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Parise A, Cresca S, Magistrato A. Molecular dynamics simulations for the structure-based drug design: targeting small-GTPases proteins. Expert Opin Drug Discov 2024:1-21. [PMID: 39105536 DOI: 10.1080/17460441.2024.2387856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/30/2024] [Indexed: 08/07/2024]
Abstract
INTRODUCTION Molecular Dynamics (MD) simulations can support mechanism-based drug design. Indeed, MD simulations by capturing biomolecule motions at finite temperatures can reveal hidden binding sites, accurately predict drug-binding poses, and estimate the thermodynamics and kinetics, crucial information for drug discovery campaigns. Small-Guanosine Triphosphate Phosphohydrolases (GTPases) regulate a cascade of signaling events, that affect most cellular processes. Their deregulation is linked to several diseases, making them appealing drug targets. The broad roles of small-GTPases in cellular processes and the recent approval of a covalent KRas inhibitor as an anticancer agent renewed the interest in targeting small-GTPase with small molecules. AREA COVERED This review emphasizes the role of MD simulations in elucidating small-GTPase mechanisms, assessing the impact of cancer-related variants, and discovering novel inhibitors. EXPERT OPINION The application of MD simulations to small-GTPases exemplifies the role of MD simulations in the structure-based drug design process for challenging biomolecular targets. Furthermore, AI and machine learning-enhanced MD simulations, coupled with the upcoming power of quantum computing, are promising instruments to target elusive small-GTPases mutations and splice variants. This powerful synergy will aid in developing innovative therapeutic strategies associated to small-GTPases deregulation, which could potentially be used for personalized therapies and in a tissue-agnostic manner to treat tumors with mutations in small-GTPases.
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Affiliation(s)
- Angela Parise
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Sofia Cresca
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche (CNR) - Istituto Officina dei Materiali (IOM), c/o International School for Advanced Studies (SISSA), Trieste, Italy
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2
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Goswami R, Gupta A, Bednova O, Coulombe G, Patel D, Rotello VM, Leyton JV. Nuclear localization signal-tagged systems: relevant nuclear import principles in the context of current therapeutic design. Chem Soc Rev 2024; 53:204-226. [PMID: 38031452 PMCID: PMC10798298 DOI: 10.1039/d1cs00269d] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Nuclear targeting of therapeutics provides a strategy for enhancing efficacy of molecules active in the nucleus and minimizing off-target effects. 'Active' nuclear-directed transport and efficient translocations across nuclear pore complexes provide the most effective means of maximizing nuclear localization. Nuclear-targeting systems based on nuclear localization signal (NLS) motifs have progressed significantly since the beginning of the current millennium. Here, we offer a roadmap for understanding the basic mechanisms of nuclear import in the context of actionable therapeutic design for developing NLS-therapeutics with improved treatment efficacy.
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Affiliation(s)
- Ritabrita Goswami
- Department of Chemistry, University of Massachusetts, Massachusetts, USA.
| | - Aarohi Gupta
- Department of Chemistry, University of Massachusetts, Massachusetts, USA.
| | - Olga Bednova
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec, Canada
| | - Gaël Coulombe
- Service des stages et du développement professionnel, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dipika Patel
- Service des stages et du développement professionnel, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts, Massachusetts, USA.
| | - Jeffrey V Leyton
- École des sciences pharmaceutiques, Université d'Ottawa, Ottawa, Ontario, Canada.
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
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3
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Tai L, Yin G, Sun F, Zhu Y. Cryo-electron microscopy reveals the structure of the nuclear pore complex. J Mol Biol 2023; 435:168051. [PMID: 36933820 DOI: 10.1016/j.jmb.2023.168051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
The nuclear pore complex (NPC) is a giant protein assembly that penetrates the double layers of the nuclear membrane. The overall structure of the NPC has approximately eightfold symmetry and is formed by approximately 30 nucleoporins. The great size and complexity of the NPC have hindered the study of its structure for many years until recent breakthroughs were achieved by integrating the latest high-resolution cryo-electron microscopy (cryo-EM), the emerging artificial intelligence-based modeling and all other available structural information from crystallography and mass spectrometry. Here, we review our latest knowledge of the NPC architecture and the history of its structural study from in vitro to in situ with progressively improved resolutions by cryo-EM, with a particular focus on the latest subnanometer-resolution structural studies. The future directions for structural studies of NPCs are also discussed.
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Affiliation(s)
- Linhua Tai
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Yin
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong 510005, China.
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli CE, Buczak K, Schmidt FH, Margiotta E, Mackmull MT, Hagen WJH, Hummer G, Kosinski J, Beck M. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science 2022; 376:eabm9506. [PMID: 35679397 DOI: 10.1126/science.abm9506] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The eukaryotic nucleus pro-tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa, the human NPC is one of the larg-est protein complexes. Its ~1000 proteins are taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs). They can be roughly categorized into two classes. Scaf-fold NUPs contain folded domains and form a cylindrical scaffold architecture around a central channel. Intrinsically disordered NUPs line the scaffold and extend into the central channel, where they interact with cargo complexes. The NPC architecture is highly dynamic. It responds to changes in nuclear envelope tension with conforma-tional breathing that manifests in dilation and constriction movements. Elucidating the scaffold architecture, ultimately at atomic resolution, will be important for gaining a more precise understanding of NPC function and dynamics but imposes a substantial chal-lenge for structural biologists. RATIONALE Considerable progress has been made toward this goal by a joint effort in the field. A synergistic combination of complementary approaches has turned out to be critical. In situ structural biology techniques were used to reveal the overall layout of the NPC scaffold that defines the spatial reference for molecular modeling. High-resolution structures of many NUPs were determined in vitro. Proteomic analysis and extensive biochemical work unraveled the interaction network of NUPs. Integra-tive modeling has been used to combine the different types of data, resulting in a rough outline of the NPC scaffold. Previous struc-tural models of the human NPC, however, were patchy and limited in accuracy owing to several challenges: (i) Many of the high-resolution structures of individual NUPs have been solved from distantly related species and, consequently, do not comprehensively cover their human counterparts. (ii) The scaf-fold is interconnected by a set of intrinsically disordered linker NUPs that are not straight-forwardly accessible to common structural biology techniques. (iii) The NPC scaffold intimately embraces the fused inner and outer nuclear membranes in a distinctive topol-ogy and cannot be studied in isolation. (iv) The conformational dynamics of scaffold NUPs limits the resolution achievable in structure determination. RESULTS In this study, we used artificial intelligence (AI)-based prediction to generate an exten-sive repertoire of structural models of human NUPs and their subcomplexes. The resulting models cover various domains and interfaces that so far remained structurally uncharac-terized. Benchmarking against previous and unpublished x-ray and cryo-electron micros-copy structures revealed unprecedented accu-racy. We obtained well-resolved cryo-electron tomographic maps of both the constricted and dilated conformational states of the hu-man NPC. Using integrative modeling, we fit-ted the structural models of individual NUPs into the cryo-electron microscopy maps. We explicitly included several linker NUPs and traced their trajectory through the NPC scaf-fold. We elucidated in great detail how mem-brane-associated and transmembrane NUPs are distributed across the fusion topology of both nuclear membranes. The resulting architectural model increases the structural coverage of the human NPC scaffold by about twofold. We extensively validated our model against both earlier and new experimental data. The completeness of our model has enabled microsecond-long coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit membrane en-vironment and solvent. These simulations reveal that the NPC scaffold prevents the constriction of the otherwise stable double-membrane fusion pore to small diameters in the absence of membrane tension. CONCLUSION Our 70-MDa atomically re-solved model covers >90% of the human NPC scaffold. It captures conforma-tional changes that occur during dilation and constriction. It also reveals the precise anchoring sites for intrinsically disordered NUPs, the identification of which is a prerequisite for a complete and dy-namic model of the NPC. Our study exempli-fies how AI-based structure prediction may accelerate the elucidation of subcellular ar-chitecture at atomic resolution. [Figure: see text].
