151
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Heikkinen T, Kämpjärvi K, Keskitalo S, von Nandelstadh P, Liu X, Rantanen V, Pitkänen E, Kinnunen M, Kuusanmäki H, Kontro M, Turunen M, Mäkinen N, Taipale J, Heckman C, Lehti K, Mustjoki S, Varjosalo M, Vahteristo P. Somatic MED12 Nonsense Mutation Escapes mRNA Decay and Reveals a Motif Required for Nuclear Entry. Hum Mutat 2017; 38:269-274. [PMID: 28054750 DOI: 10.1002/humu.23157] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/01/2016] [Indexed: 11/06/2022]
Abstract
MED12 is a key component of the transcription-regulating Mediator complex. Specific missense and in-frame insertion/deletion mutations in exons 1 and 2 have been identified in uterine leiomyomas, breast tumors, and chronic lymphocytic leukemia. Here, we characterize the first MED12 5' end nonsense mutation (c.97G>T, p.E33X) identified in acute lymphoblastic leukemia and show that it escapes nonsense-mediated mRNA decay (NMD) by using an alternative translation initiation site. The resulting N-terminally truncated protein is unable to enter the nucleus due to the lack of identified nuclear localization signal (NLS). The absence of NLS prevents the mutant MED12 protein to be recognized by importin-α and subsequent loading into the nuclear pore complex. Due to this mislocalization, all interactions between the MED12 mutant and other Mediator components are lost. Our findings provide new mechanistic insights into the MED12 functions and indicate that somatic nonsense mutations in early exons may avoid NMD.
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Affiliation(s)
- Tuomas Heikkinen
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Medicum, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Kati Kämpjärvi
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Medicum, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Pernilla von Nandelstadh
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ville Rantanen
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Institute of Biomedicine, University of Helsinki, Helsinki, Finland
| | - Esa Pitkänen
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Medicum, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Matias Kinnunen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Heikki Kuusanmäki
- Hematology Research Unit Helsinki, Department of Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Mika Kontro
- Hematology Research Unit Helsinki, Department of Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Mikko Turunen
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Netta Mäkinen
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Medicum, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Jussi Taipale
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Caroline Heckman
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Kaisa Lehti
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Finnish Cancer Institute, Helsinki, Finland.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Department of Hematology, University of Helsinki and Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.,Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Pia Vahteristo
- Research Programs Unit, Genome-Scale Biology, University of Helsinki, Helsinki, Finland.,Medicum, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
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152
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Raices M, D'Angelo MA. Nuclear pore complexes and regulation of gene expression. Curr Opin Cell Biol 2017; 46:26-32. [PMID: 28088069 DOI: 10.1016/j.ceb.2016.12.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/09/2016] [Accepted: 12/21/2016] [Indexed: 12/31/2022]
Abstract
Nuclear pore complexes (NPCs), are large multiprotein channels that penetrate the nuclear envelope connecting the nucleus to the cytoplasm. Accumulating evidence shows that besides their main role in regulating the exchange of molecules between these two compartments, NPCs and their components also play important transport-independent roles, including gene expression regulation, chromatin organization, DNA repair, RNA processing and quality control, and cell cycle control. Here, we will describe the recent findings about the role of these structures in the regulation of gene expression.
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Affiliation(s)
- Marcela Raices
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, 10901 N. Torrey Pines Road, La Jolla, 92037 CA, United States
| | - Maximiliano A D'Angelo
- Sanford Burnham Prebys Medical Discovery Institute, Development, Aging and Regeneration Program, 10901 N. Torrey Pines Road, La Jolla, 92037 CA, United States.
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153
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Tamura K, Fukao Y, Hatsugai N, Katagiri F, Hara-Nishimura I. Nup82 functions redundantly with Nup136 in a salicylic acid-dependent defense response of Arabidopsis thaliana. Nucleus 2017; 8:301-311. [PMID: 28071978 DOI: 10.1080/19491034.2017.1279774] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The nuclear pore complex (NPC) comprises more than 30 nucleoporins (Nups). NPC mediates macromolecular trafficking between the nucleoplasm and the cytoplasm, but specific roles of individual Nups are poorly understood in higher plants. Here, we show that the novel nucleoporin unique to angiosperm plants (designated as Nup82) functions in a salicylic acid-dependent defense in a redundant manner with Nup136, which is a component of the nuclear basket in the NPC. Arabidopsis thaliana Nup82 had a similar amino acid sequence to the N-terminal half of Nup136 and a Nup82-GFP fusion was localized on the nuclear envelope. Immunoprecipitation and bimolecular fluorescence complementation analyses revealed that Nup82 interacts with the NPC components Nup136 and RAE1. The double knockout mutant nup82 nup136 showed severe growth defects, while the single knockout mutant nup82 did not, suggesting that Nup82 functions redundantly with Nup136. nup82 nup136 impaired benzothiadiazole (an analog of salicylic acid)-induced resistance to the virulent bacteria Pseudomonas syringae pv. tomato DC3000. Furthermore, transcriptome analysis of nup82 nup136 indicates that deficiency of Nup82 and Nup136 causes noticeable downregulation of immune-related genes. These results suggest that Nup82 and Nup136 are redundantly involved in transcriptional regulation of salicylic acid-responsive genes through nuclear transport of signaling molecules.
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Affiliation(s)
- Kentaro Tamura
- a Department of Botany , Graduate School of Science, Kyoto University , Kyoto , Japan
| | - Yoichiro Fukao
- b Department of Bioinformatics , College of Life Sciences, Ritsumeikan University , Shiga , Japan
| | - Noriyuki Hatsugai
- c Department of Plant Biology , Microbial and Plant Genomics Institute, University of Minnesota , St. Paul , MN , USA
| | - Fumiaki Katagiri
- c Department of Plant Biology , Microbial and Plant Genomics Institute, University of Minnesota , St. Paul , MN , USA
| | - Ikuko Hara-Nishimura
- a Department of Botany , Graduate School of Science, Kyoto University , Kyoto , Japan
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154
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Abstract
To complete its life cycle, HIV-1 enters the nucleus of the host cell as reverse-transcribed viral DNA. The nucleus is a complex environment, in which chromatin is organized to support different structural and functional aspects of cell physiology. As such, it represents a challenge for an incoming viral genome, which needs to be integrated into cellular DNA to ensure productive infection. Integration of the viral genome into host DNA depends on the enzymatic activity of HIV-1 integrase and involves different cellular factors that influence the selection of integration sites. The selection of integration site has functional consequences for viral transcription, which usually follows the integration event. However, in resting CD4+ T cells, the viral genome can be silenced for long periods of time, which leads to the generation of a latent reservoir of quiescent integrated HIV-1 DNA. Integration represents the only nuclear event in the viral life cycle that can be pharmacologically targeted with current therapies, and the aspects that connect HIV-1 nuclear entry to HIV-1 integration and viral transcription are only beginning to be elucidated.
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155
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Long Q, Liao YH, Xie Y, Liang W, Cheng X, Yuan J, Yu M. Coxsackievirus B3 Directly Induced Th17 Cell Differentiation by Inhibiting Nup98 Expression in Patients with Acute Viral Myocarditis. Front Cell Infect Microbiol 2016; 6:171. [PMID: 28018858 PMCID: PMC5145863 DOI: 10.3389/fcimb.2016.00171] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
Th17 cells play a key role in the progression of coxsackievirus B3 (CVB3)-induced acute viral myocarditis (AVMC). However, the direct effect of virus on Th17 cell differentiation is still unknown. Recently, nucleoporin (Nup) 98 has been proved to be associated with lymphocyte differentiation. Therefore, we investigated whether Nup98 mediated Th17 cell differentiation in AVMC. In our study, patients with AVMC and healthy controls were recruited. The results showed that CVB3 could enter into the CD4+ T cells in AVMC patients and healthy controls. After transfecting purified CD4+ T cells with CVB3 in vitro, the Th17 cell frequency, IL-17 secretion, and RORγT synthesis were increased while the Nup98 levels were decreased. Furthermore, down-regulating Nup98 expression by siRNA-Nup98 in CD4+ T cells resulted in the elevated Th17 cell frequency and IL-17 secretion, along with enhanced levels of RORγT, dissociative p300/CBP, and acetylated Stat3. Up-regulation of Nup98 expression by pcDNA3.1-Nup98 showed the opposite effects. Our results suggested that CVB3 directly induced CD4+ T cell differentiation into Th17 cells by inhibiting Nup98 expression, representing a therapeutic target in AVMC.
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Affiliation(s)
- Qi Long
- Laboratory of Cardiovascular Immunology, Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
| | - Yu-Hua Liao
- Laboratory of Cardiovascular Immunology, Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
| | - Yu Xie
- Laboratory of Cardiovascular Immunology, Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
| | - Wei Liang
- Laboratory of Cardiovascular Immunology, Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
| | - Xiang Cheng
- Laboratory of Cardiovascular Immunology, Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
| | - Jing Yuan
- Laboratory of Cardiovascular Immunology, Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
| | - Miao Yu
- Laboratory of Cardiovascular Immunology, Institute of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
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156
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Ibarra A, Benner C, Tyagi S, Cool J, Hetzer MW. Nucleoporin-mediated regulation of cell identity genes. Genes Dev 2016; 30:2253-2258. [PMID: 27807035 PMCID: PMC5110992 DOI: 10.1101/gad.287417.116] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 10/07/2016] [Indexed: 01/21/2023]
Abstract
Here, Ibarra et al. investigate the contribution of nuclear envelope components to the regulation of cell type-specific gene expression and show a role for NPC components in the regulation of cell type-specific gene expression The authors found that nucleoporin-associated superenhancers localize preferentially to the nuclear periphery, and, in the absence of nucleoporins, transcriptional changes of SE-associated genes were observed. The organization of the genome in the three-dimensional space of the nucleus is coupled with cell type-specific gene expression. However, how nuclear architecture influences transcription that governs cell identity remains unknown. Here, we show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers (SE), regulatory structures that drive the expression of key genes that specify cell identity. We found that nucleoporin-associated SEs localize preferentially to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic transcriptional changes of SE-associated genes. Our results reveal a crucial role of NPC components in the regulation of cell type-specifying genes and highlight nuclear architecture as a regulatory layer of genome functions in cell fate.
