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Li Y, Zhu J, Zhai F, Kong L, Li H, Jin X. Advances in the understanding of nuclear pore complexes in human diseases. J Cancer Res Clin Oncol 2024; 150:374. [PMID: 39080077 PMCID: PMC11289042 DOI: 10.1007/s00432-024-05881-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Nuclear pore complexes (NPCs) are sophisticated and dynamic protein structures that straddle the nuclear envelope and act as gatekeepers for transporting molecules between the nucleus and the cytoplasm. NPCs comprise up to 30 different proteins known as nucleoporins (NUPs). However, a growing body of research has suggested that NPCs play important roles in gene regulation, viral infections, cancer, mitosis, genetic diseases, kidney diseases, immune system diseases, and degenerative neurological and muscular pathologies. PURPOSE In this review, we introduce the structure and function of NPCs. Then We described the physiological and pathological effects of each component of NPCs which provide a direction for future clinical applications. METHODS The literatures from PubMed have been reviewed for this article. CONCLUSION This review summarizes current studies on the implications of NPCs in human physiology and pathology, highlighting the mechanistic underpinnings of NPC-associated diseases.
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Affiliation(s)
- Yuxuan Li
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China
| | - Jie Zhu
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Fengguang Zhai
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China
| | - Lili Kong
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China
| | - Hong Li
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China.
| | - Xiaofeng Jin
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, 315040, Zhejiang, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, Zhejiang, China.
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2
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Oishi A, Nakagawa S, Tamura K. Nucleoporin 50 proteins affect longevity and salinity stress tolerance in seeds. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:60-72. [PMID: 37849222 DOI: 10.1093/jxb/erad396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023]
Abstract
Nucleoporin 50 (Nup50) is an evolutionarily conserved protein that is a constituent of the nuclear pore complex (NPC); however, its physiological role in plants is unclear. Arabidopsis has two Nup50 proteins, Nup50a and Nup50b, which are highly expressed in developing seeds. Green fluoresceent protein (GFP)-fused Nup50a and Nup50b are localized exclusively in the nucleopolasm, implying an additional function beyond the NPC in the nuclear envelope. To investigate the function of Nup50s, we employed the CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] system to generate a nup50a nup50b double mutant, which exhibited premature translation termination of both Nup50 proteins. While the mutant showed no significant abnormal phenotype during vegetative growth, the nup50a nup50b seeds had an abnormal shape compared with the wild type. Comparative transcriptomics using immature seeds revealed that Nup50s regulate the expression of various genes, including cell wall-related genes. The nup50a nup50b seeds exhibited reduced seed longevity and salinity stress tolerance. Tetrazolium uptake and mucilage release assays implied that the nup50a nup50b seeds had greater water permeability than the wild type. Taken together, our results imply that Nup50s play a critical role in seed formation by regulating gene expression.
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Affiliation(s)
- Ayumi Oishi
- School of Food and Nutritional Sciences, Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Shitomi Nakagawa
- School of Food and Nutritional Sciences, Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kentaro Tamura
- School of Food and Nutritional Sciences, Department of Environmental and Life Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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3
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Liu J, Chen Y, Nong B, Luo X, Cui K, Li Z, Zhang P, Tan W, Yang Y, Ma W, Liang P, Songyang Z. CRISPR-assisted transcription activation by phase-separation proteins. Protein Cell 2023; 14:874-887. [PMID: 36905356 PMCID: PMC10691850 DOI: 10.1093/procel/pwad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/11/2023] [Indexed: 03/12/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has been widely used for genome engineering and transcriptional regulation in many different organisms. Current CRISPR-activation (CRISPRa) platforms often require multiple components because of inefficient transcriptional activation. Here, we fused different phase-separation proteins to dCas9-VPR (dCas9-VP64-P65-RTA) and observed robust increases in transcriptional activation efficiency. Notably, human NUP98 (nucleoporin 98) and FUS (fused in sarcoma) IDR domains were best at enhancing dCas9-VPR activity, with dCas9-VPR-FUS IDR (VPRF) outperforming the other CRISPRa systems tested in this study in both activation efficiency and system simplicity. dCas9-VPRF overcomes the target strand bias and widens gRNA designing windows without affecting the off-target effect of dCas9-VPR. These findings demonstrate the feasibility of using phase-separation proteins to assist in the regulation of gene expression and support the broad appeal of the dCas9-VPRF system in basic and clinical applications.
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Affiliation(s)
- Jiaqi Liu
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuxi Chen
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Baoting Nong
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiao Luo
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kaixin Cui
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhan Li
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pengfei Zhang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | | | - Yue Yang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Puping Liang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zhou Songyang
- State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
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4
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Yang Y, Guo L, Chen L, Gong B, Jia D, Sun Q. Nuclear transport proteins: structure, function, and disease relevance. Signal Transduct Target Ther 2023; 8:425. [PMID: 37945593 PMCID: PMC10636164 DOI: 10.1038/s41392-023-01649-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 11/12/2023] Open
Abstract
Proper subcellular localization is crucial for the functioning of biomacromolecules, including proteins and RNAs. Nuclear transport is a fundamental cellular process that regulates the localization of many macromolecules within the nuclear or cytoplasmic compartments. In humans, approximately 60 proteins are involved in nuclear transport, including nucleoporins that form membrane-embedded nuclear pore complexes, karyopherins that transport cargoes through these complexes, and Ran system proteins that ensure directed and rapid transport. Many of these nuclear transport proteins play additional and essential roles in mitosis, biomolecular condensation, and gene transcription. Dysregulation of nuclear transport is linked to major human diseases such as cancer, neurodegenerative diseases, and viral infections. Selinexor (KPT-330), an inhibitor targeting the nuclear export factor XPO1 (also known as CRM1), was approved in 2019 to treat two types of blood cancers, and dozens of clinical trials of are ongoing. This review summarizes approximately three decades of research data in this field but focuses on the structure and function of individual nuclear transport proteins from recent studies, providing a cutting-edge and holistic view on the role of nuclear transport proteins in health and disease. In-depth knowledge of this rapidly evolving field has the potential to bring new insights into fundamental biology, pathogenic mechanisms, and therapeutic approaches.
