metazoan cell cycle. They are assembled into the re-forming nuclear envelope (NE) at the exit from mitosis and into an intact, expanding NE during interphase. Here, we show that a soluble internal fragment of the membrane nucleoporin POM121 has a dominant-negative effect on both modes of assembly in a cell-free reconstitution system. The soluble POM121 fragment binds chromatin at sites that are distinct from ELYS-Nup107-160 'seeding' sites and prevents membrane enclosure and NPC formation. Importin-β negatively regulates chromatin binding by the POM121 fragment through a conserved NLS motif and is also shown to affect the recruitment of the endogenous membrane protein to chromatin in the full assembly system. When an intact NE is present before the addition of the dominant-negative fragment, NPCs are inserted into the NE but membrane expansion is inhibited. This results in densely packed NPCs with no intervening membrane patches, as visualized by scanning electron microscopy. We conclude that POM121 plays an important role in both modes of assembly and links nuclear membrane formation and expansion to nuclear pore biogenesis.
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Affiliation(s)
- Lihi Shaulov
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
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31
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Mizuguchi C, Oka M, Moriyama T, Tachibana T, Yoneda Y. Specific monoclonal antibody against the nuclear pore complex protein, Nup96. Hybridoma (Larchmt) 2010; 29:551-3. [PMID: 21133806 DOI: 10.1089/hyb.2010.0065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Nup96 is a component of the Nup107-160 complex, the largest subunit of the nuclear pore complex. Nup96 is generated as a precursor protein with Nup98. However, the mechanism by which Nup96 contributes to cell function is not clear. We report here on the preparation of a monoclonal antibody (MAb) directed against mouse Nup96. The antibody was produced by the hybridization of mouse myeloma cells with lymph node cells from an immunized rat. The antibody, MAb 4H5, specifically recognized Nup96, as evidenced by immunoblotting using the whole cell lysates. In immunostaining using MAb 4H5, a nuclear rim staining pattern was observed. This antibody will be useful in immunoblotting and immunolocalization experiments, as well as further analyses of the biological function and cellular dynamics of this protein.
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Affiliation(s)
- Chiaki Mizuguchi
- Biomolecular Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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32
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Mitchell JM, Mansfeld J, Capitanio J, Kutay U, Wozniak RW. Pom121 links two essential subcomplexes of the nuclear pore complex core to the membrane. ACTA ACUST UNITED AC 2010; 191:505-21. [PMID: 20974814 PMCID: PMC3003318 DOI: 10.1083/jcb.201007098] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pom121 anchors core structures of the NPC to the membrane through its binding to the β-propeller domains of Nup155 and Nup160. Nuclear pore complexes (NPCs) control the movement of molecules across the nuclear envelope (NE). We investigated the molecular interactions that exist at the interface between the NPC scaffold and the pore membrane. We show that key players mediating these interactions in mammalian cells are the nucleoporins Nup155 and Nup160. Nup155 depletion massively alters NE structure, causing a dramatic decrease in NPC numbers and the improper targeting of membrane proteins to the inner nuclear membrane. The role of Nup155 in assembly is likely closely linked to events at the membrane as we show that Nup155 interacts with pore membrane proteins Pom121 and NDC1. Furthermore, we demonstrate that the N terminus of Pom121 directly binds the β-propeller regions of Nup155 and Nup160. We propose a model in which the interactions of Pom121 with Nup155 and Nup160 are predicted to assist in the formation of the nuclear pore and the anchoring of the NPC to the pore membrane.
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Affiliation(s)
- Jana M Mitchell
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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33
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Fichtman B, Ramos C, Rasala B, Harel A, Forbes DJ. Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis. Mol Biol Cell 2010; 21:4197-211. [PMID: 20926687 PMCID: PMC2993748 DOI: 10.1091/mbc.e10-04-0309] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.