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Affiliation(s)
- Shyamal Mosalaganti
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Agnieszka Obarska-Kosinska
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,European Molecular Biology Laboratory Hamburg, 22607 Hamburg, Germany
| | - Marc Siggel
- European Molecular Biology Laboratory Hamburg, 22607 Hamburg, Germany.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Reiya Taniguchi
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Christian E Zimmerli
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Katarzyna Buczak
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Florian H Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Erica Margiotta
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Marie-Therese Mackmull
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,European Molecular Biology Laboratory Hamburg, 22607 Hamburg, Germany.,Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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Nag N, Sasidharan S, Uversky VN, Saudagar P, Tripathi T. Phase separation of FG-nucleoporins in nuclear pore complexes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119205. [PMID: 34995711 DOI: 10.1016/j.bbamcr.2021.119205] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/14/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022]
Abstract
The nuclear envelope (NE) is a bilayer membrane that separates and physically isolates the genetic material from the cytoplasm. Nuclear pore complexes (NPCs) are cylindrical structures embedded in the NE and remain the sole channel of communication between the nucleus and the cytoplasm. The interior of NPCs contains densely packed intrinsically disordered FG-nucleoporins (FG-Nups), consequently forming a permeability barrier. This barrier facilitates the selection and specificity of the cargoes that are imported, exported, or shuttled through the NPCs. Recent studies have revealed that FG-Nups undergo the process of liquid-liquid phase separation into liquid droplets. Moreover, these liquid droplets mimic the permeability barrier observed in the interior of NPCs. This review highlights the phase separation of FG-Nups occurring inside the NPCs rooted in the NE. We discuss the phase separation of FG-Nups and compare the different aspects contributing to their phase separation. Furthermore, several diseases caused by the aberrant phase separation of the proteins are examined with respect to NEs. By understanding the fundamental process of phase separation at the nuclear membrane, the review seeks to explore the parameters influencing this phenomenon as well as its importance, ultimately paving the way for better research on the structure-function relationship of biomolecular condensates.
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Affiliation(s)
- Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Santanu Sasidharan
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, India.
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
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Lange J, Wood-Kaczmar A, Ali A, Farag S, Ghosh R, Parker J, Casey C, Uno Y, Kunugi A, Ferretti P, Andre R, Tabrizi SJ. Mislocalization of Nucleocytoplasmic Transport Proteins in Human Huntington's Disease PSC-Derived Striatal Neurons. Front Cell Neurosci 2021; 15:742763. [PMID: 34658796 PMCID: PMC8519404 DOI: 10.3389/fncel.2021.742763] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/09/2021] [Indexed: 11/17/2022] Open
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene (HTT). Disease progression is characterized by the loss of vulnerable neuronal populations within the striatum. A consistent phenotype across HD models is disruption of nucleocytoplasmic transport and nuclear pore complex (NPC) function. Here we demonstrate that high content imaging is a suitable method for detecting mislocalization of lamin-B1, RAN and RANGAP1 in striatal neuronal cultures thus allowing a robust, unbiased, highly powered approach to assay nuclear pore deficits. Furthermore, nuclear pore deficits extended to the selectively vulnerable DARPP32 + subpopulation neurons, but not to astrocytes. Striatal neuron cultures are further affected by changes in gene and protein expression of RAN, RANGAP1 and lamin-B1. Lowering total HTT using HTT-targeted anti-sense oligonucleotides partially restored gene expression, as well as subtly reducing mislocalization of proteins involved in nucleocytoplasmic transport. This suggests that mislocalization of RAN, RANGAP1 and lamin-B1 cannot be normalized by simply reducing expression of CAG-expanded HTT in the absence of healthy HTT protein.
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Affiliation(s)
- Jenny Lange
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Alison Wood-Kaczmar
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Aneesa Ali
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Sahar Farag
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Rhia Ghosh
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Jennifer Parker
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Caroline Casey
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Yumiko Uno
- Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Akiyoshi Kunugi
- Neuroscience Drug Discovery Unit, Takeda Pharmaceutical Company Limited, Fujisawa, Japan
| | - Patrizia Ferretti
- Stem Cell and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Ralph Andre
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Sarah J. Tabrizi
- Huntington’s Disease Centre, Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
- UK Dementia Research Institute, University College London, London, United Kingdom
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7
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Anderson EN, Morera AA, Kour S, Cherry JD, Ramesh N, Gleixner A, Schwartz JC, Ebmeier C, Old W, Donnelly CJ, Cheng JP, Kline AE, Kofler J, Stein TD, Pandey UB. Traumatic injury compromises nucleocytoplasmic transport and leads to TDP-43 pathology. eLife 2021; 10:e67587. [PMID: 34060470 PMCID: PMC8169113 DOI: 10.7554/elife.67587] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/14/2021] [Indexed: 12/14/2022] Open
Abstract
Traumatic brain injury (TBI) is a predisposing factor for many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD), and chronic traumatic encephalopathy (CTE). Although defects in nucleocytoplasmic transport (NCT) is reported ALS and other neurodegenerative diseases, whether defects in NCT occur in TBI remains unknown. We performed proteomic analysis on Drosophila exposed to repeated TBI and identified resultant alterations in several novel molecular pathways. TBI upregulated nuclear pore complex (NPC) and nucleocytoplasmic transport (NCT) proteins as well as alter nucleoporin stability. Traumatic injury disrupted RanGAP1 and NPC protein distribution in flies and a rat model and led to coaggregation of NPC components and TDP-43. In addition, trauma-mediated NCT defects and lethality are rescued by nuclear export inhibitors. Importantly, genetic upregulation of nucleoporins in vivo and in vitro triggered TDP-43 cytoplasmic mislocalization, aggregation, and altered solubility and reduced motor function and lifespan of animals. We also found NUP62 pathology and elevated NUP62 concentrations in postmortem brain tissues of patients with mild or severe CTE as well as co-localization of NUP62 and TDP-43 in CTE. These findings indicate that TBI leads to NCT defects, which potentially mediate the TDP-43 pathology in CTE.
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Affiliation(s)
- Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Andrés A Morera
- Department of Chemistry and Biochemistry, University of ArizonaTucsonUnited States
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Jonathan D Cherry
- Department of Pathology and Laboratory Medicine, Boston University School of MedicineBostonUnited States
- Boston VA Healthcare SystemBostonUnited States
| | - Nandini Ramesh
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Amanda Gleixner
- Department of Neurobiology, University of Pittsburgh School of MedicinePittsburghUnited States
- LiveLike Lou Center for ALS Research, Brain Institute, University of Pittsburgh School of MedicinePittsburghUnited States
| | - Jacob C Schwartz
- Department of Chemistry and Biochemistry, University of ArizonaTucsonUnited States
| | - Christopher Ebmeier
- Molecular, Cellular & Developmental Biology, University of ColoradoBoulderUnited States
| | - William Old
- Molecular, Cellular & Developmental Biology, University of ColoradoBoulderUnited States
| | - Christopher J Donnelly
- Department of Neurobiology, University of Pittsburgh School of MedicinePittsburghUnited States
- LiveLike Lou Center for ALS Research, Brain Institute, University of Pittsburgh School of MedicinePittsburghUnited States
| | - Jeffrey P Cheng
- Physical Medicine & Rehabilitation; Safar Center for Resuscitation Research, University of PittsburghPittsburghUnited States
| | - Anthony E Kline
- Physical Medicine & Rehabilitation; Safar Center for Resuscitation Research, University of PittsburghPittsburghUnited States
- Center for Neuroscience; Center for the Neural Basis of Cognition; Critical Care Medicine, University of PittsburghPittsburghUnited States
| | - Julia Kofler
- Department of Pathology, University of PittsburghPittsburghUnited States
| | - Thor D Stein
- Department of Pathology and Laboratory Medicine, Boston University School of MedicineBostonUnited States
- Boston VA Healthcare SystemBostonUnited States
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
- Department of Human Genetics, University of Pittsburgh School of Public HealthPittsburghUnited States
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8
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Taniue K, Akimitsu N. Aberrant phase separation and cancer. FEBS J 2021; 289:17-39. [PMID: 33583140 DOI: 10.1111/febs.15765] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/24/2021] [Accepted: 02/12/2021] [Indexed: 01/10/2023]
Abstract
Eukaryotic cells are intracellularly divided into numerous compartments or organelles, which coordinate specific molecules and biological reactions. Membrane-bound organelles are physically separated by lipid bilayers from the surrounding environment. Biomolecular condensates, also referred to membraneless organelles, are micron-scale cellular compartments that lack membranous enclosures but function to concentrate proteins and RNA molecules, and these are involved in diverse processes. Liquid-liquid phase separation (LLPS) driven by multivalent weak macromolecular interactions is a critical principle for the formation of biomolecular condensates, and a multitude of combinations among multivalent interactions may drive liquid-liquid phase transition (LLPT). Dysregulation of LLPS and LLPT leads to aberrant condensate and amyloid formation, which causes many human diseases, including neurodegeneration and cancer. Here, we describe recent findings regarding abnormal forms of biomolecular condensates and aggregation via aberrant LLPS and LLPT of cancer-related proteins in cancer development driven by mutation and fusion of genes. Moreover, we discuss the regulatory mechanisms by which aberrant LLPS and LLPT occur in cancer and the drug candidates targeting these mechanisms. Further understanding of the molecular events regulating how biomolecular condensates and aggregation form in cancer tissue is critical for the development of therapeutic strategies against tumorigenesis.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Japan.,Division of Gastroenterology and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, Japan
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9
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Diez L, Wegmann S. Nuclear Transport Deficits in Tau-Related Neurodegenerative Diseases. Front Neurol 2020; 11:1056. [PMID: 33101165 PMCID: PMC7546323 DOI: 10.3389/fneur.2020.01056] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Tau is a cytosolic microtubule binding protein that is highly abundant in the axons of the central nervous system. However, alternative functions of tau also in other cellular compartments are suggested, for example, in the nucleus, where interactions of tau with specific nuclear entities such as DNA, the nucleolus, and the nuclear envelope have been reported. We would like to review the current knowledge about tau-nucleus interactions and lay out possible neurotoxic mechanisms that are based on the (pathological) interactions of tau with the nucleus.
