1
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Keeley O, Coyne AN. Nuclear and degradative functions of the ESCRT-III pathway: implications for neurodegenerative disease. Nucleus 2024; 15:2349085. [PMID: 38700207 PMCID: PMC11073439 DOI: 10.1080/19491034.2024.2349085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024] Open
Abstract
The ESCRT machinery plays a pivotal role in membrane-remodeling events across multiple cellular processes including nuclear envelope repair and reformation, nuclear pore complex surveillance, endolysosomal trafficking, and neuronal pruning. Alterations in ESCRT-III functionality have been associated with neurodegenerative diseases including Frontotemporal Dementia (FTD), Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Disease (AD). In addition, mutations in specific ESCRT-III proteins have been identified in FTD/ALS. Thus, understanding how disruptions in the fundamental functions of this pathway and its individual protein components in the human central nervous system (CNS) may offer valuable insights into mechanisms underlying neurodegenerative disease pathogenesis and identification of potential therapeutic targets. In this review, we discuss ESCRT components, dynamics, and functions, with a focus on the ESCRT-III pathway. In addition, we explore the implications of altered ESCRT-III function for neurodegeneration with a primary emphasis on nuclear surveillance and endolysosomal trafficking within the CNS.
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Affiliation(s)
- Olivia Keeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alyssa N. Coyne
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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2
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Kotb NM, Ulukaya G, Chavan A, Nguyen SC, Proskauer L, Joyce EF, Hasson D, Jagannathan M, Rangan P. Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis. Genes Dev 2024; 38:436-454. [PMID: 38866556 PMCID: PMC11216175 DOI: 10.1101/gad.351402.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ cell genes during differentiation, and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we found that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ cell genes into a silenced state and activating a group of oocyte genes and nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, cross-talk between genome architecture and NPCs is essential for successful cell fate transitions.
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Affiliation(s)
- Noor M Kotb
- Department of Biomedical Sciences/Wadsworth Center, University at Albany State University of New York (SUNY), Albany, New York 12202, USA
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York 12202, USA
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
| | - Gulay Ulukaya
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ankita Chavan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8092 Zürich, Switzerland
| | - Son C Nguyen
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lydia Proskauer
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York 12202, USA
| | - Eric F Joyce
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dan Hasson
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Madhav Jagannathan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8092 Zürich, Switzerland
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA;
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3
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Dubey SK, Lloyd TE, Tapadia MG. Disrupted nuclear import of cell cycle proteins in Huntington's/PolyQ disease causes neurodevelopment defects in cellular and Drosophila model. Heliyon 2024; 10:e26393. [PMID: 38434042 PMCID: PMC10906312 DOI: 10.1016/j.heliyon.2024.e26393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/15/2024] [Accepted: 02/12/2024] [Indexed: 03/05/2024] Open
Abstract
Huntington's disease is caused by an expansion of CAG repeats in exon 1 of the huntingtin gene encoding an extended PolyQ tract within the Huntingtin protein (mHtt). This expansion results in selective degeneration of striatal medium spiny projection neurons in the basal ganglia. The mutation causes abnormalities during neurodevelopment in human and mouse models. Here, we report that mHtt/PolyQ aggregates inhibit the cell cycle in the Drosophila brain during development. PolyQ aggregates disrupt the nuclear pore complexes of the cells preventing the translocation of cell cycle proteins such as Cyclin E, E2F and PCNA from cytoplasm to the nucleus, thus affecting cell cycle progression. PolyQ aggregates also disrupt the nuclear pore complex and nuclear import in mHtt expressing mammalian CAD neurons. PolyQ toxicity and cell cycle defects can be restored by enhancing RanGAP-mediated nuclear import, suggesting a potential therapeutic approach for this disease.
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Affiliation(s)
- Sandeep Kumar Dubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Thomas E. Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madhu G. Tapadia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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4
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Huang P, Zhang X, Cheng Z, Wang X, Miao Y, Huang G, Fu YF, Feng X. The nuclear pore Y-complex functions as a platform for transcriptional regulation of FLOWERING LOCUS C in Arabidopsis. THE PLANT CELL 2024; 36:346-366. [PMID: 37877462 PMCID: PMC10827314 DOI: 10.1093/plcell/koad271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023]
Abstract
The nuclear pore complex (NPC) has multiple functions beyond the nucleo-cytoplasmic transport of large molecules. Subnuclear compartmentalization of chromatin is critical for gene expression in animals and yeast. However, the mechanism by which the NPC regulates gene expression is poorly understood in plants. Here we report that the Y-complex (Nup107-160 complex, a subcomplex of the NPC) self-maintains its nucleoporin homeostasis and modulates FLOWERING LOCUS C (FLC) transcription via changing histone modifications at this locus. We show that Y-complex nucleoporins are intimately associated with FLC chromatin through their interactions with histone H2A at the nuclear membrane. Fluorescence in situ hybridization assays revealed that Nup96, a Y-complex nucleoporin, enhances FLC positioning at the nuclear periphery. Nup96 interacted with HISTONE DEACETYLASE 6 (HDA6), a key repressor of FLC expression via histone modification, at the nuclear membrane to attenuate HDA6-catalyzed deposition at the FLC locus and change histone modifications. Moreover, we demonstrate that Y-complex nucleoporins interact with RNA polymerase II to increase its occupancy at the FLC locus, facilitating transcription. Collectively, our findings identify an attractive mechanism for the Y-complex in regulating FLC expression via tethering the locus at the nuclear periphery and altering its histone modification.
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Affiliation(s)
- Penghui Huang
- Zhejiang Lab, Research Institute of Intelligent Computing, Hangzhou 310012, China
- MARA Key Laboratory of Soybean Biology (Beijing), State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaomei Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyuan Cheng
- CAS Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Xu Wang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261325, China
| | - Yuchen Miao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Guowen Huang
- Department of Biological Sciences and Chemical Engineering, Hunan University of Science and Engineering, Yongzhou 425100, Hunan, China
| | - Yong-Fu Fu
- MARA Key Laboratory of Soybean Biology (Beijing), State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xianzhong Feng
- Zhejiang Lab, Research Institute of Intelligent Computing, Hangzhou 310012, China
- CAS Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
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5
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Raveh B, Eliasian R, Rashkovits S, Russel D, Hayama R, Sparks SE, Singh D, Lim R, Villa E, Rout MP, Cowburn D, Sali A. Integrative spatiotemporal map of nucleocytoplasmic transport. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.31.573409. [PMID: 38260487 PMCID: PMC10802240 DOI: 10.1101/2023.12.31.573409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The Nuclear Pore Complex (NPC) facilitates rapid and selective nucleocytoplasmic transport of molecules as large as ribosomal subunits and viral capsids. It is not clear how key emergent properties of this transport arise from the system components and their interactions. To address this question, we constructed an integrative coarse-grained Brownian dynamics model of transport through a single NPC, followed by coupling it with a kinetic model of Ran-dependent transport in an entire cell. The microscopic model parameters were fitted to reflect experimental data and theoretical information regarding the transport, without making any assumptions about its emergent properties. The resulting reductionist model is validated by reproducing several features of transport not used for its construction, such as the morphology of the central transporter, rates of passive and facilitated diffusion as a function of size and valency, in situ radial distributions of pre-ribosomal subunits, and active transport rates for viral capsids. The model suggests that the NPC functions essentially as a virtual gate whose flexible phenylalanine-glycine (FG) repeat proteins raise an entropy barrier to diffusion through the pore. Importantly, this core functionality is greatly enhanced by several key design features, including 'fuzzy' and transient interactions, multivalency, redundancy in the copy number of FG nucleoporins, exponential coupling of transport kinetics and thermodynamics in accordance with the transition state theory, and coupling to the energy-reliant RanGTP concentration gradient. These design features result in the robust and resilient rate and selectivity of transport for a wide array of cargo ranging from a few kilodaltons to megadaltons in size. By dissecting these features, our model provides a quantitative starting point for rationally modulating the transport system and its artificial mimics.
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6
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Schertzer M, Jullien L, Pinto AL, Calado RT, Revy P, Londoño-Vallejo A. Human RTEL1 Interacts with KPNB1 (Importin β) and NUP153 and Connects Nuclear Import to Nuclear Envelope Stability in S-Phase. Cells 2023; 12:2798. [PMID: 38132118 PMCID: PMC10741959 DOI: 10.3390/cells12242798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/29/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023] Open
Abstract
Regulator of TElomere Length Helicase 1 (RTEL1) is a helicase required for telomere maintenance and genome replication and repair. RTEL1 has been previously shown to participate in the nuclear export of small nuclear RNAs. Here we show that RTEL1 deficiency leads to a nuclear envelope destabilization exclusively in cells entering S-phase and in direct connection to origin firing. We discovered that inhibiting protein import also leads to similar, albeit non-cell cycle-related, nuclear envelope disruptions. Remarkably, overexpression of wild-type RTEL1, or of its C-terminal part lacking the helicase domain, protects cells against nuclear envelope anomalies mediated by protein import inhibition. We identified distinct domains in the C-terminus of RTEL1 essential for the interaction with KPNB1 (importin β) and NUP153, respectively, and we demonstrated that, on its own, the latter domain can promote the dynamic nuclear internalization of peptides that freely diffuse through the nuclear pore. Consistent with putative functions exerted in protein import, RTEL1 can be visualized on both sides of the nuclear pore using high-resolution microscopy. In all, our work points to an unanticipated, helicase-independent, role of RTEL1 in connecting both nucleocytoplasmic trafficking and nuclear envelope integrity to genome replication initiation in S-phase.
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Affiliation(s)
- Michael Schertzer
- Institut Curie, PSL Research University, CNRS, UMR3244, F-75005 Paris, France;
- Sorbonne Universités, CNRS, UMR3244, F-75005 Paris, France
| | - Laurent Jullien
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Contre le Cancer, F-75006 Paris, France; (L.J.); (P.R.)
- Paris Descartes–Sorbonne Paris Cité University, Imagine Institute, F-75015 Paris, France
| | - André L. Pinto
- Department of Medical Imaging, Hematology, and Oncology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto 14049-900, Brazil; (A.L.P.); (R.T.C.)
| | - Rodrigo T. Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto 14049-900, Brazil; (A.L.P.); (R.T.C.)
| | - Patrick Revy
- INSERM UMR 1163, Laboratory of Genome Dynamics in the Immune System, Equipe Labellisée Ligue Contre le Cancer, F-75006 Paris, France; (L.J.); (P.R.)
- Paris Descartes–Sorbonne Paris Cité University, Imagine Institute, F-75015 Paris, France
| | - Arturo Londoño-Vallejo
- Institut Curie, PSL Research University, CNRS, UMR3244, F-75005 Paris, France;
- Sorbonne Universités, CNRS, UMR3244, F-75005 Paris, France
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7
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Kotb NM, Ulukaya G, Chavan A, Nguyen SC, Proskauer L, Joyce E, Hasson D, Jagannathan M, Rangan P. Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567233. [PMID: 38014330 PMCID: PMC10680722 DOI: 10.1101/2023.11.15.567233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we find that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ-cell genes into a silenced state and activating a group of oocyte genes and Nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, crosstalk between genome architecture and NPCs is essential for successful cell fate transitions.