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Affiliation(s)
- Boris Fichtman
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0347, USA
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Hermo L, Pelletier RM, Cyr DG, Smith CE. Surfing the wave, cycle, life history, and genes/proteins expressed by testicular germ cells. Part 5: intercellular junctions and contacts between germs cells and Sertoli cells and their regulatory interactions, testicular cholesterol, and genes/proteins associated with more than one germ cell generation. Microsc Res Tech 2010; 73:409-94. [PMID: 19941291 DOI: 10.1002/jemt.20786] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the testis, cell adhesion and junctional molecules permit specific interactions and intracellular communication between germ and Sertoli cells and apposed Sertoli cells. Among the many adhesion family of proteins, NCAM, nectin and nectin-like, catenins, and cadherens will be discussed, along with gap junctions between germ and Sertoli cells and the many members of the connexin family. The blood-testis barrier separates the haploid spermatids from blood borne elements. In the barrier, the intercellular junctions consist of many proteins such as occludin, tricellulin, and claudins. Changes in the expression of cell adhesion molecules are also an essential part of the mechanism that allows germ cells to move from the basal compartment of the seminiferous tubule to the adluminal compartment thus crossing the blood-testis barrier and well-defined proteins have been shown to assist in this process. Several structural components show interactions between germ cells to Sertoli cells such as the ectoplasmic specialization which are more closely related to Sertoli cells and tubulobulbar complexes that are processes of elongating spermatids embedded into Sertoli cells. Germ cells also modify several Sertoli functions and this also appears to be the case for residual bodies. Cholesterol plays a significant role during spermatogenesis and is essential for germ cell development. Lastly, we list genes/proteins that are expressed not only in any one specific generation of germ cells but across more than one generation.
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Affiliation(s)
- Louis Hermo
- Faculty of Medicine, Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada H3A 2B2.
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35
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Bocock JP, Carmicle S, Madamba E, Erickson AH. Nuclear targeting of an endosomal E3 ubiquitin ligase. Traffic 2010; 11:756-66. [PMID: 20230530 DOI: 10.1111/j.1600-0854.2010.01060.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ring finger protein 13 (RNF13) is an E3 ubiquitin ligase embedded in endosome membranes. The protein undergoes constitutive post-translational proteolysis, making its detection difficult unless cells are incubated with a proteasome inhibitor to allow biosynthetic forms to accumulate. When cells were treated with phorbol 12-myristate 13-acetate (PMA), RNF13 avoided proteolysis. A similar stabilization was seen on ionomycin treatment of cells. Drug treatment stabilized both the full-length protein and a membrane-embedded C-terminal fragment generated following ectodomain shedding. Immunofluorescence staining revealed that PMA treatment caused the protein to accumulate in recycling endosomes, where it colocalized with transferrin receptor, and on the inner nuclear membrane, where it colocalized with lamin B. Expression of dominant-negative Rab11 inhibited nuclear localization, suggesting RNF13 was targeted to the inner nuclear membrane through recycling endosomes. New protein synthesis was necessary for this targeting. Nuclear localization was confirmed by immunoelectron microscopy and by purification of the inner nuclear membrane. Stress-induced transport of an endosomal protein to the inner nuclear membrane is a novel mechanism for introduction of regulatory proteins to the DNA environment. RNF13, with its ubiquitin ligase-active RING domain, has the potential to turn over key nuclear proteins in response to signals received at the plasma membrane.