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Affiliation(s)
- Lisa Diez
- German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases, Berlin, Germany
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10
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Moore S, Rabichow BE, Sattler R. The Hitchhiker's Guide to Nucleocytoplasmic Trafficking in Neurodegeneration. Neurochem Res 2020; 45:1306-1327. [PMID: 32086712 DOI: 10.1007/s11064-020-02989-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022]
Abstract
The widespread nature of nucleocytoplasmic trafficking defects and protein accumulation suggests distinct yet overlapping mechanisms in a variety of neurodegenerative diseases. Detailed understanding of the cellular pathways involved in nucleocytoplasmic transport and its dysregulation are essential for elucidating neurodegenerative pathogenesis and pinpointing potential areas for therapeutic intervention. The transport of cargos from the nucleus to the cytoplasm is generally regulated by the structure and function of the nuclear pore as well as the karyopherin α/β, importin, exportin, and mRNA export mechanisms. The disruption of these crucial transport mechanisms has been extensively described in the context of neurodegenerative diseases. One common theme in neurodegeneration is the cytoplasmic aggregation of proteins, including nuclear RNA binding proteins, repeat expansion associated gene products, and tau. These cytoplasmic aggregations are partly a consequence of failed nucleocytoplasmic transport machinery, but can also further disrupt transport, creating cyclical feed-forward mechanisms that exacerbate neurodegeneration. Here we describe the canonical mechanisms that regulate nucleocytoplasmic trafficking as well as how these mechanisms falter in neurodegenerative diseases.
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Affiliation(s)
- Stephen Moore
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Benjamin E Rabichow
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Rita Sattler
- Department of Neurobiology, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA.
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11
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Blasius TL, Takao D, Verhey KJ. NPHP proteins are binding partners of nucleoporins at the base of the primary cilium. PLoS One 2019; 14:e0222924. [PMID: 31553752 PMCID: PMC6760808 DOI: 10.1371/journal.pone.0222924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 09/09/2019] [Indexed: 12/21/2022] Open
Abstract
Cilia are microtubule-based organelles that protrude from the surface of eukaryotic cells to generate motility and to sense and respond to environmental cues. In order to carry out these functions, the complement of proteins in the cilium must be specific for the organelle. Regulation of protein entry into primary cilia has been shown to utilize mechanisms and components of nuclear gating, including nucleoporins of the nuclear pore complex (NPC). We show that nucleoporins also localize to the base of motile cilia on the surface of trachea epithelial cells. How nucleoporins are anchored at the cilium base has been unclear as transmembrane nucleoporins, which anchor nucleoporins at the nuclear envelope, have not been found to localize at the cilium. Here we use the directed yeast two-hybrid assay to identify direct interactions between nucleoporins and nephronophthisis proteins (NPHPs) which localize to the cilium base and contribute to cilium assembly and identity. We validate NPHP-nucleoporin interactions in mammalian cells using the knocksideways assay and demonstrate that the interactions occur at the base of the primary cilium using bimolecular fluorescence complementation. We propose that NPHP proteins anchor nucleoporins at the base of primary cilia to regulate protein entry into the organelle.
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Affiliation(s)
- T. Lynne Blasius
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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12
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Nucleus–cytoplasm cross‐talk in the aging brain. J Neurosci Res 2019; 98:247-261. [DOI: 10.1002/jnr.24446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/10/2019] [Accepted: 05/06/2019] [Indexed: 12/13/2022]
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13
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Inactivation of Cyclic AMP Response Element Transcription Caused by Constitutive p38 Activation Is Mediated by Hyperphosphorylation-Dependent CRTC2 Nucleocytoplasmic Transport. Mol Cell Biol 2019; 39:MCB.00554-18. [PMID: 30782776 DOI: 10.1128/mcb.00554-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/01/2019] [Indexed: 01/05/2023] Open
Abstract
The p38 signal transduction pathway can be activated transiently or constitutively, depending on the contexts in which the activation occurs. However, the biological consequence of constitutive activation of p38 is largely unknown. After screening 300 transcriptional cofactors, we identified CRTC2 as a downstream substrate of constitutively activated p38. Constitutive, rather than transient, activation of p38 led to hyperphosphorylation of CRTC2, resulting in CRTC2 cytosolic relocation and subsequent inactivation of cyclic AMP response element (CRE)-mediated transcription. Interestingly, the cytosolic translocation of CRTC2 depended on phosphorylation accumulation at multiple sites (≥11 phosphoserine/phosphothreonine residues) but not on specific sites. The hyperphosphorylation-driven nucleocytoplasmic transport of CRTC2 may not be a rare case of nuclear export of proteins, as we also observed that constitutively activated p38 promoted FOS nuclear export in a hyperphosphorylation-dependent manner. Collectively, our study uncovered a previously unknown mechanism of inactivation of selected transcription, which results from hyperphosphorylation-driven nucleocytoplasmic transport of cofactors or transcription factors mediated by constitutively active kinase.
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14
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Thaller DJ, Allegretti M, Borah S, Ronchi P, Beck M, Lusk CP. An ESCRT-LEM protein surveillance system is poised to directly monitor the nuclear envelope and nuclear transport system. eLife 2019; 8:e45284. [PMID: 30942170 PMCID: PMC6461442 DOI: 10.7554/elife.45284] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022] Open
Abstract
The integrity of the nuclear membranes coupled to the selective barrier of nuclear pore complexes (NPCs) are essential for the segregation of nucleoplasm and cytoplasm. Mechanical membrane disruption or perturbation to NPC assembly triggers an ESCRT-dependent surveillance system that seals nuclear pores: how these pores are sensed and sealed is ill defined. Using a budding yeast model, we show that the ESCRT Chm7 and the integral inner nuclear membrane (INM) protein Heh1 are spatially segregated by nuclear transport, with Chm7 being actively exported by Xpo1/Crm1. Thus, the exposure of the INM triggers surveillance with Heh1 locally activating Chm7. Sites of Chm7 hyperactivation show fenestrated sheets at the INM and potential membrane delivery at sites of nuclear envelope herniation. Our data suggest that perturbation to the nuclear envelope barrier would lead to local nuclear membrane remodeling to promote membrane sealing. Our findings have implications for disease mechanisms linked to NPC assembly and nuclear envelope integrity.
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Affiliation(s)
- David J Thaller
- Department of Cell BiologyYale School of MedicineNew HavenUnited States
| | - Matteo Allegretti
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryMeyerhofstrasseGermany
| | - Sapan Borah
- Department of Cell BiologyYale School of MedicineNew HavenUnited States
| | - Paolo Ronchi
- Electron Microscopy Core FacilityEuropean Molecular Biology LaboratoryMeyerhofstrasseGermany
| | - Martin Beck
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryMeyerhofstrasseGermany
| | - C Patrick Lusk
- Department of Cell BiologyYale School of MedicineNew HavenUnited States
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15
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Canela-Pérez I, López-Villaseñor I, Mendoza L, Cevallos AM, Hernández R. Nuclear localization signals in trypanosomal proteins. Mol Biochem Parasitol 2019; 229:15-23. [PMID: 30772422 DOI: 10.1016/j.molbiopara.2019.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/14/2019] [Accepted: 02/09/2019] [Indexed: 01/04/2023]
Abstract
The nuclear import of proteins in eukaryotic cells is a fundamental biological process. While it has been analysed to different extents in model eukaryotic organisms, this event has rarely been studied in the early divergent protozoa of the order Kinetoplastida. The work presented here represents an overview of nuclear import in these important species of human pathogens. Initially, an in silico study of classical nuclear localization signals within the published nuclear proteomes of Trypanosoma brucei and Trypanosoma cruzi was carried out. The basic amino acids that comprise the monopartite and bipartite classical nuclear localization signals (cNLS) in trypanosomal proteins are similar to the consensus sequences observed for the nuclear proteins of yeasts, animals and plants. In addition, a summarized description of published studies that experimentally address the NLS of nuclear proteins in trypanosomatids is presented, and the clear occurrence of non-classical NLS (NLS that lack the consensus motifs of basic amino acids) in the analysed reports indicate a complex scenario for the types of receptors in these species. In general, the information presented here agrees with the hypothetical appearance of mechanisms for the recognition of nuclear proteins in early eukaryotic evolution.
