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Schooley A, Venev SV, Aksenova V, Navarrete E, Dasso M, Dekker J. Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613305. [PMID: 39345587 PMCID: PMC11429855 DOI: 10.1101/2024.09.16.613305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Identity-specific interphase chromosome conformation must be re-established each time a cell divides. To understand how interphase folding is inherited, we developed an experimental approach that physically segregates mediators of G1 folding that are intrinsic to mitotic chromosomes from cytoplasmic factors. Proteins essential for nuclear transport, RanGAP1 and Nup93, were degraded in pro-metaphase arrested DLD-1 cells to prevent the establishment of nucleo-cytoplasmic transport during mitotic exit and isolate the decondensing mitotic chromatin of G1 daughter cells from the cytoplasm. Using this approach, we discover a transient folding intermediate entirely driven by chromosome-intrinsic factors. In addition to conventional compartmental segregation, this chromosome-intrinsic folding program leads to prominent genome-scale microcompartmentalization of mitotically bookmarked and cell type-specific cis-regulatory elements. This microcompartment conformation is formed during telophase and subsequently modulated by a second folding program driven by factors inherited through the cytoplasm in G1. This nuclear import-dependent folding program includes cohesin and factors involved in transcription and RNA processing. The combined and inter-dependent action of chromosome-intrinsic and cytoplasmic inherited folding programs determines the interphase chromatin conformation as cells exit mitosis.
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Affiliation(s)
- Allana Schooley
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
| | - Sergey V. Venev
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4480, USA
| | - Emily Navarrete
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology; Cambridge, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-4480, USA
| | - Job Dekker
- Department of Systems Biology, University of Massachusetts Chan Medical School; Worcester, USA
- Howard Hughes Medical Institute; Chevy Chase, USA
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2
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Solà Colom M, Fu Z, Gunkel P, Güttler T, Trakhanov S, Srinivasan V, Gregor K, Pleiner T, Görlich D. A checkpoint function for Nup98 in nuclear pore formation suggested by novel inhibitory nanobodies. EMBO J 2024; 43:2198-2232. [PMID: 38649536 PMCID: PMC11148069 DOI: 10.1038/s44318-024-00081-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
Nuclear pore complex (NPC) biogenesis is a still enigmatic example of protein self-assembly. We now introduce several cross-reacting anti-Nup nanobodies for imaging intact nuclear pore complexes from frog to human. We also report a simplified assay that directly tracks postmitotic NPC assembly with added fluorophore-labeled anti-Nup nanobodies. During interphase, NPCs are inserted into a pre-existing nuclear envelope. Monitoring this process is challenging because newly assembled NPCs are indistinguishable from pre-existing ones. We overcame this problem by inserting Xenopus-derived NPCs into human nuclear envelopes and using frog-specific anti-Nup nanobodies for detection. We further asked whether anti-Nup nanobodies could serve as NPC assembly inhibitors. Using a selection strategy against conserved epitopes, we obtained anti-Nup93, Nup98, and Nup155 nanobodies that block Nup-Nup interfaces and arrest NPC assembly. We solved structures of nanobody-target complexes and identified roles for the Nup93 α-solenoid domain in recruiting Nup358 and the Nup214·88·62 complex, as well as for Nup155 and the Nup98 autoproteolytic domain in NPC scaffold assembly. The latter suggests a checkpoint linking pore formation to the assembly of the Nup98-dominated permeability barrier.
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Affiliation(s)
- Mireia Solà Colom
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- AI Proteins, 20 Overland St., Boston, MA, USA
| | - Zhenglin Fu
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Philip Gunkel
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Thomas Güttler
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Octapharma Biopharmaceuticals, Im Neuenheimer Feld 590, 69120, Heidelberg, Germany
| | - Sergei Trakhanov
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Vasundara Srinivasan
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Universität Hamburg, Hamburg, Germany
| | - Kathrin Gregor
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Tino Pleiner
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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3
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Nguyen TD, Rao MK, Dhyani SP, Banks JM, Winek MA, Michalkiewicz J, Lee MY. Nucleoporin93 (Nup93) Limits Yap Activity to Prevent Endothelial Cell Senescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566598. [PMID: 38014013 PMCID: PMC10680655 DOI: 10.1101/2023.11.10.566598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Endothelial cells (ECs) form the innermost lining of the vasculature and serve a pivotal role in preventing age-related vascular disease. Endothelial health relies on the proper nucleocytoplasmic shuttling of transcription factors via nuclear pore complexes (NPCs). Emerging studies report NPC degradation with natural aging, suggesting impaired nucleocytoplasmic transport in age-related EC dysfunction. We herein identify nucleoporin93 (Nup93), a crucial structural NPC protein, as an indispensable player for vascular protection. Endothelial Nup93 protein levels are significantly reduced in the vasculature of aged mice, paralleling observations of Nup93 loss when using in vitro models of endothelial aging. Mechanistically, we find that loss of Nup93 impairs NPC transport, leading to the nuclear accumulation of Yap and downstream inflammation. Collectively, our findings indicate maintenance of endothelial Nup93 as a key determinant of EC health, where aging targets endothelial Nup93 levels to impair NPC function as a novel mechanism for EC senescence and vascular aging.
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4
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Penzo A, Palancade B. Puzzling out nuclear pore complex assembly. FEBS Lett 2023; 597:2705-2727. [PMID: 37548888 DOI: 10.1002/1873-3468.14713] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Nuclear pore complexes (NPCs) are sophisticated multiprotein assemblies embedded within the nuclear envelope and controlling the exchanges of molecules between the cytoplasm and the nucleus. In this review, we summarize the mechanisms by which these elaborate complexes are built from their subunits, the nucleoporins, based on our ever-growing knowledge of NPC structural organization and on the recent identification of additional features of this process. We present the constraints faced during the production of nucleoporins, their gathering into oligomeric complexes, and the formation of NPCs within nuclear envelopes, and review the cellular strategies at play, from co-translational assembly to the enrolment of a panel of cofactors. Remarkably, the study of NPCs can inform our perception of the biogenesis of multiprotein complexes in general - and vice versa.
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Affiliation(s)
- Arianna Penzo
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
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5
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Neely AE, Zhang Y, Blumensaadt LA, Mao H, Brenner B, Sun C, Zhang HF, Bao X. Nucleoporin downregulation modulates progenitor differentiation independent of nuclear pore numbers. Commun Biol 2023; 6:1033. [PMID: 37853046 PMCID: PMC10584948 DOI: 10.1038/s42003-023-05398-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 09/28/2023] [Indexed: 10/20/2023] Open
Abstract
Nucleoporins (NUPs) comprise nuclear pore complexes, gateways for nucleocytoplasmic transport. As primary human keratinocytes switch from the progenitor state towards differentiation, most NUPs are strongly downregulated, with NUP93 being the most downregulated NUP in this process. To determine if this NUP downregulation is accompanied by a reduction in nuclear pore numbers, we leveraged Stochastic Optical Reconstruction Microscopy. No significant changes in nuclear pore numbers were detected using three independent NUP antibodies; however, NUP reduction in other subcellular compartments such as the cytoplasm was identified. To investigate how NUP reduction influences keratinocyte differentiation, we knocked down NUP93 in keratinocytes in the progenitor-state culture condition. NUP93 knockdown diminished keratinocytes' clonogenicity and epidermal regenerative capacity, without drastically affecting nuclear pore numbers or permeability. Using transcriptome profiling, we identified that NUP93 knockdown induces differentiation genes related to both mechanical and immune barrier functions, including the activation of known NF-κB target genes. Consistently, keratinocytes with NUP93 knockdown exhibited increased nuclear localization of the NF-κB p65/p50 transcription factors, and increased NF-κB reporter activity. Taken together, these findings highlight the gene regulatory roles contributed by differential NUP expression levels in keratinocyte differentiation, independent of nuclear pore numbers.
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Affiliation(s)
- Amy E Neely
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Yang Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
- Molecular Analytics and Photonics (MAP) Lab, Department of Textile Engineering, Chemistry and Science, North Carolina State University, Raleigh, NC, 27606, USA.
| | - Laura A Blumensaadt
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Hongjing Mao
- Molecular Analytics and Photonics (MAP) Lab, Department of Textile Engineering, Chemistry and Science, North Carolina State University, Raleigh, NC, 27606, USA
| | - Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA.
- Department of Dermatology, Northwestern University, Chicago, IL, 60611, USA.
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6
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Madheshiya PK, Shukla E, Singh J, Bawaria S, Ansari MY, Chauhan R. Insights into the role of Nup62 and Nup93 in assembling cytoplasmic ring and central transport channel of the nuclear pore complex. Mol Biol Cell 2022; 33:ar139. [PMID: 36222862 PMCID: PMC9727814 DOI: 10.1091/mbc.e22-01-0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The nuclear pore complex (NPC) is a highly modular assembly of 34 distinct nucleoporins (Nups) to form a versatile transport channel between the nucleus and the cytoplasm. Among them, Nup62 is known as an essential component for nuclear transport, Nup93 for proper nuclear envelope assembly. These Nups constitute various NPC subcomplexes such as the central transport channel (CTC), the cytoplasmic ring (CR), and the inner ring (IR). However, how they play their roles in NPC assembly and transport activity is not clear. Here we delineated the interacting regions and conducted biochemical reconstitution and structural characterization of the mammalian CR complex to reveal its intrinsic dynamic behavior and a distinct "4"-shaped architecture resembling the CTC complex. Our in vitro reconstitution data demonstrate that the Nup62 coiled-coil domain is critical to form both Nup62322-525 •Nup88517-742 and Nup62322-525•Nup88517-742•Nup214693-926 heterotrimers and both can bind to Nup931-150. We therefore propose that Nup93 acts as a "sensor" to bind to Nup62 shared heterotrimers including the Nup62•Nup54 heterotrimer of the CTC, which was not shown previously to be an interacting partner. Altogether, our biochemical study suggests that Nup62 via its coiled-coil domain is central to form compositionally distinct yet structurally similar heterotrimers and Nup93 binds these diverse heterotrimers nonselectively.