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Affiliation(s)
- Arkaitz Ibarra
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Chris Benner
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Swati Tyagi
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jonah Cool
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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157
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Proteomic analysis of the signaling pathway mediated by the heterotrimeric Gα protein Pga1 of Penicillium chrysogenum. Microb Cell Fact 2016; 15:173. [PMID: 27716202 PMCID: PMC5053351 DOI: 10.1186/s12934-016-0564-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/21/2016] [Indexed: 11/18/2022] Open
Abstract
Background The heterotrimeric Gα protein Pga1-mediated signaling pathway regulates the entire developmental program in Penicillium chrysogenum, from spore germination to the formation of conidia. In addition it participates in the regulation of penicillin biosynthesis. We aimed to advance the understanding of this key signaling pathway using a proteomics approach, a powerful tool to identify effectors participating in signal transduction pathways. Results Penicillium chrysogenum mutants with different levels of activity of the Pga1-mediated signaling pathway were used to perform comparative proteomic analyses by 2D-DIGE and LC–MS/MS. Thirty proteins were identified which showed differences in abundance dependent on Pga1 activity level. By modifying the intracellular levels of cAMP we could establish cAMP-dependent and cAMP-independent pathways in Pga1-mediated signaling. Pga1 was shown to regulate abundance of enzymes in primary metabolic pathways involved in ATP, NADPH and cysteine biosynthesis, compounds that are needed for high levels of penicillin production. An in vivo phosphorylated protein containing a pleckstrin homology domain was identified; this protein is a candidate for signal transduction activity. Proteins with possible roles in purine metabolism, protein folding, stress response and morphogenesis were also identified whose abundance was regulated by Pga1 signaling. Conclusions Thirty proteins whose abundance was regulated by the Pga1-mediated signaling pathway were identified. These proteins are involved in primary metabolism, stress response, development and signal transduction. A model describing the pathways through which Pga1 signaling regulates different cellular processes is proposed. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0564-x) contains supplementary material, which is available to authorized users.
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158
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Stratigi K, Chatzidoukaki O, Garinis GA. DNA damage-induced inflammation and nuclear architecture. Mech Ageing Dev 2016; 165:17-26. [PMID: 27702596 DOI: 10.1016/j.mad.2016.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/20/2016] [Accepted: 09/25/2016] [Indexed: 12/12/2022]
Abstract
Nuclear architecture and the chromatin state affect most-if not all- DNA-dependent transactions, including the ability of cells to sense DNA lesions and restore damaged DNA back to its native form. Recent evidence points to functional links between DNA damage sensors, DNA repair mechanisms and the innate immune responses. The latter raises the question of how such seemingly disparate processes operate within the intrinsically complex nuclear landscape and the chromatin environment. Here, we discuss how DNA damage-induced immune responses operate within chromatin and the distinct sub-nuclear compartments highlighting their relevance to chronic inflammation.
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Affiliation(s)
- Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Ourania Chatzidoukaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece; Department of Biology, University of Crete, Vassilika Vouton, GR71409, Heraklion, Crete, Greece.
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159
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Abstract
The nuclear pore complex (NPC) mediates the shuttle transport of macromolecules between the nucleus and cytoplasm in eukaryotic cells. The permeability barrier formed by intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG-Nups) in the NPC functions as the critical selective control for nucleocytoplasmic transport. Signal-independent small molecules (< 40 kDa) passively diffuse through the pore, but passage of large cargo molecules is inhibited unless they are chaperoned by nuclear transport receptors (NTRs). NTRs are capable of interacting with FG-Nups and guide the cargos to cross the barrier by facilitated diffusion. The native conformation of the FG-Nups permeability barrier and the competition among multiple NTRs interacting with this barrier in the native NPCs are the 2 core questions still being highly debated in the field. Recently, we applied high-speed super-resolution fluorescence microscopy to map out the natural structure of the FG-Nups barrier and determined the competition among multiple NTRs as they interact with the barrier in the native NPCs. In this extra-view article, we will review the current understanding in the configuration and function of FG-Nups barrier and highlight the new evidence obtained recently to answer the core questions in nucleocytoplasmic transport.
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Affiliation(s)
- Christina Li
- a Department of Biology , Temple University , Philadelphia , PA , USA
| | | | - Weidong Yang
- a Department of Biology , Temple University , Philadelphia , PA , USA
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160
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Beck M, Baumeister W. Cryo-Electron Tomography: Can it Reveal the Molecular Sociology of Cells in Atomic Detail? Trends Cell Biol 2016; 26:825-837. [PMID: 27671779 DOI: 10.1016/j.tcb.2016.08.006] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
Traditionally, macromolecular structure determination is performed ex situ, that is, with purified materials. But, there are strong incentives to develop approaches to study them in situ in their native functional context. In recent years, cryo-electron tomography (cryo-ET) has emerged as a powerful method for visualizing the molecular organization of unperturbed cellular landscapes with the potential to attain near-atomic resolution. Here, we review recent work on several macromolecular assemblies, demonstrating the power of in situ studies. We also highlight technical challenges and discuss ways to meet them.
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Affiliation(s)
- Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, D-82152 Martinsried (Planegg), Germany.
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161
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Oliveira LN, Casaletti L, Báo SN, Borges CL, de Sousa Lima P, de Almeida Soares CM. Characterizing the nuclear proteome of Paracoccidioides spp. Fungal Biol 2016; 120:1209-24. [PMID: 27647238 DOI: 10.1016/j.funbio.2016.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Paracoccidioidomycosis is an endemic disease in Latin America, caused by thermo dimorphic fungi of the genus Paracoccidioides. Although previous proteome analyses of Paracoccidioides spp. have been carried out, the nuclear subproteome of this pathogen has not been described. In this way, we aimed to characterize the nuclear proteome of Paracoccidioides species, in the yeast form. For that, yeast cells were disrupted and submitted to cell fractionation. The purity of the nuclear fraction was confirmed by fluorescence and electron microscopy. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) allowed the identification of 867 proteins. In order to support our enrichment method for nuclear proteins, bioinformatics analysis were applied that allowed the identification of 281 proteins with nuclear localization. The analysis revealed proteins related to DNA maintenance, gene expression, synthesis and processing of messenger and ribosomal RNAs, likewise proteins of nuclear-cytoplasmic traffic. It was also possible to detect some proteins that are poorly expressed, like transcription factors involved in important roles such as resistance to abiotic stress, sporulation, cellular growth and DNA and chromatin maintenance. This is the first descriptive nuclear proteome of Paracoccidioides spp. that can be useful as an important platform base for fungi-specific nuclear processes.
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Affiliation(s)
- Lucas Nojosa Oliveira
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Luciana Casaletti
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil; Escola de Engenharia, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, 74605-010, Brazil
| | - Sônia Nair Báo
- Laboratório de Microscopia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Distrito Federal, 70910-900, Brazil
| | - Clayton Luiz Borges
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Patrícia de Sousa Lima
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil
| | - Célia Maria de Almeida Soares
- Laboratório de Biologia Molecular, Instituto de Ciências Biológicas, ICB II, Campus II, Universidade Federal de Goiás, Goiânia, Goiás, 74690-900, Brazil.
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162
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Del Viso F, Huang F, Myers J, Chalfant M, Zhang Y, Reza N, Bewersdorf J, Lusk CP, Khokha MK. Congenital Heart Disease Genetics Uncovers Context-Dependent Organization and Function of Nucleoporins at Cilia. Dev Cell 2016; 38:478-92. [PMID: 27593162 PMCID: PMC5021619 DOI: 10.1016/j.devcel.2016.08.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 07/07/2016] [Accepted: 08/08/2016] [Indexed: 01/21/2023]
Abstract
Human genomics is identifying candidate genes for congenital heart disease (CHD), but discovering the underlying mechanisms remains challenging. In a patient with CHD and heterotaxy (Htx), a disorder of left-right patterning, we previously identified a duplication in Nup188. However, a mechanism to explain how a component of the nuclear pore complex (NPC) could cause Htx/CHD was undefined. Here, we show that knockdown of Nup188 or its binding partner Nup93 leads to a loss of cilia during embryonic development while leaving NPC function largely intact. Many data, including the localization of endogenous Nup188/93 at cilia bases, support their direct role at cilia. Super-resolution imaging of Nup188 shows two barrel-like structures with dimensions and organization incompatible with an NPC-like ring, arguing against a proposed "ciliary pore complex." We suggest that the nanoscale organization and function of nucleoporins are context dependent in a way that is required for the structure of the heart.
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Affiliation(s)
- Florencia Del Viso
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Fang Huang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Jordan Myers
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Madeleine Chalfant
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Nooreen Reza
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - C Patrick Lusk
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
| | - Mustafa K Khokha
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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163
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Tie HC, Madugula V, Lu L. The development of a single molecule fluorescence standard and its application in estimating the stoichiometry of the nuclear pore complex. Biochem Biophys Res Commun 2016; 478:1694-9. [PMID: 27613095 DOI: 10.1016/j.bbrc.2016.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
Abstract
We report here an image-based method to quantify the stoichiometry of diffraction-limited sub-cellular protein complexes in vivo under spinning disk confocal microscopy. A GFP single molecule fluorescence standard was first established by immobilizing His-tagged GFP molecules onto the glass surface via nickel nitrilotriacetic acid functionalized polyethylene glycol. When endogenous nucleoporins were knocked down and replaced by the exogenously expressed and knockdown-resistant GFP-nucleoporins, the stoichiometry of the nucleoporin was estimated by the ratio of its fluorescence intensity to that of the GFP single molecules. Our measured stoichiometry of Nup35, Nup93, Nup133 and Nup88 is 23, 18, 14 and 9 and there are possibly16 copies of Nup107-160 complex per nuclear pore complex.