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Affiliation(s)
- Israel Canela-Pérez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Luis Mendoza
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Ana María Cevallos
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, CP 04360, México.
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16
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Kim YJ, Somers DE. Luciferase-Based Screen for Post-translational Control Factors in the Regulation of the Pseudo-Response Regulator PRR7. FRONTIERS IN PLANT SCIENCE 2019; 10:667. [PMID: 31191580 PMCID: PMC6540683 DOI: 10.3389/fpls.2019.00667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/02/2019] [Indexed: 05/04/2023]
Abstract
Control of protein turnover is a key post-translational control point in the oscillatory network of the circadian clock. Some elements, such as TOC1 and PRR5 are engaged by a well-described F-box protein, ZEITLUPE, dedicated to their proteolytic turnover to shape their expression profile to a specific time of night. For most other clock components the regulation of their protein abundance is unknown, though turnover is often rapid and often lags the cycling of the respective mRNA. Here we report the design and results of an unbiased genetic screen in Arabidopsis to uncover proteolytic regulatory factors of PSEUDO-RESPONSE REGULATOR 7 (PRR7), a transcriptional repressor that peaks in the late afternoon. We performed EMS mutagenesis on a transgenic line expressing a PRR7::PRR7-luciferase (PRR7-LUC) translational fusion that accurately recapitulates the diurnal and circadian oscillations of the endogenous PRR7 protein. Using continuous luciferase imaging under constant light, we recovered mutants that alter the PRR7-LUC waveform and some that change period. We have identified novel alleles of ELF3 and ELF4, core components of the ELF3-ELF4-LUX Evening Complex (EC), that dampen the oscillation of PRR7-LUC. We report the characterization of two new hypomorphic alleles of ELF3 that help to understand the relationship between molecular potency and phenotype.
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17
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Lari A, Farzam F, Bensidoun P, Oeffinger M, Zenklusen D, Grunwald D, Montpetit B. Live-Cell Imaging of mRNP-NPC Interactions in Budding Yeast. Methods Mol Biol 2019; 2038:131-150. [PMID: 31407282 DOI: 10.1007/978-1-4939-9674-2_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single-molecule resolution imaging has become an important tool in the study of cell biology. Aptamer-based approaches (e.g., MS2 and PP7) allow for detection of single RNA molecules in living cells and have been used to study various aspects of mRNA metabolism, including mRNP nuclear export. Here we outline an imaging protocol for the study of interactions between mRNPs and nuclear pore complexes (NPCs) in the yeast S. cerevisiae, including mRNP export. We describe in detail the steps that allow for high-resolution live-cell mRNP imaging and measurement of mRNP interactions with NPCs using simultaneous two-color imaging. Our protocol discusses yeast strain construction, choice of marker proteins to label the nuclear pore complex, as well as imaging conditions that allow high signal-to-noise data acquisition. Moreover, we describe various aspects of postacquisition image analysis for single molecule tracking and image registration allowing for the characterization of mRNP-NPC interactions.
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Affiliation(s)
- Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Farzin Farzam
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Pierre Bensidoun
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
| | - Marlene Oeffinger
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
- Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA.
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18
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Abstract
In metazoans, the assembly of kinetochores on centrometric chromatin and the dismantling of nuclear pore complexes are processes that have to be tightly coordinated to ensure the proper assembly of the mitotic spindle and a successful mitosis. It is therefore noteworthy that these two macromolecular assemblies share a subset of constituents. One of these multifaceted components is Cenp-F, a protein implicated in cancer and developmental pathologies. During the cell cycle, Cenp-F localizes in multiple cellular structures including the nuclear envelope in late G2/early prophase and kinetochores throughout mitosis. We recently characterized the molecular determinants of Cenp-F interaction with Nup133, a structural nuclear pore constituent. In parallel with two other independent studies, we further elucidated the mechanisms governing Cenp-F kinetochore recruitment that mainly relies on its interaction with Bub1, with redundant contribution of Cenp-E upon acute microtubule depolymerisation. Here we synthesize the current literature regarding the dual location of Cenp-F at nuclear pores and kinetochores and extend our discussion to the regulation of these NPC and kinetochore localizations by mitotic kinase and spindle microtubules.
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Affiliation(s)
- Alessandro Berto
- a Institut Jacques Monod , UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité , Paris , France.,b Ecole Doctorale Structure et Dynamique des Systèmes Vivants (#577) , Univ Paris Sud, Université Paris-Saclay , Orsay , France
| | - Valérie Doye
- a Institut Jacques Monod , UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité , Paris , France
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19
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Eftekharzadeh B, Daigle JG, Kapinos LE, Coyne A, Schiantarelli J, Carlomagno Y, Cook C, Miller SJ, Dujardin S, Amaral AS, Grima JC, Bennett RE, Tepper K, DeTure M, Vanderburg CR, Corjuc BT, DeVos SL, Gonzalez JA, Chew J, Vidensky S, Gage FH, Mertens J, Troncoso J, Mandelkow E, Salvatella X, Lim RYH, Petrucelli L, Wegmann S, Rothstein JD, Hyman BT. Tau Protein Disrupts Nucleocytoplasmic Transport in Alzheimer's Disease. Neuron 2018; 99:925-940.e7. [PMID: 30189209 PMCID: PMC6240334 DOI: 10.1016/j.neuron.2018.07.039] [Citation(s) in RCA: 262] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/14/2018] [Accepted: 07/20/2018] [Indexed: 10/28/2022]
Abstract
Tau is the major constituent of neurofibrillary tangles in Alzheimer's disease (AD), but the mechanism underlying tau-associated neural damage remains unclear. Here, we show that tau can directly interact with nucleoporins of the nuclear pore complex (NPC) and affect their structural and functional integrity. Pathological tau impairs nuclear import and export in tau-overexpressing transgenic mice and in human AD brain tissue. Furthermore, the nucleoporin Nup98 accumulates in the cell bodies of some tangle-bearing neurons and can facilitate tau aggregation in vitro. These data support the hypothesis that tau can directly interact with NPC components, leading to their mislocalization and consequent disruption of NPC function. This raises the possibility that NPC dysfunction contributes to tau-induced neurotoxicity in AD and tauopathies.
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Affiliation(s)
- Bahareh Eftekharzadeh
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - J Gavin Daigle
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | | | - Alyssa Coyne
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Julia Schiantarelli
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Yari Carlomagno
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Casey Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Sean J Miller
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Simon Dujardin
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ana S Amaral
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jonathan C Grima
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Rachel E Bennett
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Katharina Tepper
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Michael DeTure
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| | - Charles R Vanderburg
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Bianca T Corjuc
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sarah L DeVos
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jose Antonio Gonzalez
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jeannie Chew
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Svetlana Vidensky
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jerome Mertens
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Juan Troncoso
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE) and CAESAR Research Center, 53175 Bonn, Germany
| | | | | | | | - Susanne Wegmann
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
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20
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Identification of the Novel Nup188-brr7 Allele in a Screen for Cold-Sensitive mRNA Export Mutants in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2018; 8:2991-3003. [PMID: 30021831 PMCID: PMC6118305 DOI: 10.1534/g3.118.200447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The maturation and export of mRNA from the nucleus through the nuclear pore complex is critical for maintaining an appropriate proteome in all eukaryotic cells. Here we summarize a previously unpublished screen in S. cerevisiae that utilized an established dT50 in situ hybridization assay to identify cold-sensitive mutants that accumulated bulk poly A RNA in the nucleus. The screen identified seven mutants in six complementation groups, including the brr6-1 strain that we described previously. In addition to brr6-1, we identified novel alleles of the key transport gene GLE1 and NUP188, a component of the Nic96 nucleoporin complex. Notably, we show that the nup188-brr7 allele causes defects in select protein import pathways as well as mRNA export. Given recent structural and functional evidence linking the Nic96 complex to transport components, this mutant may be particularly useful to the transport community.