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Affiliation(s)
| | - Ekta Shukla
- National Centre for Cell Science, Pune 411007, Maharashtra, India
| | - Jyotsana Singh
- National Centre for Cell Science, Pune 411007, Maharashtra, India
| | | | | | - Radha Chauhan
- National Centre for Cell Science, Pune 411007, Maharashtra, India,*Address correspondence to: Radha Chauhan ()
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7
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Bierzynska A, Bull K, Miellet S, Dean P, Neal C, Colby E, McCarthy HJ, Hegde S, Sinha MD, Bugarin Diz C, Stirrups K, Megy K, Mapeta R, Penkett C, Marsh S, Forrester N, Afzal M, Stark H, BioResource NIHR, Williams M, Welsh GI, Koziell AB, Hartley PS, Saleem MA. Exploring the relevance of NUP93 variants in steroid-resistant nephrotic syndrome using next generation sequencing and a fly kidney model. Pediatr Nephrol 2022; 37:2643-2656. [PMID: 35211795 PMCID: PMC9489583 DOI: 10.1007/s00467-022-05440-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 12/10/2021] [Accepted: 12/21/2021] [Indexed: 10/24/2022]
Abstract
BACKGROUND Variants in genes encoding nuclear pore complex (NPC) proteins are a newly identified cause of paediatric steroid-resistant nephrotic syndrome (SRNS). Recent reports describing NUP93 variants suggest these could be a significant cause of paediatric onset SRNS. We report NUP93 cases in the UK and demonstrate in vivo functional effects of Nup93 depletion in a fly (Drosophila melanogaster) nephrocyte model. METHODS Three hundred thirty-seven paediatric SRNS patients from the National cohort of patients with Nephrotic Syndrome (NephroS) were whole exome and/or whole genome sequenced. Patients were screened for over 70 genes known to be associated with Nephrotic Syndrome (NS). D. melanogaster Nup93 knockdown was achieved by RNA interference using nephrocyte-restricted drivers. RESULTS Six novel homozygous and compound heterozygous NUP93 variants were detected in 3 sporadic and 2 familial paediatric onset SRNS characterised histologically by focal segmental glomerulosclerosis (FSGS) and progressing to kidney failure by 12 months from clinical diagnosis. Silencing of the two orthologs of human NUP93 expressed in D. melanogaster, Nup93-1, and Nup93-2 resulted in significant signal reduction of up to 82% in adult pericardial nephrocytes with concomitant disruption of NPC protein expression. Additionally, nephrocyte morphology was highly abnormal in Nup93-1 and Nup93-2 silenced flies surviving to adulthood. CONCLUSION We expand the spectrum of NUP93 variants detected in paediatric onset SRNS and demonstrate its incidence within a national cohort. Silencing of either D. melanogaster Nup93 ortholog caused a severe nephrocyte phenotype, signaling an important role for the nucleoporin complex in podocyte biology. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Agnieszka Bierzynska
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Katherine Bull
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sara Miellet
- Department of Life and Environmental Science, Bournemouth University, Talbot Campus, Fern Barrow, Poole, Dorset BH12 5BB England, UK
- Illawarra Health and Medical Research Institute, Molecular Horizons and School of Medicine, University of Wollongong, Wollongong, Australia
| | - Philip Dean
- Bristol Genetics Laboratory, North Bristol National Health Service Trust, Bristol, UK
| | - Chris Neal
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Elizabeth Colby
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Hugh J. McCarthy
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
- School of Medicine, University of Sydney and Children’s Hospital at Westmead, Westmead, Australia
| | - Shivaram Hegde
- Children’s Kidney Centre, University Hospital of Wales, Cardiff, UK
| | - Manish D. Sinha
- Department of Paediatric Nephrology, Evelina London Children’s Hospital, Guy’s and St, Thomas’ Hospital, London, UK
| | - Carmen Bugarin Diz
- School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, SE1 7EH UK
| | - Kathleen Stirrups
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
| | - Karyn Megy
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Rutendo Mapeta
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Chris Penkett
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
| | - Sarah Marsh
- Bristol Genetics Laboratory, North Bristol National Health Service Trust, Bristol, UK
| | - Natalie Forrester
- Illawarra Health and Medical Research Institute, Molecular Horizons and School of Medicine, University of Wollongong, Wollongong, Australia
| | - Maryam Afzal
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Hannah Stark
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
| | - NIHR BioResource
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
| | - Maggie Williams
- Bristol Genetics Laboratory, North Bristol National Health Service Trust, Bristol, UK
| | - Gavin I. Welsh
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Ania B. Koziell
- Department of Paediatric Nephrology, Evelina London Children’s Hospital, Guy’s and St, Thomas’ Hospital, London, UK
- School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, SE1 7EH UK
| | - Paul S. Hartley
- Department of Life and Environmental Science, Bournemouth University, Talbot Campus, Fern Barrow, Poole, Dorset BH12 5BB England, UK
| | - Moin A. Saleem
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
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8
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Huang G, Zhan X, Zeng C, Liang K, Zhu X, Zhao Y, Wang P, Wang Q, Zhou Q, Tao Q, Liu M, Lei J, Yan C, Shi Y. Cryo-EM structure of the inner ring from the Xenopus laevis nuclear pore complex. Cell Res 2022; 32:451-460. [PMID: 35301439 PMCID: PMC9061766 DOI: 10.1038/s41422-022-00633-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/08/2022] [Indexed: 02/06/2023] Open
Abstract
Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an average resolution of 4.2 Å. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188. Four molecules of Nup93 each places an extended helix into the axial groove of Nup205 or Nup188, together constituting the central scaffold. The channel nucleoporin hetero-trimer of Nup62/58/54 is anchored on the central scaffold. Six Nup155 molecules interact with the central scaffold and together with the NDC1-ALADIN hetero-dimers anchor the IR subunit to the nuclear envelope and to outer rings. The scarce inter-subunit contacts may allow sufficient latitude in conformation and diameter of the IR. Our structure reveals the molecular basis for the IR subunit assembly of a vertebrate NPC.
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Affiliation(s)
- Gaoxingyu Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China.
| | - Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Chao Zeng
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Ke Liang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Xuechen Zhu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Yanyu Zhao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Pan Wang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Qifan Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Qiang Zhou
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China
| | - Qinghua Tao
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China
| | - Minhao Liu
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yigong Shi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang, China.
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Beijing, China.
- Tsinghua University-Peking University Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China.
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9
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Raices M, D'Angelo MA. Structure, Maintenance, and Regulation of Nuclear Pore Complexes: The Gatekeepers of the Eukaryotic Genome. Cold Spring Harb Perspect Biol 2022; 14:a040691. [PMID: 34312247 PMCID: PMC8789946 DOI: 10.1101/cshperspect.a040691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, the genetic material is segregated inside the nucleus. This compartmentalization of the genome requires a transport system that allows cells to move molecules across the nuclear envelope, the membrane-based barrier that surrounds the chromosomes. Nuclear pore complexes (NPCs) are the central component of the nuclear transport machinery. These large protein channels penetrate the nuclear envelope, creating a passage between the nucleus and the cytoplasm through which nucleocytoplasmic molecule exchange occurs. NPCs are one of the largest protein assemblies of eukaryotic cells and, in addition to their critical function in nuclear transport, these structures also play key roles in many cellular processes in a transport-independent manner. Here we will review the current knowledge of the NPC structure, the cellular mechanisms that regulate their formation and maintenance, and we will provide a brief description of a variety of processes that NPCs regulate.
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Affiliation(s)
- Marcela Raices
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
| | - Maximiliano A D'Angelo
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
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10
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Cason RK, Williams A, Chryst-Stangl M, Wu G, Huggins K, Brathwaite KE, Lane BM, Greenbaum LA, D'Agati VD, Gbadegesin RA. Collapsing Focal Segmental Glomerulosclerosis in Siblings With Compound Heterozygous Variants in NUP93 Expand the Spectrum of Kidney Phenotypes Associated With Nucleoporin Gene Mutations. Front Pediatr 2022; 10:915174. [PMID: 35874595 PMCID: PMC9301271 DOI: 10.3389/fped.2022.915174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/07/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Focal segmental glomerulosclerosis (FSGS) is a major cause of end stage kidney disease, with the collapsing form having the worst prognosis. Study of families with hereditary FSGS has provided insight into disease mechanisms. METHODS In this report, we describe a sibling pair with NUP93 mutations and collapsing FSGS (cFSGS). For each brother, we performed next generation sequencing and segregation analysis by direct sequencing. To determine if the variants found in the index family are a common cause of cFSGS, we screened 7 patients with cFSGS, gleaned from our cohort of 200 patients with FSGS, for variants in NUP93 as well as for APOL1 high-risk genotypes. RESULTS We identified segregating compound heterozygous NUP93 variants (1) c.1772G > T p.G591V, 2) c.2084T > C p.L695S) in the two brothers. We did not find any pathogenic variants in the seven patients with cFSGS from our cohort, and as expected five of these seven patients carried the APOL1 high-risk genotype. CONCLUSION To the best of our knowledge, this is the first report of cFSGS in patients with NUP93 mutations, based on this report, mutations in NUP93 and other nucleoporin genes should be considered when evaluating a child with familial cFSGS. Determining the mechanisms by which these variants cause cFSGS may provide insight into the pathogenesis of the more common primary and virus-mediated forms of cFSGS.