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Affiliation(s)
- Hieng Chiong Tie
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Viswanadh Madugula
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Lei Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
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164
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Wu Z, Jin Z, Zhang X, Shen N, Wang J, Zhao Y, Mei L. Nup62, associated with spindle microtubule rather than spindle matrix, is involved in chromosome alignment and spindle assembly during mitosis. Cell Biol Int 2016; 40:968-75. [PMID: 27298184 DOI: 10.1002/cbin.10633] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022]
Abstract
An increasing number of the active mitotic functions of nucleoporins in the distinct steps of mitosis have been assigned over the past few years. As one of FG-repeats containing nucleoporins, Nup62 has been found to be involved in nuclear transport, cell migration, virus infection, and cell cycle regulation. However, the role and mechanism of Nup62 in mitotic regulation have not been fully revealed. In this paper, it was revealed that a fraction of Nup62 was associated with mitotic spindle microtubule instead of spindle matrix, and the localization of Nup62 in the mitotic spindle depended on its three coiled-coil domains rather than Crm1, although Nup62 strongly interacted with Crm1 during mitosis. Moreover, depletion of Nup62 by small interference of RNA seriously induced the defects of chromosome alignment and spindle assembly although the bipolar spindle was observed in most of the Nup62 knock-down cells. Notably, congression of polar chromosome defect was observed in more than 30% of Nup62 knock-down cells. These findings revealed that Nup62 was a novel mitotic spindle associated nucleoporin and involved in chromosome alignment and spindle assembly.
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Affiliation(s)
- Zhige Wu
- Department of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - Zhihua Jin
- Department of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - Xinhong Zhang
- Department of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - Na Shen
- Department of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - Jinbo Wang
- Department of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - Yingxian Zhao
- Department of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
| | - Lehe Mei
- Department of Biotechnology and Chemical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China
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165
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Zhong J, Zhu X, Luo K, Li L, Tang M, Liu Y, Zhou Z, Huang Y. Direct Cytoplasmic Delivery and Nuclear Targeting Delivery of HPMA-MT Conjugates in a Microtubules Dependent Fashion. Mol Pharm 2016; 13:3069-79. [PMID: 27417390 DOI: 10.1021/acs.molpharmaceut.6b00181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
As the hearts of tumor cells, the nucleus is the ultimate target of many chemotherapeutic agents and genes. However, nuclear drug delivery is always hampered by multiple intracellular obstacles, such as low efficiency of lysosome escape and insufficient nuclear trafficking. Herein, an N-(2-hydroxypropyl) methacrylamide (HPMA) polymer-based drug delivery system was designed, which could achieve direct cytoplasmic delivery by a nonendocytic pathway and transport into the nucleus in a microtubules dependent fashion. A special targeting peptide (MT), derived from an endogenic parathyroid hormone-related protein, was conjugated to the polymer backbone, which could accumulate into the nucleus a by microtubule-mediated pathway. The in vitro studies found that low temperature and NaN3 could not influence the cell internalization of the conjugates. Besides, no obvious overlay of the conjugates with lysosome demonstrated that the polymer conjugates could enter the tumor cell cytoplasm by a nonendocytic pathway, thus avoiding the drug degradation in the lysosome. Furthermore, after suppression of the microtubule dynamics with microtubule stabilizing docetaxel (DTX) and destabilizing nocodazole (Noc), the nuclear accumulation of polymeric conjugates was significantly inhibited. Living cells fluorescence recovery after photobleaching study found that the nuclear import rate of conjugates was 2-fold faster compared with the DTX and Noc treated groups. These results demonstrated that the conjugates transported into the nucleus in a microtubules dependent way. Therefore, in addition to direct cytoplasmic delivery, our peptide conjugated polymeric platform could simultaneously mediate nuclear drug accumulation, which may open a new path for further intracellular genes/peptides delivery.
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Affiliation(s)
- Jiaju Zhong
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministery of Education), West China School of Pharmacy, Sichuan University , NO. 17, Block 3, South Renmin Road, Chengdu 610041, P.R. China
| | - Xi Zhu
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministery of Education), West China School of Pharmacy, Sichuan University , NO. 17, Block 3, South Renmin Road, Chengdu 610041, P.R. China
| | - Kui Luo
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital, Sichuan University , Chengdu 610041, China
| | - Lian Li
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministery of Education), West China School of Pharmacy, Sichuan University , NO. 17, Block 3, South Renmin Road, Chengdu 610041, P.R. China
| | - Manlin Tang
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministery of Education), West China School of Pharmacy, Sichuan University , NO. 17, Block 3, South Renmin Road, Chengdu 610041, P.R. China
| | - Yanxi Liu
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministery of Education), West China School of Pharmacy, Sichuan University , NO. 17, Block 3, South Renmin Road, Chengdu 610041, P.R. China
| | - Zhou Zhou
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministery of Education), West China School of Pharmacy, Sichuan University , NO. 17, Block 3, South Renmin Road, Chengdu 610041, P.R. China
| | - Yuan Huang
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministery of Education), West China School of Pharmacy, Sichuan University , NO. 17, Block 3, South Renmin Road, Chengdu 610041, P.R. China
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166
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A Novel Mutation in Nucleoporin 35 Causes Murine Degenerative Colonic Smooth Muscle Myopathy. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:2254-61. [PMID: 27427419 DOI: 10.1016/j.ajpath.2016.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/01/2016] [Accepted: 04/26/2016] [Indexed: 11/21/2022]
Abstract
Chronic intestinal pseudo-obstruction (CIPO) is a rare but life-threatening disease characterized by severe intestinal dysmotility. Histopathologic studies in CIPO patients have identified several different mechanisms that appear to be involved in the dysmotility, including defects in neurons, smooth muscle, or interstitial cells of Cajal. Currently there are few mouse models of the various forms of CIPO. We generated a mouse with a point mutation in the RNA recognition motif of the Nup35 gene, which encodes a component of the nuclear pore complex. Nup35 mutants developed a severe megacolon and exhibited a reduced lifespan. Histopathologic examination revealed a degenerative myopathy that developed after birth and specifically affected smooth muscle in the colon; smooth muscle in the small bowel and the bladder were not affected. Furthermore, no defects were found in enteric neurons or interstitial cells of Cajal. Nup35 mice are likely to be a valuable model for the subtype of CIPO characterized by degenerative myopathy. Our study also raises the possibility that Nup35 polymorphisms could contribute to some cases of CIPO.
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167
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Herpes simplex virus 1 induces egress channels through marginalized host chromatin. Sci Rep 2016; 6:28844. [PMID: 27349677 PMCID: PMC5378911 DOI: 10.1038/srep28844] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/24/2016] [Indexed: 01/13/2023] Open
Abstract
Lytic infection with herpes simplex virus type 1 (HSV-1) induces profound modification of the cell nucleus including formation of a viral replication compartment and chromatin marginalization into the nuclear periphery. We used three-dimensional soft X-ray tomography, combined with cryogenic fluorescence, confocal and electron microscopy, to analyse the transformation of peripheral chromatin during HSV-1 infection. Our data showed an increased presence of low-density gaps in the marginalized chromatin at late infection. Advanced data analysis indicated the formation of virus-nucleocapsid-sized (or wider) channels extending through the compacted chromatin of the host. Importantly, confocal and electron microscopy analysis showed that these gaps frequently contained viral nucleocapsids. These results demonstrated that HSV-1 infection induces the formation of channels penetrating the compacted layer of cellular chromatin and allowing for the passage of progeny viruses to the nuclear envelope, their site of nuclear egress.
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168
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Lucic B, Lusic M. Connecting HIV-1 integration and transcription: a step toward new treatments. FEBS Lett 2016; 590:1927-39. [PMID: 27224516 DOI: 10.1002/1873-3468.12226] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 12/12/2022]
Abstract
Thanks to the current combined antiretroviral therapy (cART), HIV-1 infection has become a manageable although chronic disease. The reason for this lies in the fact that long-lived cellular reservoirs persist in patients on cART. Despite numerous efforts to understand molecular mechanisms that contribute to viral latency, the important question of how and when latency is established remains unanswered. Related to this is the connection between HIV-1 integration and the capacity of the provirus to enter the latent state. In this review, we will give an overview of these nuclear events in the viral life cycle in the light of current therapeutic approaches, which aim to either reactivate the provirus or even excise the proviral DNA from the cellular genome.
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Affiliation(s)
- Bojana Lucic
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg and German Center for Infection Research (DZIF), Germany
| | - Marina Lusic
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg and German Center for Infection Research (DZIF), Germany
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169
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Fradkin LG, Budnik V. This bud's for you: mechanisms of cellular nucleocytoplasmic trafficking via nuclear envelope budding. Curr Opin Cell Biol 2016; 41:125-31. [PMID: 27236823 DOI: 10.1016/j.ceb.2016.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/03/2016] [Accepted: 05/05/2016] [Indexed: 11/27/2022]
Abstract
The nuclear envelope (NE) physically separates the cytoplasmic and nuclear compartments. While this barrier provides advantages, it also presents a challenge for the nuclear export of large ribonucleoprotein (RNP) complexes. Decades-old dogma holds that all such border-crossing is via the nuclear pore complex (NPC). However, the diameter of the NPC central channel limits the passage of large cargos. Here, we review evidence that such large RNPs employ an endogenous NE-budding pathway, previously thought to be exclusive to the nuclear egress of Herpes viruses. We discuss this and other models proposed, the likelihood that this pathway is conserved, and the consequences of disrupting NE-budding for synapse development, localized translation of synaptic mRNAs, and laminopathies inducing accelerated aging.