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21
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A SUMO-dependent feedback loop senses and controls the biogenesis of nuclear pore subunits. Nat Commun 2018; 9:1665. [PMID: 29695777 PMCID: PMC5916902 DOI: 10.1038/s41467-018-03673-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 03/05/2018] [Indexed: 11/29/2022] Open
Abstract
While the activity of multiprotein complexes is crucial for cellular metabolism, little is known about the mechanisms that collectively control the expression of their components. Here, we investigate the regulations targeting the biogenesis of the nuclear pore complex (NPC), the macromolecular assembly mediating nucleocytoplasmic exchanges. Systematic analysis of RNA-binding proteins interactomes, together with in vivo and in vitro assays, reveal that a subset of NPC mRNAs are specifically bound by Hek2, a yeast hnRNP K-like protein. Hek2-dependent translational repression and protein turnover are further shown to finely tune the levels of NPC subunits. Strikingly, mutations or physiological perturbations altering pore integrity decrease the levels of the NPC-associated SUMO protease Ulp1, and trigger the accumulation of sumoylated versions of Hek2 unable to bind NPC mRNAs. Our results support the existence of a quality control mechanism involving Ulp1 as a sensor of NPC integrity and Hek2 as a repressor of NPC biogenesis. The nuclear pore complex is crucial for mediating nucleocytoplasmic exchanges. Here the authors use budding yeast to reveal a mechanism responsible of maintaining nucleoporin homeostasis by sensing changes in the complex integrity and further altering the metabolism of the corresponding mRNAs.
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22
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Abstract
The ERK1 and ERK2 (ERK1/2) cascade is a central signaling pathway activated by a wide variety of extracellular agents that transmit the messages of G Protein Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Being such a central pathway, the activity of the cascade is well regulated, including by dynamic changes of the subcellular localization of components of the ERK1/2 cascade. In resting cells, ERK1/2 are localized in the cytosol due to their interactions with different anchoring proteins. After stimulation, ERK1/2 are phosphorylated by MEK1/2 on their regulatory TEY motif, which permits their detachment from the anchoring proteins. This detachment exposes ERK1/2 to additional phosphorylation on two serine residues (SPS motif) within the nuclear translocation signal (NTS) of the kinases. This additional phosphorylation allows ERK1/2 to interact with importin7, which consequently promotes their translocation to the nucleus. More studies are still required in order to better understand the mechanism and consequence of the nuclear translocation of ERK1/2. In this chapter, we describe some of the techniques used to study nuclear translocation of ERK1/2 in mammalian cells. We briefly mention methods such as digitonin permeabilization and cellular fractionation, as well as overexpression of reporter constructs. More thoroughly, we describe immunofluorescence, immunoprecipitation, and proximity ligation assay (PLA) approaches that are routinely used in our laboratory. Hopefully, the increase of knowledge based on these methods will open more opportunities for the identification of new therapeutic targets for diseases where the ERK1/2 cascade is dysregulated, such as cancer, neurodegenerative diseases, and diabetes.
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Affiliation(s)
- Denise A Berti
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Rony Seger
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, 76100, Israel.
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23
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Sellés J, Penrad-Mobayed M, Guillaume C, Fuger A, Auvray L, Faklaris O, Montel F. Nuclear pore complex plasticity during developmental process as revealed by super-resolution microscopy. Sci Rep 2017; 7:14732. [PMID: 29116248 PMCID: PMC5677124 DOI: 10.1038/s41598-017-15433-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/26/2017] [Indexed: 02/08/2023] Open
Abstract
Nuclear Pore Complex (NPC) is of paramount importance for cellular processes since it is the unique gateway for molecular exchange through the nucleus. Unraveling the modifications of the NPC structure in response to physiological cues, also called nuclear pore plasticity, is key to the understanding of the selectivity of this molecular machinery. As a step towards this goal, we use the optical super-resolution microscopy method called direct Stochastic Optical Reconstruction Microscopy (dSTORM), to analyze oocyte development impact on the internal structure and large-scale organization of the NPC. Staining of the FG-Nups proteins and the gp210 proteins allowed us to pinpoint a decrease of the global diameter by measuring the mean diameter of the central channel and the luminal ring of the NPC via autocorrelation image processing. Moreover, by using an angular and radial density function we show that development of the Xenopus laevis oocyte is correlated with a progressive decrease of the density of NPC and an ordering on a square lattice.
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Affiliation(s)
- Julien Sellés
- Matière et Systèmes Complexes, Université Paris Diderot/CNRS (UMR 7057), 75205, Paris, Cedex 13, France
- Institut Jacques Monod, Université Paris Diderot/CNRS, UMR 7592, 15 rue Hélène Brion, 75205, Paris, CEDEX 13, France
| | - May Penrad-Mobayed
- Institut Jacques Monod, Université Paris Diderot/CNRS, UMR 7592, 15 rue Hélène Brion, 75205, Paris, CEDEX 13, France
| | - Cyndélia Guillaume
- Matière et Systèmes Complexes, Université Paris Diderot/CNRS (UMR 7057), 75205, Paris, Cedex 13, France
| | - Alica Fuger
- Matière et Systèmes Complexes, Université Paris Diderot/CNRS (UMR 7057), 75205, Paris, Cedex 13, France
| | - Loïc Auvray
- Matière et Systèmes Complexes, Université Paris Diderot/CNRS (UMR 7057), 75205, Paris, Cedex 13, France
| | - Orestis Faklaris
- ImagoSeine core facility, Institut Jacques Monod, Université Paris Diderot/CNRS, UMR 7592, 15 rue Hélène Brion, 75205, Paris, CEDEX 13, France
| | - Fabien Montel
- Matière et Systèmes Complexes, Université Paris Diderot/CNRS (UMR 7057), 75205, Paris, Cedex 13, France.
- Univ Lyon, Ens de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69342, Lyon, France.
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24
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Moleiro L, Mell M, Bocanegra R, López-Montero I, Fouquet P, Hellweg T, Carrascosa J, Monroy F. Permeability modes in fluctuating lipid membranes with DNA-translocating pores. Adv Colloid Interface Sci 2017; 247:543-554. [PMID: 28735883 DOI: 10.1016/j.cis.2017.07.009] [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: 07/03/2017] [Revised: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 10/19/2022]
Abstract
Membrane pores can significantly alter not only the permeation dynamics of biological membranes but also their elasticity. Large membrane pores able to transport macromolecular contents represent an interesting model to test theoretical predictions that assign active-like (non-equilibrium) behavior to the permeability contributions to the enhanced membrane fluctuations existing in permeable membranes [Maneville et al. Phys. Rev. Lett. 82, 4356 (1999)]. Such high-amplitude active contributions arise from the forced transport of solvent and solutes through the open pores, which becomes even dominant at large permeability. In this paper, we present a detailed experimental analysis of the active shape fluctuations that appear in highly permeable lipid vesicles with large macromolecular pores inserted in the lipid membrane, which are a consequence of transport permeability events occurred in an osmotic gradient. The experimental results are found in quantitative agreement with theory, showing a remarkable dependence with the density of membrane pores and giving account of mechanical compliances and permeability rates that are compatible with the large size of the membrane pore considered. The presence of individual permeation events has been detected in the fluctuation time-series, from which a stochastic distribution of the permeation events compatible with a shot-noise has been deduced. The non-equilibrium character of the membrane fluctuations in a permeation field, even if the membrane pores are mere passive transporters, is clearly demonstrated. Finally, a bio-nano-technology outlook of the proposed synthetic concept is given on the context of prospective uses as active membrane DNA-pores exploitable in gen-delivery applications based on lipid vesicles.
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25
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Grima JC, Daigle JG, Arbez N, Cunningham KC, Zhang K, Ochaba J, Geater C, Morozko E, Stocksdale J, Glatzer JC, Pham JT, Ahmed I, Peng Q, Wadhwa H, Pletnikova O, Troncoso JC, Duan W, Snyder SH, Ranum LPW, Thompson LM, Lloyd TE, Ross CA, Rothstein JD. Mutant Huntingtin Disrupts the Nuclear Pore Complex. Neuron 2017; 94:93-107.e6. [PMID: 28384479 PMCID: PMC5595097 DOI: 10.1016/j.neuron.2017.03.023] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/30/2017] [Accepted: 03/13/2017] [Indexed: 01/01/2023]
Abstract
Huntington's disease (HD) is caused by an expanded CAG repeat in the Huntingtin (HTT) gene. The mechanism(s) by which mutant HTT (mHTT) causes disease is unclear. Nucleocytoplasmic transport, the trafficking of macromolecules between the nucleus and cytoplasm, is tightly regulated by nuclear pore complexes (NPCs) made up of nucleoporins (NUPs). Previous studies offered clues that mHTT may disrupt nucleocytoplasmic transport and a mutation of an NUP can cause HD-like pathology. Therefore, we evaluated the NPC and nucleocytoplasmic transport in multiple models of HD, including mouse and fly models, neurons transfected with mHTT, HD iPSC-derived neurons, and human HD brain regions. These studies revealed severe mislocalization and aggregation of NUPs and defective nucleocytoplasmic transport. HD repeat-associated non-ATG (RAN) translation proteins also disrupted nucleocytoplasmic transport. Additionally, overexpression of NUPs and treatment with drugs that prevent aberrant NUP biology also mitigated this transport defect and neurotoxicity, providing future novel therapy targets.