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Affiliation(s)
- Jeffrey P Bocock
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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Buch C, Lindberg R, Figueroa R, Gudise S, Onischenko E, Hallberg E. An integral protein of the inner nuclear membrane localizes to the mitotic spindle in mammalian cells. J Cell Sci 2009; 122:2100-7. [DOI: 10.1242/jcs.047373] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Here, we characterize a transmembrane protein of the nuclear envelope that we name spindle-associated membrane protein 1 (Samp1). The protein is conserved in metazoa and fission yeast and is homologous to Net5 in rat and Ima1 in Schizosaccharomyces pombe. We show that, in human cells, the protein is a membrane-spanning polypeptide with an apparent molecular mass of 43 kDa. This is consistent with a predicted polypeptide of 392 amino acids that has five transmembrane segments and its C-terminus exposed to the nucleoplasm. During interphase, Samp1 was specifically distributed in the inner nuclear membrane. Post-transcriptional silencing of Samp1 expression resulted in separation of centrosomes from the nuclear envelope, indicating that it is functionally connected to the cytoskeleton. At the onset of mitosis, most of the protein dispersed out into the ER, as expected. However, during mitosis, a significant fraction of the protein specifically localized to the polar regions of the mitotic spindle. We demonstrate for the first time, in human cells, the existence of a membranous structure overlapping with the mitotic spindle. Interestingly, another integral inner nuclear membrane protein, emerin, was absent from the spindle-associated membranes. Thus, Samp1 defines a specific membrane domain associated with the mitotic spindle.
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Affiliation(s)
- Charlotta Buch
- Department of Biosciences and Nutrition, Karolinska Institute, SE-141 57 Huddinge, Sweden
- Life Sciences, Södertörns University, SE-141 89 Huddinge, Sweden
| | - Robert Lindberg
- Life Sciences, Södertörns University, SE-141 89 Huddinge, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ricardo Figueroa
- Life Sciences, Södertörns University, SE-141 89 Huddinge, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Santhosh Gudise
- Department of Biosciences and Nutrition, Karolinska Institute, SE-141 57 Huddinge, Sweden
- Life Sciences, Södertörns University, SE-141 89 Huddinge, Sweden
| | - Evgeny Onischenko
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Einar Hallberg
- Life Sciences, Södertörns University, SE-141 89 Huddinge, Sweden
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Korfali N, Fairley EAL, Swanson SK, Florens L, Schirmer EC. Use of sequential chemical extractions to purify nuclear membrane proteins for proteomics identification. Methods Mol Biol 2009; 528:201-225. [PMID: 19153695 DOI: 10.1007/978-1-60327-310-7_15] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The nuclear envelope (NE) is a double membrane system that is both a part of the endoplasmic reticulum and part of the nucleus. As its constituent proteins tend to be highly complexed with nuclear and cytoplasmic components, it is notoriously difficult to purify. Two methods can reduce this difficulty for the identification of nuclear membrane proteins: comparison to contaminating membranes and chemical extractions to enrich for certain groups of proteins. The purification of nuclear envelopes and contaminating microsomal membranes is described here along with procedures for chemical extraction using salt and detergent, chaotropes, or alkaline solutions. Each extraction method enriches for different combinations of nuclear envelope proteins. Finally, we describe the analysis of these fractions with MudPIT, a proteomics methodology that avoids gel extraction of bands to facilitate identification of minor proteins and membrane proteins that do not resolve well on gels. Together these three approaches can significantly increase the output of proteomics studies aimed at identifying the protein complement of subcellular membrane systems.
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Affiliation(s)
- Nadia Korfali
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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38
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Abstract
PAX5, a master regulator of B-cell development, was recently shown to be involved in several leukemia-associated rearrangements, which result in fusion genes encoding chimeric proteins that antagonize PAX5 transcriptional activity. In a population-based fluorescence in situ hybridization screening study of 446 childhood acute lymphoblastic leukemia (ALL) patients, we now show that PAX5 rearrangements occur at an incidence of about 2.5% of B-cell precursor ALL. Identification of several novel PAX5 partner genes, including POM121, BRD1, DACH1, HIPK1 and JAK2 brings the number of distinct PAX5 in-frame fusions to at least 12. Our data show that these not only comprise transcription factors but also structural proteins and genes involved in signal transduction, which at least in part have not been implicated in tumorigenesis.