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Affiliation(s)
- Rachel K Cason
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Anna Williams
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Megan Chryst-Stangl
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Guanghong Wu
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Kinsie Huggins
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Kaye E Brathwaite
- Division of Pediatric Nephrology, Children's Hospital at Montefiore, The Bronx, NY, United States
| | - Brandon M Lane
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Larry A Greenbaum
- Division of Pediatric Nephrology, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, United States
| | - Vivette D D'Agati
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Rasheed A Gbadegesin
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
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11
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Hamed M, Antonin W. Dunking into the Lipid Bilayer: How Direct Membrane Binding of Nucleoporins Can Contribute to Nuclear Pore Complex Structure and Assembly. Cells 2021; 10:3601. [PMID: 34944108 PMCID: PMC8700311 DOI: 10.3390/cells10123601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 02/07/2023] Open
Abstract
Nuclear pore complexes (NPCs) mediate the selective and highly efficient transport between the cytoplasm and the nucleus. They are embedded in the two membrane structure of the nuclear envelope at sites where these two membranes are fused to pores. A few transmembrane proteins are an integral part of NPCs and thought to anchor these complexes in the nuclear envelope. In addition, a number of nucleoporins without membrane spanning domains interact with the pore membrane. Here we review our current knowledge of how these proteins interact with the membrane and how this interaction can contribute to NPC assembly, stability and function as well as shaping of the pore membrane.
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Affiliation(s)
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany;
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12
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Röhrl JM, Arnold R, Djabali K. Nuclear Pore Complexes Cluster in Dysmorphic Nuclei of Normal and Progeria Cells during Replicative Senescence. Cells 2021; 10:cells10010153. [PMID: 33466669 PMCID: PMC7828780 DOI: 10.3390/cells10010153] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/10/2021] [Accepted: 01/11/2021] [Indexed: 01/10/2023] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare premature aging disease caused by a mutation in LMNA. A G608G mutation in exon 11 of LMNA is responsible for most HGPS cases, generating a truncated protein called “progerin”. Progerin is permanently farnesylated and accumulates in HGPS cells, causing multiple cellular defects such as nuclear dysmorphism, a thickened lamina, loss of heterochromatin, premature senescence, and clustering of Nuclear Pore Complexes (NPC). To identify the mechanism of NPC clustering in HGPS cells, we evaluated post-mitotic NPC assembly in control and HGPS cells and found no defects. Next, we examined the occurrence of NPC clustering in control and HGPS cells during replicative senescence. We reported that NPC clustering occurs solely in the dysmorphic nuclei of control and HGPS cells. Hence, NPC clustering occurred at a higher frequency in HGPS cells compared to control cells at early passages; however, in late cultures with similar senescence index, NPCs clustering occurred at a similar rate in both control and HGPS. Our results show that progerin does not disrupt post-mitotic reassembly of NPCs. However, NPCs frequently cluster in dysmorphic nuclei with a high progerin content. Additionally, nuclear envelope defects that arise during replicative senescence cause NPC clustering in senescent cells with dysmorphic nuclei.
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13
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Sonawane PJ, S Dewangan P, Madheshiya PK, Chopra K, Kumar M, Niranjan S, Ansari MY, Singh J, Bawaria S, Banerjee M, Chauhan R. Molecular and structural analysis of central transport channel in complex with Nup93 of nuclear pore complex. Protein Sci 2020; 29:2510-2527. [PMID: 33085133 DOI: 10.1002/pro.3983] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/10/2020] [Accepted: 10/19/2020] [Indexed: 12/23/2022]
Abstract
The central transport channel (CTC) of nuclear pore complexes (NPCs) is made up of three nucleoporins Nup62, Nup58 and Nup54. In which manner and capacity, these nucleoporins form the CTC, is not yet clear. We explored the CTC Nups from various species and observed that distinct biochemical characteristics of CTC Nups are evolutionarily conserved. Moreover, comparative biochemical analysis of CTC complexes showed various stoichiometric combinations of Nup62, Nup54 and Nup58 coexisting together. We observed the conserved amino-terminal domain of mammalian Nup93 is crucial for the anchorage of CTC and its localization to NPCs. We could reconstitute and purify mammalian CTC·Nup93 quaternary complex by co-expressing full length or N-terminal domain of Nup93 along with CTC complex. Further, we characterized CTC·Nup93 complex using small angle X-ray scattering and electron microscopy that revealed a "V" shape of CTC·Nup93 complex. Overall, this study demonstrated for the first time evolutionarily conserved plasticity and stoichiometric diversity in CTC Nups.
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Affiliation(s)
- Parshuram J Sonawane
- National Center for Cell Science, Savitribai Phule University of Pune Campus, Pune, India
| | - Pravin S Dewangan
- National Center for Cell Science, Savitribai Phule University of Pune Campus, Pune, India
| | | | - Kriti Chopra
- National Center for Cell Science, Savitribai Phule University of Pune Campus, Pune, India
| | - Mohit Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Sangeeta Niranjan
- National Center for Cell Science, Savitribai Phule University of Pune Campus, Pune, India
| | - Mohammed Yousuf Ansari
- National Center for Cell Science, Savitribai Phule University of Pune Campus, Pune, India
| | - Jyotsana Singh
- National Center for Cell Science, Savitribai Phule University of Pune Campus, Pune, India
| | - Shrankhla Bawaria
- National Center for Cell Science, Savitribai Phule University of Pune Campus, Pune, India
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Radha Chauhan
- National Center for Cell Science, Savitribai Phule University of Pune Campus, Pune, India
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14
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Mossaid I, Chatel G, Martinelli V, Vaz M, Fahrenkrog B. Mitotic checkpoint protein Mad1 is required for early Nup153 recruitment to chromatin and nuclear envelope integrity. J Cell Sci 2020; 133:jcs249243. [PMID: 33023979 DOI: 10.1242/jcs.249243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/24/2020] [Indexed: 11/20/2022] Open
Abstract
Nucleoporin Nup153 is a multifunctional protein and a known binding partner of mitotic checkpoint protein Mad1 (also known as MAD1L1). The functional relevance of their interaction has remained elusive. Here, we have further dissected the interface and functional interplay of Nup153 and Mad1. Using in situ proximity ligation assays, we found that the presence of a nuclear envelope (NE) is a prerequisite for the Nup153-Mad1 association. Time-lapse microscopy revealed that depletion of Mad1 delayed recruitment of Nup153 to anaphase chromatin, which was often accompanied by a prolongation of anaphase. Furthermore, as seen by electron microscopic and three-dimensional structured illumination investigations, Nup153 and Mad1 depletion led to alterations in NE architecture, characterised by a change of membrane curvature at nuclear pore complexes (NPCs) and an expansion of the spacing between inner and outer nuclear membranes. Nup153 depletion, but not Mad1 depletion, caused defects in interphase NPC assembly, with partial displacement of cytoplasmic nucleoporins and a reduction in NPC density. Taken together, our results suggest that Nup153 has separable roles in NE and NPC formation: in post-mitotic NE re-formation in concert with Mad1 and in interphase NPC assembly, independent of Mad1.
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Affiliation(s)
- Ikram Mossaid
- Institute of Molecular Biology and Medicine, Laboratory Biologie du Noyau, Université Libre de Bruxelles, 6041 Charleroi, Belgium
| | - Guillaume Chatel
- Institute of Molecular Biology and Medicine, Laboratory Biologie du Noyau, Université Libre de Bruxelles, 6041 Charleroi, Belgium
| | - Valérie Martinelli
- Institute of Molecular Biology and Medicine, Laboratory Biologie du Noyau, Université Libre de Bruxelles, 6041 Charleroi, Belgium
| | - Marcela Vaz
- Institute of Molecular Biology and Medicine, Laboratory Biologie du Noyau, Université Libre de Bruxelles, 6041 Charleroi, Belgium
| | - Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Laboratory Biologie du Noyau, Université Libre de Bruxelles, 6041 Charleroi, Belgium
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15
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Sakuma S, Raices M, Borlido J, Guglielmi V, Zhu EYS, D'Angelo MA. Inhibition of Nuclear Pore Complex Formation Selectively Induces Cancer Cell Death. Cancer Discov 2020; 11:176-193. [PMID: 32988961 DOI: 10.1158/2159-8290.cd-20-0581] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/03/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022]
Abstract
Nuclear pore complexes (NPC) are the central mediators of nucleocytoplasmic transport. Increasing evidence shows that many cancer cells have increased numbers of NPCs and become addicted to the nuclear transport machinery. How reducing NPC numbers affects the physiology of normal and cancer cells and whether it could be exploited for cancer therapies has not been investigated. We report that inhibition of NPC formation, a process mostly restricted to proliferating cells, causes selective cancer cell death, prevents tumor growth, and induces tumor regression. Although cancer cells die in response to NPC assembly inhibition, normal cells undergo a reversible cell-cycle arrest that allows them to survive. Mechanistically, reducing NPC numbers results in multiple alterations contributing to cancer cell death, including abnormalities in nuclear transport, catastrophic alterations in gene expression, and the selective accumulation of DNA damage. Our findings uncover the NPC formation process as a novel targetable pathway in cancer cells. SIGNIFICANCE: Reducing NPC numbers in cancer cells induces death, prevents tumor growth, and results in tumor regression. Conversely, normal cells undergo a reversible cell-cycle arrest in response to inhibition of NPC assembly. These findings expose the potential of targeting NPC formation in cancer.This article is highlighted in the In This Issue feature, p. 1.
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Affiliation(s)
- Stephen Sakuma
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Marcela Raices
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Joana Borlido
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Valeria Guglielmi
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Ethan Y S Zhu
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Maximiliano A D'Angelo
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California.