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Affiliation(s)
- Yang Yang
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lu Guo
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Chen
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bo Gong
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, Chengdu, China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China.
| | - Qingxiang Sun
- Department of Pulmonary and Critical Care Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, China.
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5
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Coyne AN, Rothstein JD. Nuclear pore complexes - a doorway to neural injury in neurodegeneration. Nat Rev Neurol 2022; 18:348-362. [PMID: 35488039 PMCID: PMC10015220 DOI: 10.1038/s41582-022-00653-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 12/13/2022]
Abstract
The genetic underpinnings and end-stage pathological hallmarks of neurodegenerative diseases are increasingly well defined, but the cellular pathophysiology of disease initiation and propagation remains poorly understood, especially in sporadic forms of these diseases. Altered nucleocytoplasmic transport is emerging as a prominent pathomechanism of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis, Alzheimer disease, frontotemporal dementia and Huntington disease. The nuclear pore complex (NPC) and interactions between its individual nucleoporin components and nuclear transport receptors regulate nucleocytoplasmic transport, as well as genome organization and gene expression. Specific nucleoporin abnormalities have been identified in sporadic and familial forms of neurodegenerative disease, and these alterations are thought to contribute to disrupted nucleocytoplasmic transport. The specific nucleoporins and nucleocytoplasmic transport proteins that have been linked to different neurodegenerative diseases are partially distinct, suggesting that NPC injury contributes to the cellular specificity of neurodegenerative disease and could be an early initiator of the pathophysiological cascades that underlie neurodegenerative disease. This concept is consistent with the fact that rare genetic mutations in some nucleoporins cause cell-type-specific neurological disease. In this Review, we discuss nucleoporin and NPC disruptions and consider their impact on cellular function and the pathophysiology of neurodegenerative disease.
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Affiliation(s)
- Alyssa N Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jeffrey D Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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6
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Holzer G, Antonin W. Nup50 plays more than one instrument. Cell Cycle 2022; 21:1785-1794. [PMID: 35549614 PMCID: PMC9359400 DOI: 10.1080/15384101.2022.2074742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Nup50 is nuclear pore complex component localized to the nuclear side of the pore and in the nucleoplasm. It has been characterized as an auxiliary factor in nuclear transport reactions. Our recent work indicates that it interacts with and stimulates RCC1, the sole guanine nucleotide exchange factor for the GTPase Ran. Here, we discuss how this interaction might contribute to Nup50 function in nuclear transport but also its other functions like control of gene expression, cell cycle and DNA damage repair.
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Affiliation(s)
- Guillaume Holzer
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
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7
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Holzer G, De Magistris P, Gramminger C, Sachdev R, Magalska A, Schooley A, Scheufen A, Lennartz B, Tatarek‐Nossol M, Lue H, Linder MI, Kutay U, Preisinger C, Moreno‐Andres D, Antonin W. The nucleoporin Nup50 activates the Ran guanine nucleotide exchange factor RCC1 to promote NPC assembly at the end of mitosis. EMBO J 2021; 40:e108788. [PMID: 34725842 PMCID: PMC8634129 DOI: 10.15252/embj.2021108788] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
During mitotic exit, thousands of nuclear pore complexes (NPCs) assemble concomitant with the nuclear envelope to build a transport-competent nucleus. Here, we show that Nup50 plays a crucial role in NPC assembly independent of its well-established function in nuclear transport. RNAi-mediated downregulation in cells or immunodepletion of Nup50 protein in Xenopus egg extracts interferes with NPC assembly. We define a conserved central region of 46 residues in Nup50 that is crucial for Nup153 and MEL28/ELYS binding, and for NPC interaction. Surprisingly, neither NPC interaction nor binding of Nup50 to importin α/β, the GTPase Ran, or chromatin is crucial for its function in the assembly process. Instead, an N-terminal fragment of Nup50 can stimulate the Ran GTPase guanine nucleotide exchange factor RCC1 and NPC assembly, indicating that Nup50 acts via the Ran system in NPC reformation at the end of mitosis. In support of this conclusion, Nup50 mutants defective in RCC1 binding and stimulation cannot replace the wild-type protein in in vitro NPC assembly assays, whereas excess RCC1 can compensate the loss of Nup50.