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Affiliation(s)
- Noor M. Kotb
- Department of Biomedical Sciences/Wadsworth Center, University at Albany SUNY, Albany, NY 12202
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Gulay Ulukaya
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) core
| | - Ankita Chavan
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8092 Zurich
| | - Son C. Nguyen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
| | - Lydia Proskauer
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202
- Current address: Biochemistry and Molecular Biology Department, University of Massachusetts Amherst, Amherst, MA 01003
| | - Eric Joyce
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
| | - Dan Hasson
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) core
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madhav Jagannathan
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8092 Zurich
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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8
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Yang Y, Guo L, Chen L, Gong B, Jia D, Sun Q. Nuclear transport proteins: structure, function, and disease relevance. Signal Transduct Target Ther 2023; 8:425. [PMID: 37945593 PMCID: PMC10636164 DOI: 10.1038/s41392-023-01649-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 11/12/2023] Open
Abstract
Proper subcellular localization is crucial for the functioning of biomacromolecules, including proteins and RNAs. Nuclear transport is a fundamental cellular process that regulates the localization of many macromolecules within the nuclear or cytoplasmic compartments. In humans, approximately 60 proteins are involved in nuclear transport, including nucleoporins that form membrane-embedded nuclear pore complexes, karyopherins that transport cargoes through these complexes, and Ran system proteins that ensure directed and rapid transport. Many of these nuclear transport proteins play additional and essential roles in mitosis, biomolecular condensation, and gene transcription. Dysregulation of nuclear transport is linked to major human diseases such as cancer, neurodegenerative diseases, and viral infections. Selinexor (KPT-330), an inhibitor targeting the nuclear export factor XPO1 (also known as CRM1), was approved in 2019 to treat two types of blood cancers, and dozens of clinical trials of are ongoing. This review summarizes approximately three decades of research data in this field but focuses on the structure and function of individual nuclear transport proteins from recent studies, providing a cutting-edge and holistic view on the role of nuclear transport proteins in health and disease. In-depth knowledge of this rapidly evolving field has the potential to bring new insights into fundamental biology, pathogenic mechanisms, and therapeutic approaches.
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Affiliation(s)
- Yang Yang
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lu Guo
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Chen
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bo Gong
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.
| | - Qingxiang Sun
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, China.
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9
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Penzo A, Dubarry M, Brocas C, Zheng M, Mangione RM, Rougemaille M, Goncalves C, Lautier O, Libri D, Simon MN, Géli V, Dubrana K, Palancade B. A R-loop sensing pathway mediates the relocation of transcribed genes to nuclear pore complexes. Nat Commun 2023; 14:5606. [PMID: 37730746 PMCID: PMC10511428 DOI: 10.1038/s41467-023-41345-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023] Open
Abstract
Nuclear pore complexes (NPCs) have increasingly recognized interactions with the genome, as exemplified in yeast, where they bind transcribed or damaged chromatin. By combining genome-wide approaches with live imaging of model loci, we uncover a correlation between NPC association and the accumulation of R-loops, which are genotoxic structures formed through hybridization of nascent RNAs with their DNA templates. Manipulating hybrid formation demonstrates that R-loop accumulation per se, rather than transcription or R-loop-dependent damages, is the primary trigger for relocation to NPCs. Mechanistically, R-loop-dependent repositioning involves their recognition by the ssDNA-binding protein RPA, and SUMO-dependent interactions with NPC-associated factors. Preventing R-loop-dependent relocation leads to lethality in hybrid-accumulating conditions, while NPC tethering of a model hybrid-prone locus attenuates R-loop-dependent genetic instability. Remarkably, this relocation pathway involves molecular factors similar to those required for the association of stalled replication forks with NPCs, supporting the existence of convergent mechanisms for sensing transcriptional and genotoxic stresses.
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Affiliation(s)
- Arianna Penzo
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Marion Dubarry
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue, 13273, Marseille, France
- Univ Lyon, Université Claude Bernard Lyon 1, INSA-Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, F-69622, Villeurbanne, France
| | - Clémentine Brocas
- Université Paris Cité, Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Myriam Zheng
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Raphaël M Mangione
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Mathieu Rougemaille
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Coralie Goncalves
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Ophélie Lautier
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France
| | - Domenico Libri
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Marie-Noëlle Simon
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue, 13273, Marseille, France
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR7258, Centre National de la Recherche Scientifique (CNRS), Aix Marseille University, Institut Paoli-Calmettes, Equipe Labélisée Ligue, 13273, Marseille, France
| | - Karine Dubrana
- Université Paris Cité, Université Paris-Saclay, INSERM, iRCM/IBFJ CEA, UMR Stabilité Génétique Cellules Souches et Radiations, Fontenay-aux-Roses, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013, Paris, France.
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10
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Cesur MF, Basile A, Patil KR, Çakır T. A new metabolic model of Drosophila melanogaster and the integrative analysis of Parkinson's disease. Life Sci Alliance 2023; 6:e202201695. [PMID: 37236669 PMCID: PMC10215973 DOI: 10.26508/lsa.202201695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
High conservation of the disease-associated genes between flies and humans facilitates the common use of Drosophila melanogaster to study metabolic disorders under controlled laboratory conditions. However, metabolic modeling studies are highly limited for this organism. We here report a comprehensively curated genome-scale metabolic network model of Drosophila using an orthology-based approach. The gene coverage and metabolic information of the draft model derived from a reference human model were expanded via Drosophila-specific KEGG and MetaCyc databases, with several curation steps to avoid metabolic redundancy and stoichiometric inconsistency. Furthermore, we performed literature-based curations to improve gene-reaction associations, subcellular metabolite locations, and various metabolic pathways. The performance of the resulting Drosophila model (8,230 reactions, 6,990 metabolites, and 2,388 genes), iDrosophila1 (https://github.com/SysBioGTU/iDrosophila), was assessed using flux balance analysis in comparison with the other currently available fly models leading to superior or comparable results. We also evaluated the transcriptome-based prediction capacity of iDrosophila1, where differential metabolic pathways during Parkinson's disease could be successfully elucidated. Overall, iDrosophila1 is promising to investigate system-level metabolic alterations in response to genetic and environmental perturbations.
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Affiliation(s)
- Müberra Fatma Cesur
- Systems Biology and Bioinformatics Program, Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
| | - Arianna Basile
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Kiran Raosaheb Patil
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Tunahan Çakır
- Systems Biology and Bioinformatics Program, Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey
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11
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Kim S, Phan S, Shaw TR, Ellisman MH, Veatch SL, Barmada SJ, Pappas SS, Dauer WT. TorsinA is essential for the timing and localization of neuronal nuclear pore complex biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538491. [PMID: 37162852 PMCID: PMC10168336 DOI: 10.1101/2023.04.26.538491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Nuclear pore complexes (NPCs) regulate information transfer between the nucleus and cytoplasm. NPC defects are linked to several neurological diseases, but the processes governing NPC biogenesis and spatial organization are poorly understood. Here, we identify a temporal window of strongly upregulated NPC biogenesis during neuronal maturation. We demonstrate that the AAA+ protein torsinA, whose loss of function causes the neurodevelopmental movement disorder DYT-TOR1A (DYT1) dystonia, coordinates NPC spatial organization during this period without impacting total NPC density. Using a new mouse line in which endogenous Nup107 is Halo-Tagged, we find that torsinA is essential for correct localization of NPC formation. In the absence of torsinA, the inner nuclear membrane buds excessively at sites of mislocalized, nascent NPCs, and NPC assembly completion is delayed. Our work implies that NPC spatial organization and number are independently regulated and suggests that torsinA is critical for the normal localization and assembly kinetics of NPCs.
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Affiliation(s)
- Sumin Kim
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Sébastien Phan
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA
| | - Thomas R. Shaw
- Department of Biophysics, University of Michigan, Ann Arbor, MI
| | - Mark H. Ellisman
- National Center for Microscopy and Imaging Research, Center for Research on Biological Systems, Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA
| | - Sarah L. Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, MI
| | - Sami J. Barmada
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI
- Department of Neurology, University of Michigan, Ann Arbor, MI
| | - Samuel S. Pappas
- Peter O’Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX
- Department of Neurology, UT Southwestern, Dallas, TX
| | - William T. Dauer
- Peter O’Donnell Jr. Brain Institute, UT Southwestern, Dallas, TX
- Department of Neurology, UT Southwestern, Dallas, TX
- Department of Neuroscience, UT Southwestern, Dallas, TX
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12
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Kumar MS, Stallworth KM, Murthy AC, Lim SM, Li N, Jain A, Munro JB, Fawzi NL, Lagier-Tourenne C, Bosco DA. Interactions between FUS and the C-terminal Domain of Nup62 are Sufficient for their Co-phase Separation into Amorphous Assemblies. J Mol Biol 2023; 435:167972. [PMID: 36690069 PMCID: PMC10329203 DOI: 10.1016/j.jmb.2023.167972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/29/2022] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
Deficient nucleocytoplasmic transport is emerging as a pathogenic feature of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), including in ALS caused by mutations in Fused in Sarcoma (FUS). Recently, both wild-type and ALS-linked mutant FUS were shown to directly interact with the phenylalanine-glycine (FG)-rich nucleoporin 62 (Nup62) protein, where FUS WT/ Nup62 interactions were enriched within the nucleus but ALS-linked mutant FUS/ Nup62 interactions were enriched within the cytoplasm of cells. Nup62 is a central channel Nup that has a prominent role in forming the selectivity filter within the nuclear pore complex and in regulating effective nucleocytoplasmic transport. Under conditions where FUS phase separates into liquid droplets in vitro, the addition of Nup62 caused the synergistic formation of amorphous assemblies containing both FUS and Nup62. Here, we examined the molecular determinants of this process using recombinant FUS and Nup62 proteins and biochemical approaches. We demonstrate that the structured C-terminal domain of Nup62 containing an alpha-helical coiled-coil region plays a dominant role in binding FUS and is sufficient for inducing the formation of FUS/Nup62 amorphous assemblies. In contrast, the natively unstructured, F/G repeat-rich N-terminal domain of Nup62 modestly contributed to FUS/Nup62 phase separation behavior. Expression of individual Nup62 domain constructs in human cells confirmed that the Nup62 C-terminal domain is essential for localization of the protein to the nuclear envelope. Our results raise the possibility that interactions between FUS and the C-terminal domain of Nup62 can influence the function of Nup62 under physiological and/or pathological conditions.
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Affiliation(s)
- Meenakshi Sundaram Kumar
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA; Biochemistry and Molecular Biotechnology Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Karly M Stallworth
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA
| | - Anastasia C Murthy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Su Min Lim
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Nan Li
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Aastha Jain
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James B Munro
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS at Mass General, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, MA 01605, USA.
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13
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Yang J, Griffin A, Qiang Z, Ren J. Organelle-targeted therapies: a comprehensive review on system design for enabling precision oncology. Signal Transduct Target Ther 2022; 7:379. [PMID: 36402753 PMCID: PMC9675787 DOI: 10.1038/s41392-022-01243-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/21/2022] Open
Abstract
Cancer is a major threat to human health. Among various treatment methods, precision therapy has received significant attention since the inception, due to its ability to efficiently inhibit tumor growth, while curtailing common shortcomings from conventional cancer treatment, leading towards enhanced survival rates. Particularly, organelle-targeted strategies enable precise accumulation of therapeutic agents in organelles, locally triggering organelle-mediated cell death signals which can greatly reduce the therapeutic threshold dosage and minimize side-effects. In this review, we comprehensively discuss history and recent advances in targeted therapies on organelles, specifically including nucleus, mitochondria, lysosomes and endoplasmic reticulum, while focusing on organelle structures, organelle-mediated cell death signal pathways, and design guidelines of organelle-targeted nanomedicines based on intervention mechanisms. Furthermore, a perspective on future research and clinical opportunities and potential challenges in precision oncology is presented. Through demonstrating recent developments in organelle-targeted therapies, we believe this article can further stimulate broader interests in multidisciplinary research and technology development for enabling advanced organelle-targeted nanomedicines and their corresponding clinic translations.