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16
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Chopra K, Burdak B, Sharma K, Kembhavi A, Mande SC, Chauhan R. CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information. Biomolecules 2020; 10:biom10060938. [PMID: 32580303 PMCID: PMC7356028 DOI: 10.3390/biom10060938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/27/2022] Open
Abstract
Decrypting the interface residues of the protein complexes provides insight into the functions of the proteins and, hence, the overall cellular machinery. Computational methods have been devised in the past to predict the interface residues using amino acid sequence information, but all these methods have been majorly applied to predict for prokaryotic protein complexes. Since the composition and rate of evolution of the primary sequence is different between prokaryotes and eukaryotes, it is important to develop a method specifically for eukaryotic complexes. Here, we report a new hybrid pipeline for predicting the protein-protein interaction interfaces in a pairwise manner from the amino acid sequence information of the interacting proteins. It is based on the framework of Co-evolution, machine learning (Random Forest), and Network Analysis named CoRNeA trained specifically on eukaryotic protein complexes. We use Co-evolution, physicochemical properties, and contact potential as major group of features to train the Random Forest classifier. We also incorporate the intra-contact information of the individual proteins to eliminate false positives from the predictions keeping in mind that the amino acid sequence of a protein also holds information for its own folding and not only the interface propensities. Our prediction on example datasets shows that CoRNeA not only enhances the prediction of true interface residues but also reduces false positive rates significantly.
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Affiliation(s)
- Kriti Chopra
- National Centre for Cell Science, Pune 411007, Maharashtra, India; (K.C.); (B.B.)
| | - Bhawna Burdak
- National Centre for Cell Science, Pune 411007, Maharashtra, India; (K.C.); (B.B.)
| | - Kaushal Sharma
- Inter-University Centre for Astronomy and Astrophysics, Pune 411007, Maharashtra, India; (K.S.); (A.K.)
| | - Ajit Kembhavi
- Inter-University Centre for Astronomy and Astrophysics, Pune 411007, Maharashtra, India; (K.S.); (A.K.)
| | - Shekhar C. Mande
- Council of Scientific and Industrial Research (CSIR), New Delhi 110001, India;
| | - Radha Chauhan
- National Centre for Cell Science, Pune 411007, Maharashtra, India; (K.C.); (B.B.)
- Correspondence: ; Tel.: +91-20-25708255
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17
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Monwan W, Kawasaki T, Hasan MZ, Ori D, Kawai T. Identification of nucleoporin 93 (Nup93) that mediates antiviral innate immune responses. Biochem Biophys Res Commun 2020; 521:1077-1082. [PMID: 31733835 DOI: 10.1016/j.bbrc.2019.11.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/05/2019] [Indexed: 01/28/2023]
Abstract
RIG-I-like receptors (RLRs) are cytoplasmic sensors for viral RNA that elicit antiviral innate immune responses. RLR signaling culminates in the activation of the protein kinase TBK1, which mediates phosphorylation and nuclear translocation of IRF3 that regulates expression of type I interferon genes. Here, we found that Nucleoporin 93 (Nup93), components of nuclear pore complex (NPC), plays an important role in RLR-mediated antiviral responses. Nup93-deficient RAW264.7 macrophage cells exhibited decreased expression of Ifnb1 and Cxcl10 genes after treatment with a synthetic RLR agonist stimulation as well as Newcastle Disease Virus infection. Silencing Nup93 in murine primary macrophages and embryonic fibroblasts also resulted in reduced expression of these genes. IRF3 nuclear translocation during RLR signaling was impaired in Nup93-deficient RAW264.7 cells. Notably, the activation of TBK1 during RLR signaling was also decreased in Nup93-deficient cells. We found that Nup93 formed a complex with TBK1, and Nup93 overexpression enhanced TBK1-mediated IFNβ promoter activation. Taken together, our findings suggest that Nup93 regulates antiviral innate immunity by enhancing TBK1 activity and IRF3 nuclear translocation.
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Affiliation(s)
- Warunthorn Monwan
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Nara, 630-0192, Japan
| | - Takumi Kawasaki
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Nara, 630-0192, Japan.
| | - Md Zobaer Hasan
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Nara, 630-0192, Japan
| | - Daisuke Ori
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Nara, 630-0192, Japan
| | - Taro Kawai
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Nara, 630-0192, Japan.
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18
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Rempel IL, Steen A, Veenhoff LM. Poor old pores-The challenge of making and maintaining nuclear pore complexes in aging. FEBS J 2020; 287:1058-1075. [PMID: 31912972 PMCID: PMC7154712 DOI: 10.1111/febs.15205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/20/2019] [Accepted: 01/06/2020] [Indexed: 12/11/2022]
Abstract
The nuclear pore complex (NPC) is the sole gateway to the nuclear interior, and its function is essential to all eukaryotic life. Controlling the functionality of NPCs is a tremendous challenge for cells. Firstly, NPCs are large structures, and their complex assembly does occasionally go awry. Secondly, once assembled, some components of the NPC persist for an extremely long time and, as a result, are susceptible to accumulate damage. Lastly, a significant proportion of the NPC is composed of intrinsically disordered proteins that are prone to aggregation. In this review, we summarize how the quality of NPCs is guarded in young cells and discuss the current knowledge on the fate of NPCs during normal aging in different tissues and organisms. We discuss the extent to which current data supports a hypothesis that NPCs are poorly maintained during aging of nondividing cells, while in dividing cells the main challenge is related to the assembly of new NPCs. Our survey of current knowledge points toward NPC quality control as an important node in aging of both dividing and nondividing cells. Here, the loss of protein homeostasis during aging is central and the NPC appears to both be impacted by, and to drive, this process.
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Affiliation(s)
- Irina L Rempel
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, The Netherlands
| | - Anton Steen
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, The Netherlands
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19
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Ouyang X, Hao X, Liu S, Hu J, Hu L. Expression of Nup93 is associated with the proliferation, migration and invasion capacity of cervical cancer cells. Acta Biochim Biophys Sin (Shanghai) 2019; 51:1276-1285. [PMID: 31774908 DOI: 10.1093/abbs/gmz131] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 01/15/2023] Open
Abstract
Cervical cancer is a prevalent and devastating malignancy in females worldwide. Nucleoporin 93 (Nup93), a member of the nuclear pore complex, plays an important role in transport across the nuclear pore. Several nucleoporins have been linked to cancer. However, the oncogenic role and underlying mechanism of Nup93 in cervical cancer development have not been reported. In this study, the expression of Nup93 was analyzed by quantitative real-time polymerase chain reaction (qPCR), western blot analysis, and immunohistochemical staining in cervical cancer tissues and cell lines. We found that the expression of Nup93 was higher in cervical cancer samples, compared to normal cervical samples. The knockdown of Nup93 inhibited cell proliferation, migration, and invasion capacity of cervical cancer cells. At the same time, we also found that silencing of Nup93 could inhibit cellular migration and invasion by regulating cytoskeleton actin and Rho family proteins. Nup93 also participated in the IL-6/STAT3 signaling pathway. In addition, down-regulation of Nup93 prevented tumor formation in mice in vivo. Thus, Nup93 may be a carcinogenic gene and serve as a potential therapeutic target for cervical cancer.
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Affiliation(s)
- Xiaolan Ouyang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaoming Hao
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Shuaibin Liu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jianguo Hu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Lina Hu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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20
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Biallelic Variants in the Nuclear Pore Complex Protein NUP93 Are Associated with Non-progressive Congenital Ataxia. THE CEREBELLUM 2019; 18:422-432. [PMID: 30741391 DOI: 10.1007/s12311-019-1010-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Nuclear pore complexes (NPCs) are the gateways of the nuclear envelope mediating transport between cytoplasm and nucleus. They form huge complexes of 125 MDa in vertebrates and consist of about 30 different nucleoporins present in multiple copies in each complex. Here, we describe pathogenic variants in the nucleoporin 93 (NUP93) associated with an autosomal recessive form of congenital ataxia. Two rare compound heterozygous variants of NUP93 were identified by whole exome sequencing in two brothers with isolated cerebellar atrophy: one missense variant (p.R537W) results in a protein which does not localize to NPCs and cannot functionally replace the wild type protein, whereas the variant (p.F699L) apparently supports NPC assembly. In addition to its recently described pathological role in steroid-resistant nephrotic syndrome, our work identifies NUP93 as a candidate gene for non-progressive congenital ataxia.
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21
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Yang L, Zhang JH, Zhang XL, Lao GJ, Su GM, Wang L, Li YL, Ye WC, He J. Tandem mass tag-based quantitative proteomic analysis of lycorine treatment in highly pathogenic avian influenza H5N1 virus infection. PeerJ 2019; 7:e7697. [PMID: 31592345 PMCID: PMC6778435 DOI: 10.7717/peerj.7697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/19/2019] [Indexed: 12/14/2022] Open
Abstract
Highly pathogenic H5N1 influenza viruses (HPAIV) cause rapid systemic illness and death in susceptible animals, leading to a disease with high morbidity and mortality rates. Although vaccines and drugs are the best solution to prevent this threat, a more effective treatment for H5 strains of influenza has yet to be developed. Therefore, the development of therapeutics/drugs that combat H5N1 influenza virus infection is becoming increasingly important. Lycorine, the major component of Amaryllidaceae alkaloids, exhibits better protective effects against A/CK/GD/178/04 (H5N1) (GD178) viruses than the commercial neuraminidase (NA) inhibitor oseltamivir in our prior study. Lycorine demonstrates outstanding antiviral activity because of its inhibitory activity against the export of viral ribonucleoprotein complexes (vRNPs) from the nucleus. However, how lycorine affects the proteome of AIV infected cells is unknown. Therefore, we performed a comparative proteomic analysis to identify changes in protein expression in AIV-infected Madin-Darby Canine Kidney cells treated with lycorine. Three groups were designed: mock infection group (M), virus infection group (V), and virus infection and lycorine-treated after virus infection group (L). The multiplexed tandem mass tag (TMT) approach was employed to analyze protein level in this study. In total, 5,786 proteins were identified from the three groups of cells by using TMT proteomic analysis. In the V/M group, 1,101 proteins were identified, of which 340 differentially expressed proteins (DEPs) were determined during HPAIV infection; among the 1,059 proteins identified from the lycorine-treated group, 258 proteins presented significant change. Here, 71 proteins showed significant upregulation or downregulation of expression in the virus-infected/mock and virus-infected/lycorine-treated comparisons, and the proteins in each fraction were functionally classified further. Interestingly, lycorine treatment decreased the levels of the nuclear pore complex protein 93 (Nup93, E2RSV7), which is associated with nuclear–cytoplasmic transport. In addition, Western blot experiments confirmed that the expression of Nup93 was significantly downregulated in lycorine treatment but induced after viral infection. Our results may provide new insights into how lycorine may trap vRNPs in the nucleus and suggest new potential therapeutic targets for influenza virus.