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Affiliation(s)
- Guillaume Holzer
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Paola De Magistris
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
- Present address:
Department of BionanoscienceKavli Institute of NanoscienceDelftthe Netherlands
| | | | - Ruchika Sachdev
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - Adriana Magalska
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - Allana Schooley
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | - Anja Scheufen
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Birgitt Lennartz
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Marianna Tatarek‐Nossol
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Hongqi Lue
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Monika I Linder
- Institute of BiochemistryETH ZurichZurichSwitzerland
- Present address:
Department of PediatricsDr. von Hauner Children's Hospital and Gene CenterUniversity Hospital, LMUMunichGermany
| | - Ulrike Kutay
- Institute of BiochemistryETH ZurichZurichSwitzerland
| | - Christian Preisinger
- Proteomics FacilityInterdisciplinary Centre for Clinical Research (IZKF)Medical SchoolRWTH Aachen UniversityAachenGermany
| | - Daniel Moreno‐Andres
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
| | - Wolfram Antonin
- Institute of Biochemistry and Molecular Cell BiologyMedical SchoolRWTH Aachen UniversityAachenGermany
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8
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Gao X, Yu S, Guan Y, Shen Y, Xu L. Nucleoporin 50 mediates Kcna4 transcription to regulate cardiac electrical activity. J Cell Sci 2021; 134:271877. [PMID: 34409458 DOI: 10.1242/jcs.256818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
Emerging evidence has demonstrated that nucleoporins (Nups) play a pivotal role in cell-type-specific gene regulation, but how they control the expression and activity of ion channel genes in the heart remains unclear. Here, we show that Nup50, which is localized in the nucleus of cardiomyocytes, selectively induces an increase in the transcription and translation of Kcna4. The Kcna4 gene encodes a K+ voltage-gated channel of shaker-related subfamily member 4 and is essential for regulating the action potential in cardiac membranes. Using immunofluorescence imaging, luciferase assays and chromatin immunoprecipitation assays, we identified that the direct binding of the FG-repeat domain within Nup50 to the proximity of the Kcna4 promoter was required to activate the transcription and subsequent translation of Kcna4. Functionally, Nup50 overexpression increased the currents of KCNA4-encoded Ito,s channels, and reverse knockdown of Nup50 resulted in a remarkable decrease in the amplitude of Ito,s currents in cardiomyocytes. Moreover, a positive correlation between Nup50 and Kcna4 mRNA and protein expression was observed in heart tissues subjected to ischemic insults. These findings provide insights into the homeostatic control of cardiac electrophysiology through Nup-mediated regulation.
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Affiliation(s)
- Xueting Gao
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China.,Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Shuai Yu
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China.,Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Yi Guan
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China.,Institute of Medical Genetics, Tongji University, Shanghai 200092, China
| | - Yunli Shen
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China
| | - Liang Xu
- Department of Cardiology, East Hospital, Tongji University School of Medicine, Shanghai 200120, China.,Key Laboratory of Arrhythmias of the Ministry of Education of China, Tongji University School of Medicine, Shanghai 200120, China.,Institute of Medical Genetics, Tongji University, Shanghai 200092, China
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9
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Jibiki K, Kodama TS, Suenaga A, Kawase Y, Shibazaki N, Nomoto S, Nagasawa S, Nagashima M, Shimodan S, Kikuchi R, Okayasu M, Takashita R, Mehmood R, Saitoh N, Yoneda Y, Akagi KI, Yasuhara N. Importin α2 association with chromatin: Direct DNA binding via a novel DNA-binding domain. Genes Cells 2021; 26:945-966. [PMID: 34519142 DOI: 10.1111/gtc.12896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 12/18/2022]
Abstract
The nuclear transport of proteins is important for facilitating appropriate nuclear functions. The importin α family proteins play key roles in nuclear transport as transport receptors for copious nuclear proteins. Additionally, these proteins possess other functions, including chromatin association and gene regulation. However, these nontransport functions of importin α are not yet fully understood, especially their molecular-level mechanisms and consequences for functioning with chromatin. Here, we report the novel molecular characteristics of importin α binding to diverse DNA sequences in chromatin. We newly identified and characterized a DNA-binding domain-the Nucleic Acid Associating Trolley pole domain (NAAT domain)-in the N-terminal region of importin α within the conventional importin β binding (IBB) domain that is necessary for nuclear transport of cargo proteins. Furthermore, we found that the DNA binding of importin α synergistically coupled the recruitment of its cargo protein to DNA. This is the first study to delineate the interaction between importin α and chromatin DNA via the NAAT domain, indicating the bifunctionality of the importin α N-terminal region for nuclear transport and chromatin association.
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Affiliation(s)
- Kazuya Jibiki
- Graduate School of Integrated Basic Sciences, Nihon University, Tokyo, Japan
| | - Takashi S Kodama
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | - Atsushi Suenaga
- Graduate School of Integrated Basic Sciences, Nihon University, Tokyo, Japan.,Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | - Yota Kawase
- Graduate School of Integrated Basic Sciences, Nihon University, Tokyo, Japan
| | - Noriko Shibazaki
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | - Shin Nomoto
- Graduate School of Integrated Basic Sciences, Nihon University, Tokyo, Japan
| | - Seiya Nagasawa
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | - Misaki Nagashima
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | - Shieri Shimodan
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | - Renan Kikuchi
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | - Mina Okayasu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | - Ruka Takashita
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | - Rashid Mehmood
- Department of Life Sciences, College of Science and General Studies, Alfaisal University, Riyadh, Saudi Arabia
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Yoshihiro Yoneda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | - Ken-Ichi Akagi
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan.,Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Noriko Yasuhara
- Graduate School of Integrated Basic Sciences, Nihon University, Tokyo, Japan.,Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
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10
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Phan TK, Fonseka P, Tixeira R, Pathan M, Ang CS, Ozkocak DC, Mathivanan S, Poon IKH. Pannexin-1 channel regulates nuclear content packaging into apoptotic bodies and their size. Proteomics 2021; 21:e2000097. [PMID: 33661579 DOI: 10.1002/pmic.202000097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/04/2021] [Accepted: 02/25/2021] [Indexed: 12/23/2022]
Abstract
Apoptotic bodies (ApoBDs), which are large extracellular vesicles exclusively released by apoptotic cells, possess therapeutically exploitable properties including biomolecule loadability and transferability. However, current limited understanding of ApoBD biology has hindered its exploration for clinical use. Particularly, as ApoBD-accompanying cargoes (e.g., nucleic acids and proteins) have major influence on their functionality, further insights into the mechanism of biomolecule sorting into ApoBDs are critical to unleash their therapeutic potential. Previous studies suggested pannexin 1 (PANX1) channel, a negative regulator of ApoBD biogenesis, can modify synaptic vesicle contents. We also reported that trovafloxacin (a PANX1 inhibitor) increases proportion of ApoBDs containing DNA. Therefore, we sought to define the role of PANX1 in regulating the sorting of nuclear content into ApoBDs. Here, using flow cytometry and label-free quantitative proteomic analyses, we showed that targeting PANX1 activity during apoptosis, via either pharmacological inhibition or genetic disruption, resulted in enrichment of both DNA and nuclear proteins in ApoBDs that were unexpectedly smaller in size. Our data suggest that PANX1, besides being a key regulator of ApoBD formation, also functions as a negative regulator of nuclear content packaging and modulator of ApoBD size. Together, our findings provide further insights into ApoBD biology and form a novel conceptual framework for ApoBD-based therapies through pharmacologically manipulating ApoBD contents.