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Affiliation(s)
- Lee G Fradkin
- Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA
| | - Vivian Budnik
- Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA.
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170
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Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH, Hetzer MW. Evolution of a transcriptional regulator from a transmembrane nucleoporin. Genes Dev 2016; 30:1155-71. [PMID: 27198230 PMCID: PMC4888837 DOI: 10.1101/gad.280941.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/26/2016] [Indexed: 11/24/2022]
Abstract
Franks et al. identify a widely expressed variant of the transmembrane nucleoporin Pom121 (named sPom121, for “soluble Pom121”) that arose by genomic rearrangement before the divergence of hominoids. Instead of localizing to the NPC, sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified transcriptional regulator, at gene promoters to control transcription of its target genes in human cells. Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo–cytoplasmic transport, recent research suggests that certain NPC proteins have additionally acquired the role of affecting gene expression at the nuclear periphery and in the nucleoplasm in metazoans. Here we identify a widely expressed variant of the transmembrane nucleoporin (Nup) Pom121 (named sPom121, for “soluble Pom121”) that arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead, sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified transcriptional regulator, at gene promoters to control transcription of its target genes in human cells. Interestingly, sPom121 transcripts appear independently in several mammalian species, suggesting convergent innovation of Nup-mediated transcription regulation during mammalian evolution. Our findings implicate alternate transcription initiation as a mechanism to increase the functional diversity of NPC components.
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Affiliation(s)
- Tobias M Franks
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Chris Benner
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Iñigo Narvaiza
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Maria C N Marchetto
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Janet M Young
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Harmit S Malik
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Fred H Gage
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California 92037, USA; Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, California 92093, USA
| | - Martin W Hetzer
- Laboratory of Molecular and Cellular Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA
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171
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Kosinski J, Mosalaganti S, von Appen A, Teimer R, DiGuilio AL, Wan W, Bui KH, Hagen WJ, Briggs JAG, Glavy JS, Hurt E, Beck M. Molecular architecture of the inner ring scaffold of the human nuclear pore complex. Science 2016; 352:363-365. [PMID: 27081072 PMCID: PMC8926079 DOI: 10.1126/science.aaf0643] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/19/2016] [Indexed: 07/21/2023]
Abstract
Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar.
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Affiliation(s)
- Jan Kosinski
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Shyamal Mosalaganti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Alexander von Appen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Roman Teimer
- Biochemistry Center of Heidelberg University, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Amanda L. DiGuilio
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 507 River Street, Hoboken, NJ 07030, USA
| | - William Wan
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Khanh Huy Bui
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Wim J.H. Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - John A. G. Briggs
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Joseph S. Glavy
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, 507 River Street, Hoboken, NJ 07030, USA
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, Im Neuenheimer Feld 328, D-69120 Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
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172
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Nucleoporin genes in human diseases. Eur J Hum Genet 2016; 24:1388-95. [PMID: 27071718 DOI: 10.1038/ejhg.2016.25] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 02/04/2016] [Accepted: 03/01/2016] [Indexed: 12/22/2022] Open
Abstract
Nuclear pore complexes (NPCs) are large channels spanning the nuclear envelope that mediate nucleocytoplasmic transport. They are composed of multiple copies of ~30 proteins termed nucleoporins (NUPs). Alterations in NUP genes are linked to several human neoplastic and non-neoplastic diseases. This review focuses on NUPs, their genes, localization, function in the NPC and involvement in human diseases.
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173
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Wang WM, Liu PQ, Xu YJ, Xiao S. Protein trafficking during plant innate immunity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:284-98. [PMID: 26345282 DOI: 10.1111/jipb.12426] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/06/2015] [Indexed: 05/20/2023]
Abstract
Plants have evolved a sophisticated immune system to fight against pathogenic microbes. Upon detection of pathogen invasion by immune receptors, the immune system is turned on, resulting in production of antimicrobial molecules including pathogenesis-related (PR) proteins. Conceivably, an efficient immune response depends on the capacity of the plant cell's protein/membrane trafficking network to deploy the right defense-associated molecules in the right place at the right time. Recent research in this area shows that while the abundance of cell surface immune receptors is regulated by endocytosis, many intracellular immune receptors, when activated, are partitioned between the cytoplasm and the nucleus for induction of defense genes and activation of programmed cell death, respectively. Vesicle transport is an essential process for secretion of PR proteins to the apoplastic space and targeting of defense-related proteins to the plasma membrane or other endomembrane compartments. In this review, we discuss the various aspects of protein trafficking during plant immunity, with a focus on the immunity proteins on the move and the major components of the trafficking machineries engaged.
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Affiliation(s)
- Wen-Ming Wang
- Rice Research Institute & Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peng-Qiang Liu
- Rice Research Institute & Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yong-Ju Xu
- Rice Research Institute & Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research & Department of Plant Science and Landscape Architecture, University of Maryland, Rockville, MD, 20850, USA
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174
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Closing a gap in the nuclear envelope. Curr Opin Cell Biol 2016; 40:90-97. [PMID: 27016712 DOI: 10.1016/j.ceb.2016.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/13/2016] [Accepted: 03/05/2016] [Indexed: 11/22/2022]
Abstract
The nuclear envelope (NE) ensures nucleo-cytoplasmic compartmentalization, with trafficking of macromolecules across this double membrane controlled by embedded nuclear pore complexes (NPCs). The NE and associated proteins are dismantled during open mitosis and reestablishment of this barrier during mitotic exit requires dynamic remodeling of endoplasmic reticulum (ER) membranes and coordination with NPC reformation, with NPC deposition continuing during subsequent interphase. In this review, we discuss recent progress in our understanding of NE reformation and nuclear pore complex generation, with special focus on work implicating the endosomal sorting complex required for transport (ESCRT) membrane remodeling machinery in these events.
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175
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Gallemí M, Galstyan A, Paulišić S, Then C, Ferrández-Ayela A, Lorenzo-Orts L, Roig-Villanova I, Wang X, Micol JL, Ponce MR, Devlin PF, Martínez-García JF. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development 2016; 143:1623-31. [PMID: 26989173 DOI: 10.1242/dev.130211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 03/03/2016] [Indexed: 12/28/2022]
Abstract
When plants grow in close proximity basic resources such as light can become limiting. Under such conditions plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). Following genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporins, participates positively in the control of the hypocotyl elongation response to plant proximity, a role that can be considered dependent on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport independent and that it might rely on its dynamic localization within and outside of the NPC. These results provide mechanistic insights in to how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling.
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Affiliation(s)
- Marçal Gallemí
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Anahit Galstyan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Sandi Paulišić
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Christiane Then
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | | | - Laura Lorenzo-Orts
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Irma Roig-Villanova
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Xuewen Wang
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Jose Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Maria Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Paul F Devlin
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Jaime F Martínez-García
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Ps. Lluís Companys 10, 08010 Barcelona, Spain
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176
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Mechanisms of Nuclear Export in Cancer and Resistance to Chemotherapy. Cancers (Basel) 2016; 8:cancers8030035. [PMID: 26985906 PMCID: PMC4810119 DOI: 10.3390/cancers8030035] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 03/03/2016] [Accepted: 03/08/2016] [Indexed: 01/14/2023] Open
Abstract
Tumour suppressor proteins, such as p53, BRCA1, and ABC, play key roles in preventing the development of a malignant phenotype, but those that function as transcriptional regulators need to enter the nucleus in order to function. The export of proteins between the nucleus and cytoplasm is complex. It occurs through nuclear pores and exported proteins need a nuclear export signal (NES) to bind to nuclear exportin proteins, including CRM1 (Chromosomal Region Maintenance protein 1), and the energy for this process is provided by the RanGTP/RanGDP gradient. Due to the loss of DNA repair and cell cycle checkpoints, drug resistance is a major problem in cancer treatment, and often an initially successful treatment will fail due to the development of resistance. An important mechanism underlying resistance is nuclear export, and a number of strategies that can prevent nuclear export may reverse resistance. Examples include inhibitors of CRM1, antibodies to the nuclear export signal, and alteration of nuclear pore structure. Each of these are considered in this review.
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177
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Musser SM, Grünwald D. Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches. J Mol Biol 2016; 428:2091-119. [PMID: 26944195 DOI: 10.1016/j.jmb.2016.02.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/05/2016] [Accepted: 02/17/2016] [Indexed: 01/06/2023]
Abstract
Due to its central role in macromolecular trafficking and nucleocytoplasmic information transfer, the nuclear pore complex (NPC) has been studied in great detail using a wide spectrum of methods. Consequently, many aspects of its architecture, general function, and role in the life cycle of a cell are well understood. Over the last decade, fluorescence microscopy methods have enabled the real-time visualization of single molecules interacting with and transiting through the NPC, allowing novel questions to be examined with nanometer precision. While initial single-molecule studies focused primarily on import pathways using permeabilized cells, it has recently proven feasible to investigate the export of mRNAs in living cells. Single-molecule assays can address questions that are difficult or impossible to answer by other means, yet the complexity of nucleocytoplasmic transport requires that interpretation be based on a firm genetic, biochemical, and structural foundation. Moreover, conceptually simple single-molecule experiments remain technically challenging, particularly with regard to signal intensity, signal-to-noise ratio, and the analysis of noise, stochasticity, and precision. We discuss nuclear transport issues recently addressed by single-molecule microscopy, evaluate the limits of existing assays and data, and identify open questions for future studies. We expect that single-molecule fluorescence approaches will continue to be applied to outstanding nucleocytoplasmic transport questions, and that the approaches developed for NPC studies are extendable to additional complex systems and pathways within cells.