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Affiliation(s)
- Li Yang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, China.,College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jia Hao Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao Li Zhang
- College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Guang Jie Lao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Guan Ming Su
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lei Wang
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, China
| | - Yao Lan Li
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, China
| | - Wen Cai Ye
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, China
| | - Jun He
- Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou, China.,Institute of Laboratory Animal Science, Jinan University, Guangzhou, China
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22
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Molecular assay for an intronic variant in NUP93 that causes steroid resistant nephrotic syndrome. J Hum Genet 2019; 64:673-679. [PMID: 31015583 DOI: 10.1038/s10038-019-0606-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 04/13/2019] [Accepted: 04/14/2019] [Indexed: 01/09/2023]
Abstract
Advances in molecular genetics have revealed that approximately 30% of cases with steroid-resistant nephrotic syndrome (SRNS) are caused by single-gene mutations. More than 50 genes are responsible for SRNS. One such gene is the nucleoporin, 93-KD (NUP93). Thus far, few studies have reported mutations of NUP93 in SRNS. Here, we describe an NUP93 biallelic mutation in a 9-year-old boy with focal segmental glomerular sclerosis (FSGS). Notably, one mutation comprised an intronic variant; we conducted in vivo and in vitro analysis to characterize this variant. We found two heterozygous mutations in NUP93: c.2137-18G>A in intron 19 and a novel nonsense mutation c.727A>T (p.Lys243*) in exon 8. We conducted RNA sequencing and in vitro splicing assays by using minigene construction, combined with protein expression analysis to determine the pathogenicity of the intronic variant. Both RNA sequencing and in vitro splicing assay showed exon 20-skipping by the intronic variant. In protein expression analysis, aberrant subcellular localization with small punctate vesicles in the cytoplasm was observed for the intronic variant. Taken together, we concluded that c.2137-18G>A was linked to pathogenicity due to aberrant splicing. NUP93 variants are quite rare; however, we have shown that even intronic variants in NUP93 can cause SRNS. This study provides a fundamental approach to validate the intronic variant, as well as new insights regarding the clinical spectrum of SRNS caused by rare gene variants.
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23
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Abstract
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange. They are exceptionally large protein complexes that fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. About 30 different protein components, termed nucleoporins, assemble in multiple copies into an intricate cylindrical architecture. Here, we review our current knowledge of the structure of nucleoporins and how those come together in situ. We delineate architectural principles on several hierarchical organization levels, including isoforms, posttranslational modifications, nucleoporins, and higher-order oligomerization of nucleoporin subcomplexes. We discuss how cells exploit this modularity to faithfully assemble NPCs.
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Affiliation(s)
- Bernhard Hampoelz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , ,
| | - Amparo Andres-Pons
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , , .,Current affiliation: Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland;
| | - Panagiotis Kastritis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , , .,Current affiliation: ZIK HALOmem, Martin Luther University of Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; , , .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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24
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Meng Q, Gao J, Zhu H, He H, Lu Z, Hong M, Zhou H. The proteomic study of serially passaged human skin fibroblast cells uncovers down-regulation of the chromosome condensin complex proteins involved in replicative senescence. Biochem Biophys Res Commun 2018; 505:1112-1120. [PMID: 30336977 DOI: 10.1016/j.bbrc.2018.10.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/10/2018] [Indexed: 01/09/2023]
Abstract
Dermal fibroblast is one of the major constitutive cells of skin and plays a central role in skin senescence. The replicative senescence of fibroblasts may cause skin aging, bad wound healing, skin diseases and even cancer. In this study, a label-free quantitative proteomic approach was employed to analyzing the serial passaged human skin fibroblast (CCD-1079Sk) cells, resulting in 3371 proteins identified. Of which, 280 proteins were significantly changed in early passage (6 passages, P6), middle passage (12 passages, P12) and late passage (21 passages, P21), with a time-dependent decrease or increase tendency. Bioinformatic analysis demonstrated that the chromosome condensin complex, including structural maintenance of chromosomes protein 2 (SMC2) and structural maintenance of chromosomes protein 4 (SMC4), were down-regulated in the serially passaged fibroblast cells. The qRT-PCR and Western Blot experiments confirmed that the expression of these two proteins were significantly down-regulated in a time-dependent manner in the subculture of human skin fibroblasts (HSFb cells). In summary, we used serially passaged human skin fibroblast cells coupled with quantitative proteomic approach to profile the protein expression pattern in the temporal progress of replicative senescence in HSFb cells and revealed that the down-regulation of the chromosome condensin complex subunits, such as SMC2 and SMC4, may play an important role in the fibroblast senescence.
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Affiliation(s)
- Qian Meng
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing, 100049, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Hongwen Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Han He
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China
| | - Zhi Lu
- Technology Center, Shanghai Inoherb Co. Ltd, 121 Chengyin Road, Shanghai, 200083, China.
| | - Minhua Hong
- Technology Center, Shanghai Inoherb Co. Ltd, 121 Chengyin Road, Shanghai, 200083, China.
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China; University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing, 100049, China.
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25
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Furusawa Y, Yamada S, Kawaoka Y. Host Factor Nucleoporin 93 Is Involved in the Nuclear Export of Influenza Virus RNA. Front Microbiol 2018; 9:1675. [PMID: 30087672 PMCID: PMC6066526 DOI: 10.3389/fmicb.2018.01675] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/04/2018] [Indexed: 11/13/2022] Open
Abstract
Influenza virus replication relies on the functions of host factors. In our previous study, we identified host factors involved in virus replication and began analyses of their roles in this process. In this study, we focused on Nucleoporin 93 (NUP93) and revealed its importance in influenza virus replication. NUP93 knockdown mediated by siRNAs reduced viral replication and decreased the efficiency of the early step of the viral life cycle. NUP93 did not appear to be important for virus binding, internalization, or the nuclear import of viral ribonucleoprotein (vRNP); however, in NUP93-depleted cells, viral RNA accumulated in the nucleus. These results suggest that NUP93 is involved in the nuclear export of viral RNA.
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Affiliation(s)
- Yuri Furusawa
- Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shinya Yamada
- Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, United States.,Department of Special Pathogens, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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26
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Kopeina GS, Prokhorova EA, Lavrik IN, Zhivotovsky B. Alterations in the nucleocytoplasmic transport in apoptosis: Caspases lead the way. Cell Prolif 2018; 51:e12467. [PMID: 29947118 DOI: 10.1111/cpr.12467] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/19/2018] [Indexed: 12/13/2022] Open
Abstract
Apoptosis is a mode of regulated cell death that is indispensable for the morphogenesis, development and homeostasis of multicellular organisms. Caspases are cysteine-dependent aspartate-specific proteases, which function as initiators and executors of apoptosis. Caspases are cytosolic proteins that can cleave substrates located in different intracellular compartments during apoptosis. Many years ago, the involvement of caspases in the regulation of nuclear changes, a hallmark of apoptosis, was documented. Accumulated data suggest that apoptosis-associated alterations in nucleocytoplasmic transport are also linked to caspase activity. Here, we aim to discuss the current state of knowledge regarding this process. Particular attention will be focused on caspase nuclear entry and their functions in the demolition of the nucleus upon apoptotic stimuli.
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Affiliation(s)
- Gelina S Kopeina
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | | | - Inna N Lavrik
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia.,Translational Inflammation Research, Medical Faculty, Otto von Guericke University, Magdeburg, Germany
| | - Boris Zhivotovsky
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia.,Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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27
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De Magistris P, Tatarek-Nossol M, Dewor M, Antonin W. A self-inhibitory interaction within Nup155 and membrane binding are required for nuclear pore complex formation. J Cell Sci 2018; 131:jcs.208538. [PMID: 29150488 DOI: 10.1242/jcs.208538] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/13/2017] [Indexed: 01/02/2023] Open
Abstract
Nuclear pore complexes (NPCs) are gateways through the nuclear envelope. How they form into a structure containing three rings and integrate into the nuclear envelope remains a challenging paradigm for coordinated assembly of macro-complexes. In vertebrates, the cytoplasmic and nucleoplasmic rings of NPCs are mostly formed by multiple copies of the Nup107-Nup160 complex, whereas the central, or inner ring is composed of Nup53, Nup93, Nup155 and the two paralogues Nup188 and Nup205. Inner ring assembly is only partially understood. Using in vitro nuclear assembly reactions, we show that direct pore membrane binding of Nup155 is crucial for NPC formation. Replacing full-length Nup155 with its N-terminal β-propeller allows assembly of the outer ring components to the NPC backbone that also contains Nup53. However, further assembly, especially recruitment of the Nup93 and Nup62 complexes, is blocked. Self-interaction between the N- and C-terminal domains of Nup155 has an auto-inhibitory function that prevents interaction between the N-terminus of Nup155 and the C-terminal region of Nup53. Nup93 can overcome this block by binding to Nup53, thereby promoting formation of the inner ring and the NPC.