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Affiliation(s)
- Jingjing Yang
- grid.24516.340000000123704535Institute of Nano and Biopolymeric Materials, School of Materials Science and Engineering, Tongji University, 201804 Shanghai, China
| | - Anthony Griffin
- grid.267193.80000 0001 2295 628XSchool of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, MS 39406 USA
| | - Zhe Qiang
- grid.267193.80000 0001 2295 628XSchool of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, MS 39406 USA
| | - Jie Ren
- grid.24516.340000000123704535Institute of Nano and Biopolymeric Materials, School of Materials Science and Engineering, Tongji University, 201804 Shanghai, China
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14
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Richards L, Lord CL, Benton ML, Capra JA, Nordman JT. Nucleoporins facilitate ORC loading onto chromatin. Cell Rep 2022; 41:111590. [PMID: 36351393 PMCID: PMC10040217 DOI: 10.1016/j.celrep.2022.111590] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/10/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
The origin recognition complex (ORC) binds throughout the genome to initiate DNA replication. In metazoans, it is still unclear how ORC is targeted to specific loci to facilitate helicase loading and replication initiation. Here, we perform immunoprecipitations coupled with mass spectrometry for ORC2 in Drosophila embryos. Surprisingly, we find that ORC2 associates with multiple subunits of the Nup107-160 subcomplex of the nuclear pore. Bioinformatic analysis reveals that, relative to all modENCODE factors, nucleoporins are among the most enriched factors at ORC2 binding sites. Critically, depletion of the nucleoporin Elys, a member of the Nup107-160 complex, decreases ORC2 loading onto chromatin. Depleting Elys also sensitizes cells to replication fork stalling, which could reflect a defect in establishing dormant replication origins. Our work reveals a connection between ORC, replication initiation, and nucleoporins, suggesting a function for nucleoporins in metazoan replication initiation.
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Affiliation(s)
- Logan Richards
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Christopher L Lord
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | | | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, UCSF, San Francisco, CA 94143, USA
| | - Jared T Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA.
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15
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Bierzynska A, Bull K, Miellet S, Dean P, Neal C, Colby E, McCarthy HJ, Hegde S, Sinha MD, Bugarin Diz C, Stirrups K, Megy K, Mapeta R, Penkett C, Marsh S, Forrester N, Afzal M, Stark H, BioResource NIHR, Williams M, Welsh GI, Koziell AB, Hartley PS, Saleem MA. Exploring the relevance of NUP93 variants in steroid-resistant nephrotic syndrome using next generation sequencing and a fly kidney model. Pediatr Nephrol 2022; 37:2643-2656. [PMID: 35211795 PMCID: PMC9489583 DOI: 10.1007/s00467-022-05440-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 12/10/2021] [Accepted: 12/21/2021] [Indexed: 10/24/2022]
Abstract
BACKGROUND Variants in genes encoding nuclear pore complex (NPC) proteins are a newly identified cause of paediatric steroid-resistant nephrotic syndrome (SRNS). Recent reports describing NUP93 variants suggest these could be a significant cause of paediatric onset SRNS. We report NUP93 cases in the UK and demonstrate in vivo functional effects of Nup93 depletion in a fly (Drosophila melanogaster) nephrocyte model. METHODS Three hundred thirty-seven paediatric SRNS patients from the National cohort of patients with Nephrotic Syndrome (NephroS) were whole exome and/or whole genome sequenced. Patients were screened for over 70 genes known to be associated with Nephrotic Syndrome (NS). D. melanogaster Nup93 knockdown was achieved by RNA interference using nephrocyte-restricted drivers. RESULTS Six novel homozygous and compound heterozygous NUP93 variants were detected in 3 sporadic and 2 familial paediatric onset SRNS characterised histologically by focal segmental glomerulosclerosis (FSGS) and progressing to kidney failure by 12 months from clinical diagnosis. Silencing of the two orthologs of human NUP93 expressed in D. melanogaster, Nup93-1, and Nup93-2 resulted in significant signal reduction of up to 82% in adult pericardial nephrocytes with concomitant disruption of NPC protein expression. Additionally, nephrocyte morphology was highly abnormal in Nup93-1 and Nup93-2 silenced flies surviving to adulthood. CONCLUSION We expand the spectrum of NUP93 variants detected in paediatric onset SRNS and demonstrate its incidence within a national cohort. Silencing of either D. melanogaster Nup93 ortholog caused a severe nephrocyte phenotype, signaling an important role for the nucleoporin complex in podocyte biology. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Agnieszka Bierzynska
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Katherine Bull
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sara Miellet
- Department of Life and Environmental Science, Bournemouth University, Talbot Campus, Fern Barrow, Poole, Dorset BH12 5BB England, UK
- Illawarra Health and Medical Research Institute, Molecular Horizons and School of Medicine, University of Wollongong, Wollongong, Australia
| | - Philip Dean
- Bristol Genetics Laboratory, North Bristol National Health Service Trust, Bristol, UK
| | - Chris Neal
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Elizabeth Colby
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Hugh J. McCarthy
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
- School of Medicine, University of Sydney and Children’s Hospital at Westmead, Westmead, Australia
| | - Shivaram Hegde
- Children’s Kidney Centre, University Hospital of Wales, Cardiff, UK
| | - Manish D. Sinha
- Department of Paediatric Nephrology, Evelina London Children’s Hospital, Guy’s and St, Thomas’ Hospital, London, UK
| | - Carmen Bugarin Diz
- School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, SE1 7EH UK
| | - Kathleen Stirrups
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
| | - Karyn Megy
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Rutendo Mapeta
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Chris Penkett
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
| | - Sarah Marsh
- Bristol Genetics Laboratory, North Bristol National Health Service Trust, Bristol, UK
| | - Natalie Forrester
- Illawarra Health and Medical Research Institute, Molecular Horizons and School of Medicine, University of Wollongong, Wollongong, Australia
| | - Maryam Afzal
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Hannah Stark
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
| | - NIHR BioResource
- NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, CB2 0QQ UK
| | - Maggie Williams
- Bristol Genetics Laboratory, North Bristol National Health Service Trust, Bristol, UK
| | - Gavin I. Welsh
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
| | - Ania B. Koziell
- Department of Paediatric Nephrology, Evelina London Children’s Hospital, Guy’s and St, Thomas’ Hospital, London, UK
- School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King’s College London, London, SE1 7EH UK
| | - Paul S. Hartley
- Department of Life and Environmental Science, Bournemouth University, Talbot Campus, Fern Barrow, Poole, Dorset BH12 5BB England, UK
| | - Moin A. Saleem
- Bristol Renal and Children’s Renal Unit, Bristol Medical School, University of Bristol, Whitson Street, Bristol, BS1 3NY UK
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16
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Lüdke D, Yan Q, Rohmann PFW, Wiermer M. NLR we there yet? Nucleocytoplasmic coordination of NLR-mediated immunity. THE NEW PHYTOLOGIST 2022; 236:24-42. [PMID: 35794845 DOI: 10.1111/nph.18359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Plant intracellular nucleotide-binding leucine-rich repeat immune receptors (NLRs) perceive the activity of pathogen-secreted effector molecules that, when undetected, promote colonisation of hosts. Signalling from activated NLRs converges with and potentiates downstream responses from activated pattern recognition receptors (PRRs) that sense microbial signatures at the cell surface. Efficient signalling of both receptor branches relies on the host cell nucleus as an integration point for transcriptional reprogramming, and on the macromolecular transport processes that mediate the communication between cytoplasm and nucleoplasm. Studies on nuclear pore complexes (NPCs), the nucleoporin proteins (NUPs) that compose NPCs, and nuclear transport machinery constituents that control nucleocytoplasmic transport, have revealed that they play important roles in regulating plant immune responses. Here, we discuss the contributions of nucleoporins and nuclear transport receptor (NTR)-mediated signal transduction in plant immunity with an emphasis on NLR immune signalling across the nuclear compartment boundary and within the nucleus. We also highlight and discuss cytoplasmic and nuclear functions of NLRs and their signalling partners and further consider the potential implications of NLR activation and resistosome formation in both cellular compartments for mediating plant pathogen resistance and programmed host cell death.
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Affiliation(s)
- Daniel Lüdke
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Julia-Lermontowa-Weg 3, 37077, Goettingen, Germany
| | - Qiqi Yan
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Julia-Lermontowa-Weg 3, 37077, Goettingen, Germany
| | - Philipp F W Rohmann
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Julia-Lermontowa-Weg 3, 37077, Goettingen, Germany
| | - Marcel Wiermer
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Julia-Lermontowa-Weg 3, 37077, Goettingen, Germany
- Biochemistry of Plant-Microbe Interactions, Dahlem Centre of Plant Sciences, Institute of Biology, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195, Berlin, Germany
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17
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Dutta S, Polavaram NS, Islam R, Bhattacharya S, Bodas S, Mayr T, Roy S, Albala SAY, Toma MI, Darehshouri A, Borkowetz A, Conrad S, Fuessel S, Wirth M, Baretton GB, Hofbauer LC, Ghosh P, Pienta KJ, Klinkebiel DL, Batra SK, Muders MH, Datta K. Neuropilin-2 regulates androgen-receptor transcriptional activity in advanced prostate cancer. Oncogene 2022; 41:3747-3760. [PMID: 35754042 PMCID: PMC9979947 DOI: 10.1038/s41388-022-02382-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 01/22/2023]
Abstract
Aberrant transcriptional activity of androgen receptor (AR) is one of the dominant mechanisms for developing of castration-resistant prostate cancer (CRPC). Analyzing AR-transcriptional complex related to CRPC is therefore important towards understanding the mechanism of therapy resistance. While studying its mechanism, we observed that a transmembrane protein called neuropilin-2 (NRP2) plays a contributory role in forming a novel AR-transcriptional complex containing nuclear pore proteins. Using immunogold electron microscopy, high-resolution confocal microscopy, chromatin immunoprecipitation, proteomics, and other biochemical techniques, we delineated the molecular mechanism of how a specific splice variant of NRP2 becomes sumoylated upon ligand stimulation and translocates to the inner nuclear membrane. This splice variant of NRP2 then stabilizes the complex between AR and nuclear pore proteins to promote CRPC specific gene expression. Both full-length and splice variants of AR have been identified in this specific transcriptional complex. In vitro cell line-based assays indicated that depletion of NRP2 not only destabilizes the AR-nuclear pore protein interaction but also inhibits the transcriptional activities of AR. Using an in vivo bone metastasis model, we showed that the inhibition of NRP2 led to the sensitization of CRPC cells toward established anti-AR therapies such as enzalutamide. Overall, our finding emphasize the importance of combinatorial inhibition of NRP2 and AR as an effective therapeutic strategy against treatment refractory prostate cancer.