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Affiliation(s)
- Thanh Kha Phan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Pamali Fonseka
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Rochelle Tixeira
- VIB-UGent Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Mohashin Pathan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Dilara Ceyda Ozkocak
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ivan Ka Ho Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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11
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Lyngdoh DL, Nag N, Uversky VN, Tripathi T. Prevalence and functionality of intrinsic disorder in human FG-nucleoporins. Int J Biol Macromol 2021; 175:156-170. [PMID: 33548309 DOI: 10.1016/j.ijbiomac.2021.01.218] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/19/2021] [Accepted: 01/31/2021] [Indexed: 11/27/2022]
Abstract
The nuclear-cytoplasmic transport of biomolecules is assisted by the nuclear pores composed of evolutionarily conserved proteins termed nucleoporins (Nups). The central Nups, characterized by multiple FG-repeats, are highly dynamic and contain a high level of intrinsically disordered regions (IDPRs). FG-Nups bind several protein partners and play critical roles in molecular interactions and the regulation of cellular functions through their IDPRs. In the present study, we performed a multiparametric bioinformatics analysis to characterize the prevalence and functionality of IDPRs in human FG-Nups. These analyses revealed that the sequence of all FG-Nups contained >50% IDPRs (except Nup54 and Nup358). Nup98, Nup153, and POM121 were extremely disordered with ~80% IDPRs. The functional disorder-based binding regions in the FG-Nups were identified. The phase separation behavior of FG-Nups indicated that all FG-Nups have the potential to undergo liquid-to-liquid phase separation that could stabilize their liquid state. The inherent structural flexibility in FG-Nups is mechanistically and functionally advantageous. Since certain FG-Nups interact with disease-relevant protein aggregates, their complexes can be exploited for drug design. Furthermore, consideration of the FG-Nups from the intrinsic disorder perspective provides critical information that can guide future experimental studies to uncover novel pathways associated with diseases linked with protein misfolding and aggregation.
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Affiliation(s)
- Denzelle Lee Lyngdoh
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Niharika Nag
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, United States
| | - Timir Tripathi
- Molecular and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India.
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12
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Lange A, Fasken MB, Stewart M, Corbett AH. Dissecting the roles of Cse1 and Nup2 in classical NLS-cargo release in vivo. Traffic 2020; 21:622-635. [PMID: 32734712 PMCID: PMC7891619 DOI: 10.1111/tra.12759] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 01/26/2023]
Abstract
The importin α/β transport machinery mediates the nuclear import of cargo proteins that bear a classical nuclear localization sequence (cNLS). These cargo proteins are linked to the major nuclear protein import factor, importin‐β, by the importin‐α adapter, after which cargo/carrier complexes enter the nucleus through nuclear pores. In the nucleus, cargo is released by the action of RanGTP and the nuclear pore protein Nup2, after which the importins are recycled to the cytoplasm for further transport cycles. The nuclear export of importin‐α is mediated by Cse1/CAS. Here, we exploit structures of functionally important complexes to identify residues that are critical for these interactions and provide insight into how cycles of protein import and recycling of importin‐α occur in vivo using a Saccharomyces cerevisiae model. We examine how these molecular interactions impact protein localization, cargo import, function and complex formation. We show that reversing the charge of key residues in importin‐α (Arg44) or Cse1 (Asp220) results in loss of function of the respective proteins and impairs complex formation both in vitro and in vivo. To extend these results, we show that basic residues in the Nup2 N‐terminus are required for both Nup2 interaction with importin‐α and Nup2 function. These results provide a more comprehensive mechanistic model of how Cse1, RanGTP and Nup2 function in concert to mediate cNLS‐cargo release in the nucleus. Directional transport of cargoes between the nucleus and cytoplasm is mediated by receptors that bind cargo in one compartment and release cargo into a destination compartment. Cargoes that contain a cNLS are recognized by importin‐α in the cytoplasm. Release factors including the importin‐α export receptor, Cse1, and a nuclear pore complex protein, Nup2, ensure efficient cargo delivery into the nucleus. Interactions defined by previous structural studies are required for productive interactions between importin‐α, Cse1, and Nup2 to occur in vivo.