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Affiliation(s)
- Paola De Magistris
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany.,Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Marianna Tatarek-Nossol
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Manfred Dewor
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, 72076 Tübingen, Germany .,Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
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28
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Mimura Y, Takemoto S, Tachibana T, Ogawa Y, Nishimura M, Yokota H, Imamoto N. A statistical image analysis framework for pore-free islands derived from heterogeneity distribution of nuclear pore complexes. Sci Rep 2017; 7:16315. [PMID: 29176624 PMCID: PMC5701208 DOI: 10.1038/s41598-017-16386-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/13/2017] [Indexed: 11/26/2022] Open
Abstract
Nuclear pore complexes (NPCs) maintain cellular homeostasis by mediating nucleocytoplasmic transport. Although cyclin-dependent kinases (CDKs) regulate NPC assembly in interphase, the location of NPC assembly on the nuclear envelope is not clear. CDKs also regulate the disappearance of pore-free islands, which are nuclear envelope subdomains; this subdomain gradually disappears with increase in homogeneity of the NPC in response to CDK activity. However, a causal relationship between pore-free islands and NPC assembly remains unclear. Here, we elucidated mechanisms underlying NPC assembly from a new perspective by focusing on pore-free islands. We proposed a novel framework for image-based analysis to automatically determine the detailed ‘landscape’ of pore-free islands from a large quantity of images, leading to the identification of NPC intermediates that appear in pore-free islands with increased frequency in response to CDK activity. Comparison of the spatial distribution between simulated and the observed NPC intermediates within pore-free islands showed that their distribution was spatially biased. These results suggested that the disappearance of pore-free islands is highly related to de novo NPC assembly and indicated the existence of specific regulatory mechanisms for the spatial arrangement of NPC assembly on nuclear envelopes.
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Affiliation(s)
| | - Satoko Takemoto
- Image Processing Research Team, RIKEN Centre for Advanced Photonics, Saitama, Japan
| | - Taro Tachibana
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan
| | - Yutaka Ogawa
- Cellular Dynamics Laboratory, RIKEN, Saitama, Japan
| | - Masaomi Nishimura
- Image Processing Research Team, RIKEN Centre for Advanced Photonics, Saitama, Japan
| | - Hideo Yokota
- Image Processing Research Team, RIKEN Centre for Advanced Photonics, Saitama, Japan.
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN, Saitama, Japan.
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29
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Linder MI, Köhler M, Boersema P, Weberruss M, Wandke C, Marino J, Ashiono C, Picotti P, Antonin W, Kutay U. Mitotic Disassembly of Nuclear Pore Complexes Involves CDK1- and PLK1-Mediated Phosphorylation of Key Interconnecting Nucleoporins. Dev Cell 2017; 43:141-156.e7. [PMID: 29065306 PMCID: PMC5654724 DOI: 10.1016/j.devcel.2017.08.020] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 07/04/2017] [Accepted: 08/25/2017] [Indexed: 01/09/2023]
Abstract
During interphase, the nuclear envelope (NE) serves as a selective barrier between cytosol and nucleoplasm. When vertebrate cells enter mitosis, the NE is dismantled in the process of nuclear envelope breakdown (NEBD). Disassembly of nuclear pore complexes (NPCs) is a key aspect of NEBD, required for NE permeabilization and formation of a cytoplasmic mitotic spindle. Here, we show that both CDK1 and polo-like kinase 1 (PLK1) support mitotic NPC disintegration by hyperphosphorylation of Nup98, the gatekeeper nucleoporin, and Nup53, a central nucleoporin linking the inner NPC scaffold to the pore membrane. Multisite phosphorylation of Nup53 critically contributes to its liberation from its partner nucleoporins, including the pore membrane protein NDC1. Initial steps of NPC disassembly in semi-permeabilized cells can be reconstituted by a cocktail of mitotic kinases including cyclinB-CDK1, NIMA, and PLK1, suggesting that the unzipping of nucleoporin interactions by protein phosphorylation is an important principle underlying mitotic NE permeabilization.
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Affiliation(s)
- Monika I Linder
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Mario Köhler
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Paul Boersema
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Marion Weberruss
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Cornelia Wandke
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Joseph Marino
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Caroline Ashiono
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, 52074 Aachen, Germany
| | - Ulrike Kutay
- Institute of Biochemistry, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.
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30
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Dewangan PS, Sonawane PJ, Chouksey AR, Chauhan R. The Nup62 Coiled-Coil Motif Provides Plasticity for Triple-Helix Bundle Formation. Biochemistry 2017; 56:2803-2811. [PMID: 28406021 DOI: 10.1021/acs.biochem.6b01050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The central transport channel of the vertebrate nuclear pore complex (NPC) consists of nucleoporins: Nup62, Nup54, and Nup58. The coiled-coil domains in α-helical regions of these nucleoporins are thought to be crucial for several protein-protein interactions in the NPC subcomplexes. In this study, we determined the crystal structure of the coiled-coil domain of rat Nup62 fragment (residues 362-425) to 2.4 Å resolution. The crystal structure shows the conserved coiled-coil domain as a parallel three-helix bundle for the Nup62(362-425) fragment. On the basis of our size exclusion chromatography coupled to multiangle light scattering analysis and glutaraldehyde cross-linking experiments, we conclude that the Nup62(362-425) fragment displays dynamic behavior in solution and can also exist in either homodimeric or homotrimeric states. Our comparative analysis of the rat Nup62(362-425) homotrimeric structure with previously reported heterotrimeric structures [rat Nup62(362-425)·Nup54(346-407) and Xenopus Nup62(358-485)·Nup54(315-450)·Nup58(283-406) complexes] demonstrates the structural basis for parallel triple-helix bundle formation for Nup62 with different partners. Moreover, we show that the coiled-coil domain of Nup62 is sufficient for interaction with the coiled-coil domain of rat Exo70, a protein in an exocyst complex. On the basis of these observations, we suggest the plausible chain replacement mechanism that yields to diverse protein assemblies with Nup62. In summary, the coiled-coil motif present in Nup62 imparts the ability to form a homotrimer and heterotrimers either with Nup54 or with Nup54-Nup58 within the NPCs as well as with Exo70 beyond the NPCs. These complexes of Nup62 suggest the crucial role of the coiled-coil motifs in providing plasticity to various modular assemblies.
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Affiliation(s)
- Pravin S Dewangan
- National Centre for Cell Science , S. P. Pune University Campus, Ganeshkhind, Pune 411007, India
| | - Parshuram J Sonawane
- National Centre for Cell Science , S. P. Pune University Campus, Ganeshkhind, Pune 411007, India
| | - Ankita R Chouksey
- National Centre for Cell Science , S. P. Pune University Campus, Ganeshkhind, Pune 411007, India
| | - Radha Chauhan
- National Centre for Cell Science , S. P. Pune University Campus, Ganeshkhind, Pune 411007, India
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31
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Labade AS, Karmodiya K, Sengupta K. HOXA repression is mediated by nucleoporin Nup93 assisted by its interactors Nup188 and Nup205. Epigenetics Chromatin 2016; 9:54. [PMID: 27980680 PMCID: PMC5135769 DOI: 10.1186/s13072-016-0106-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022] Open
Abstract
Background The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associated with human chromosomes 5, 7 and 16 and with the promoters of the HOXA gene as revealed by ChIP-on-chip studies using tiling microarrays for these chromosomes. However, the functional consequences of the association of Nup93 with HOXA is unknown. Results Here, we examined the association of Nup93 with the HOXA gene cluster and its consequences on HOXA gene expression in diploid colorectal cancer cells (DLD1). Nup93 showed a specific enrichment ~1 Kb upstream of the transcription start site of each of the HOXA1, HOXA3 and HOXA5 promoters, respectively. Furthermore, the association of Nup93 with HOXA was assisted by its interacting partners Nup188 and Nup205. The depletion of the Nup93 sub-complex significantly upregulated HOXA gene expression levels. However, expression levels of a control gene locus (GLCCI1) on human chromosome 7 were unaffected. Three-dimensional fluorescence in situ hybridization (3D-FISH) analyses revealed that the depletion of the Nup93 sub-complex (but not Nup98) disengages the HOXA gene locus from the nuclear periphery, suggesting a potential role for Nup93 in tethering and repressing the HOXA gene cluster. Consistently, Nup93 knockdown increased active histone marks (H3K9ac), decreased repressive histone marks (H3K27me3) on the HOXA1 promoter and increased transcription elongation marks (H3K36me3) within the HOXA1 gene. Moreover, the combined depletion of Nup93 and CTCF (a known organizer of HOXA gene cluster) but not Nup93 alone, significantly increased GLCCI1 gene expression levels. Taken together, this suggests a novel role for Nup93 and its interactors in repressing the HOXA gene cluster. Conclusions This study reveals that the nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 mediates the repression of HOXA gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0106-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ajay S Labade
- Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India
| | - Krishanpal Karmodiya
- Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India
| | - Kundan Sengupta
- Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India
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32
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Patil V, Pal J, Somasundaram K. Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing. Oncotarget 2016; 6:43452-71. [PMID: 26496030 PMCID: PMC4791243 DOI: 10.18632/oncotarget.6171] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 10/05/2015] [Indexed: 01/22/2023] Open
Abstract
Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM- EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes- ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.