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Affiliation(s)
- Samikshan Dutta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Navatha Shree Polavaram
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ridwan Islam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sreyashi Bhattacharya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sanika Bodas
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Thomas Mayr
- Rudolf Becker Laboratory for Prostate Cancer Research, Medical Faculty, University of Bonn, Germany,Institute of Pathology, Medical Faculty, University of Bonn, Germany,Institute of Pathology, Technische Universitaet Dresden, Dresden, Germany
| | - Sohini Roy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Marieta I. Toma
- Institute of Pathology, Medical Faculty, University of Bonn, Germany,Institute of Pathology, Technische Universitaet Dresden, Dresden, Germany
| | - Anza Darehshouri
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Angelika Borkowetz
- Department of Urology, Technische Universitaet Dresden, Dresden, Germany
| | - Stefanie Conrad
- Division of Endocrinology and Metabolic Bone Diseases, Department of Medicine III, Technische Universitaet Dresden, Dresden, Germany,Center for Healthy Aging, Technische Universitaet Dresden, Dresden, Germany
| | - Susanne Fuessel
- Department of Urology, Technische Universitaet Dresden, Dresden, Germany
| | - Manfred Wirth
- Department of Urology, Technische Universitaet Dresden, Dresden, Germany
| | - Gustavo B. Baretton
- Institute of Pathology, Technische Universitaet Dresden, Dresden, Germany,German Cancer Consortium (DKTK), partner site Dresden and German Research Center (DKFZ), Heidelberg, Germany,Tumor and Normal Tissue Bank of the University Cancer Center (UCC), University Hospital and Faculty of Medicine, Technische Universitaet Dresden, Germany
| | - Lorenz C. Hofbauer
- Division of Endocrinology and Metabolic Bone Diseases, Department of Medicine III, Technische Universitaet Dresden, Dresden, Germany,Center for Healthy Aging, Technische Universitaet Dresden, Dresden, Germany,German Cancer Consortium (DKTK), partner site Dresden and German Research Center (DKFZ), Heidelberg, Germany
| | - Paramita Ghosh
- Department of Biochemistry and Molecular Medicine, University of California Davis
| | - Kenneth J. Pienta
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David L Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michael H. Muders
- Rudolf Becker Laboratory for Prostate Cancer Research, Medical Faculty, University of Bonn, Germany,Institute of Pathology, Medical Faculty, University of Bonn, Germany,Institute of Pathology, Technische Universitaet Dresden, Dresden, Germany
| | - Kaustubh Datta
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA.
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18
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Sawh AN, Mango SE. Chromosome organization in 4D: insights from C. elegans development. Curr Opin Genet Dev 2022; 75:101939. [PMID: 35759905 DOI: 10.1016/j.gde.2022.101939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 05/20/2022] [Accepted: 05/27/2022] [Indexed: 11/03/2022]
Abstract
Eukaryotic genome organization is ordered and multilayered, from the nucleosome to chromosomal scales. These layers are not static during development, but are remodeled over time and between tissues. Thus, animal model studies with high spatiotemporal resolution are necessary to understand the various forms and functions of genome organization in vivo. In C. elegans, sequencing- and imaging-based advances have provided insight on how histone modifications, regulatory elements, and large-scale chromosome conformations are established and changed. Recent observations include unexpected physiological roles for topologically associating domains, different roles for the nuclear lamina at different chromatin scales, cell-type-specific enhancer and promoter regulatory grammars, and prevalent compartment variability in early development. Here, we summarize these and other recent findings in C. elegans, and suggest future avenues of research to enrich our in vivo knowledge of the forms and functions of nuclear organization.
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Affiliation(s)
- Ahilya N Sawh
- Biozentrum, University of Basel, 4056 Basel-Stadt, Switzerland.
| | - Susan E Mango
- Biozentrum, University of Basel, 4056 Basel-Stadt, Switzerland.
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19
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Gomar-Alba M, Pozharskaia V, Cichocki B, Schaal C, Kumar A, Jacquel B, Charvin G, Igual JC, Mendoza M. Nuclear pore complex acetylation regulates mRNA export and cell cycle commitment in budding yeast. EMBO J 2022; 41:e110271. [PMID: 35735140 PMCID: PMC9340480 DOI: 10.15252/embj.2021110271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 11/27/2022] Open
Abstract
Nuclear pore complexes (NPCs) mediate communication between the nucleus and the cytoplasm, and regulate gene expression by interacting with transcription and mRNA export factors. Lysine acetyltransferases (KATs) promote transcription through acetylation of chromatin‐associated proteins. We find that Esa1, the KAT subunit of the yeast NuA4 complex, also acetylates the nuclear pore basket component Nup60 to promote mRNA export. Acetylation of Nup60 recruits the mRNA export factor Sac3, the scaffolding subunit of the Transcription and Export 2 (TREX‐2) complex, to the nuclear basket. The Esa1‐mediated nuclear export of mRNAs in turn promotes entry into S phase, which is inhibited by the Hos3 deacetylase in G1 daughter cells to restrain their premature commitment to a new cell division cycle. This mechanism is not only limited to G1/S‐expressed genes but also inhibits the expression of the nutrient‐regulated GAL1 gene specifically in daughter cells. Overall, these results reveal how acetylation can contribute to the functional plasticity of NPCs in mother and daughter yeast cells. In addition, our work demonstrates dual gene expression regulation by the evolutionarily conserved NuA4 complex, at the level of transcription and at the stage of mRNA export by modifying the nucleoplasmic entrance to nuclear pores.
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Affiliation(s)
- Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Spain
| | - Vasilisa Pozharskaia
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Bogdan Cichocki
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Celia Schaal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Arun Kumar
- Department of Cell Biology, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Basile Jacquel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - J Carlos Igual
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, Burjassot, Spain
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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20
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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: 123] [Impact Index Per Article: 61.5] [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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21
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Coyne AN, Rothstein JD. Nuclear pore complexes - a doorway to neural injury in neurodegeneration. Nat Rev Neurol 2022; 18:348-362. [PMID: 35488039 PMCID: PMC10015220 DOI: 10.1038/s41582-022-00653-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 12/13/2022]
Abstract
The genetic underpinnings and end-stage pathological hallmarks of neurodegenerative diseases are increasingly well defined, but the cellular pathophysiology of disease initiation and propagation remains poorly understood, especially in sporadic forms of these diseases. Altered nucleocytoplasmic transport is emerging as a prominent pathomechanism of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer disease, frontotemporal dementia and Huntington disease. The nuclear pore complex (NPC) and interactions between its individual nucleoporin components and nuclear transport receptors regulate nucleocytoplasmic transport, as well as genome organization and gene expression. Specific nucleoporin abnormalities have been identified in sporadic and familial forms of neurodegenerative disease, and these alterations are thought to contribute to disrupted nucleocytoplasmic transport. The specific nucleoporins and nucleocytoplasmic transport proteins that have been linked to different neurodegenerative diseases are partially distinct, suggesting that NPC injury contributes to the cellular specificity of neurodegenerative disease and could be an early initiator of the pathophysiological cascades that underlie neurodegenerative disease. This concept is consistent with the fact that rare genetic mutations in some nucleoporins cause cell-type-specific neurological disease. In this Review, we discuss nucleoporin and NPC disruptions and consider their impact on cellular function and the pathophysiology of neurodegenerative disease.
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Affiliation(s)
- Alyssa N Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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22
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A Nuclear Belt Fastens on Neural Cell Fate. Cells 2022; 11:cells11111761. [PMID: 35681456 PMCID: PMC9179901 DOI: 10.3390/cells11111761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/20/2022] [Accepted: 05/21/2022] [Indexed: 12/22/2022] Open
Abstract
Successful embryonic and adult neurogenesis require proliferating neural stem and progenitor cells that are intrinsically and extrinsically guided into a neuronal fate. In turn, migration of new-born neurons underlies the complex cytoarchitecture of the brain. Proliferation and migration are therefore essential for brain development, homeostasis and function in adulthood. Among several tightly regulated processes involved in brain formation and function, recent evidence points to the nuclear envelope (NE) and NE-associated components as critical new contributors. Classically, the NE was thought to merely represent a barrier mediating selective exchange between the cytoplasm and nucleoplasm. However, research over the past two decades has highlighted more sophisticated and diverse roles for NE components in progenitor fate choice and migration of their progeny by tuning gene expression via interactions with chromatin, transcription factors and epigenetic factors. Defects in NE components lead to neurodevelopmental impairments, whereas age-related changes in NE components are proposed to influence neurodegenerative diseases. Thus, understanding the roles of NE components in brain development, maintenance and aging is likely to reveal new pathophysiological mechanisms for intervention. Here, we review recent findings for the previously underrepresented contribution of the NE in neuronal commitment and migration, and envision future avenues for investigation.
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23
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Using Single Molecule RNA FISH to Determine Nuclear Export and Transcription Phenotypes in Drosophila Tissues. Methods Mol Biol 2022; 2502:113-125. [PMID: 35412235 DOI: 10.1007/978-1-0716-2337-4_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single molecule RNA fluorescence in situ hybridization (smRNA FISH) is a widely used method for examining cellular localization of RNA and assessing gene expression outputs. The Nuclear Pore Complex (NPC) is a nuclear macro-complex known to both mediate nucleocytoplasmic transport and influence transcription via interactions with chromatin. Consequently, depletion of NPC proteins can result in defects in either transcription or nuclear export of mRNA. To distinguish between these two different functions of NPC components, it is preferable to analyze transcription and mRNA export simultaneously or in the same cell. Here, we present a smRNA FISH protocol with downstream custom MATLAB image analysis for application in Drosophila larval salivary gland tissues. This method can detect both nuclear export and transcriptional phenotypes in the same cell and as a single assay, and can be adapted to many other cell types and organisms.
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24
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Pascual-Garcia P, Little SC, Capelson M. Nup98-dependent transcriptional memory is established independently of transcription. eLife 2022; 11:e63404. [PMID: 35289742 PMCID: PMC8923668 DOI: 10.7554/elife.63404] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/26/2022] [Indexed: 12/31/2022] Open
Abstract
Cellular ability to mount an enhanced transcriptional response upon repeated exposure to external cues is termed transcriptional memory, which can be maintained epigenetically through cell divisions and can depend on a nuclear pore component Nup98. The majority of mechanistic knowledge on transcriptional memory has been derived from bulk molecular assays. To gain additional perspective on the mechanism and contribution of Nup98 to memory, we used single-molecule RNA FISH (smFISH) to examine the dynamics of transcription in Drosophila cells upon repeated exposure to the steroid hormone ecdysone. We combined smFISH with mathematical modeling and found that upon hormone exposure, cells rapidly activate a low-level transcriptional response, but simultaneously begin a slow transition into a specialized memory state characterized by a high rate of expression. Strikingly, our modeling predicted that this transition between non-memory and memory states is independent of the transcription stemming from initial activation. We confirmed this prediction experimentally by showing that inhibiting transcription during initial ecdysone exposure did not interfere with memory establishment. Together, our findings reveal that Nup98's role in transcriptional memory is to stabilize the forward rate of conversion from low to high expressing state, and that induced genes engage in two separate behaviors - transcription itself and the establishment of epigenetically propagated transcriptional memory.