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Affiliation(s)
- Jonathan C Grima
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - J Gavin Daigle
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicolas Arbez
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathleen C Cunningham
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ke Zhang
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joseph Ochaba
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Charlene Geater
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Eva Morozko
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Jennifer Stocksdale
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Jenna C Glatzer
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jacqueline T Pham
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ishrat Ahmed
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qi Peng
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Harsh Wadhwa
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Olga Pletnikova
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Juan C Troncoso
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wenzhen Duan
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Solomon H Snyder
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Laura P W Ranum
- Center for NeuroGenetics, Departments of Molecular Genetics and Microbiology and Neurology, College of Medicine, Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Leslie M Thompson
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA
| | - Thomas E Lloyd
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christopher A Ross
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey D Rothstein
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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26
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Abstract
The nuclear pore complex (NPC) mediates the shuttle transport of macromolecules between the nucleus and cytoplasm in eukaryotic cells. The permeability barrier formed by intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG-Nups) in the NPC functions as the critical selective control for nucleocytoplasmic transport. Signal-independent small molecules (< 40 kDa) passively diffuse through the pore, but passage of large cargo molecules is inhibited unless they are chaperoned by nuclear transport receptors (NTRs). NTRs are capable of interacting with FG-Nups and guide the cargos to cross the barrier by facilitated diffusion. The native conformation of the FG-Nups permeability barrier and the competition among multiple NTRs interacting with this barrier in the native NPCs are the 2 core questions still being highly debated in the field. Recently, we applied high-speed super-resolution fluorescence microscopy to map out the natural structure of the FG-Nups barrier and determined the competition among multiple NTRs as they interact with the barrier in the native NPCs. In this extra-view article, we will review the current understanding in the configuration and function of FG-Nups barrier and highlight the new evidence obtained recently to answer the core questions in nucleocytoplasmic transport.
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Affiliation(s)
- Christina Li
- a Department of Biology , Temple University , Philadelphia , PA , USA
| | | | - Weidong Yang
- a Department of Biology , Temple University , Philadelphia , PA , USA
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27
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Prpar Mihevc S, Darovic S, Kovanda A, Bajc Česnik A, Župunski V, Rogelj B. Nuclear trafficking in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Brain 2016; 140:13-26. [PMID: 27497493 DOI: 10.1093/brain/aww197] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis and frontotemporal lobar degeneration are two ends of a phenotypic spectrum of disabling, relentlessly progressive and ultimately fatal diseases. A key characteristic of both conditions is the presence of TDP-43 (encoded by TARDBP) or FUS immunoreactive cytoplasmic inclusions in neuronal and glial cells. This cytoplasmic mislocalization of otherwise predominantly nuclear RNA binding proteins implies a perturbation of the nucleocytoplasmic shuttling as a possible event in the pathogenesis. Compromised nucleocytoplasmic shuttling has recently also been associated with a hexanucleotide repeat expansion mutation in C9orf72, which is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal lobar degeneration, and leads to accumulation of cytoplasmic TDP-43 inclusions. Mutation in C9orf72 may disrupt nucleocytoplasmic shuttling on the level of C9ORF72 protein, the transcribed hexanucleotide repeat RNA, and/or dipeptide repeat proteins translated form the hexanucleotide repeat RNA. These defects of nucleocytoplasmic shuttling may therefore, constitute the common ground of the underlying disease mechanisms in different molecular subtypes of amyotrophic lateral sclerosis and frontotemporal lobar degeneration.
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Affiliation(s)
- Sonja Prpar Mihevc
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Simona Darovic
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Anja Kovanda
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Ana Bajc Česnik
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Vera Župunski
- 2 Faculty of Chemistry and Chemical Technology, Večna pot 113, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Boris Rogelj
- 1 Department of Biotechnology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia .,2 Faculty of Chemistry and Chemical Technology, Večna pot 113, University of Ljubljana, SI-1000 Ljubljana, Slovenia.,3 Biomedical Research Institute BRIS, Puhova 10, SI-1000 Ljubljana, Slovenia
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28
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Zahn R, Osmanović D, Ehret S, Araya Callis C, Frey S, Stewart M, You C, Görlich D, Hoogenboom BW, Richter RP. A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies. eLife 2016; 5. [PMID: 27058170 PMCID: PMC4874776 DOI: 10.7554/elife.14119] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/07/2016] [Indexed: 11/13/2022] Open
Abstract
The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior - a key element for the transport selectivity of the NPC - was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface.
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Affiliation(s)
- Raphael Zahn
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain
| | - Dino Osmanović
- London Centre for Nanotechnology, University College London, London, United Kingdom.,Department of Physics and Astronomy, University College London, London, United Kingdom.,Department of Physics, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Severin Ehret
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain
| | | | - Steffen Frey
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Murray Stewart
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Changjiang You
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, United Kingdom.,Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Ralf P Richter
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain.,Laboratory of Interdisciplinary Physics, University Grenoble Alpes - CNRS, Grenoble, France.,Max-Planck-Institute for Intelligent Systems, Stuttgart, Germany
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29
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Blondot ML, Bruss V, Kann M. Intracellular transport and egress of hepatitis B virus. J Hepatol 2016; 64:S49-S59. [PMID: 27084037 DOI: 10.1016/j.jhep.2016.02.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/27/2016] [Accepted: 02/03/2016] [Indexed: 12/23/2022]
Abstract
Hepatitis B virus (HBV) replicates its genomic information in the nucleus via transcription and therefore has to deliver its partially double stranded DNA genome into the nucleus. Like other viruses with a nuclear replication phase, HBV genomes are transported inside the viral capsids first through the cytoplasm towards the nuclear envelope. Following the arrival at the nuclear pore, the capsids are transported through, using classical cellular nuclear import pathways. The arrest of nuclear import at the nucleoplasmic side of the nuclear pore is unique, however, and is where the capsids efficiently disassemble leading to genome release. In the latter phase of the infection, newly formed nucleocapsids in the cytosol have to move to budding sites at intracellular membranes carrying the three viral envelope proteins. Capsids containing single stranded nucleic acid are not enveloped, in contrast to empty and double stranded DNA containing capsids. A small linear domain in the large envelope protein and two areas on the capsid surface have been mapped, where point mutations strongly block nucleocapsid envelopment. It is possible that these domains are involved in the envelope--with capsid interactions driving the budding process. Like other enveloped viruses, HBV also uses the cellular endosomal sorting complexes required for transport (ESCRT) machinery for catalyzing budding through the membrane and away from the cytosol.
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Affiliation(s)
- Marie-Lise Blondot
- Univ. de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France; CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France
| | - Volker Bruss
- Institute for Virology, Helmholtz Zentrum München, Technische Universität Muenchen, Neuherberg, Germany
| | - Michael Kann
- Univ. de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France; CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, Bordeaux, France; CHU de Bordeaux, Bordeaux, France.
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30
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Boeynaems S, Bogaert E, Michiels E, Gijselinck I, Sieben A, Jovičić A, De Baets G, Scheveneels W, Steyaert J, Cuijt I, Verstrepen KJ, Callaerts P, Rousseau F, Schymkowitz J, Cruts M, Van Broeckhoven C, Van Damme P, Gitler AD, Robberecht W, Van Den Bosch L. Drosophila screen connects nuclear transport genes to DPR pathology in c9ALS/FTD. Sci Rep 2016; 6:20877. [PMID: 26869068 PMCID: PMC4751451 DOI: 10.1038/srep20877] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/11/2016] [Indexed: 12/12/2022] Open
Abstract
Hexanucleotide repeat expansions in C9orf72 are the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD) (c9ALS/FTD). Unconventional translation of these repeats produces dipeptide repeat proteins (DPRs) that may cause neurodegeneration. We performed a modifier screen in Drosophila and discovered a critical role for importins and exportins, Ran-GTP cycle regulators, nuclear pore components, and arginine methylases in mediating DPR toxicity. These findings provide evidence for an important role for nucleocytoplasmic transport in the pathogenic mechanism of c9ALS/FTD.