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Liu HL, De Souza CPC, Osmani AH, Osmani SA. The three fungal transmembrane nuclear pore complex proteins of Aspergillus nidulans are dispensable in the presence of an intact An-Nup84-120 complex. Mol Biol Cell 2008; 20:616-30. [PMID: 19019988 DOI: 10.1091/mbc.e08-06-0628] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In Aspergillus nidulans nuclear pore complexes (NPCs) undergo partial mitotic disassembly such that 12 NPC proteins (Nups) form a core structure anchored across the nuclear envelope (NE). To investigate how the NPC core is maintained, we affinity purified the major core An-Nup84-120 complex and identified two new fungal Nups, An-Nup37 and An-ELYS, previously thought to be vertebrate specific. During mitosis the An-Nup84-120 complex locates to the NE and spindle pole bodies but, unlike vertebrate cells, does not concentrate at kinetochores. We find that mutants lacking individual An-Nup84-120 components are sensitive to the membrane destabilizer benzyl alcohol (BA) and high temperature. Although such mutants display no defects in mitotic spindle formation, they undergo mitotic specific disassembly of the NPC core and transient aggregation of the mitotic NE, suggesting the An-Nup84-120 complex might function with membrane. Supporting this, we show cells devoid of all known fungal transmembrane Nups (An-Ndc1, An-Pom152, and An-Pom34) are viable but that An-ndc1 deletion combined with deletion of individual An-Nup84-120 components is either lethal or causes sensitivity to treatments expected to destabilize membrane. Therefore, the An-Nup84-120 complex performs roles, perhaps at the NPC membrane as proposed previously, that become essential without the An-Ndc1 transmembrane Nup.
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Affiliation(s)
- Hui-Lin Liu
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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40
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Batrakou DG, Kerr ARW, Schirmer EC. Comparative proteomic analyses of the nuclear envelope and pore complex suggests a wide range of heretofore unexpected functions. J Proteomics 2008; 72:56-70. [PMID: 18852071 DOI: 10.1016/j.jprot.2008.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 08/26/2008] [Accepted: 09/18/2008] [Indexed: 12/31/2022]
Abstract
Since the discovery of several inherited diseases linked to the nuclear envelope the number of functions ascribed to this subcellular organelle has skyrocketed. However the molecular pathways underlying these functions are not clear in most cases, perhaps because of missing components. Several recent proteomic analyses of the nuclear envelope and nuclear pore complex proteomes have yielded not only enough missing components to potentially elucidate these pathways, but suggest an exponentially greater number of functions at the nuclear periphery than ever imagined. Many of these functions appear to derive from recapitulation of pathways utilized at the plasma membrane and from other membrane systems. Additionally, many proteins identified in the comparative nuclear envelope studies have sequence characteristics suggesting that they might also contribute to nuclear pore complex functions. In particular, the striking enrichment for proteins in the nuclear envelope fractions that carry phenylalanine-glycine (FG) repeats may be significant for the mechanism of nuclear transport. In retrospect, these findings are only surprising in context of the notion held for many years that the nuclear envelope was only a barrier protecting the genome. In fact, it is arguably the most complex membrane organelle in the cell.
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Affiliation(s)
- Dzmitry G Batrakou
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
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41
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Abstract
Because of its many connections to other cell systems, the nuclear envelope (NE)is essentially impossible to purify to homogeneity. To circumvent these problems, we developed a subtractive proteomics approach in which the fraction of interest and a fraction known to contaminate the fraction of interest are separately analyzed, and proteins identified in both fractions are subtracted from the data set. This requires that the contaminating fraction can be purified to homogeneity. In this case, microsomal membranes (MMs) are used to represent endoplasmic reticulum contamination, allowing the identification of transmembrane proteins specific to the NE. To circumvent problems commonly associated with analyzing membrane proteins, the multidimensional protein identification technology (MudPIT) proteomics methodology is employed.