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Affiliation(s)
- Pau Pascual-Garcia
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Shawn C Little
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Maya Capelson
- Department of Cell and Developmental Biology, Penn Epigenetics Institute, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
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25
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Wu X, Han J, Guo C. Function of Nuclear Pore Complexes in Regulation of Plant Defense Signaling. Int J Mol Sci 2022; 23:ijms23063031. [PMID: 35328452 PMCID: PMC8953349 DOI: 10.3390/ijms23063031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/06/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
In eukaryotes, the nucleus is the regulatory center of cytogenetics and metabolism, and it is critical for fundamental biological processes, including DNA replication and transcription, protein synthesis, and biological macromolecule transportation. The eukaryotic nucleus is surrounded by a lipid bilayer called the nuclear envelope (NE), which creates a microenvironment for sophisticated cellular processes. The NE is perforated by the nuclear pore complex (NPC), which is the channel for biological macromolecule bi-directional transport between the nucleus and cytoplasm. It is well known that NPC is the spatial designer of the genome and the manager of genomic function. Moreover, the NPC is considered to be a platform for the continual adaptation and evolution of eukaryotes. So far, a number of nucleoporins required for plant-defense processes have been identified. Here, we first provide an overview of NPC organization in plants, and then discuss recent findings in the plant NPC to elaborate on and dissect the distinct defensive functions of different NPC subcomponents in plant immune defense, growth and development, hormone signaling, and temperature response. Nucleoporins located in different components of NPC have their unique functions, and the link between the NPC and nucleocytoplasmic trafficking promotes crosstalk of different defense signals in plants. It is necessary to explore appropriate components of the NPC as potential targets for the breeding of high-quality and broad spectrum resistance crop varieties.
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Affiliation(s)
- Xi Wu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China;
| | - Junyou Han
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun 130062, China;
- Correspondence: (J.H.); (C.G.)
| | - Changkui Guo
- Laboratory of Plant Molecular and Developmental Biology, Zhejiang A & F University, Hangzhou 311300, China
- Correspondence: (J.H.); (C.G.)
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26
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Shared genetic loci for body fat storage and adipocyte lipolysis in humans. Sci Rep 2022; 12:3666. [PMID: 35256633 PMCID: PMC8901764 DOI: 10.1038/s41598-022-07291-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
Total body fat and central fat distribution are heritable traits and well-established predictors of adverse metabolic outcomes. Lipolysis is the process responsible for the hydrolysis of triacylglycerols stored in adipocytes. To increase our understanding of the genetic regulation of body fat distribution and total body fat, we set out to determine if genetic variants associated with body mass index (BMI) or waist-hip-ratio adjusted for BMI (WHRadjBMI) in genome-wide association studies (GWAS) mediate their effect by influencing adipocyte lipolysis. We utilized data from the recent GWAS of spontaneous and isoprenaline-stimulated lipolysis in the unique GENetics of Adipocyte Lipolysis (GENiAL) cohort. GENiAL consists of 939 participants who have undergone abdominal subcutaneous adipose biopsy for the determination of spontaneous and isoprenaline-stimulated lipolysis in adipocytes. We report 11 BMI and 15 WHRadjBMI loci with SNPs displaying nominal association with lipolysis and allele-dependent gene expression in adipose tissue according to in silico analysis. Functional evaluation of candidate genes in these loci by small interfering RNAs (siRNA)-mediated knock-down in adipose-derived stem cells identified ZNF436 and NUP85 as intrinsic regulators of lipolysis consistent with the associations observed in the clinical cohorts. Furthermore, candidate genes in another BMI-locus (STX17) and two more WHRadjBMI loci (NID2, GGA3, GRB2) control lipolysis alone, or in conjunction with lipid storage, and may hereby be involved in genetic control of body fat. The findings expand our understanding of how genetic variants mediate their impact on the complex traits of fat storage and distribution.
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27
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Zhao JS, Shi S, Qu HY, Keckesova Z, Cao ZJ, Yang LX, Yu X, Feng L, Shi Z, Krakowiak J, Mao RY, Shen YT, Fan YM, Fu TM, Ye C, Xu D, Gao X, You J, Li W, Liang T, Lu Z, Feng YX. Glutamine synthetase licenses APC/C-mediated mitotic progression to drive cell growth. Nat Metab 2022; 4:239-253. [PMID: 35145325 DOI: 10.1038/s42255-021-00524-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 12/22/2021] [Indexed: 11/09/2022]
Abstract
Tumors can reprogram the functions of metabolic enzymes to fuel malignant growth; however, beyond their conventional functions, key metabolic enzymes have not been found to directly govern cell mitosis. Here, we report that glutamine synthetase (GS) promotes cell proliferation by licensing mitotic progression independently of its metabolic function. GS depletion, but not impairment of its enzymatic activity, results in mitotic arrest and multinucleation across multiple lung and liver cancer cell lines, patient-derived organoids and xenografted tumors. Mechanistically, GS directly interacts with the nuclear pore protein NUP88 to prevent its binding to CDC20. Such interaction licenses activation of the CDC20-mediated anaphase-promoting complex or cyclosome to ensure proper metaphase-to-anaphase transition. In addition, GS is overexpressed in human non-small cell lung cancer and its depletion reduces tumor growth in mice and increases the efficacy of microtubule-targeted chemotherapy. Our findings highlight a moonlighting function of GS in governing mitosis and illustrate how an essential metabolic enzyme promotes cell proliferation and tumor development, beyond its main metabolic function.
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Affiliation(s)
- Jiang-Sha Zhao
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
| | - Shuo Shi
- Shanghai Advanced Institute of Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Hai-Yan Qu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Zuzana Keckesova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Zi-Jian Cao
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Li-Xian Yang
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaofu Yu
- Department of Thoracic Radiotherapy, Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Limin Feng
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhong Shi
- Department of Medical Oncology, Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
| | - Joanna Krakowiak
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center Houston, Houston, TX, USA
| | - Ruo-Ying Mao
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi-Tong Shen
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu-Meng Fan
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Tian-Min Fu
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Ohio, OH, USA
| | - Cunqi Ye
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Daqian Xu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Xiaofei Gao
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Jia You
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center Houston, Houston, TX, USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas, Houston, TX, USA
| | - Tingbo Liang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
| | - Zhimin Lu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
| | - Yu-Xiong Feng
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
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28
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Abstract
The nuclear envelope is composed of the nuclear membranes, nuclear lamina, and nuclear pore complexes. Laminopathies are diseases caused by mutations in genes encoding protein components of the lamina and these other nuclear envelope substructures. Mutations in the single gene encoding lamin A and C, which are expressed in most differentiated somatic cells, cause diseases affecting striated muscle, adipose tissue, peripheral nerve, and multiple systems with features of accelerated aging. Mutations in genes encoding other nuclear envelope proteins also cause an array of diseases that selectively affect different tissues or organs. In some instances, the molecular and cellular consequences of laminopathy-causing mutations are known. However, even when these are understood, mechanisms explaining specific tissue or organ pathology remain enigmatic. Current mechanistic hypotheses focus on how alterations in the nuclear envelope may affect gene expression, including via the regulation of signaling pathways, or cellular mechanics, including responses to mechanical stress.
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Affiliation(s)
- Ji-Yeon Shin
- Department of Medicine and Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Howard J. Worman
- Department of Medicine and Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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29
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SUMO-Based Regulation of Nuclear Positioning to Spatially Regulate Homologous Recombination Activities at Replication Stress Sites. Genes (Basel) 2021; 12:genes12122010. [PMID: 34946958 PMCID: PMC8701742 DOI: 10.3390/genes12122010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/20/2022] Open
Abstract
DNA lesions have properties that allow them to escape their nuclear compartment to achieve DNA repair in another one. Recent studies uncovered that the replication fork, when its progression is impaired, exhibits increased mobility when changing nuclear positioning and anchors to nuclear pore complexes, where specific types of homologous recombination pathways take place. In yeast models, increasing evidence points out that nuclear positioning is regulated by small ubiquitin-like modifier (SUMO) metabolism, which is pivotal to maintaining genome integrity at sites of replication stress. Here, we review how SUMO-based pathways are instrumental to spatially segregate the subsequent steps of homologous recombination during replication fork restart. In particular, we discussed how routing towards nuclear pore complex anchorage allows distinct homologous recombination pathways to take place at halted replication forks.
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30
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Labade AS, Salvi A, Kar S, Karmodiya K, Sengupta K. Nup93 and CTCF modulate spatiotemporal dynamics and function of the HOXA gene locus during differentiation. J Cell Sci 2021; 134:273378. [PMID: 34746948 DOI: 10.1242/jcs.259307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/30/2021] [Indexed: 11/20/2022] Open
Abstract
Nucleoporins regulate nuclear transport and are also involved in DNA damage, repair, cell cycle, chromatin organization, and gene expression. Here, we studied the role of nucleoporin Nup93 and the chromatin organizer CTCF in regulating HOXA expression during differentiation. ChIP sequencing revealed a significant overlap between Nup93 and CTCF peaks. Interestingly, Nup93 and CTCF are associated with the 3' and 5'HOXA genes respectively. Depletions of Nup93 and CTCF antagonistically modulate expression levels of 3'and 5'HOXA genes in undifferentiated NT2/D1 cells. Nup93 also regulates the localization of the HOXA gene locus, which disengages from the nuclear periphery upon Nup93 but not CTCF depletion, consistent with its upregulation. The dynamic association of Nup93 and CTCF with the HOXA locus during differentiation correlates with its spatial positioning and expression. While Nup93 tethers the HOXA locus to the nuclear periphery, CTCF potentially regulates looping of the HOXA gene cluster in a temporal manner. In summary, Nup93 and CTCF complement one another in modulating the spatiotemporal dynamics and function of the HOXA gene locus during differentiation.
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Affiliation(s)
- Ajay S Labade
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Adwait Salvi
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Saswati Kar
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
| | - Kundan Sengupta
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008 Maharashtra, INDIA
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31
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Chen M, Long Q, Borrie MS, Sun H, Zhang C, Yang H, Shi D, Gartenberg MR, Deng W. Nucleoporin TPR promotes tRNA nuclear export and protein synthesis in lung cancer cells. PLoS Genet 2021; 17:e1009899. [PMID: 34793452 PMCID: PMC8639082 DOI: 10.1371/journal.pgen.1009899] [Citation(s) in RCA: 3] [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: 04/07/2021] [Revised: 12/02/2021] [Accepted: 10/21/2021] [Indexed: 12/26/2022] Open
Abstract
The robust proliferation of cancer cells requires vastly elevated levels of protein synthesis, which relies on a steady supply of aminoacylated tRNAs. Delivery of tRNAs to the cytoplasm is a highly regulated process, but the machinery for tRNA nuclear export is not fully elucidated. In this study, using a live cell imaging strategy that visualizes nascent transcripts from a specific tRNA gene in yeast, we identified the nuclear basket proteins Mlp1 and Mlp2, two homologs of the human TPR protein, as regulators of tRNA export. TPR expression is significantly increased in lung cancer tissues and correlated with poor prognosis. Consistently, knockdown of TPR inhibits tRNA nuclear export, protein synthesis and cell growth in lung cancer cell lines. We further show that NXF1, a well-known mRNA nuclear export factor, associates with tRNAs and mediates their transport through nuclear pores. Collectively, our findings uncover a conserved mechanism that regulates nuclear export of tRNAs, which is a limiting step in protein synthesis in eukaryotes.