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Affiliation(s)
- Vikas Patil
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Jagriti Pal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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33
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Del Viso F, Huang F, Myers J, Chalfant M, Zhang Y, Reza N, Bewersdorf J, Lusk CP, Khokha MK. Congenital Heart Disease Genetics Uncovers Context-Dependent Organization and Function of Nucleoporins at Cilia. Dev Cell 2016; 38:478-92. [PMID: 27593162 PMCID: PMC5021619 DOI: 10.1016/j.devcel.2016.08.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 07/07/2016] [Accepted: 08/08/2016] [Indexed: 01/21/2023]
Abstract
Human genomics is identifying candidate genes for congenital heart disease (CHD), but discovering the underlying mechanisms remains challenging. In a patient with CHD and heterotaxy (Htx), a disorder of left-right patterning, we previously identified a duplication in Nup188. However, a mechanism to explain how a component of the nuclear pore complex (NPC) could cause Htx/CHD was undefined. Here, we show that knockdown of Nup188 or its binding partner Nup93 leads to a loss of cilia during embryonic development while leaving NPC function largely intact. Many data, including the localization of endogenous Nup188/93 at cilia bases, support their direct role at cilia. Super-resolution imaging of Nup188 shows two barrel-like structures with dimensions and organization incompatible with an NPC-like ring, arguing against a proposed "ciliary pore complex." We suggest that the nanoscale organization and function of nucleoporins are context dependent in a way that is required for the structure of the heart.
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Affiliation(s)
- Florencia Del Viso
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Fang Huang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Jordan Myers
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Madeleine Chalfant
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Nooreen Reza
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - C Patrick Lusk
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
| | - Mustafa K Khokha
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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34
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Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL, Wan W, Bui KH, Hagen WJ, Briggs JAG, Glavy JS, Hurt E, Beck M. Molecular architecture of the inner ring scaffold of the human nuclear pore complex. Science 2016; 352:363-365. [PMID: 27081072 PMCID: PMC8926079 DOI: 10.1126/science.aaf0643] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/19/2016] [Indexed: 07/21/2023]
Abstract
Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar.
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Affiliation(s)
- Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Alexander von Appen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Roman Teimer
- Biochemistry Center of Heidelberg University, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Amanda L. DiGuilio
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 507 River Street, Hoboken, NJ 07030, USA
| | - William Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Wim J.H. Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - John A. G. Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Joseph S. Glavy
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 507 River Street, Hoboken, NJ 07030, USA
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
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35
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Mutations in nuclear pore genes NUP93, NUP205 and XPO5 cause steroid-resistant nephrotic syndrome. Nat Genet 2016; 48:457-65. [PMID: 26878725 PMCID: PMC4811732 DOI: 10.1038/ng.3512] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/22/2016] [Indexed: 12/26/2022]
Abstract
Nucleoporins are essential components of the nuclear pore complex (NPC). Only a few diseases have been attributed to NPC dysfunction. Steroid-resistant nephrotic syndrome (SRNS), a frequent cause of chronic kidney disease, is caused by dysfunction of glomerular podocytes. Here we identify in eight families with SRNS mutations in NUP93, its interaction partner NUP205 or XPO5 (encoding exportin 5) as hitherto unrecognized monogenic causes of SRNS. NUP93 mutations caused disrupted NPC assembly. NUP93 knockdown reduced the presence of NUP205 in the NPC, and, reciprocally, a NUP205 alteration abrogated NUP93 interaction. We demonstrate that NUP93 and exportin 5 interact with the signaling protein SMAD4 and that NUP93 mutations abrogated interaction with SMAD4. Notably, NUP93 mutations interfered with BMP7-induced SMAD transcriptional reporter activity. We hereby demonstrate that mutations of NUP genes cause a distinct renal disease and identify aberrant SMAD signaling as a new disease mechanism of SRNS, opening a potential new avenue for treatment.
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36
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Weberruss M, Antonin W. Perforating the nuclear boundary – how nuclear pore complexes assemble. J Cell Sci 2016; 129:4439-4447. [DOI: 10.1242/jcs.194753] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
ABSTRACT
The nucleus is enclosed by the nuclear envelope, a double membrane which creates a selective barrier between the cytoplasm and the nuclear interior. Its barrier and transport characteristics are determined by nuclear pore complexes (NPCs) that are embedded within the nuclear envelope, and control molecular exchange between the cytoplasm and nucleoplasm. In this Commentary, we discuss the biogenesis of these huge protein assemblies from approximately one thousand individual proteins. We will summarize current knowledge about distinct assembly modes in animal cells that are characteristic for different cell cycle phases and their regulation.
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Affiliation(s)
- Marion Weberruss
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
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37
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Pleiner T, Bates M, Trakhanov S, Lee CT, Schliep JE, Chug H, Böhning M, Stark H, Urlaub H, Görlich D. Nanobodies: site-specific labeling for super-resolution imaging, rapid epitope-mapping and native protein complex isolation. eLife 2015; 4:e11349. [PMID: 26633879 PMCID: PMC4755751 DOI: 10.7554/elife.11349] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/02/2015] [Indexed: 12/23/2022] Open
Abstract
Nanobodies are single-domain antibodies of camelid origin. We generated nanobodies against the vertebrate nuclear pore complex (NPC) and used them in STORM imaging to locate individual NPC proteins with <2 nm epitope-label displacement. For this, we introduced cysteines at specific positions in the nanobody sequence and labeled the resulting proteins with fluorophore-maleimides. As nanobodies are normally stabilized by disulfide-bonded cysteines, this appears counterintuitive. Yet, our analysis showed that this caused no folding problems. Compared to traditional NHS ester-labeling of lysines, the cysteine-maleimide strategy resulted in far less background in fluorescence imaging, it better preserved epitope recognition and it is site-specific. We also devised a rapid epitope-mapping strategy, which relies on crosslinking mass spectrometry and the introduced ectopic cysteines. Finally, we used different anti-nucleoporin nanobodies to purify the major NPC building blocks – each in a single step, with native elution and, as demonstrated, in excellent quality for structural analysis by electron microscopy. The presented strategies are applicable to any nanobody and nanobody-target.
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Affiliation(s)
- Tino Pleiner
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Mark Bates
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sergei Trakhanov
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Chung-Tien Lee
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Jan Erik Schliep
- 3D Electron Cryo-Microscopy Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Hema Chug
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marc Böhning
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Holger Stark
- 3D Electron Cryo-Microscopy Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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38
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Schellhaus AK, De Magistris P, Antonin W. Nuclear Reformation at the End of Mitosis. J Mol Biol 2015; 428:1962-85. [PMID: 26423234 DOI: 10.1016/j.jmb.2015.09.016] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/17/2015] [Accepted: 09/19/2015] [Indexed: 12/17/2022]
Abstract
Cells have developed highly sophisticated ways to accurately pass on their genetic information to the daughter cells. In animal cells, which undergo open mitosis, the nuclear envelope breaks down at the beginning of mitosis and the chromatin massively condenses to be captured and segregated by the mitotic spindle. These events have to be reverted in order to allow the reformation of a nucleus competent for DNA transcription and replication, as well as all other nuclear processes occurring in interphase. Here, we summarize our current knowledge of how, in animal cells, the highly compacted mitotic chromosomes are decondensed at the end of mitosis and how a nuclear envelope, including functional nuclear pore complexes, reassembles around these decondensing chromosomes.
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Affiliation(s)
| | - Paola De Magistris
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany.
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39
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Breuer M, Ohkura H. A negative loop within the nuclear pore complex controls global chromatin organization. Genes Dev 2015; 29:1789-94. [PMID: 26341556 PMCID: PMC4573852 DOI: 10.1101/gad.264341.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/12/2015] [Indexed: 12/23/2022]
Abstract
The nuclear pore complex (NPC) tethers chromatin to create an environment for gene regulation, but little is known about how this activity is regulated to avoid excessive tethering of the genome. Here we propose a negative regulatory loop within the NPC controlling the chromatin attachment state, in which Nup155 and Nup93 recruit Nup62 to suppress chromatin tethering by Nup155. Depletion of Nup62 severely disrupts chromatin distribution in the nuclei of female germlines and somatic cells, which can be reversed by codepleting Nup155. Thus, this universal regulatory system within the NPC is crucial to control large-scale chromatin organization in the nucleus.
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Affiliation(s)
- Manuel Breuer
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Hiroyuki Ohkura
- The Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
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40
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Schooley A, Moreno-Andrés D, De Magistris P, Vollmer B, Antonin W. The lysine demethylase LSD1 is required for nuclear envelope formation at the end of mitosis. J Cell Sci 2015. [PMID: 26224877 DOI: 10.1242/jcs.173013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The metazoan nucleus breaks down and reassembles during each cell division. Upon mitotic exit, the successful reestablishment of an interphase nucleus requires the coordinated reorganization of chromatin and formation of a functional nuclear envelope. Here, we report that the histone demethylase LSD1 (also known as KDM1A) plays a crucial role in nuclear assembly at the end of mitosis. Downregulation of LSD1 in cells extends telophase and impairs nuclear pore complex assembly. In vitro, LSD1 demethylase activity is required for the recruitment of MEL28 (also known as ELYS and AHCTF1) and nuclear envelope precursor vesicles to chromatin, crucial steps in nuclear reassembly. Accordingly, the formation of a closed nuclear envelope and nuclear pore complex assembly are impaired upon depletion of LSD1 or inhibition of its activity. Our results identify histone demethylation by LSD1 as a new regulatory mechanism linking the chromatin state and nuclear envelope formation at the end of mitosis.