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Affiliation(s)
- Allison Lange
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Murray Stewart
- Cambridge Biomedical Campus, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia, USA
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13
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Khan AU, Qu R, Ouyang J, Dai J. Role of Nucleoporins and Transport Receptors in Cell Differentiation. Front Physiol 2020; 11:239. [PMID: 32308628 PMCID: PMC7145948 DOI: 10.3389/fphys.2020.00239] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
Bidirectional molecular movements between the nucleus and cytoplasm take place through nuclear pore complexes (NPCs) embedded in the nuclear membrane. These macromolecular structures are composed of several nucleoporins, which form seven different subcomplexes based on their biochemical affinity. These nucleoporins are integral components of the complex, not only allowing passive transport but also interacting with importin, exportin, and other molecules that are required for transport of protein in various cellular processes. Transport of different proteins is carried out either dependently or independently on transport receptors. As well as facilitating nucleocytoplasmic transport, nucleoporins also play an important role in cell differentiation, possibly by their direct gene interaction. This review will cover the general role of nucleoporins (whether its dependent or independent) and nucleocytoplasmic transport receptors in cell differentiation.
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14
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Mayol GF, Revuelta MV, Salusso A, Touz MC, Rópolo AS. Evidence of nuclear transport mechanisms in the protozoan parasite Giardia lamblia. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1867:118566. [PMID: 31672613 DOI: 10.1016/j.bbamcr.2019.118566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/26/2019] [Accepted: 10/15/2019] [Indexed: 11/28/2022]
Abstract
Nuclear-cytoplasmic trafficking of proteins is a highly regulated process that modulates multiple biological processes in eukaryotic cells. In Giardia lamblia, shuttling has been described from the cytoplasm to nuclei of proteins during the biological cell cycle of the parasite. This suggests that a mechanism of nucleocytoplasmic transport is present and functional in G. lamblia. By means of computational biology analyses, we found that there are only two genes for nuclear transport in this parasite, named Importin α and Importin β. When these transporters were overexpressed, both localized close to the nuclear envelope, and no change was observed in trophozoite growth rate. However, during the encystation process, both transporters induced an increase in the number of cysts produced. Importazole and Ivermectin, two known specific inhibitors of importins, separately influenced the encysting process by inducing an arrest in the trophozoite stage that prevents the production of cysts. This effect was more noticeable when Ivermectin, an anti-parasitic drug, was used. Finally, we tested whether the enzyme arginine deiminase, which shuttles from the cytoplasm to the nuclei during encystation, was influenced by these transporters. We found that treatment with each of the inhibitors abrogates arginine deiminase nuclear translocation and favors perinuclear localization. This suggests that Importin α and Importin β are key transporters during the encystation process and are involved, at least, in the transport of arginine deiminase into the nuclei. Considering the effect produced by Ivermectin during growth and encystation, we postulate that this drug could be used to treat giardiasis.
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Affiliation(s)
- Gonzalo Federico Mayol
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Victoria Revuelta
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Agostina Salusso
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Carolina Touz
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Andrea Silvana Rópolo
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina.
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15
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Solomon DA, Stepto A, Au WH, Adachi Y, Diaper DC, Hall R, Rekhi A, Boudi A, Tziortzouda P, Lee YB, Smith B, Bridi JC, Spinelli G, Dearlove J, Humphrey DM, Gallo JM, Troakes C, Fanto M, Soller M, Rogelj B, Parsons RB, Shaw CE, Hortobágyi T, Hirth F. A feedback loop between dipeptide-repeat protein, TDP-43 and karyopherin-α mediates C9orf72-related neurodegeneration. Brain 2019; 141:2908-2924. [PMID: 30239641 PMCID: PMC6158706 DOI: 10.1093/brain/awy241] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/02/2018] [Indexed: 12/13/2022] Open
Abstract
Accumulation and aggregation of TDP-43 is a major pathological hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. TDP-43 inclusions also characterize patients with GGGGCC (G4C2) hexanucleotide repeat expansion in C9orf72 that causes the most common genetic form of amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD). Functional studies in cell and animal models have identified pathogenic mechanisms including repeat-induced RNA toxicity and accumulation of G4C2-derived dipeptide-repeat proteins. The role of TDP-43 dysfunction in C9ALS/FTD, however, remains elusive. We found G4C2-derived dipeptide-repeat protein but not G4C2-RNA accumulation caused TDP-43 proteinopathy that triggered onset and progression of disease in Drosophila models of C9ALS/FTD. Timing and extent of TDP-43 dysfunction was dependent on levels and identity of dipeptide-repeat proteins produced, with poly-GR causing early and poly-GA/poly-GP causing late onset of disease. Accumulating cytosolic, but not insoluble aggregated TDP-43 caused karyopherin-α2/4 (KPNA2/4) pathology, increased levels of dipeptide-repeat proteins and enhanced G4C2-related toxicity. Comparable KPNA4 pathology was observed in both sporadic frontotemporal dementia and C9ALS/FTD patient brains characterized by its nuclear depletion and cytosolic accumulation, irrespective of TDP-43 or dipeptide-repeat protein aggregates. These findings identify a vicious feedback cycle for dipeptide-repeat protein-mediated TDP-43 and subsequent KPNA pathology, which becomes self-sufficient of the initiating trigger and causes C9-related neurodegeneration.