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42
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Rasala BA, Ramos C, Harel A, Forbes DJ. Capture of AT-rich chromatin by ELYS recruits POM121 and NDC1 to initiate nuclear pore assembly. Mol Biol Cell 2008; 19:3982-96. [PMID: 18596237 DOI: 10.1091/mbc.e08-01-0012] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Assembly of the nuclear pore, gateway to the genome, from its component subunits is a complex process. In higher eukaryotes, nuclear pore assembly begins with the binding of ELYS/MEL-28 to chromatin and recruitment of the large critical Nup107-160 pore subunit. The choreography of steps that follow is largely speculative. Here, we set out to molecularly define early steps in nuclear pore assembly, beginning with chromatin binding. Point mutation analysis indicates that pore assembly is exquisitely sensitive to the change of only two amino acids in the AT-hook motif of ELYS. The dependence on AT-rich chromatin for ELYS binding is borne out by the use of two DNA-binding antibiotics. AT-binding Distamycin A largely blocks nuclear pore assembly, whereas GC-binding Chromomycin A(3) does not. Next, we find that recruitment of vesicles containing the key integral membrane pore proteins POM121 and NDC1 to the forming nucleus is dependent on chromatin-bound ELYS/Nup107-160 complex, whereas recruitment of gp210 vesicles is not. Indeed, we reveal an interaction between the cytoplasmic domain of POM121 and the Nup107-160 complex. Our data thus suggest an order for nuclear pore assembly of 1) AT-rich chromatin sites, 2) ELYS, 3) the Nup107-160 complex, and 4) POM121- and NDC1-containing membrane vesicles and/or sheets, followed by (5) assembly of the bulk of the remaining soluble pore subunits.
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Affiliation(s)
- Beth A Rasala
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0347, USA
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43
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Hieda M, Isokane M, Koizumi M, Higashi C, Tachibana T, Shudou M, Taguchi T, Hieda Y, Higashiyama S. Membrane-anchored growth factor, HB-EGF, on the cell surface targeted to the inner nuclear membrane. ACTA ACUST UNITED AC 2008; 180:763-9. [PMID: 18299347 PMCID: PMC2373455 DOI: 10.1083/jcb.200710022] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Heparin-binding EGF-like growth factor (HB-EGF) is synthesized as a type I transmembrane protein (proHB-EGF) and expressed on the cell surface. The ectodomain shedding of proHB-EGF at the extracellular region on the plasma membrane yields a soluble EGF receptor ligand and a transmembrane-cytoplasmic fragment (HB-EGF-CTF). The cytoplasmic domain of proHB-EGF (HB-EGF-cyto) interacts with transcriptional repressors to reverse their repressive activities. However, how HB-EGF-cyto accesses transcriptional repressors is yet unknown. The present study demonstrates that, after exposure to shedding stimuli, both HB-EGF-CTF and unshed proHB-EGF translocate to the nuclear envelope. Immunoelectron microscopy and digitonin-permeabilized cells showed that HB-EGF-cyto signals are at the inner nuclear membrane. A short sequence element within the HB-EGF-cyto allows a transmembrane protein to localize to the nuclear envelope. The dominant-active form of Rab5 and Rab11 suppressed nuclear envelope targeting. Collectively, these data demonstrate that membrane-anchored HB-EGF is targeted to the inner nuclear membrane via a retrograde membrane trafficking pathway.
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Affiliation(s)
- Miki Hieda
- Department of Biochemistry and Molecular Genetics, Ehime University Graduate School of Medicine, Ehime 791-0295, Japan
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44
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Purification of Nuclei and Preparation of Nuclear Envelopes from Skeletal Muscle. THE NUCLEUS 2008; 463:23-41. [DOI: 10.1007/978-1-59745-406-3_2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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45
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Vaillant DC, Paulin-Levasseur M. Evaluation of mammalian cell-free systems of nuclear disassembly and assembly. J Histochem Cytochem 2007; 56:157-73. [PMID: 17967934 DOI: 10.1369/jhc.7a7330.2007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mammalian cell-free systems are very useful for the biochemical and structural study of nuclear disassembly and assembly. Through experimental manipulations, the role of specific proteins in these processes can be studied. Recently, we intended to examine the involvement of integral and peripheral inner nuclear membrane proteins in nuclear disassembly and assembly. However, we could not achieve proper disassembly when isolated interphase HeLa nuclei were exposed to mitotic soluble extracts obtained from the same cell line and containing cyclin B1. Homogenates of synchronized mitotic HeLa cells left to reassemble their nuclei generated incomplete nuclear envelopes on chromatin masses. Digitonin-permeabilized mitotic cells also assembled incomplete nuclei, generating a lot of cytoplasmic inclusions of inner nuclear membrane proteins as an intermediate. These results were therefore used as a basis for a critical evaluation of mammalian cell-free systems. We present here evidence that cell synchronization itself can interfere with the progress of nuclear assembly, possibly by causing aberrant nuclear disassembly and/or by inducing the formation of an abnormal number of mitotic spindles.