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Affiliation(s)
- Miao Chen
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Qian Long
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Melinda S. Borrie
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Haohui Sun
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Changlin Zhang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Han Yang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Dingbo Shi
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Marc R. Gartenberg
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
- The Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Wuguo Deng
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
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32
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Bonnet A, Chaput C, Palmic N, Palancade B, Lesage P. A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription. PLoS Genet 2021; 17:e1009889. [PMID: 34723966 PMCID: PMC8585004 DOI: 10.1371/journal.pgen.1009889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/11/2021] [Accepted: 10/18/2021] [Indexed: 11/19/2022] Open
Abstract
Beyond their canonical function in nucleocytoplasmic exchanges, nuclear pore complexes (NPCs) regulate the expression of protein-coding genes. Here, we have implemented transcriptomic and molecular methods to specifically address the impact of the NPC on retroelements, which are present in multiple copies in genomes. We report a novel function for the Nup84 complex, a core NPC building block, in specifically restricting the transcription of LTR-retrotransposons in yeast. Nup84 complex-dependent repression impacts both Copia and Gypsy Ty LTR-retrotransposons, all over the S. cerevisiae genome. Mechanistically, the Nup84 complex restricts the transcription of Ty1, the most active yeast retrotransposon, through the tethering of the SUMO-deconjugating enzyme Ulp1 to NPCs. Strikingly, the modest accumulation of Ty1 RNAs caused by Nup84 complex loss-of-function is sufficient to trigger an important increase of Ty1 cDNA levels, resulting in massive Ty1 retrotransposition. Altogether, our study expands our understanding of the complex interactions between retrotransposons and the NPC, and highlights the importance for the cells to keep retrotransposons under tight transcriptional control.
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Affiliation(s)
- Amandine Bonnet
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Carole Chaput
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Noé Palmic
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Pascale Lesage
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U944, CNRS UMR 7212, Paris, France
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33
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Wu S, Chen K, Xu T, Ma K, Gao L, Fu C, Zhang W, Jing C, Ren C, Deng M, Chen Y, Zhou Y, Pan W, Jia X. Tpr Deficiency Disrupts Erythroid Maturation With Impaired Chromatin Condensation in Zebrafish Embryogenesis. Front Cell Dev Biol 2021; 9:709923. [PMID: 34722501 PMCID: PMC8548687 DOI: 10.3389/fcell.2021.709923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Vertebrate erythropoiesis involves nuclear and chromatin condensation at the early stages of terminal differentiation, which is a unique process to distinguish mature erythrocytes from erythroblasts. However, the underlying mechanisms of chromatin condensation during erythrocyte maturation remain elusive. Here, we reported a novel zebrafish mutant cas7 with erythroid maturation deficiency. Positional cloning showed that a single base mutation in tprb gene, which encodes nucleoporin translocated promoter region (Tpr), is responsible for the disrupted erythroid maturation and upregulation of erythroid genes, including ae1-globin and be1-globin. Further investigation revealed that deficient erythropoiesis in tprb cas7 mutant was independent on HIF signaling pathway. The proportion of euchromatin was significantly increased, whereas the percentage of heterochromatin was markedly decreased in tprb cas7 mutant. In addition, TPR knockdown in human K562 cells also disrupted erythroid differentiation and dramatically elevated the expression of globin genes, which suggests that the functions of TPR in erythropoiesis are highly conserved in vertebrates. Taken together, this study revealed that Tpr played vital roles in chromatin condensation and gene regulation during erythroid maturation in vertebrates.
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Affiliation(s)
- Shuang Wu
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Kai Chen
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Tao Xu
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
- Central Laboratory, Qingdao Agricultural University, Qingdao, China
| | - Ke Ma
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Lei Gao
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Cong Fu
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Wenjuan Zhang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Changbin Jing
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Chunguang Ren
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Min Deng
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yi Chen
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi Zhou
- Stem Cell Program, Hematology/Oncology Program at Children’s Hospital Boston, Harvard Medical School, Boston, MA, United States
| | - Weijun Pan
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoe Jia
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
- Inner Mongolia Key Laboratory of Hypoxic Translational Medicine, Baotou Medical College, Baotou, China
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34
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Coordination of transcription, processing, and export of highly expressed RNAs by distinct biomolecular condensates. Emerg Top Life Sci 2021; 4:281-291. [PMID: 32338276 PMCID: PMC7733674 DOI: 10.1042/etls20190160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/30/2022]
Abstract
Genes under control of super-enhancers are expressed at extremely high levels and are frequently associated with nuclear speckles. Recent data suggest that the high concentration of unphosphorylated RNA polymerase II (Pol II) and Mediator recruited to super-enhancers create phase-separated condensates. Transcription initiates within or at the surface of these phase-separated droplets and the phosphorylation of Pol II, associated with transcription initiation and elongation, dissociates Pol II from these domains leading to engagement with nuclear speckles, which are enriched with RNA processing factors. The transitioning of Pol II from transcription initiation domains to RNA processing domains effectively co-ordinates transcription and processing of highly expressed RNAs which are then rapidly exported into the cytoplasm.
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35
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Colussi C, Grassi C. Epigenetic regulation of neural stem cells: The emerging role of nucleoporins. STEM CELLS (DAYTON, OHIO) 2021; 39:1601-1614. [PMID: 34399020 PMCID: PMC9290943 DOI: 10.1002/stem.3444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/28/2021] [Indexed: 11/06/2022]
Abstract
Nucleoporins (Nups) are components of the nuclear pore complex that, besides regulating nucleus-cytoplasmic transport, emerged as a hub for chromatin interaction and gene expression modulation. Specifically, Nups act in a dynamic manner both at specific gene level and in the topological organization of chromatin domains. As such, they play a fundamental role during development and determination of stemness/differentiation balance in stem cells. An increasing number of reports indicate the implication of Nups in many central nervous system functions with great impact on neurogenesis, neurophysiology, and neurological disorders. Nevertheless, the role of Nup-mediated epigenetic regulation in embryonic and adult neural stem cells (NSCs) is a field largely unexplored and the comprehension of their mechanisms of action is only beginning to be unveiled. After a brief overview of epigenetic mechanisms, we will present and discuss the emerging role of Nups as new effectors of neuroepigenetics and as dynamic platform for chromatin function with specific reference to the biology of NSCs.
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Affiliation(s)
- Claudia Colussi
- Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti" (IASI)-CNR, Rome, Italy
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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36
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Lin YC, Kumar MS, Ramesh N, Anderson EN, Nguyen AT, Kim B, Cheung S, McDonough JA, Skarnes WC, Lopez-Gonzalez R, Landers JE, Fawzi NL, Mackenzie IR, Lee EB, Nickerson JA, Grunwald D, Pandey UB, Bosco DA. Interactions between ALS-linked FUS and nucleoporins are associated with defects in the nucleocytoplasmic transport pathway. Nat Neurosci 2021; 24:1077-1088. [PMID: 34059832 PMCID: PMC8832378 DOI: 10.1038/s41593-021-00859-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/16/2021] [Indexed: 02/05/2023]
Abstract
Nucleocytoplasmic transport (NCT) decline occurs with aging and neurodegeneration. Here, we investigated the NCT pathway in models of amyotrophic lateral sclerosis-fused in sarcoma (ALS-FUS). Expression of ALS-FUS led to a reduction in NCT and nucleoporin (Nup) density within the nuclear membrane of human neurons. FUS and Nups were found to interact independently of RNA in cells and to alter the phase-separation properties of each other in vitro. FUS-Nup interactions were not localized to nuclear pores, but were enriched in the nucleus of control neurons versus the cytoplasm of mutant neurons. Our data indicate that the effect of ALS-linked mutations on the cytoplasmic mislocalization of FUS, rather than on the physiochemical properties of the protein itself, underlie our reported NCT defects. An aberrant interaction between mutant FUS and Nups is underscored by studies in Drosophila, whereby reduced Nup expression rescued multiple toxic FUS-induced phenotypes, including abnormal nuclear membrane morphology in neurons.
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Affiliation(s)
- Yen-Chen Lin
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA
| | - Meenakshi Sundaram Kumar
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA
| | - Nandini Ramesh
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, 15261, USA
| | - Eric N. Anderson
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Aivi T. Nguyen
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Boram Kim
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simon Cheung
- Department of Pathology, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | | | | | - Rodrigo Lopez-Gonzalez
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA
| | - Nicolas L. Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, 02912, USA
| | - Ian R.A. Mackenzie
- Department of Pathology, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - Edward B. Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jeffrey A. Nickerson
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, 01605, USA
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Udai B. Pandey
- Division of Child Neurology, Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Daryl A. Bosco
- Department of Neurology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, 01605, USA,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA,Lead Contact,To whom correspondence should be addressed: Daryl A. Bosco: Department of Neurology, University of Massachusetts Medical Center, Worcester, MA 01605; ; Tel. (774) 455-3745; Fax. (508) 856-6750
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37
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Padilla-Mejia NE, Koreny L, Holden J, Vancová M, Lukeš J, Zoltner M, Field MC. A hub-and-spoke nuclear lamina architecture in trypanosomes. J Cell Sci 2021; 134:jcs251264. [PMID: 34151975 PMCID: PMC8255026 DOI: 10.1242/jcs.251264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 05/10/2021] [Indexed: 01/11/2023] Open
Abstract
The nuclear lamina supports many functions, including maintaining nuclear structure and gene expression control, and correct spatio-temporal assembly is vital to meet these activities. Recently, multiple lamina systems have been described that, despite independent evolutionary origins, share analogous functions. In trypanosomatids the two known lamina proteins, NUP-1 and NUP-2, have molecular masses of 450 and 170 kDa, respectively, which demands a distinct architecture from the ∼60 kDa lamin-based system of metazoa and other lineages. To uncover organizational principles for the trypanosome lamina we generated NUP-1 deletion mutants to identify domains and their arrangements responsible for oligomerization. We found that both the N- and C-termini act as interaction hubs, and that perturbation of these interactions impacts additional components of the lamina and nuclear envelope. Furthermore, the assembly of NUP-1 terminal domains suggests intrinsic organizational capacity. Remarkably, there is little impact on silencing of telomeric variant surface glycoprotein genes. We suggest that both terminal domains of NUP-1 have roles in assembling the trypanosome lamina and propose a novel architecture based on a hub-and-spoke configuration.
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Affiliation(s)
| | - Ludek Koreny
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jennifer Holden
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Marie Vancová
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Department of Parasitology, Faculty of Science, Charles University in Prague, BIOCEV 252 50, Vestec, Czech Republic
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
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38
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Cavazza T, Takeda Y, Politi AZ, Aushev M, Aldag P, Baker C, Choudhary M, Bucevičius J, Lukinavičius G, Elder K, Blayney M, Lucas-Hahn A, Niemann H, Herbert M, Schuh M. Parental genome unification is highly error-prone in mammalian embryos. Cell 2021; 184:2860-2877.e22. [PMID: 33964210 PMCID: PMC8162515 DOI: 10.1016/j.cell.2021.04.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 02/05/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022]
Abstract
Most human embryos are aneuploid. Aneuploidy frequently arises during the early mitotic divisions of the embryo, but its origin remains elusive. Human zygotes that cluster their nucleoli at the pronuclear interface are thought to be more likely to develop into healthy euploid embryos. Here, we show that the parental genomes cluster with nucleoli in each pronucleus within human and bovine zygotes, and clustering is required for the reliable unification of the parental genomes after fertilization. During migration of intact pronuclei, the parental genomes polarize toward each other in a process driven by centrosomes, dynein, microtubules, and nuclear pore complexes. The maternal and paternal chromosomes eventually cluster at the pronuclear interface, in direct proximity to each other, yet separated. Parental genome clustering ensures the rapid unification of the parental genomes on nuclear envelope breakdown. However, clustering often fails, leading to chromosome segregation errors and micronuclei, incompatible with healthy embryo development.