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Affiliation(s)
- Steven Boeynaems
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,VIB, Vesalius Research Center, Laboratory of Neurobiology, B-3000 Leuven, Belgium
| | - Elke Bogaert
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,VIB, Vesalius Research Center, Laboratory of Neurobiology, B-3000 Leuven, Belgium
| | - Emiel Michiels
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,VIB, Vesalius Research Center, Laboratory of Neurobiology, B-3000 Leuven, Belgium
| | - Ilse Gijselinck
- Department of Molecular Genetics, VIB, B-2610 Antwerp, Belgium.,Institute Born-Bunge, University of Antwerp, B-2610 Antwerp, Belgium
| | - Anne Sieben
- Department of Molecular Genetics, VIB, B-2610 Antwerp, Belgium.,Institute Born-Bunge, University of Antwerp, B-2610 Antwerp, Belgium.,Department of Neurology, University Hospital Ghent and University of Ghent, B-9000 Ghent, Belgium
| | - Ana Jovičić
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Greet De Baets
- Switch Laboratory, VIB, B-3000 Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Wendy Scheveneels
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,VIB, Vesalius Research Center, Laboratory of Neurobiology, B-3000 Leuven, Belgium
| | - Jolien Steyaert
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,VIB, Vesalius Research Center, Laboratory of Neurobiology, B-3000 Leuven, Belgium
| | - Ivy Cuijt
- Department of Molecular Genetics, VIB, B-2610 Antwerp, Belgium.,Institute Born-Bunge, University of Antwerp, B-2610 Antwerp, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory of Systems Biology, Gaston Geenslaan 1, B-3001 Leuven, Belgium.,KU Leuven - University of Leuven, Department of Microbial and Molecular Systems, Laboratory for Genetics and Genomics, Gaston Geenslaan 1, B-3001 Leuven, Belgium
| | - Patrick Callaerts
- KU Leuven - University of Leuven, Department of Human Genetics, Laboratory of Behavioral and Developmental Genetics, B-3000 Leuven, Belgium.,VIB Center for the Biology of Disease, B-3000 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB, B-3000 Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB, B-3000 Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium
| | - Marc Cruts
- Department of Molecular Genetics, VIB, B-2610 Antwerp, Belgium.,Institute Born-Bunge, University of Antwerp, B-2610 Antwerp, Belgium
| | - Christine Van Broeckhoven
- Department of Molecular Genetics, VIB, B-2610 Antwerp, Belgium.,Institute Born-Bunge, University of Antwerp, B-2610 Antwerp, Belgium
| | - Philip Van Damme
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,VIB, Vesalius Research Center, Laboratory of Neurobiology, B-3000 Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, B-3000 Leuven, Belgium
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Wim Robberecht
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,VIB, Vesalius Research Center, Laboratory of Neurobiology, B-3000 Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, B-3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- KU Leuven - University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), B-3000 Leuven, Belgium.,VIB, Vesalius Research Center, Laboratory of Neurobiology, B-3000 Leuven, Belgium
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31
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Faustino RS, Behfar A, Groenendyk J, Wyles SP, Niederlander N, Reyes S, Puceat M, Michalak M, Terzic A, Perez-Terzic C. Calreticulin secures calcium-dependent nuclear pore competency required for cardiogenesis. J Mol Cell Cardiol 2016; 92:63-74. [PMID: 26826378 DOI: 10.1016/j.yjmcc.2016.01.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 12/24/2022]
Abstract
Calreticulin deficiency causes myocardial developmental defects that culminate in an embryonic lethal phenotype. Recent studies have linked loss of this calcium binding chaperone to failure in myofibrillogenesis through an as yet undefined mechanism. The purpose of the present study was to identify cellular processes corrupted by calreticulin deficiency that precipitate dysregulation of cardiac myofibrillogenesis related to acquisition of cardiac phenotype. In an embryonic stem cell knockout model, calreticulin deficit (crt(-/-)) compromised nucleocytoplasmic transport of nuclear localization signal-dependent and independent pathways, disrupting nuclear import of the cardiac transcription factor MEF2C. The expression of nucleoporins and associated nuclear transport proteins in derived crt(-/-) cardiomyocytes revealed an abnormal nuclear pore complex (NPC) configuration. Altered protein content in crt(-/-) cells resulted in remodeled NPC architecture that caused decreased pore diameter and diminished probability of central channel occupancy versus wild type counterparts. Ionophore treatment of impaired calcium handling in crt(-/-) cells corrected nuclear pore microarchitecture and rescued nuclear import resulting in normalized myofibrillogenesis. Thus, calreticulin deficiency alters nuclear pore function and structure, impeding myofibrillogenesis in nascent cardiomyocytes through a calcium dependent mechanism. This essential role of calreticulin in nucleocytoplasmic communication competency ties its regulatory action with proficiency of cardiac myofibrillogenesis essential for proper cardiac development.
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Affiliation(s)
- Randolph S Faustino
- Center for Regenerative Medicine, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Atta Behfar
- Center for Regenerative Medicine, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Jody Groenendyk
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Saranya P Wyles
- Center for Regenerative Medicine, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Nicolas Niederlander
- Center for Regenerative Medicine, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Santiago Reyes
- Center for Regenerative Medicine, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | | | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Andre Terzic
- Center for Regenerative Medicine, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Carmen Perez-Terzic
- Center for Regenerative Medicine, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA; Department of Physical Medicine and Rehabilitation, Mayo Clinic, Rochester, MN, USA; Rehabilitation Research Center, Rochester, MN, USA.
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32
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Smith C, Lari A, Derrer CP, Ouwehand A, Rossouw A, Huisman M, Dange T, Hopman M, Joseph A, Zenklusen D, Weis K, Grunwald D, Montpetit B. In vivo single-particle imaging of nuclear mRNA export in budding yeast demonstrates an essential role for Mex67p. J Cell Biol 2015; 211:1121-30. [PMID: 26694837 PMCID: PMC4687877 DOI: 10.1083/jcb.201503135] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/17/2015] [Indexed: 11/22/2022] Open
Abstract
Many messenger RNA export proteins have been identified; yet the spatial and temporal activities of these proteins and how they determine directionality of messenger ribonucleoprotein (mRNP) complex export from the nucleus remain largely undefined. Here, the bacteriophage PP7 RNA-labeling system was used in Saccharomyces cerevisiae to follow single-particle mRNP export events with high spatial precision and temporal resolution. These data reveal that mRNP export, consisting of nuclear docking, transport, and cytoplasmic release from a nuclear pore complex (NPC), is fast (∼ 200 ms) and that upon arrival in the cytoplasm, mRNPs are frequently confined near the nuclear envelope. Mex67p functions as the principal mRNP export receptor in budding yeast. In a mex67-5 mutant, delayed cytoplasmic release from NPCs and retrograde transport of mRNPs was observed. This proves an essential role for Mex67p in cytoplasmic mRNP release and directionality of transport.
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Affiliation(s)
- Carlas Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Azra Lari
- Department of Cell Biology, University of Alberta, T6G 2H7 Edmonton, Alberta, Canada
| | | | - Anette Ouwehand
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Ammeret Rossouw
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Maximiliaan Huisman
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Thomas Dange
- Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Mark Hopman
- Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Aviva Joseph
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Daniel Zenklusen
- Departement de Biochimie et Medecine Moleculaire, Universite de Montreal, H3T 1J4 Montreal, Quebec, Canada
| | - Karsten Weis
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland Department of Cell and Developmental Biology, University of California, Berkeley, Berkeley, CA 94720
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605 Department Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, T6G 2H7 Edmonton, Alberta, Canada
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33
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Abstract
Breuer and Ohkura propose a negative regulatory loop within the nuclear pore complex (NPC) controlling the chromatin attachment state, in which Nup155 and Nup93 recruit Nup62 to suppress chromatin tethering by Nup155. 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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Morchoisne-Bolhy S, Geoffroy MC, Bouhlel IB, Alves A, Audugé N, Baudin X, Van Bortle K, Powers MA, Doye V. Intranuclear dynamics of the Nup107-160 complex. Mol Biol Cell 2015; 26:2343-56. [PMID: 25904327 PMCID: PMC4462950 DOI: 10.1091/mbc.e15-02-0060] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/14/2015] [Indexed: 12/11/2022] Open
Abstract
The Nup107-160 nuclear pore subcomplex (Y-complex) and the chromatin-binding nucleoporin Elys dynamically colocalize with Nup98 and the export factor CRM1 in nuclear GLFG bodies present in HeLa sublines. Thus, in addition to its structural role at the NPC and its mitotic functions, the Y-complex may also act inside the nucleus during interphase. Nup98 is a glycine-leucine-phenylalanine-glycine (GLFG) repeat–containing nucleoporin that, in addition to nuclear transport, contributes to multiple aspects of gene regulation. Previous studies revealed its dynamic localization within intranuclear structures known as GLFG bodies. Here we show that the mammalian Nup107-160 complex (Y-complex), a major scaffold module of the nuclear pore, together with its partner Elys, colocalizes with Nup98 in GLFG bodies. The frequency and size of GLFG bodies vary among HeLa sublines, and we find that an increased level of Nup98 is associated with the presence of bodies. Recruitment of the Y-complex and Elys into GLFG bodies requires the C-terminal domain of Nup98. During cell division, Y-Nup–containing GLFG bodies are disassembled in mitotic prophase, significantly ahead of nuclear pore disassembly. FRAP studies revealed that, unlike at nuclear pores, the Y-complex shuttles into and out of GLFG bodies. Finally, we show that within the nucleoplasm, a fraction of Nup107, a key component of the Y-complex, displays reduced mobility, suggesting interaction with other nuclear components. Together our data uncover a previously neglected intranuclear pool of the Y-complex that may underscore a yet-uncharacterized function of these nucleoporins inside the nucleus, even in cells that contain no detectable GLFG bodies.