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Affiliation(s)
- Daniel A Solomon
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Alan Stepto
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Wing Hei Au
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Yoshitsugu Adachi
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Danielle C Diaper
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Rachel Hall
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Anjeet Rekhi
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Adel Boudi
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Paraskevi Tziortzouda
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Youn-Bok Lee
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Bradley Smith
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Jessika C Bridi
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Greta Spinelli
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Jonah Dearlove
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Dickon M Humphrey
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Jean-Marc Gallo
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Claire Troakes
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Manolis Fanto
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Boris Rogelj
- Jozef Stefan Institute, Department of Biotechnology and Biomedical Research Institute BRIS and University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, Slovenia
| | - Richard B Parsons
- King's College London, School of Cancer Studies and Pharmaceutical Sciences, London, UK
| | - Christopher E Shaw
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Tibor Hortobágyi
- MTA-DE Cerebrovascular and Neurodegenerative Research Group, Departments of Neurology and Neuropathology, University of Debrecen, Debrecen, Hungary.,King's College London, Department of Old Age Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - Frank Hirth
- King's College London, Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, UK
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16
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Suresh S, Osmani SA. Poring over chromosomes: mitotic nuclear pore complex segregation. Curr Opin Cell Biol 2019; 58:42-49. [PMID: 30798206 DOI: 10.1016/j.ceb.2019.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/09/2019] [Accepted: 01/18/2019] [Indexed: 01/23/2023]
Abstract
Eukaryotic cells rely on flux of macromolecules between the nucleus and the cytoplasm for growth and survival. Bidirectional transport is achieved through Nuclear Pore Complexes (NPCs) embedded in the Nuclear Envelope (NE). NPC proteins perform other cellular functions during mitosis, chromatin organization, DNA repair and gene regulation. Dysregulation of NPC number, or defects in their structure and function, are linked to numerous diseases but how NPCs are faithfully inherited during mitosis is poorly understood. In this review, we discuss recent insights to mechanisms of mammalian mitotic NPC segregation and NPC assembly as well as mitotic NPC inheritance via the mitotic chromatin located NPC protein Nup2 in Aspergillus nidulans. We suggest mitotic Nup2 chromatin-based mechanisms could also operate in vertebrate cells.
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Affiliation(s)
- Subbulakshmi Suresh
- Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
| | - Stephen A Osmani
- Department of Molecular Genetics, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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17
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Sheng KL, Pridham KJ, Sheng Z, Lamouille S, Varghese RT. Functional Blockade of Small GTPase RAN Inhibits Glioblastoma Cell Viability. Front Oncol 2019; 8:662. [PMID: 30671385 PMCID: PMC6331428 DOI: 10.3389/fonc.2018.00662] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/13/2018] [Indexed: 11/13/2022] Open
Abstract
Glioblastoma, the most common malignant tumor in the brain, lacks effective treatments and is currently incurable. To identify novel drug targets for this deadly cancer, the publicly available results of RNA interference screens from the Project Achilles database were analyzed. Ten candidate genes were identified as survival genes in 15 glioblastoma cell lines. RAN, member RAS oncogene family (RAN) was expressed in glioblastoma at the highest level among all candidates based upon cDNA microarray data. However, Kaplan-Meier survival analysis did not show any correlation between RAN mRNA levels and patient survival. Because RAN is a small GTPase that regulates nuclear transport controlled by karyopherin subunit beta 1 (KPNB1), RAN was further analyzed together with KPNB1. Indeed, GBM patients with high levels of RAN also had more KPNB1 and levels of KPNB1 alone did not relate to patient prognosis. Through a Cox multivariate analysis, GBM patients with high levels of RAN and KPNB1 showed significantly shorter life expectancy when temozolomide and promoter methylation of O6-methylguanine DNA methyltransferase were used as covariates. These results indicate that RAN and KPNB1 together are associated with drug resistance and GBM poor prognosis. Furthermore, the functional blockade of RAN and KPNB1 by importazole remarkably suppressed cell viability and activated apoptosis in GBM cells expressing high levels of RAN, while having a limited effect on astrocytes and GBM cells with undetectable RAN. Together, our results demonstrate that RAN activity is important for GBM survival and the functional blockade of RAN/KPNB1 is an appealing therapeutic approach.
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Affiliation(s)
- Kevin L Sheng
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, United States
| | - Kevin J Pridham
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, United States
| | - Zhi Sheng
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, United States.,Department of Internal Medicine, Virginia Tech Carilion School of Medicine, Roanoke, VA, United States.,Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA, United States.,Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States.,Faculty of Health Science, Virginia Tech, Blacksburg, VA, United States
| | - Samy Lamouille
- Fralin Biomedical Research Institute at VTC, Roanoke, VA, United States.,Basic Science Education, Virginia Tech Carilion School of Medicine, Roanoke, VA, United States.,Department of Biological Sciences, College of Science, Virginia Tech, Blacksburg, VA, United States
| | - Robin T Varghese
- Department of Biological Affairs and Research, Edward Via College of Osteopathic Medicine, Blacksburg, VA, United States
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18
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Phosphoproteomic identification and functional characterization of protein kinase substrates by 2D-DIGE and Phos-tag PAGE. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:57-61. [DOI: 10.1016/j.bbapap.2018.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/22/2022]
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19
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Suresh S, Markossian S, Osmani AH, Osmani SA. Nup2 performs diverse interphase functions in Aspergillus nidulans. Mol Biol Cell 2018; 29:3144-3154. [PMID: 30355026 PMCID: PMC6340215 DOI: 10.1091/mbc.e18-04-0223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The nuclear pore complex (NPC) protein Nup2 plays interphase nuclear transport roles and in Aspergillus nidulans also functions to bridge NPCs at mitotic chromatin for their faithful coinheritance to daughter G1 nuclei. In this study, we further investigate the interphase functions of Nup2 in A. nidulans. Although Nup2 is not required for nuclear import of all nuclear proteins after mitosis, it is required for normal G1 nuclear accumulation of the NPC nuclear basket–associated components Mad2 and Mlp1 as well as the THO complex protein Tho2. Targeting of Mlp1 to nuclei partially rescues the interphase delay seen in nup2 mutants indicating that some of the interphase defects in Nup2-deleted cells are due to Mlp1 mislocalization. Among the inner nuclear membrane proteins, Nup2 affects the localization of Ima1, orthologues of which are involved in nuclear movement. Interestingly, nup2 mutant G1 nuclei also exhibit an abnormally long period of extensive to-and-fro movement immediately after mitosis in a manner dependent on the microtubule cytoskeleton. This indicates that Nup2 is required to limit the transient postmitotic nuclear migration typical of many filamentous fungi. The findings reveal that Nup2 is a multifunctional protein that performs diverse functions during both interphase and mitosis in A. nidulans.