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Affiliation(s)
- Tommaso Cavazza
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Yuko Takeda
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, NE1 4EP Newcastle upon Tyne, UK
| | - Antonio Z Politi
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Magomet Aushev
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, NE1 4EP Newcastle upon Tyne, UK
| | - Patrick Aldag
- Institute of Farm Animal Genetics, Biotechnology, Friedrich-Loeffler-Institute, Mariensee, 31535 Neustadt, Germany
| | | | - Meenakshi Choudhary
- Newcastle Fertility Centre at Life, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4EP Newcastle upon Tyne, UK
| | - Jonas Bucevičius
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | | | - Kay Elder
- Bourn Hall Clinic, CB23 2TN Cambridge, UK
| | | | - Andrea Lucas-Hahn
- Institute of Farm Animal Genetics, Biotechnology, Friedrich-Loeffler-Institute, Mariensee, 31535 Neustadt, Germany
| | - Heiner Niemann
- Institute of Farm Animal Genetics, Biotechnology, Friedrich-Loeffler-Institute, Mariensee, 31535 Neustadt, Germany
| | - Mary Herbert
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, NE1 4EP Newcastle upon Tyne, UK; Newcastle Fertility Centre at Life, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4EP Newcastle upon Tyne, UK
| | - Melina Schuh
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
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39
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Kittisopikul M, Shimi T, Tatli M, Tran JR, Zheng Y, Medalia O, Jaqaman K, Adam SA, Goldman RD. Computational analyses reveal spatial relationships between nuclear pore complexes and specific lamins. J Cell Biol 2021; 220:e202007082. [PMID: 33570570 PMCID: PMC7883741 DOI: 10.1083/jcb.202007082] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/15/2020] [Accepted: 01/05/2021] [Indexed: 12/29/2022] Open
Abstract
Nuclear lamin isoforms form fibrous meshworks associated with nuclear pore complexes (NPCs). Using datasets prepared from subpixel and segmentation analyses of 3D-structured illumination microscopy images of WT and lamin isoform knockout mouse embryo fibroblasts, we determined with high precision the spatial association of NPCs with specific lamin isoform fibers. These relationships are retained in the enlarged lamin meshworks of Lmna-/- and Lmnb1-/- fibroblast nuclei. Cryo-ET observations reveal that the lamin filaments composing the fibers contact the nucleoplasmic ring of NPCs. Knockdown of the ring-associated nucleoporin ELYS induces NPC clusters that exclude lamin A/C fibers but include LB1 and LB2 fibers. Knockdown of the nucleoporin TPR or NUP153 alters the arrangement of lamin fibers and NPCs. Evidence that the number of NPCs is regulated by specific lamin isoforms is presented. Overall the results demonstrate that lamin isoforms and nucleoporins act together to maintain the normal organization of lamin meshworks and NPCs within the nuclear envelope.
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Affiliation(s)
- Mark Kittisopikul
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Takeshi Shimi
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
- Cell Biology Center and World Research Hub Initiative, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Meltem Tatli
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Joseph Riley Tran
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | - Yixian Zheng
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Khuloud Jaqaman
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Stephen A. Adam
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Robert D. Goldman
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL
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40
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Rebensburg SV, Wei G, Larue RC, Lindenberger J, Francis AC, Annamalai AS, Morrison J, Shkriabai N, Huang SW, KewalRamani V, Poeschla EM, Melikyan GB, Kvaratskhelia M. Sec24C is an HIV-1 host dependency factor crucial for virus replication. Nat Microbiol 2021; 6:435-444. [PMID: 33649557 PMCID: PMC8012256 DOI: 10.1038/s41564-021-00868-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
Early events of the human immunodeficiency virus 1 (HIV-1) lifecycle, such as post-entry virus trafficking, uncoating and nuclear import, are poorly characterized because of limited understanding of virus-host interactions. Here, we used mass spectrometry-based proteomics to delineate cellular binding partners of curved HIV-1 capsid lattices and identified Sec24C as an HIV-1 host dependency factor. Gene deletion and complementation in Jurkat cells revealed that Sec24C facilitates infection and markedly enhances HIV-1 spreading infection. Downregulation of Sec24C in HeLa cells substantially reduced HIV-1 core stability and adversely affected reverse transcription, nuclear import and infectivity. Live-cell microscopy showed that Sec24C co-trafficked with HIV-1 cores in the cytoplasm during virus ingress. Biochemical assays demonstrated that Sec24C directly and specifically interacted with hexameric capsid lattices. A 2.3-Å resolution crystal structure of Sec24C228-242 in the complex with a capsid hexamer revealed that the Sec24C FG-motif bound to a pocket comprised of two adjoining capsid subunits. Combined with previous data1-4, our findings indicate that a capsid-binding FG-motif is conserved in unrelated proteins present in the cytoplasm (Sec24C), the nuclear pore (Nup153; refs. 3,4) and the nucleus (CPSF6; refs. 1,2). We propose that these virus-host interactions during HIV-1 trafficking across different cellular compartments are crucial for productive infection of target cells.
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Affiliation(s)
- Stephanie V Rebensburg
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Guochao Wei
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ross C Larue
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Jared Lindenberger
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ashwanth C Francis
- Department of Pediatrics, Infectious Diseases, Emory University, Atlanta, GA, USA
| | - Arun S Annamalai
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - James Morrison
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Nikoloz Shkriabai
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Szu-Wei Huang
- Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Vineet KewalRamani
- Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gregory B Melikyan
- Department of Pediatrics, Infectious Diseases, Emory University, Atlanta, GA, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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41
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Nunes V, Ferreira JG. From the cytoskeleton to the nucleus: An integrated view on early spindle assembly. Semin Cell Dev Biol 2021; 117:42-51. [PMID: 33726956 DOI: 10.1016/j.semcdb.2021.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/01/2022]
Abstract
Accurate chromosome segregation requires a complete restructuring of cellular organization. Microtubules remodel to assemble a mitotic spindle and the actin cytoskeleton rearranges to form a stiff actomyosin cortex. These cytoplasmic events must be spatially and temporally coordinated with mitotic chromosome condensation and nuclear envelope permeabilization, in order to ensure mitotic timing and fidelity. Here, we discuss the main cytoskeletal and nuclear events that occur during mitotic entry in proliferating animal cells, focusing on their coordinated contribution for early mitotic spindle assembly. We will also explore recent progress in understanding their regulatory biochemical and mechanical pathways.
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Affiliation(s)
- Vanessa Nunes
- Instituto de Investigação e Inovação em Saúde - i3S, University of Porto, Porto, Portugal; BiotechHealth PhD Programe, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Jorge G Ferreira
- Instituto de Investigação e Inovação em Saúde - i3S, University of Porto, Porto, Portugal; Departamento de Biomedicina, Faculdade de Medicina, University of Porto, Porto, Portugal.
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Liu L, Wang T. Male gametophyte development in flowering plants: A story of quarantine and sacrifice. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153365. [PMID: 33548696 DOI: 10.1016/j.jplph.2021.153365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 05/19/2023]
Abstract
Over 160 years ago, scientists made the first microscopic observations of angiosperm pollen. Unlike in animals, male meiosis in angiosperms produces a haploid microspore that undergoes one asymmetric division to form a vegetative cell and a generative cell. These two cells have distinct fates: the vegetative cell exits the cell cycle and elongates to form a tip-growing pollen tube; the generative cell divides once more in the pollen grain or within the growing pollen tube to form a pair of sperm cells. The concept that male germ cells are less active than the vegetative cell came from biochemical analyses and pollen structure anatomy early in the last century and is supported by the pollen transcriptome data of the last decade. However, the mechanism of how and when the transcriptional repression in male germ cells occurs is still not fully understood. In this review, we provide a brief account of the cytological and metabolic differentiation between the vegetative cell and male germ cells, with emphasis on the role of temporary callose walls, dynamic nuclear pore density, transcription repression, and histone variants. We further discuss the intercellular movement of small interfering RNA (siRNA) derived from transposable elements (TEs) and reexamine the function of TE expression in male germ cells.
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Affiliation(s)
- Lingtong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China.
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Kumanski S, Viart BT, Kossida S, Moriel-Carretero M. Lipid Droplets Are a Physiological Nucleoporin Reservoir. Cells 2021; 10:472. [PMID: 33671805 PMCID: PMC7926788 DOI: 10.3390/cells10020472] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
Lipid Droplets (LD) are dynamic organelles that originate in the Endoplasmic Reticulum and mostly bud off toward the cytoplasm, where they store neutral lipids for energy and protection purposes. LD also have diverse proteins on their surface, many of which are necessary for the their correct homeostasis. However, these organelles also act as reservoirs of proteins that can be made available elsewhere in the cell. In this sense, they act as sinks that titrate key regulators of many cellular processes. Among the specialized factors that reside on cytoplasmic LD are proteins destined for functions in the nucleus, but little is known about them and their impact on nuclear processes. By screening for nuclear proteins in publicly available LD proteomes, we found that they contain a subset of nucleoporins from the Nuclear Pore Complex (NPC). Exploring this, we demonstrate that LD act as a physiological reservoir, for nucleoporins, that impacts the conformation of NPCs and hence their function in nucleo-cytoplasmic transport, chromatin configuration, and genome stability. Furthermore, our in silico modeling predicts a role for LD-released fatty acids in regulating the transit of nucleoporins from LD through the cytoplasm and to nuclear pores.
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Affiliation(s)
- Sylvain Kumanski
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France;
| | - Benjamin T. Viart
- International ImMunoGeneTics Information System (IMGT®), Institut de Génétique Humaine (IGH), Université de Montpellier, Centre National de la Recherche Scientifique, 34396 Montpellier CEDEX 05, France; (B.T.V.); (S.K.)
| | - Sofia Kossida
- International ImMunoGeneTics Information System (IMGT®), Institut de Génétique Humaine (IGH), Université de Montpellier, Centre National de la Recherche Scientifique, 34396 Montpellier CEDEX 05, France; (B.T.V.); (S.K.)
| | - María Moriel-Carretero
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, 34293 Montpellier CEDEX 05, France;
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Nie M, Oravcová M, Jami‐Alahmadi Y, Wohlschlegel JA, Lazzerini‐Denchi E, Boddy MN. FAM111A induces nuclear dysfunction in disease and viral restriction. EMBO Rep 2021; 22:e50803. [PMID: 33369867 PMCID: PMC7857424 DOI: 10.15252/embr.202050803] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022] Open
Abstract
Mutations in the nuclear trypsin-like serine protease FAM111A cause Kenny-Caffey syndrome (KCS2) with hypoparathyroidism and skeletal dysplasia or perinatally lethal osteocraniostenosis (OCS). In addition, FAM111A was identified as a restriction factor for certain host range mutants of the SV40 polyomavirus and VACV orthopoxvirus. However, because FAM111A function is poorly characterized, its roles in restricting viral replication and the etiology of KCS2 and OCS remain undefined. We find that FAM111A KCS2 and OCS patient mutants are hyperactive and cytotoxic, inducing apoptosis-like phenotypes such as disruption of nuclear structure and pore distribution, in a protease-dependent manner. Moreover, wild-type FAM111A activity causes similar nuclear phenotypes, including the loss of nuclear barrier function, when SV40 host range mutants attempt to replicate in restrictive cells. Interestingly, pan-caspase inhibitors do not block these FAM111A-induced phenotypes, implying it acts independently or upstream of caspases. In this regard, we identify nucleoporins and the associated GANP transcription/replication factor as FAM111A interactors and candidate targets. Overall, we reveal a potentially unifying mechanism through which deregulated FAM111A activity restricts viral replication and causes KCS2 and OCS.