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Affiliation(s)
- Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, 1114 TAMU, College Station, TX 77843, USA.
| | - David Grünwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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178
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Kobayashi A, Hashizume C, Dowaki T, Wong RW. Therapeutic potential of mitotic interaction between the nucleoporin Tpr and aurora kinase A. Cell Cycle 2016; 14:1447-58. [PMID: 25789545 DOI: 10.1080/15384101.2015.1021518] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Spindle poles are defined by centrosomes; therefore, an abnormal number or defective structural organization of centrosomes can lead to loss of spindle bipolarity and genetic integrity. Previously, we showed that Tpr (translocated promoter region), a component of the nuclear pore complex (NPC), interacts with Mad1 and dynein to promote proper chromosome segregation during mitosis. Tpr also associates with p53 to induce autophagy. Here, we report that Tpr depletion induces mitotic catastrophe and enhances the rate of tetraploidy and polyploidy. Mechanistically, Tpr interacts, via its central domain, with Aurora A but not Aurora B kinase. In Tpr-depleted cells, the expression levels, centrosomal localization and phosphorylation of Aurora A were all reduced. Surprisingly, an Aurora A inhibitor, Alisertib (MLN8237), also disrupted centrosomal localization of Tpr and induced mitotic catastrophe and cell death in a time- and dose-dependent manner. Strikingly, over-expression of Aurora A disrupted Tpr centrosomal localization only in cells with supernumerary centrosomes but not in bipolar cells. Our results highlight the mutual regulation between Tpr and Aurora A and further confirm the importance of nucleoporin function in spindle pole organization, bipolar spindle assembly, and mitosis; functions that are beyond the conventional nucleocytoplasmic transport and NPC structural roles of nucleoporins. Furthermore, the central coiled-coil domain of Tpr binds to and sequesters extra Aurora A to safeguard bipolarity. This Tpr domain merits further investigation for its ability to inhibit Aurora kinase and as a potential therapeutic agent in cancer treatment.
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Affiliation(s)
- Akiko Kobayashi
- a Laboratory of Molecular and Cellular Biology; Department of Biology ; Faculty of Natural Systems; Kanazawa University ; Kanazawa , Ishikawa , Japan
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179
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Jahed Z, Soheilypour M, Peyro M, Mofrad MRK. The LINC and NPC relationship – it's complicated! J Cell Sci 2016; 129:3219-29. [DOI: 10.1242/jcs.184184] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT
The genetic information of eukaryotic cells is enclosed within a double-layered nuclear envelope, which comprises an inner and outer nuclear membrane. Several transmembrane proteins locate to the nuclear envelope; however, only two integral protein complexes span the nuclear envelope and connect the inside of the nucleus to the cytoplasm. The nuclear pore complex (NPC) acts as a gateway for molecular exchange between the interior of the nucleus and the cytoplasm, whereas so-called LINC complexes physically link the nucleoskeleton and the cytoskeleton. In this Commentary, we will discuss recent studies that have established direct functional associations between these two complexes. The assembly of NPCs and their even distribution throughout the nuclear envelope is dependent on components of the LINC complex. Additionally, LINC complex formation is dependent on the successful localization of inner nuclear membrane components of LINC complexes and their transport through the NPC. Furthermore, the architecture of the nuclear envelope depends on both protein complexes. Finally, we will present recent evidence showing that LINC complexes can affect nucleo-cytoplasmic transport through the NPC, further highlighting the importance of understanding the associations of these essential complexes at the nuclear envelope.
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Affiliation(s)
- Zeinab Jahed
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Mohammad Soheilypour
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Mohaddeseh Peyro
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
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180
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Takao D, Verhey KJ. Gated entry into the ciliary compartment. Cell Mol Life Sci 2016; 73:119-27. [PMID: 26472341 PMCID: PMC4959937 DOI: 10.1007/s00018-015-2058-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 11/26/2022]
Abstract
Cilia and flagella play important roles in cell motility and cell signaling. These functions require that the cilium establishes and maintains a unique lipid and protein composition. Recent work indicates that a specialized region at the base of the cilium, the transition zone, serves as both a barrier to entry and a gate for passage of select components. For at least some cytosolic proteins, the barrier and gate functions are provided by a ciliary pore complex (CPC) that shares molecular and mechanistic properties with nuclear gating. Specifically, nucleoporins of the CPC limit the diffusional entry of cytosolic proteins in a size-dependent manner and enable the active transport of large molecules and complexes via targeting signals, importins, and the small G protein Ran. For membrane proteins, the septin protein SEPT2 is part of the barrier to entry whereas the gating function is carried out and/or regulated by proteins associated with ciliary diseases (ciliopathies) such as nephronophthisis, Meckel–Gruber syndrome and Joubert syndrome. Here, we discuss the evidence behind these models of ciliary gating as well as the similarities to and differences from nuclear gating.
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Affiliation(s)
- Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA
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181
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Giacomini C, Mahajani S, Ruffilli R, Marotta R, Gasparini L. Lamin B1 protein is required for dendrite development in primary mouse cortical neurons. Mol Biol Cell 2016; 27:35-47. [PMID: 26510501 PMCID: PMC4694760 DOI: 10.1091/mbc.e15-05-0307] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/07/2015] [Accepted: 10/23/2015] [Indexed: 01/15/2023] Open
Abstract
Lamin B1, a key component of the nuclear lamina, plays an important role in brain development and function. A duplication of the human lamin B1 (LMNB1) gene has been linked to adult-onset autosomal dominant leukodystrophy, and mouse and human loss-of-function mutations in lamin B1 are susceptibility factors for neural tube defects. In the mouse, experimental ablation of endogenous lamin B1 (Lmnb1) severely impairs embryonic corticogenesis. Here we report that in primary mouse cortical neurons, LMNB1 overexpression reduces axonal outgrowth, whereas deficiency of endogenous Lmnb1 results in aberrant dendritic development. In the absence of Lmnb1, both the length and complexity of dendrites are reduced, and their growth is unresponsive to KCl stimulation. This defective dendritic outgrowth stems from impaired ERK signaling. In Lmnb1-null neurons, ERK is correctly phosphorylated, but phospho-ERK fails to translocate to the nucleus, possibly due to delocalization of nuclear pore complexes (NPCs) at the nuclear envelope. Taken together, these data highlight a previously unrecognized role of lamin B1 in dendrite development of mouse cortical neurons through regulation of nuclear shuttling of specific signaling molecules and NPC distribution.
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Affiliation(s)
- Caterina Giacomini
- Molecular Neurodegeneration Lab, Neuroscience and Brain Technologies Department, 16163 Genoa, Italy
| | - Sameehan Mahajani
- Molecular Neurodegeneration Lab, Neuroscience and Brain Technologies Department, 16163 Genoa, Italy
| | - Roberta Ruffilli
- Electron Microscopy Lab, Nanochemistry Department, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Roberto Marotta
- Electron Microscopy Lab, Nanochemistry Department, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - Laura Gasparini
- Molecular Neurodegeneration Lab, Neuroscience and Brain Technologies Department, 16163 Genoa, Italy
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182
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Mohammad RM, Muqbil I, Lowe L, Yedjou C, Hsu HY, Lin LT, Siegelin MD, Fimognari C, Kumar NB, Dou QP, Yang H, Samadi AK, Russo GL, Spagnuolo C, Ray SK, Chakrabarti M, Morre JD, Coley HM, Honoki K, Fujii H, Georgakilas AG, Amedei A, Niccolai E, Amin A, Ashraf SS, Helferich WG, Yang X, Boosani CS, Guha G, Bhakta D, Ciriolo MR, Aquilano K, Chen S, Mohammed SI, Keith WN, Bilsland A, Halicka D, Nowsheen S, Azmi AS. Broad targeting of resistance to apoptosis in cancer. Semin Cancer Biol 2015; 35 Suppl:S78-S103. [PMID: 25936818 PMCID: PMC4720504 DOI: 10.1016/j.semcancer.2015.03.001] [Citation(s) in RCA: 517] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 12/15/2022]
Abstract
Apoptosis or programmed cell death is natural way of removing aged cells from the body. Most of the anti-cancer therapies trigger apoptosis induction and related cell death networks to eliminate malignant cells. However, in cancer, de-regulated apoptotic signaling, particularly the activation of an anti-apoptotic systems, allows cancer cells to escape this program leading to uncontrolled proliferation resulting in tumor survival, therapeutic resistance and recurrence of cancer. This resistance is a complicated phenomenon that emanates from the interactions of various molecules and signaling pathways. In this comprehensive review we discuss the various factors contributing to apoptosis resistance in cancers. The key resistance targets that are discussed include (1) Bcl-2 and Mcl-1 proteins; (2) autophagy processes; (3) necrosis and necroptosis; (4) heat shock protein signaling; (5) the proteasome pathway; (6) epigenetic mechanisms; and (7) aberrant nuclear export signaling. The shortcomings of current therapeutic modalities are highlighted and a broad spectrum strategy using approaches including (a) gossypol; (b) epigallocatechin-3-gallate; (c) UMI-77 (d) triptolide and (e) selinexor that can be used to overcome cell death resistance is presented. This review provides a roadmap for the design of successful anti-cancer strategies that overcome resistance to apoptosis for better therapeutic outcome in patients with cancer.