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Affiliation(s)
- Subbulakshmi Suresh
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210.,Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065
| | - Sarine Markossian
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143
| | - Aysha H Osmani
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Stephen A Osmani
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
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20
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OKA M, YONEDA Y. Importin α: functions as a nuclear transport factor and beyond. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2018; 94:259-274. [PMID: 30078827 PMCID: PMC6117492 DOI: 10.2183/pjab.94.018] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nucleocytoplasmic transport is an essential process in eukaryotes. The molecular mechanisms underlying nuclear transport that involve the nuclear transport receptor, small GTPase Ran, and the nuclear pore complex are highly conserved from yeast to humans. On the other hand, it has become clear that the nuclear transport system diverged during evolution to achieve various physiological functions in multicellular eukaryotes. In this review, we first summarize the molecular mechanisms of nuclear transport and how these were elucidated. Then, we focus on the diverse functions of importin α, which acts not merely an import factor but also as a multi-functional protein contributing to a variety of cellular functions in higher eukaryotes.
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Affiliation(s)
- Masahiro OKA
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
| | - Yoshihiro YONEDA
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, Japan
- Correspondence should be addressed: Y. Yoneda, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan (e-mail: )
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21
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Tsypin LM, Turkewitz AP. The Co-regulation Data Harvester: automating gene annotation starting from a transcriptome database. SOFTWAREX 2017; 6:165-171. [PMID: 29104906 PMCID: PMC5663188 DOI: 10.1016/j.softx.2017.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Identifying co-regulated genes provides a useful approach for defining pathway-specific machinery in an organism. To be efficient, this approach relies on thorough genome annotation, a process much slower than genome sequencing per se. Tetrahymena thermophila, a unicellular eukaryote, has been a useful model organism and has a fully sequenced but sparsely annotated genome. One important resource for studying this organism has been an online transcriptomic database. We have developed an automated approach to gene annotation in the context of transcriptome data in T. thermophila, called the Co-regulation Data Harvester (CDH). Beginning with a gene of interest, the CDH identifies co-regulated genes by accessing the Tetrahymena transcriptome database. It then identifies their closely related genes (orthologs) in other organisms by using reciprocal BLAST searches. Finally, it collates the annotations of those orthologs' functions, which provides the user with information to help predict the cellular role of the initial query. The CDH, which is freely available, represents a powerful new tool for analyzing cell biological pathways in Tetrahymena. Moreover, to the extent that genes and pathways are conserved between organisms, the inferences obtained via the CDH should be relevant, and can be explored, in many other systems.
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22
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Suresh S, Markossian S, Osmani AH, Osmani SA. Mitotic nuclear pore complex segregation involves Nup2 in Aspergillus nidulans. J Cell Biol 2017; 216:2813-2826. [PMID: 28747316 PMCID: PMC5584150 DOI: 10.1083/jcb.201610019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 05/11/2017] [Accepted: 07/06/2017] [Indexed: 01/20/2023] Open
Abstract
Transport through nuclear pore complexes (NPCs) during interphase is facilitated by the nucleoporin Nup2 via its importin α- and Ran-binding domains. However, Aspergillus nidulans and vertebrate Nup2 also locate to chromatin during mitosis, suggestive of mitotic functions. In this study, we report that Nup2 is required for mitotic NPC inheritance in A. nidulans Interestingly, the role of Nup2 during mitotic NPC segregation is independent of its importin α- and Ran-binding domains but relies on a central targeting domain that is necessary for localization and viability. To test whether mitotic chromatin-associated Nup2 might function to bridge NPCs with chromatin during segregation, we provided an artificial link between NPCs and chromatin via Nup133 and histone H1. Using this approach, we bypassed the requirement of Nup2 for NPC segregation. This indicates that A. nidulans cells ensure accurate mitotic NPC segregation to daughter nuclei by linking mitotic DNA and NPC segregation via the mitotic specific chromatin association of Nup2.
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Affiliation(s)
- Subbulakshmi Suresh
- Department of Molecular Genetics, The Ohio State University, Columbus, OH.,Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY
| | - Sarine Markossian
- Department of Molecular Genetics, The Ohio State University, Columbus, OH
| | - Aysha H Osmani
- Department of Molecular Genetics, The Ohio State University, Columbus, OH
| | - Stephen A Osmani
- Department of Molecular Genetics, The Ohio State University, Columbus, OH
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23
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Park E, Lee B, Clurman BE, Lee K. NUP50 is necessary for the survival of primordial germ cells in mouse embryos. Reproduction 2016; 151:51-8. [DOI: 10.1530/rep-14-0649] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 10/29/2015] [Indexed: 11/08/2022]
Abstract
Nucleoporin 50 kDa (NUP50), a component of the nuclear pore complex, is highly expressed in male germ cells, but its role in germ cells is largely unknown. In this study, we analyzed the expression and function of NUP50 during the embryonic development of germ cells using NUP50-deficient mice. NUP50 was expressed in germ cells of both sexes at embryonic day 15.5 (E15.5), E13.5, and E12.5. In addition, NUP50 expression was also detected in primordial germ cells (PGCs) migrating into the genital ridges at E9.5. The gonads of Nup50−/− embryos of both sexes contained few PGCs at both E11.5 and E12.5 and no developing germ cells at E15.5. The migratory PGCs in Nup50−/− embryos at E9.5 showed increased apoptosis but a normal rate of proliferation, resulting in the progressive loss of germ cells at later stages. Taken together, these results suggest that NUP50 plays an essential role in the survival of PGCs during embryonic development.