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Affiliation(s)
- Minghua Nie
- Department of Molecular MedicineThe Scripps Research InstituteLa JollaCAUSA
| | - Martina Oravcová
- Department of Molecular MedicineThe Scripps Research InstituteLa JollaCAUSA
| | - Yasaman Jami‐Alahmadi
- Department of Biological ChemistryDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - James A Wohlschlegel
- Department of Biological ChemistryDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | | | - Michael N Boddy
- Department of Molecular MedicineThe Scripps Research InstituteLa JollaCAUSA
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Karoutas A, Akhtar A. Functional mechanisms and abnormalities of the nuclear lamina. Nat Cell Biol 2021; 23:116-126. [PMID: 33558730 DOI: 10.1038/s41556-020-00630-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Alterations in nuclear shape are present in human diseases and ageing. A compromised nuclear lamina is molecularly interlinked to altered chromatin functions and genomic instability. Whether these alterations are a cause or a consequence of the pathological state are important questions in biology. Here, we summarize the roles of nuclear envelope components in chromatin organization, phase separation and transcriptional and epigenetic regulation. Examining these functions in healthy backgrounds will guide us towards a better understanding of pathological alterations.
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Affiliation(s)
- Adam Karoutas
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Francis Crick Institute, London, UK
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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46
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Lüdke D, Rohmann PFW, Wiermer M. Nucleocytoplasmic Communication in Healthy and Diseased Plant Tissues. FRONTIERS IN PLANT SCIENCE 2021; 12:719453. [PMID: 34394173 PMCID: PMC8357054 DOI: 10.3389/fpls.2021.719453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/09/2021] [Indexed: 05/16/2023]
Abstract
The double membrane of the nuclear envelope (NE) constitutes a selective compartment barrier that separates nuclear from cytoplasmic processes. Plant viability and responses to a changing environment depend on the spatial communication between both compartments. This communication is based on the bidirectional exchange of proteins and RNAs and is regulated by a sophisticated transport machinery. Macromolecular traffic across the NE depends on nuclear transport receptors (NTRs) that mediate nuclear import (i.e. importins) or export (i.e. exportins), as well as on nuclear pore complexes (NPCs) that are composed of nucleoporin proteins (NUPs) and span the NE. In this review, we provide an overview of plant NPC- and NTR-directed cargo transport and we consider transport independent functions of NPCs and NE-associated proteins in regulating plant developmental processes and responses to environmental stresses.
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Affiliation(s)
- Daniel Lüdke
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Philipp F. W. Rohmann
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Marcel Wiermer
- Molecular Biology of Plant-Microbe Interactions Research Group, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, Göttingen, Germany
- Molecular Biology of Plant-Microbe Interactions Research Group, Göttingen Center for Molecular Biosciences, University of Göttingen, Göttingen, Germany
- *Correspondence: Marcel Wiermer,
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47
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Hong SH, Son KH, Ha SY, Wee TI, Choi SK, Won JE, Han HD, Ro Y, Park YM, Eun JW, Nam SW, Han JW, Kang K, You JS. Nucleoporin 210 Serves a Key Scaffold for SMARCB1 in Liver Cancer. Cancer Res 2020; 81:356-370. [PMID: 33239431 DOI: 10.1158/0008-5472.can-20-0568] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/19/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022]
Abstract
The roles of chromatin remodelers and their underlying mechanisms of action in cancer remain unclear. In this study, SMARCB1, known initially as a bona fide tumor suppressor gene, was investigated in liver cancer. SMARCB1 was highly upregulated in patients with liver cancer and was associated with poor prognosis. Loss- and gain-of-function studies in liver cells revealed that SMARCB1 loss led to reduced cell proliferation, wound healing capacity, and tumor growth in vivo. Although upregulated SMARCB1 appeared to contribute to switch/sucrose nonfermentable (SWI/SNF) complex stability and integrity, it did not act using its known pathways antagonism with EZH2 or association between TP53 or AMPK. SMARCB1 knockdown induced a mild reduction in global H3K27 acetylation, and chromatin immunoprecipitation sequencing of SMARCB1 and acetylated histone H3K27 antibodies before and after SMARCB1 loss identified Nucleoporin210 (NUP210) as a critical target of SMARCB1, which bound its enhancer and changed H3K27Ac enrichment and downstream gene expression, particularly cholesterol homeostasis and xenobiotic metabolism. Notably, NUP210 was not only a putative tumor supporter involved in liver cancer but also acted as a key scaffold for SMARCB1 and P300 to chromatin. Furthermore, SMARCB1 deficiency conferred sensitivity to doxorubicin and P300 inhibitor in liver cancer cells. These findings provide insights into mechanisms underlying dysregulation of chromatin remodelers and show novel associations between nucleoporins and chromatin remodelers in cancer. SIGNIFICANCE: This study reveals a novel protumorigenic role for SMARCB1 and describes valuable links between nucleoporins and chromatin remodelers in cancer by identifying NUP210 as a critical coregulator of SMARCB1 chromatin remodeling activity.
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Affiliation(s)
| | - Keun Hong Son
- College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Sang Yun Ha
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae In Wee
- School of Medicine, Konkuk University, Seoul, Korea
| | | | - Ji Eun Won
- School of Medicine, Konkuk University, Seoul, Korea
| | - Hee Dong Han
- School of Medicine, Konkuk University, Seoul, Korea
| | - Youngtae Ro
- School of Medicine, Konkuk University, Seoul, Korea
| | | | - Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, Suwon, Korea
| | - Suk Woo Nam
- Department of Pathology, College of Medicine, Catholic University, Seoul, Korea
| | - Jeung-Whan Han
- Research Center for Epigenome Regulation, School of Pharmacy, Sungkyunkwan University, Suwon, Korea
| | - Keunsoo Kang
- College of Natural Sciences, Dankook University, Cheonan, Korea
| | - Jueng Soo You
- School of Medicine, Konkuk University, Seoul, Korea.
- Research Institute of Medical Science, Konkuk University, Seoul, Korea
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Molenberghs F, Bogers JJ, De Vos WH. Confined no more: Viral mechanisms of nuclear entry and egress. Int J Biochem Cell Biol 2020; 129:105875. [PMID: 33157236 DOI: 10.1016/j.biocel.2020.105875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022]
Abstract
Viruses are obligatory intracellular parasites. For their efficient replication, many require access to the nuclear interior. Yet, only few viral particles are small enough to passively diffuse through the nuclear pore complexes, calling for alternative strategies to bypass the nuclear envelope barrier. Some viruses will await mitotic nuclear envelope breakdown to gain access, whereas others will exploit more active means, for instance by hijacking nuclear pore transport or by directly targeting constituents of the nuclear envelope so as to remodel and temporarily perturb its integrity. After replication, newly produced viral DNA complexes need to cross the same barrier to exit the nucleus and enter the cytoplasm, where the final stages of virion maturation take place. There are also different flavours to the feat of nuclear egress that vary in delicacy and intensity. In this review, we define the major entry and egress strategies that are exploited by different viruses and describe the molecular details thereof. Ultimately, a deeper understanding of these pathways may help identifying molecular targets for blocking viral reproduction or spreading.
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Affiliation(s)
- Freya Molenberghs
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences/Medicine and Health Sciences, University of Antwerp, Belgium
| | - Johannes J Bogers
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences/Medicine and Health Sciences, University of Antwerp, Belgium
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences/Medicine and Health Sciences, University of Antwerp, Belgium.
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Identification of AR-V7 downstream genes commonly targeted by AR/AR-V7 and specifically targeted by AR-V7 in castration resistant prostate cancer. Transl Oncol 2020; 14:100915. [PMID: 33096335 PMCID: PMC7581977 DOI: 10.1016/j.tranon.2020.100915] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/28/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
The entire landscape of AR-V7 target regions/genes in CRPC cells was investigated. We identified 78 AR-V7 target genes, targeted specifically by AR-V7 e.g. SLC3A2, or commonly by AR and AR-V7 e.g. NUP210. SLC3A2 and NUP210 were markedly upregulated in clinical CRPC tissues, leading to increased proliferation in CRPC.
Primary prostate cancer (PC) progresses to castration-resistant PC (CRPC) under androgen deprivation therapy, by mechanisms e.g. expression of androgen receptor (AR) splice variant-7 (AR-V7). Here we conducted comprehensive epigenome and transcriptome analyses comparing LNCaP, primary PC cells, and LNCaP95, AR-V7-expressing CRPC cells derived from LNCaP. Of 399 AR-V7 target regions identified through ChIP-seq analysis, 377 could be commonly targeted by hormone-stimulated AR, and 22 were specifically targeted by AR-V7. Among genes neighboring to these AR-V7 target regions, 78 genes were highly expressed in LNCaP95, while AR-V7 knockdown led to significant repression of these genes and suppression of growth of LNCaP95. Of the 78 AR-V7 target genes, 74 were common AR/AR-V7 target genes and 4 were specific AR-V7 target genes; their most suppressed genes by AR-V7 knockdown were NUP210 and SLC3A2, respectively, and underwent subsequent analyses. NUP210 and SLC3A2 were significantly upregulated in clinical CRPC tissues, and their knockdown resulted in significant suppression of cellular growth of LNCaP95 through apoptosis and growth arrest. Collectively, AR-V7 contributes to CRPC proliferation by activating both common AR/AR-V7 target and specific AR-V7 target, e.g. NUP210 and SLC3A2.
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50
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Wessel SR, Mohni KN, Luzwick JW, Dungrawala H, Cortez D. Functional Analysis of the Replication Fork Proteome Identifies BET Proteins as PCNA Regulators. Cell Rep 2020; 28:3497-3509.e4. [PMID: 31553917 PMCID: PMC6878991 DOI: 10.1016/j.celrep.2019.08.051] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/25/2019] [Accepted: 08/15/2019] [Indexed: 01/15/2023] Open
Abstract
Identifying proteins that function at replication forks is essential to understanding DNA replication, chromatin assembly, and replication-coupled DNA repair mechanisms. Combining quantitative mass spectrometry in multiple cell types with stringent statistical cutoffs, we generated a high-confidence catalog of 593 proteins that are enriched at replication forks and nascent chromatin. Loss-of-function genetic analyses indicate that 85% yield phenotypes that are consistent with activities in DNA and chromatin replication or already have described functions in these processes. We illustrate the value of this resource by identifying activities of the BET family proteins BRD2, BRD3, and BRD4 in controlling DNA replication. These proteins use their extra-terminal domains to bind and inhibit the ATAD5 complex and thereby control the amount of PCNA on chromatin.
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Affiliation(s)
- Sarah R Wessel
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Kareem N Mohni
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Jessica W Luzwick
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Huzefa Dungrawala
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.
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