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Affiliation(s)
- Ramzi M Mohammad
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States; Interim translational Research Institute, Hamad Medical Corporation, Doha, Qatar.
| | - Irfana Muqbil
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
| | - Leroy Lowe
- Getting to Know Cancer, Truro, Nova Scotia, Canada
| | - Clement Yedjou
- C-SET, [Jackson, #229] State University, Jackson, MS, United States
| | - Hsue-Yin Hsu
- Department of Life Sciences, Tzu-Chi University, Hualien, Taiwan
| | - Liang-Tzung Lin
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Markus David Siegelin
- Department of Pathology and Cell Biology, Columbia University, New York City, NY, United States
| | - Carmela Fimognari
- Dipartimento di Scienze per la Qualità della Vita Alma Mater Studiorum-Università di Bologna, Italy
| | - Nagi B Kumar
- Moffit Cancer Center, University of South Florida College of Medicine, Tampa, FL, United States
| | - Q Ping Dou
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States; Departments of Pharmacology and Pathology, Karmanos Cancer Institute, Detroit MI, United States
| | - Huanjie Yang
- The School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | | | - Gian Luigi Russo
- Institute of Food Sciences National Research Council, Avellino, Italy
| | - Carmela Spagnuolo
- Institute of Food Sciences National Research Council, Avellino, Italy
| | - Swapan K Ray
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Mrinmay Chakrabarti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - James D Morre
- Mor-NuCo, Inc, Purdue Research Park, West Lafayette, IN, United States
| | - Helen M Coley
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Kanya Honoki
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Japan
| | - Hiromasa Fujii
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Japan
| | - Alexandros G Georgakilas
- Department of Physics, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou 15780, Athens, Greece
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, university of florence, Italy
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, university of florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, UAE University, United Arab Emirates; Faculty of Science, Cairo University, Egypt
| | - S Salman Ashraf
- Department of Chemistry, College of Science, UAE University, United Arab Emirates
| | - William G Helferich
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Xujuan Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Chandra S Boosani
- Department of BioMedical Sciences, School of Medicine Creighton University, Omaha NE, United States
| | - Gunjan Guha
- School of Chemical and Bio Technology, SASTRA University, Thanjavur, India
| | - Dipita Bhakta
- School of Chemical and Bio Technology, SASTRA University, Thanjavur, India
| | | | - Katia Aquilano
- Department of Biology, University of Rome "Tor Vergata", Italy
| | - Sophie Chen
- Ovarian and Prostate Cancer Research Trust Laboratory, Guildford, Surrey, United Kingdom
| | - Sulma I Mohammed
- Department of Comparative Pathobiology and Purdue University Center for Cancer Research, Purdue, West Lafayette, IN, United States
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Ireland
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Ireland
| | - Dorota Halicka
- Department of Pathology, New York Medical College, Valhalla, NY, United States
| | - Somaira Nowsheen
- Mayo Graduate School, Mayo Medical School, Mayo Clinic Medical Scientist Training Program, Rochester, MN, United States
| | - Asfar S Azmi
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
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183
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Gong Y, Huang C, Li JZ, Grewe BF, Zhang Y, Eismann S, Schnitzer MJ. High-speed recording of neural spikes in awake mice and flies with a fluorescent voltage sensor. Science 2015; 350:1361-6. [PMID: 26586188 DOI: 10.1126/science.aab0810] [Citation(s) in RCA: 290] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 11/10/2015] [Indexed: 12/15/2022]
Abstract
Genetically encoded voltage indicators (GEVIs) are a promising technology for fluorescence readout of millisecond-scale neuronal dynamics. Previous GEVIs had insufficient signaling speed and dynamic range to resolve action potentials in live animals. We coupled fast voltage-sensing domains from a rhodopsin protein to bright fluorophores through resonance energy transfer. The resulting GEVIs are sufficiently bright and fast to report neuronal action potentials and membrane voltage dynamics in awake mice and flies, resolving fast spike trains with 0.2-millisecond timing precision at spike detection error rates orders of magnitude better than previous GEVIs. In vivo imaging revealed sensory-evoked responses, including somatic spiking, dendritic dynamics, and intracellular voltage propagation. These results empower in vivo optical studies of neuronal electrophysiology and coding and motivate further advancements in high-speed microscopy.
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Affiliation(s)
- Yiyang Gong
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA. CNC Program, Stanford University, Stanford, CA 94305, USA. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
| | - Cheng Huang
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Jin Zhong Li
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA. CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Benjamin F Grewe
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA. CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Yanping Zhang
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA. CNC Program, Stanford University, Stanford, CA 94305, USA. Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Stephan Eismann
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA. CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Mark J Schnitzer
- James H. Clark Center, Stanford University, Stanford, CA 94305, USA. CNC Program, Stanford University, Stanford, CA 94305, USA. Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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184
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A Novel Saccharomyces cerevisiae FG Nucleoporin Mutant Collection for Use in Nuclear Pore Complex Functional Experiments. G3-GENES GENOMES GENETICS 2015; 6:51-8. [PMID: 26530420 PMCID: PMC4704724 DOI: 10.1534/g3.115.023002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
FG nucleoporins (Nups) are the class of proteins that both generate the permeability barrier and mediate selective transport through the nuclear pore complex (NPC). The FG Nup family has 11 members in Saccharomyces cerevisiae, and the study of mutants lacking different FG domains has been instrumental in testing transport models. To continue analyzing the distinct functional roles of FG Nups in vivo, additional robust genetic tools are required. Here, we describe a novel collection of S. cerevisiae mutant strains in which the FG domains of different groups of Nups are absent (Δ) in the greatest number documented to date. Using this plasmid-based ΔFG strategy, we find that a GLFG domain-only pore is sufficient for viability. The resulting extensive plasmid and strain resources are available to the scientific community for future in-depth in vivo studies of NPC transport.
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185
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Kwon HK, Lee JH, Shin HJ, Kim JH, Choi S. Structural and functional analysis of cell adhesion and nuclear envelope nano-topography in cell death. Sci Rep 2015; 5:15623. [PMID: 26490051 PMCID: PMC4614995 DOI: 10.1038/srep15623] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/28/2015] [Indexed: 01/19/2023] Open
Abstract
The cell death mechanisms of necrosis and apoptosis generate biochemical and morphological changes in different manners. However, the changes that occur in cell adhesion and nuclear envelope (NE) topography, during necrosis and apoptosis, are not yet fully understood. Here, we show the different alterations in cell adhesion function, as well as the topographical changes occurring to the NE, during the necrotic and apoptotic cell death process, using the xCELLigence system and atomic force microscopy (AFM). Studies using xCELLigence technology and AFM have shown that necrotic cell death induced the expansion of the cell adhesion area, but did not affect the speed of cell adhesion. Necrotic nuclei showed a round shape and presence of nuclear pore complexes (NPCs). Moreover, we found that the process of necrosis in combination with apoptosis (termed nepoptosis here) resulted in the reduction of the cell adhesion area and cell adhesion speed through the activation of caspases. Our findings showed, for the first time, a successful characterization of NE topography and cell adhesion during necrosis and apoptosis, which may be of importance for the understanding of cell death and might aid the design of future drug delivery methods for anti-cancer therapies.
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Affiliation(s)
- Hyuk-Kwon Kwon
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Jae-Hyeok Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.,Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Hyeon-Jun Shin
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Jae-Ho Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
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186
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Yeast Integral Membrane Proteins Apq12, Brl1, and Brr6 Form a Complex Important for Regulation of Membrane Homeostasis and Nuclear Pore Complex Biogenesis. EUKARYOTIC CELL 2015; 14:1217-27. [PMID: 26432634 DOI: 10.1128/ec.00101-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/01/2015] [Indexed: 11/20/2022]
Abstract
Proper functioning of intracellular membranes is critical for many cellular processes. A key feature of membranes is their ability to adapt to changes in environmental conditions by adjusting their composition so as to maintain constant biophysical properties, including fluidity and flexibility. Similar changes in the biophysical properties of membranes likely occur when intracellular processes, such as vesicle formation and fusion, require dramatic changes in membrane curvature. Similar modifications must also be made when nuclear pore complexes (NPCs) are constructed within the existing nuclear membrane, as occurs during interphase in all eukaryotes. Here we report on the role of the essential nuclear envelope/endoplasmic reticulum (NE/ER) protein Brl1 in regulating the membrane composition of the NE/ER. We show that Brl1 and two other proteins characterized previously-Brr6, which is closely related to Brl1, and Apq12-function together and are required for lipid homeostasis. All three transmembrane proteins are localized to the NE and can be coprecipitated. As has been shown for mutations affecting Brr6 and Apq12, mutations in Brl1 lead to defects in lipid metabolism, increased sensitivity to drugs that inhibit enzymes involved in lipid synthesis, and strong genetic interactions with mutations affecting lipid metabolism. Mutations affecting Brl1 or Brr6 or the absence of Apq12 leads to hyperfluid membranes, because mutant cells are hypersensitive to agents that increase membrane fluidity. We suggest that the defects in nuclear pore complex biogenesis and mRNA export seen in these mutants are consequences of defects in maintaining the biophysical properties of the NE.
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187
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Chaumet A, Wright GD, Seet SH, Tham KM, Gounko NV, Bard F. Nuclear envelope-associated endosomes deliver surface proteins to the nucleus. Nat Commun 2015; 6:8218. [PMID: 26356418 PMCID: PMC4579783 DOI: 10.1038/ncomms9218] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/29/2015] [Indexed: 01/16/2023] Open
Abstract
Endocytosis directs molecular cargo along three main routes: recycling to the cell surface, transport to the Golgi apparatus or degradation in endolysosomes. Pseudomonas exotoxin A (PE) is a bacterial protein that typically traffics to the Golgi and then the endoplasmic reticulum before translocating to the cytosol. Here we show that a substantial fraction of internalized PE is also located in nuclear envelope-associated endosomes (NAE), which display limited mobility, exhibit a propensity to undergo fusion and readily discharge their contents into the nuclear envelope. Electron microscopy and protein trapping in the nucleus indicate that NAE mediate PE transfer into the nucleoplasm. RNAi screening further revealed that NAE-mediated transfer depends on the nuclear envelope proteins SUN1 and SUN2, as well as the Sec61 translocon complex. These data reveal a novel endosomal route from the cell surface to the nucleoplasm that facilitates the accumulation of extracellular and cell surface proteins in the nucleus.