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Affiliation(s)
| | - Marie-Claude Geoffroy
- Institut Jacques Monod, CNRS UMR7592-Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Imène B Bouhlel
- Institut Jacques Monod, CNRS UMR7592-Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Annabelle Alves
- Institut Jacques Monod, CNRS UMR7592-Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France Ecole Doctorale Gènes Génomes Cellules, Université Paris Sud, 91405 Orsay, France
| | - Nicolas Audugé
- Institut Jacques Monod, CNRS UMR7592-Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Xavier Baudin
- ImagoSeine Imaging Facility, Institut Jacques Monod, 75205 Paris, France
| | - Kevin Van Bortle
- Department of Cell Biology and Biochemistry, Cell and Developmental Biology Graduate Program, Emory University School of Medicine, Atlanta, GA 30322
| | - Maureen A Powers
- Department of Cell Biology and Biochemistry, Cell and Developmental Biology Graduate Program, Emory University School of Medicine, Atlanta, GA 30322
| | - Valérie Doye
- Institut Jacques Monod, CNRS UMR7592-Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
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Plessner M, Melak M, Chinchilla P, Baarlink C, Grosse R. Nuclear F-actin formation and reorganization upon cell spreading. J Biol Chem 2015; 290:11209-16. [PMID: 25759381 DOI: 10.1074/jbc.m114.627166] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Indexed: 12/30/2022] Open
Abstract
We recently discovered signal-regulated nuclear actin network assembly. However, in contrast to cytoplasmic actin regulation, polymeric nuclear actin structures and functions remain only poorly understood. Here we describe a novel molecular tool to visualize real-time nuclear actin dynamics by targeting the Actin-Chromobody-TagGFP to the nucleus, thus establishing a nuclear Actin-Chromobody. Interestingly, we observe nuclear actin polymerization into dynamic filaments upon cell spreading and fibronectin stimulation, both of which appear to be triggered by integrin signaling. Furthermore, we show that nucleoskeletal proteins such as the LINC (linker of nucleoskeleton and cytoskeleton) complex and components of the nuclear lamina couple cell spreading or integrin activation by fibronectin to nuclear actin polymerization. Spreading-induced nuclear actin polymerization results in serum response factor (SRF)-mediated transcription through nuclear retention of myocardin-related transcription factor A (MRTF-A). Our results reveal a signaling pathway, which links integrin activation by extracellular matrix interaction to nuclear actin polymerization through the LINC complex, and therefore suggest a role for nuclear actin polymerization in the context of cellular adhesion and mechanosensing.
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Affiliation(s)
- Matthias Plessner
- From the Institute of Pharmacology, Biochemical-Pharmacological Center (BPC), University of Marburg, Karl-von-Frisch-Strasse 1, 35043 Marburg, Germany
| | - Michael Melak
- From the Institute of Pharmacology, Biochemical-Pharmacological Center (BPC), University of Marburg, Karl-von-Frisch-Strasse 1, 35043 Marburg, Germany
| | - Pilar Chinchilla
- From the Institute of Pharmacology, Biochemical-Pharmacological Center (BPC), University of Marburg, Karl-von-Frisch-Strasse 1, 35043 Marburg, Germany
| | - Christian Baarlink
- From the Institute of Pharmacology, Biochemical-Pharmacological Center (BPC), University of Marburg, Karl-von-Frisch-Strasse 1, 35043 Marburg, Germany
| | - Robert Grosse
- From the Institute of Pharmacology, Biochemical-Pharmacological Center (BPC), University of Marburg, Karl-von-Frisch-Strasse 1, 35043 Marburg, Germany
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Sun L, Hartson SD, Matts RL. Identification of proteins associated with Aha1 in HeLa cells by quantitative proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:365-80. [PMID: 25614414 DOI: 10.1016/j.bbapap.2015.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/20/2014] [Accepted: 01/09/2015] [Indexed: 01/17/2023]
Abstract
The identification of the activator of heat shock protein 90 (Hsp90) ATPase's (Aha1) protein-protein interaction (PPI) network will provide critical insights into the relationship of Aha1 with multi-molecular complexes and shed light onto Aha1's interconnections with Hsp90-regulated biological functions. Flag-tagged Aha1 was over-expressed in HeLa cells and isolated by anti-Flag affinity pull downs, followed by trypsin digestion and identification co-adsorbing proteins by liquid chromatography-tandem mass spectroscopy (LC-MS/MS). A probability-based identification of Aha1 PPIs was generated from the LC-MS/MS analysis by using a relative quantification strategy, spectral counting (SC). By comparing the SC-based protein levels between Aha1 pull-down samples and negative controls, 164 Aha1-interacting proteins were identified that were quantitatively enriched in the pull-down samples over the controls. The identified Aha1-interacting proteins are involved in a wide number of intracellular bioprocesses, including DNA maintenance, chromatin structure, RNA processing, translation, nucleocytoplasmic and vesicle transport, among others. The interactions of 33 of the identified proteins with Aha1 were further confirmed by Western blotting, demonstrating the reliability of our affinity-purification-coupled quantitative SC-MS strategy. Our proteomic data suggests that Aha1 may participate in diverse biological pathways to facilitate Hsp90 chaperone functions in response to stress.
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Affiliation(s)
- Liang Sun
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert L Matts
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
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Bonnet A, Palancade B. Regulation of mRNA trafficking by nuclear pore complexes. Genes (Basel) 2014; 5:767-91. [PMID: 25184662 PMCID: PMC4198930 DOI: 10.3390/genes5030767] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 11/17/2022] Open
Abstract
Over the last two decades, multiple studies have explored the mechanisms governing mRNA export out of the nucleus, a crucial step in eukaryotic gene expression. During transcription and processing, mRNAs are assembled into messenger ribonucleoparticles (mRNPs). mRNPs are then exported through nuclear pore complexes (NPCs), which are large multiprotein assemblies made of several copies of a limited number of nucleoporins. A considerable effort has been put into the dissection of mRNA export through NPCs at both cellular and molecular levels, revealing the conserved contributions of a subset of nucleoporins in this process, from yeast to vertebrates. Several reports have also demonstrated the ability of NPCs to sort out properly-processed mRNPs for entry into the nuclear export pathway. Importantly, changes in mRNA export have been associated with post-translational modifications of nucleoporins or changes in NPC composition, depending on cell cycle progression, development or exposure to stress. How NPC modifications also impact on cellular mRNA export in disease situations, notably upon viral infection, is discussed.
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Affiliation(s)
- Amandine Bonnet
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, Paris F-75205, France.
| | - Benoit Palancade
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, Paris F-75205, France.
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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: 359] [Impact Index Per Article: 35.9] [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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Floch AG, Tareste D, Fuchs P, Chadrin A, Naciri I, Leger T, Schlenstedt G, Palancade B, Doye V. Nuclear pore targeting of the yeast Pom33 nucleoporin depends on karyopherin- and lipid-binding. J Cell Sci 2014; 128:305-16. [DOI: 10.1242/jcs.158915] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pom33 is an integral membrane protein of the yeast nuclear pore complex (NPC), required for proper NPC distribution and assembly. To characterize Pom33 NPC-targeting determinants, we performed immunoprecipitation experiments followed by mass spectrometry analyses. This identified a novel Pom33 partner, the nuclear import factor Kap123. In vitro experiments revealed a direct interaction between Pom33 C-terminal domain (CTD) and Kap123. In silico analysis predicted the presence of two amphipathic α-helices within Pom33-CTD. Circular dichroism and liposome co-flotation assays showed that this domain is able to fold into α-helices in the presence of liposomes and preferentially binds to highly curved lipid membranes. When expressed in yeast, under conditions abolishing Pom33-CTD membrane association, this domain behaves as a Kap123-dependent nuclear localization signal (NLS). While deletion of Pom33 C-terminal domain (Pom33ΔCTD-GFP) impairs Pom33 stability and NPC targeting, mutants affecting either Kap123 binding or the amphipathic properties of the α-helices do not display any detectable defect. However, combined impairment of lipid and Kap123 binding affects Pom33 targeting to NPCs. These data highlight the requirement of multiple determinants and mechanisms for proper NPC localization of Pom33.
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