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Affiliation(s)
- Dominique C Vaillant
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, Canada K1N 6N5
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46
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Abstract
Antinuclear antibodies are detectable in approximately 50% of subjects with primary biliary cirrhosis (PBC). Most clinical laboratories use indirect immunofluorescence microscopy to detect antinuclear antibodies and two labeling patterns that predominate in PBC are nuclear rim and multiple nuclear dots. Antibodies giving these patterns most often recognize nuclear envelope protein gp210 and nuclear body protein sp100, respectively. Fewer subjects with PBC have autoantibodies giving nuclear rim labeling that recognize nucleoporin p62 and LBR. Gp210 is an integral protein localized to the nuclear pore membranes. Approximately 25% of subjects with PBC have detectable serum anti-gp210 antibodies. The vast majority of anti-gp210 antibodies from patients with PBC recognize a stretch of only 15 amino acids in the carboxyl-terminal tail that faces the nuclear pore complex. Enzyme-linked immunosorbent assays using either recombinant protein expressed in bacteria or chemically synthesized polypeptides have been established to reliably detect these autoantibodies. Although initial studies did not find a correlation between the presence of anti-gp210 antibodies and prognosis in PBC, recent data suggest that the presence of antinuclear envelope protein antibodies correlate with an unfavorable disease course and more rapid progression.
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Affiliation(s)
- Howard J Worman
- Departments of Medicine and of Anatomy and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, USA
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47
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Onischenko EA, Crafoord E, Hallberg E. Phosphomimetic mutation of the mitotically phosphorylated serine 1880 compromises the interaction of the transmembrane nucleoporin gp210 with the nuclear pore complex. Exp Cell Res 2007; 313:2744-51. [PMID: 17559836 DOI: 10.1016/j.yexcr.2007.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 04/12/2007] [Accepted: 05/14/2007] [Indexed: 12/01/2022]
Abstract
The nuclear pore complexes (NPCs) reversibly disassemble and reassemble during mitosis. Disassembly of the NPC is accompanied by phosphorylation of many nucleoporins although the function of this is not clear. It was previously shown that in the transmembrane nucleoporin gp210 a single serine residue at position 1880 is specifically phosphorylated during mitosis. Using amino acid substitution combined with live cell imaging, time-lapse microscopy and FRAP, we investigated the role of serine 1880 in binding of gp210 to the NPC in vivo. An alanine substitution mutant (S1880A) was significantly more dynamic at the NPC compared to the wild-type protein, suggesting that serine 1880 is important for binding of gp210 to the NPC. Moreover a glutamate substitution (S1880E) closely mimicking phosphorylated serine specifically interfered with incorporation of gp210 into the NPC and compromised its post-mitotic recruitment to the nuclear envelope of daughter nuclei. Our findings are consistent with the idea that mitotic phosphorylation acts to dissociate gp210 from the structural elements of the NPC.