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Affiliation(s)
- Alexandre Chaumet
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Graham D. Wright
- Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore
- Joint IMB-IMCB Electron Microscopy Suite, 20 Biopolis Street, #B2-14 Matrix, Singapore 138671, Singapore
| | - Sze Hwee Seet
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Keit Min Tham
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Natalia V. Gounko
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Institute of Medical Biology, 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore
- Joint IMB-IMCB Electron Microscopy Suite, 20 Biopolis Street, #B2-14 Matrix, Singapore 138671, Singapore
| | - Frederic Bard
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Department of Biochemistry, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
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188
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Blanco E, Shen H, Ferrari M. Principles of nanoparticle design for overcoming biological barriers to drug delivery. Nat Biotechnol 2015; 33:941-51. [PMID: 26348965 PMCID: PMC4978509 DOI: 10.1038/nbt.3330] [Citation(s) in RCA: 4101] [Impact Index Per Article: 455.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 07/29/2015] [Indexed: 12/11/2022]
Abstract
Biological barriers to drug transport prevent successful accumulation of nanotherapeutics specifically at diseased sites, limiting efficacious responses in disease processes ranging from cancer to inflammation. Although substantial research efforts have aimed to incorporate multiple functionalities and moieties within the overall nanoparticle design, many of these strategies fail to adequately address these barriers. Obstacles, such as nonspecific distribution and inadequate accumulation of therapeutics, remain formidable challenges to drug developers. A reimagining of conventional nanoparticles is needed to successfully negotiate these impediments to drug delivery. Site-specific delivery of therapeutics will remain a distant reality unless nanocarrier design takes into account the majority, if not all, of the biological barriers that a particle encounters upon intravenous administration. By successively addressing each of these barriers, innovative design features can be rationally incorporated that will create a new generation of nanotherapeutics, realizing a paradigmatic shift in nanoparticle-based drug delivery.
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Affiliation(s)
- Elvin Blanco
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, Texas, USA
| | - Haifa Shen
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York, USA
| | - Mauro Ferrari
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
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189
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Selective Removal of FG Repeat Domains from the Nuclear Pore Complex by Enterovirus 2A(pro). J Virol 2015; 89:11069-79. [PMID: 26311873 DOI: 10.1128/jvi.00956-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 08/20/2015] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Enteroviruses proteolyze nuclear pore complex (NPC) proteins (Nups) during infection, leading to disruption of host nuclear transport pathways and alterations in nuclear permeability. To better understand how enteroviruses exert these effects on nuclear transport, the mechanisms and consequences of Nup98 proteolysis were examined. The results indicate that Nup98 is rapidly targeted for degradation following enterovirus infection and that this is mediated by the enterovirus 2A protease (2A(pro)). Incubation of bacterially expressed or in vitro-translated Nup98 with 2A(pro) results in proteolytic cleavage at multiple sites in vitro, indicating that 2A(pro) cleaves Nup98 directly. Site-directed mutagenesis of putative cleavage sites identified Gly374 and Gly552 as the sites of 2A(pro) proteolysis in Nup98 in vitro and in infected cells. Indirect immunofluorescence assays using an antibody that recognizes the N terminus of Nup98 revealed that proteolysis releases the N-terminal FG-rich region from the NPC. In contrast, similar analyses using an antibody to the C terminus indicated that this region is retained at the nuclear rim. Nup88, a core NPC component that serves as a docking site for Nup98, also remains at the NPC in infected cells. These findings support a model whereby the selective removal of Nup FG repeat domains leads to increased NPC permeability and inhibition of certain transport pathways, while retention of structural domains maintains the overall NPC structure and leaves other transport pathways unaffected. IMPORTANCE Enteroviruses are dependent upon host nuclear RNA binding proteins for efficient replication. This study examines the mechanisms responsible for alterations in nuclear transport in enterovirus-infected cells that lead to the cytoplasmic accumulation of these proteins. The results demonstrate that the enterovirus 2A protease directly cleaves the nuclear pore complex (NPC) protein, Nup98, at amino acid positions G374 and G552 both in vitro and in infected cells. Cleavage at these positions results in the selective removal of the FG-containing N terminus of Nup98 from the NPC, while the C terminus remains associated. Nup88, a core component of the NPC that serves as a docking site for the C terminus of Nup98, remains associated with the NPC in infected cells. These findings help to explain the alterations in permeability and nuclear transport in enterovirus-infected cells and how NPCs remain functional for certain trafficking pathways despite significant alterations to their compositions.
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190
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Munawar N, Olivero G, Jerman E, Doyle B, Streubel G, Wynne K, Bracken A, Cagney G. Native gel analysis of macromolecular protein complexes in cultured mammalian cells. Proteomics 2015. [PMID: 26223664 DOI: 10.1002/pmic.201500045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Native gel electrophoresis enables separation of cellular proteins in their non-denatured state. In experiments aimed at analysing proteins in higher order or multimeric assemblies (i.e. protein complexes) it offers some advantages over rival approaches, particularly as an interface technology with mass spectrometry. Here we separated fractions from HEK293 cells by native electrophoresis in order to survey protein complexes in the cytoplasmic, nuclear and chromatin environments, finding 689 proteins distributed among 217 previously described complexes. As expected, different fractions contained distinct combinations of macromolecular complexes, with subunits of the same complex tending to co-migrate. Exceptions to this observation could often be explained by the presence of subunits shared among different complexes. We investigated one identified complex, the Polycomb Repressor Complex 2 (PRC2), in more detail following affinity purification of the EZH2 subunit. This approach resulted in the identification of all previously reported members of PRC2. Overall, this work demonstrates that the use of native gel electrophoresis as an upstream separating step is an effective approach for analysis of the components and cellular distribution of protein complexes.
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Affiliation(s)
- Nayla Munawar
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
| | - Giorgio Olivero
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
| | - Emilia Jerman
- Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
| | - Benjamin Doyle
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
| | | | - Kieran Wynne
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
| | - Adrian Bracken
- Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
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191
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Munawar N, Olivero G, Jerman E, Doyle B, Streubel G, Wynne K, Bracken A, Cagney G. Native gel analysis of macromolecular protein complexes in cultured mammalian cells. Proteomics 2015. [DOI: https://doi.org/10.1002/pmic.201500045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nayla Munawar
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | - Giorgio Olivero
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | - Emilia Jerman
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
| | - Benjamin Doyle
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | | | - Kieran Wynne
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
| | - Adrian Bracken
- Smurfit Institute of Genetics; Trinity College; Dublin Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Research; University College Dublin; Belfield Ireland
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192
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Xu L, Pan L, Li J, Huang B, Feng J, Li C, Wang S, The E, Liu Y, Yuan T, Zhen L, Liang D, Liu Y, Li L, Cui Y, Jiang X, Peng L, Chen YH. Nucleoporin 35 regulates cardiomyocyte pH homeostasis by controlling Na+-H+ exchanger-1 expression. J Mol Cell Biol 2015; 7:476-85. [PMID: 26260029 DOI: 10.1093/jmcb/mjv054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 06/08/2015] [Indexed: 12/23/2022] Open
Abstract
The mammalian nuclear pore complex is comprised of ∼ 30 different nucleoporins (Nups). It governs the nuclear import of gene expression modulators and the export of mRNAs. In cardiomyocytes, Na(+)-H(+) exchanger-1 (NHE1) is an integral membrane protein that exclusively regulates intracellular pH (pHi) by exchanging one intracellular H(+) for one extracellular Na(+). However, the role of Nups in cardiac NHE1 expression remains unknown. We herein report that Nup35 regulates cardiomyocyte NHE1 expression by controlling the nucleo-cytoplasmic trafficking of nhe1 mRNA. The N-terminal domain of Nup35 determines nhe1 mRNA nuclear export by targeting the 5'-UTR (-412 to -213 nt) of nhe1 mRNA. Nup35 ablation weakens the resistance of cardiomyocytes to an acid challenge by depressing NHE1 expression. Moreover, we identify that Nup35 and NHE1 are simultaneously downregulated in ischemic cardiomyocytes both in vivo and in vitro. Enforced expression of Nup35 effectively counteracts the anoxia-induced intracellular acidification. We conclude that Nup35 selectively regulates cardiomyocyte pHi homeostasis by posttranscriptionally controlling NHE1 expression. This finding reveals a novel regulatory mechanism of cardiomyocyte pHi, and may provide insight into the therapeutic strategy for ischemic cardiac diseases.
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Affiliation(s)
- Liang Xu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Lei Pan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jun Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Bijun Huang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Jing Feng
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Changming Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Shiyi Wang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Erlinda The
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Yuan Liu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Tianyou Yuan
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Lixiao Zhen
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Dandan Liang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Yi Liu
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Li Li
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Yingyu Cui
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Xiaoyan Jiang
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Luying Peng
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
| | - Yi-Han Chen
- Key Laboratory of Arrhythmias of the Ministry of Education of China, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Institute of Medical Genetics, Tongji University, Shanghai 200092, China Department of Cardiology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China Department of Pathology and Pathophysiology, Tongji University School of Medicine, Shanghai 200092, China
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193
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Shimojima K, Okamoto N, Yamamoto T. Characteristics of 2p15-p16.1 microdeletion syndrome: Review and description of two additional patients. Congenit Anom (Kyoto) 2015; 55:125-32. [PMID: 25900130 DOI: 10.1111/cga.12112] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 04/14/2015] [Indexed: 12/14/2022]
Abstract
Many new microdeletion syndromes have been characterized in the past decade, including 2p15-p16.1 microdeletion syndrome. More than 10 patients with this syndrome have been described. Recently, we encountered two additional patients with 2p15-p16.1 microdeletion syndrome. All patients showed variable degrees of intellectual disability, with the autistic features characteristic of this syndrome. Seven out of 16 patients (44%) showed structural abnormalities in the brain, which is also an important feature of this syndrome. The shortest region of microdeletion overlap among the patients includes two genes, USP34 and XPO1. Although these genes have some functional relevance to cancer, they have not been associated with neurological functions. Diagnosis of additional patients with 2p15-p16.1 microdeletion syndrome and identification of pathogenic mutations in this region will help identify the genes responsible for the neurological features of the syndrome.