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Affiliation(s)
- Allana Schooley
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Daniel Moreno-Andrés
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Paola De Magistris
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Benjamin Vollmer
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany
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41
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Boni A, Politi AZ, Strnad P, Xiang W, Hossain MJ, Ellenberg J. Live imaging and modeling of inner nuclear membrane targeting reveals its molecular requirements in mammalian cells. J Cell Biol 2015; 209:705-20. [PMID: 26056140 PMCID: PMC4460149 DOI: 10.1083/jcb.201409133] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 05/08/2015] [Indexed: 01/08/2023] Open
Abstract
Targeting of inner nuclear membrane (INM) proteins is essential for nuclear architecture and function, yet its mechanism remains poorly understood. Here, we established a new reporter that allows real-time imaging of membrane protein transport from the ER to the INM using Lamin B receptor and Lap2β as model INM proteins. These reporters allowed us to characterize the kinetics of INM targeting and establish a mathematical model of this process and enabled us to probe its molecular requirements in an RNA interference screen of 96 candidate genes. Modeling of the phenotypes of genes involved in transport of these INM proteins predicted that it critically depended on the number and permeability of nuclear pores and the availability of nuclear binding sites, but was unaffected by depletion of most transport receptors. These predictions were confirmed with targeted validation experiments on the functional requirements of nucleoporins and nuclear lamins. Collectively, our data support a diffusion retention model of INM protein transport in mammalian cells.
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Affiliation(s)
- Andrea Boni
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Antonio Z Politi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Petr Strnad
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Wanqing Xiang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - M Julius Hossain
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
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42
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Hurt E, Beck M. Towards understanding nuclear pore complex architecture and dynamics in the age of integrative structural analysis. Curr Opin Cell Biol 2015; 34:31-8. [PMID: 25938906 DOI: 10.1016/j.ceb.2015.04.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/26/2015] [Accepted: 04/16/2015] [Indexed: 11/29/2022]
Abstract
Determining the functional architecture of the nuclear pore complex, that remains only partially understood, requires bridging across different length scales. Recent technological advances in quantitative and cross-linking mass spectrometry, super-resolution fluorescence microscopy and electron microscopy have enormously accelerated the integration of different types of data into coherent structural models. Moreover, high-resolution structural analysis of nucleoporins and their in vitro reconstitution into complexes is now facilitated by the use of thermostable orthologs. In this review we highlight how the application of such technologies has led to novel insights into nuclear pore architecture and to a paradigm shift. Today nuclear pores are not anymore seen as static facilitators of nucleocytoplasmic transport but ensembles of multiple overlaying functional states that are involved in various cellular processes.
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Affiliation(s)
- Ed Hurt
- Biochemistry Center of Heidelberg University, INF328, D-69120 Heidelberg, Germany.
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
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43
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Vollmer B, Antonin W. The diverse roles of the Nup93/Nic96 complex proteins - structural scaffolds of the nuclear pore complex with additional cellular functions. Biol Chem 2014; 395:515-28. [PMID: 24572986 DOI: 10.1515/hsz-2013-0285] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/22/2014] [Indexed: 11/15/2022]
Abstract
Nuclear pore complexes mediate the transport between the cell nucleoplasm and cytoplasm. These 125 MDa structures are among the largest assemblies found in eukaryotes, built from proteins organized in distinct subcomplexes that act as building blocks during nuclear pore complex biogenesis. In this review, we focus on one of these subcomplexes, the Nup93 complex in metazoa and its yeast counterpart, the Nic96 complex. We discuss its essential function in nuclear pore complex assembly as a linker between the nuclear membrane and the central part of the pore and its various roles in nuclear transport processes and beyond.
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44
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Kim DI, Birendra KC, Zhu W, Motamedchaboki K, Doye V, Roux KJ. Probing nuclear pore complex architecture with proximity-dependent biotinylation. Proc Natl Acad Sci U S A 2014; 111:E2453-61. [PMID: 24927568 PMCID: PMC4066523 DOI: 10.1073/pnas.1406459111] [Citation(s) in RCA: 381] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Proximity-dependent biotin identification (BioID) is a method for identifying protein associations that occur in vivo. By fusing a promiscuous biotin ligase to a protein of interest expressed in living cells, BioID permits the labeling of proximate proteins during a defined labeling period. In this study we used BioID to study the human nuclear pore complex (NPC), one of the largest macromolecular assemblies in eukaryotes. Anchored within the nuclear envelope, NPCs mediate the nucleocytoplasmic trafficking of numerous cellular components. We applied BioID to constituents of the Nup107-160 complex and the Nup93 complex, two conserved NPC subcomplexes. A strikingly different set of NPC constituents was detected depending on the position of these BioID-fusion proteins within the NPC. By applying BioID to several constituents located throughout the extremely stable Nup107-160 subcomplex, we refined our understanding of this highly conserved subcomplex, in part by demonstrating a direct interaction of Nup43 with Nup85. Furthermore, by using the extremely stable Nup107-160 structure as a molecular ruler, we defined the practical labeling radius of BioID. These studies further our understanding of human NPC organization and demonstrate that BioID is a valuable tool for exploring the constituency and organization of large protein assemblies in living cells.
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Affiliation(s)
- Dae In Kim
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - K C Birendra
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Wenhong Zhu
- Sanford-Burnham Proteomics Facility, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Khatereh Motamedchaboki
- Sanford-Burnham Proteomics Facility, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Valérie Doye
- Institut Jacques Monod, Unité Mixte de Recherche 7592, Centre National de la Recherche Scientifique, Université Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France; and
| | - Kyle J Roux
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104;Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105
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45
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Bui KH, von Appen A, DiGuilio AL, Ori A, Sparks L, Mackmull MT, Bock T, Hagen W, Andrés-Pons A, Glavy JS, Beck M. Integrated structural analysis of the human nuclear pore complex scaffold. Cell 2014; 155:1233-43. [PMID: 24315095 DOI: 10.1016/j.cell.2013.10.055] [Citation(s) in RCA: 271] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 08/22/2013] [Accepted: 10/02/2013] [Indexed: 11/28/2022]
Abstract
The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes.
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Affiliation(s)
- Khanh Huy Bui
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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46
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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: 4.3] [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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47
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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: 4.8] [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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48
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Yoshimura SH, Otsuka S, Kumeta M, Taga M, Takeyasu K. Intermolecular disulfide bonds between nucleoporins regulate karyopherin-dependent nuclear transport. J Cell Sci 2013; 126:3141-50. [PMID: 23641069 DOI: 10.1242/jcs.124172] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Disulfide (S-S) bonds play important roles in the regulation of protein function and cellular stress responses. In this study, we demonstrate that distinct sets of nucleoporins (Nups), components of the nuclear pore complex (NPC), form S-S bonds and regulate nuclear transport through the NPC. Kinetic analysis of importin β demonstrated that the permeability of the NPC was increased by dithiothreitol treatment and reduced by oxidative stress. The permeability of small proteins such as GFP was not affected by either oxidative stress or a reducing reagent. Immunoblot analysis revealed that the oxidative stress significantly induced S-S bond formation in Nups 358, 155, 153 and 62 but not 88 and 160. The direct involvement of cysteine residues in the formation of S-S bonds was confirmed by mutating conserved cysteine residues in Nup62, which abolished the formation of S-S bonds and enhanced the permeability of the NPC. Knocking down Nup62 reduced the stress-inducible S-S bonds of Nup155, suggesting that Nup62 and Nup155 are covalently coupled via S-S bonds. From these results, we propose that the inner channel of the NPC is somehow insulated from the cytoplasm and is more sensitive than the cytoplasm to the intracellular redox state.
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Affiliation(s)
- Shige H Yoshimura
- Graduate School of Biostudies, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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49
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The permeability of reconstituted nuclear pores provides direct evidence for the selective phase model. Cell 2012; 150:738-51. [PMID: 22901806 DOI: 10.1016/j.cell.2012.07.019] [Citation(s) in RCA: 232] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/05/2012] [Accepted: 06/05/2012] [Indexed: 11/20/2022]
Abstract
Nuclear pore complexes (NPCs) maintain a permeability barrier between the nucleus and the cytoplasm through FG-repeat-containing nucleoporins (Nups). We previously proposed a "selective phase model" in which the FG repeats interact with one another to form a sieve-like barrier that can be locally disrupted by the binding of nuclear transport receptors (NTRs), but not by inert macromolecules, allowing selective passage of NTRs and associated cargo. Here, we provide direct evidence for this model in a physiological context. By using NPCs reconstituted from Xenopus laevis egg extracts, we show that Nup98 is essential for maintaining the permeability barrier. Specifically, the multivalent cohesion between FG repeats is required, including cohesive FG repeats close to the anchorage point to the NPC scaffold. Our data exclude alternative models that are based solely on an interaction between the FG repeats and NTRs and indicate that the barrier is formed by a sieve-like FG hydrogel.
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50
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Building a nuclear envelope at the end of mitosis: coordinating membrane reorganization, nuclear pore complex assembly, and chromatin de-condensation. Chromosoma 2012; 121:539-54. [PMID: 23104094 PMCID: PMC3501164 DOI: 10.1007/s00412-012-0388-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/04/2012] [Accepted: 10/04/2012] [Indexed: 12/01/2022]
Abstract
The metazoan nucleus is disassembled and re-built at every mitotic cell division. The nuclear envelope, including nuclear pore complexes, breaks down at the beginning of mitosis to accommodate the capture of massively condensed chromosomes by the spindle apparatus. At the end of mitosis, a nuclear envelope is newly formed around each set of segregating and de-condensing chromatin. We review the current understanding of the membrane restructuring events involved in the formation of the nuclear membrane sheets of the envelope, the mechanisms governing nuclear pore complex assembly and integration in the nascent nuclear membranes, and the regulated coordination of these events with chromatin de-condensation.
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