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48
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Schirmer EC, Foisner R. Proteins that associate with lamins: many faces, many functions. Exp Cell Res 2007; 313:2167-79. [PMID: 17451680 DOI: 10.1016/j.yexcr.2007.03.012] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 03/05/2007] [Accepted: 03/12/2007] [Indexed: 11/27/2022]
Abstract
Lamin-associated polypeptides (LAPs) comprise inner nuclear membrane proteins tightly associated with the peripheral lamin scaffold as well as proteins forming stable complexes with lamins in the nucleoplasm. The involvement of LAPs in a wide range of human diseases may be linked to an equally bewildering range of their functions, including sterol reduction, histone modification, transcriptional repression, and Smad- and beta-catenin signaling. Many LAPs are likely to be at the center of large multi-protein complexes, components of which may dictate their functions, and a few LAPs have defined enzymatic activities. Here we discuss the definition of LAPs, review their many binding partners, elaborate their functions in nuclear architecture, chromatin organization, gene expression and signaling, and describe what is currently known about their links to human disease.
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Affiliation(s)
- Eric C Schirmer
- The Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3JR, UK
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Stavru F, Hülsmann BB, Spang A, Hartmann E, Cordes VC, Görlich D. NDC1: a crucial membrane-integral nucleoporin of metazoan nuclear pore complexes. ACTA ACUST UNITED AC 2006; 173:509-19. [PMID: 16702233 PMCID: PMC2063861 DOI: 10.1083/jcb.200601001] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
POM121 and gp210 were, until this point, the only known membrane-integral nucleoporins (Nups) of vertebrates and, thus, the only candidate anchors for nuclear pore complexes (NPCs) within the nuclear membrane. In an accompanying study (see Stavru et al. on p. 477 of this issue), we provided evidence that NPCs can exist independently of POM121 and gp210, and we predicted that vertebrate NPCs contain additional membrane-integral constituents. We identify such an additional membrane protein in the NPCs of mammals, frogs, insects, and nematodes as the orthologue to yeast Ndc1p/Cut11p. Human NDC1 (hNDC1) likely possesses six transmembrane segments, and it is located at the nuclear pore wall. Depletion of hNDC1 from human HeLa cells interferes with the assembly of phenylalanine-glycine repeat Nups into NPCs. The loss of NDC1 function in Caenorhabditis elegans also causes severe NPC defects and very high larval and embryonic mortality. However, it is not ultimately lethal. Instead, homozygous NDC1-deficient worms can be propagated. This indicates that none of the membrane-integral Nups is universally essential for NPC assembly, and suggests that NPC biogenesis is an extremely fault-tolerant process.
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Affiliation(s)
- Fabrizia Stavru
- Zentrum für Molekulare Biologie der Universität Heidelberg, D-69120 Heidelberg, Germany
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50
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Stavru F, Nautrup-Pedersen G, Cordes VC, Görlich D. Nuclear pore complex assembly and maintenance in POM121- and gp210-deficient cells. ACTA ACUST UNITED AC 2006; 173:477-83. [PMID: 16702234 PMCID: PMC2063858 DOI: 10.1083/jcb.200601002] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
So far, POM121 and gp210 are the only known anchoring sites of vertebrate nuclear pore complexes (NPCs) within the lipid bilayer of the nuclear envelope (NE) and, thus, are excellent candidates for initiating the NPC assembly process. Indeed, we demonstrate that POM121 can recruit several nucleoporins, such as Nup62 or Nup358, to ectopic assembly sites. It thus appears to act as a nucleation site for the assembly of NPC substructures. Nonetheless, we observed functional NPCs and intact NEs in severely POM121-depleted cells. Double knockdowns of gp210 and POM121 in HeLa cells, as well as depletion of POM121 from human fibroblasts, which do not express gp210, further suggest that NPCs can assemble or at least persist in a POM121- and gp210-free form. This points to extensive redundancies in protein–protein interactions within NPCs and suggests that vertebrate NPCs contain additional membrane-integral nucleoporins for anchorage within the lipid bilayer of the NE. In Stavru et al. (on p. 509 of this issue), we describe such an additional transmembrane nucleoporin as the metazoan orthologue of yeast Ndc1p.
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Affiliation(s)
- Fabrizia Stavru
- Zentrum für Molekulare Biologie der Universität Heidelberg, D-69120 Heidelberg, Germany
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