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Affiliation(s)
- Keiko Shimojima
- Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Izumi, Japan
| | - Toshiyuki Yamamoto
- Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo, Japan
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194
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Honda T, Nakajima K. Proper Level of Cytosolic Disabled-1, Which Is Regulated by Dual Nuclear Translocation Pathways, Is Important for Cortical Neuronal Migration. Cereb Cortex 2015. [PMID: 26209842 DOI: 10.1093/cercor/bhv162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Disabled-1 (Dab1) is an essential intracellular protein in the Reelin pathway. It has a nuclear localization signal (NLS; hereafter referred to as "NLS1") and 2 nuclear export signals, and shuttles between the nucleus and the cytoplasm. In this study, we found that Dab1 has an additional unidentified NLS, and that the Dab1 NLS1 mutant could translocate to the nucleus in an unconventional ATP/temperature-dependent and cytoplasmic factor/RanGTP gradient-independent manner. Additional mutations in the NLS1 mutant revealed that K(67) and K(69) are important for the nuclear transport. Furthermore, an excess of the intracellular domain of the Reelin receptors inhibited the nuclear translocation of Dab1. An in utero electroporation study showed that a large amount of Dab1 in the cytoplasm in migrating neurons inhibited the migration, and that forced transport of Dab1 into the nucleus attenuated this inhibitory effect. In addition, rescue experiments using yotari, an autosomal recessive mutant of dab1, revealed that cells expressing Dab1 NLS1 mutant tend to distribute at more superficial positions than those expressing wild-type Dab1. Taken together, these findings suggest that Dab1 has at least 2 NLSs, and that the regulation of the subcellular localization of Dab1 is important for the proper migration of excitatory neurons.
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Affiliation(s)
- Takao Honda
- Department of Anatomy, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kazunori Nakajima
- Department of Anatomy, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
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195
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Chromatin at the nuclear periphery and the regulation of genome functions. Histochem Cell Biol 2015; 144:111-22. [PMID: 26170147 DOI: 10.1007/s00418-015-1346-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2015] [Indexed: 01/01/2023]
Abstract
Chromatin is not randomly organized in the nucleus, and its spatial organization participates in the regulation of genome functions. However, this spatial organization is also not entirely fixed and modifications of chromatin architecture are implicated in physiological processes such as differentiation or senescence. One of the most striking features of chromatin architecture is the concentration of heterochromatin at the nuclear periphery. A closer examination of the association of chromatin at the nuclear periphery reveals that heterochromatin accumulates at the nuclear lamina, whereas nuclear pores are usually devoid of heterochromatin. After summarizing the current techniques used to study the attachment of chromatin at the nuclear lamina or the nuclear pores, we review the mechanisms underlying these attachments, their plasticity and their consequences on the regulation of gene expression, DNA repair and replication.
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196
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Transcriptional control of autophagy-lysosome function drives pancreatic cancer metabolism. Nature 2015; 524:361-5. [PMID: 26168401 PMCID: PMC5086585 DOI: 10.1038/nature14587] [Citation(s) in RCA: 591] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/20/2015] [Indexed: 12/11/2022]
Abstract
Activation of cellular stress response pathways to maintain metabolic homeostasis is emerging as a critical growth and survival mechanism in many cancers. The pathogenesis of pancreatic ductal adenocarcinoma (PDA) requires high levels of autophagy, a conserved self-degradative process. However, the regulatory circuits that activate autophagy and reprogram PDA cell metabolism are unknown. Here we show that autophagy induction in PDA occurs as part of a broader transcriptional program that coordinates activation of lysosome biogenesis and function, and nutrient scavenging, mediated by the MiT/TFE family of transcription factors. In human PDA cells, the MiT/TFE proteins--MITF, TFE3 and TFEB--are decoupled from regulatory mechanisms that control their cytoplasmic retention. Increased nuclear import in turn drives the expression of a coherent network of genes that induce high levels of lysosomal catabolic function essential for PDA growth. Unbiased global metabolite profiling reveals that MiT/TFE-dependent autophagy-lysosome activation is specifically required to maintain intracellular amino acid pools. These results identify the MiT/TFE proteins as master regulators of metabolic reprogramming in pancreatic cancer and demonstrate that transcriptional activation of clearance pathways converging on the lysosome is a novel hallmark of aggressive malignancy.
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197
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MacDonald WA, Sachani SS, White CR, Mann MRW. A role for chromatin topology in imprinted domain regulation. Biochem Cell Biol 2015. [PMID: 26222733 DOI: 10.1139/bcb-2015-0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.
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Affiliation(s)
- William A MacDonald
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Saqib S Sachani
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Carlee R White
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Mellissa R W Mann
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
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198
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Maizels Y, Gerlitz G. Shaping of interphase chromosomes by the microtubule network. FEBS J 2015; 282:3500-24. [PMID: 26040675 DOI: 10.1111/febs.13334] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/11/2015] [Accepted: 06/01/2015] [Indexed: 12/31/2022]
Abstract
It is well established that microtubule dynamics play a major role in chromosome condensation and localization during mitosis. During interphase, however, it is assumed that the metazoan nuclear envelope presents a physical barrier, which inhibits interaction between the microtubules located in the cytoplasm and the chromatin fibers located in the nucleus. In recent years, it has become apparent that microtubule dynamics alter chromatin structure and function during interphase as well. Microtubule motor proteins transport several transcription factors and exogenous DNA (such as plasmid DNA) from the cytoplasm to the nucleus. Various soluble microtubule components are able to translocate into the nucleus, where they bind various chromatin elements leading to transcriptional alterations. In addition, microtubules may apply force on the nuclear envelope, which is transmitted into the nucleus, leading to changes in chromatin structure. Thus, microtubule dynamics during interphase may affect chromatin spatial organization, as well as transcription, replication and repair.
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Affiliation(s)
- Yael Maizels
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Israel
| | - Gabi Gerlitz
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Israel
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199
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Zhu Y, Liu TW, Madden Z, Yuzwa SA, Murray K, Cecioni S, Zachara N, Vocadlo DJ. Post-translational O-GlcNAcylation is essential for nuclear pore integrity and maintenance of the pore selectivity filter. J Mol Cell Biol 2015; 8:2-16. [PMID: 26031751 DOI: 10.1093/jmcb/mjv033] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 04/13/2015] [Indexed: 01/12/2023] Open
Abstract
O-glycosylation of the nuclear pore complex (NPC) by O-linked N-acetylglucosamine (O-GlcNAc) is conserved within metazoans. Many nucleoporins (Nups) comprising the NPC are constitutively O-GlcNAcylated, but the functional role of this modification remains enigmatic. We show that loss of O-GlcNAc, induced by either inhibition of O-GlcNAc transferase (OGT) or deletion of the gene encoding OGT, leads to decreased cellular levels of a number of natively O-GlcNAcylated Nups. Loss of O-GlcNAc enables increased ubiquitination of these Nups and their increased proteasomal degradation. The decreased half-life of these deglycosylated Nups manifests in their gradual loss from the NPC and a downstream malfunction of the nuclear pore selective permeability barrier in both dividing and post-mitotic cells. These findings define a critical role of O-GlcNAc modification of the NPC in maintaining its composition and the function of the selectivity filter. The results implicate NPC glycosylation as a regulator of NPC function and reveal the role of conserved glycosylation of the NPC among metazoans.
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Affiliation(s)
- Yanping Zhu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Ta-Wei Liu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Zarina Madden
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Scott A Yuzwa
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Kelsey Murray
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Samy Cecioni
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Natasha Zachara
- Department of Biological Chemistry, Johns Hopkins University Medical School, Baltimore, MD 21205, USA
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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200
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Worman HJ, Schirmer EC. Nuclear membrane diversity: underlying tissue-specific pathologies in disease? Curr Opin Cell Biol 2015; 34:101-12. [PMID: 26115475 PMCID: PMC4522394 DOI: 10.1016/j.ceb.2015.06.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 06/05/2015] [Accepted: 06/10/2015] [Indexed: 11/16/2022]
Abstract
Human 'laminopathy' diseases result from mutations in genes encoding nuclear lamins or nuclear envelope (NE) transmembrane proteins (NETs). These diseases present a seeming paradox: the mutated proteins are widely expressed yet pathology is limited to specific tissues. New findings suggest tissue-specific pathologies arise because these widely expressed proteins act in various complexes that include tissue-specific components. Diverse mechanisms to achieve NE tissue-specificity include tissue-specific regulation of the expression, mRNA splicing, signaling, NE-localization and interactions of potentially hundreds of tissue-specific NETs. New findings suggest these NETs underlie tissue-specific NE roles in cytoskeletal mechanics, cell-cycle regulation, signaling, gene expression and genome organization. This view of the NE as 'specialized' in each cell type is important to understand the tissue-specific pathology of NE-linked diseases.
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Affiliation(s)
- Howard J Worman
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, USA
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
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