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Schellhaus AK, De Magistris P, Antonin W. Nuclear Reformation at the End of Mitosis. J Mol Biol 2015; 428:1962-85. [PMID: 26423234 DOI: 10.1016/j.jmb.2015.09.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/17/2015] [Accepted: 09/19/2015] [Indexed: 12/17/2022]
Abstract
Cells have developed highly sophisticated ways to accurately pass on their genetic information to the daughter cells. In animal cells, which undergo open mitosis, the nuclear envelope breaks down at the beginning of mitosis and the chromatin massively condenses to be captured and segregated by the mitotic spindle. These events have to be reverted in order to allow the reformation of a nucleus competent for DNA transcription and replication, as well as all other nuclear processes occurring in interphase. Here, we summarize our current knowledge of how, in animal cells, the highly compacted mitotic chromosomes are decondensed at the end of mitosis and how a nuclear envelope, including functional nuclear pore complexes, reassembles around these decondensing chromosomes.
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Affiliation(s)
| | - Paola De Magistris
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany
| | - Wolfram Antonin
- Friedrich Miescher Laboratory of the Max Planck Society, Spemannstrasse 39, 72076 Tübingen, Germany.
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25
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Dickmanns A, Kehlenbach RH, Fahrenkrog B. Nuclear Pore Complexes and Nucleocytoplasmic Transport: From Structure to Function to Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 320:171-233. [PMID: 26614874 DOI: 10.1016/bs.ircmb.2015.07.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleocytoplasmic transport is an essential cellular activity and occurs via nuclear pore complexes (NPCs) that reside in the double membrane of the nuclear envelope. Significant progress has been made during the past few years in unravelling the ultrastructural organization of NPCs and their constituents, the nucleoporins, by cryo-electron tomography and X-ray crystallography. Mass spectrometry and genomic approaches have provided deeper insight into the specific regulation and fine tuning of individual nuclear transport pathways. Recent research has also focused on the roles nucleoporins play in health and disease, some of which go beyond nucleocytoplasmic transport. Here we review emerging results aimed at understanding NPC architecture and nucleocytoplasmic transport at the atomic level, elucidating the specific function individual nucleoporins play in nuclear trafficking, and finally lighting up the contribution of nucleoporins and nuclear transport receptors in human diseases, such as cancer and certain genetic disorders.
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Affiliation(s)
- Achim Dickmanns
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Göttingen, Göttingen, Germany
| | - Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
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26
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Abstract
Nucleocytoplasmic transport is crucial not only for basic cellular activities but also for the physiological adaptation of cells to various environmental stimuli that affect development, cell-fate determination, or disease development. The basic transport mechanisms have been revealed during the past two decades through the identification and biochemical characterizations of factors mediating the transport, dissecting the transport process and examining the function of nuclear pore complexes (NPCs). In this chapter, we describe methods for a nuclear transport reconstitution assay using digitonin-permeabilized mammalian cells. The transport assay can be generally conducted in the lab without special equipment. The assay system is efficient and significantly contributes to the study of nucleocytoplasmic transport.
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Markossian S, Suresh S, Osmani AH, Osmani SA. Nup2 requires a highly divergent partner, NupA, to fulfill functions at nuclear pore complexes and the mitotic chromatin region. Mol Biol Cell 2014; 26:605-21. [PMID: 25540430 PMCID: PMC4325833 DOI: 10.1091/mbc.e14-09-1359] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Among nuclear pore proteins, Nup2 is unique because it transfers to the mitotic chromatin region to fulfill unknown functions. Analysis of Nup2 and a novel targeting partner, NupA, shows that they are required for normal anaphase and nucleokinesis. Their functions also involve an import pathway for Mad1 but apparently not general nuclear protein import. Chromatin and nuclear pore complexes (NPCs) undergo dramatic changes during mitosis, which in vertebrates and Aspergillus nidulans involves movement of Nup2 from NPCs to the chromatin region to fulfill unknown functions. This transition is shown to require the Cdk1 mitotic kinase and be promoted prematurely by ectopic expression of the NIMA kinase. Nup2 localizes with a copurifying partner termed NupA, a highly divergent yet essential NPC protein. NupA and Nup2 locate throughout the chromatin region during prophase but during anaphase move to surround segregating DNA. NupA function is shown to involve targeting Nup2 to its interphase and mitotic locations. Deletion of either Nup2 or NupA causes identical mitotic defects that initiate a spindle assembly checkpoint (SAC)–dependent mitotic delay and also cause defects in karyokinesis. These mitotic problems are not caused by overall defects in mitotic NPC disassembly–reassembly or general nuclear import. However, without Nup2 or NupA, although the SAC protein Mad1 locates to its mitotic locations, it fails to locate to NPCs normally in G1 after mitosis. Collectively the study provides new insight into the roles of Nup2 and NupA during mitosis and in a surveillance mechanism that regulates nucleokinesis when mitotic defects occur after SAC fulfillment.
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Affiliation(s)
- Sarine Markossian
- Laboratory of Gene Regulation and Development, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | | | - Aysha H Osmani
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210
| | - Stephen A Osmani
- Department of Molecular Genetics, Ohio State University, Columbus, OH 43210
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28
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Buchwalter AL, Liang Y, Hetzer MW. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Mol Biol Cell 2014; 25:2472-84. [PMID: 24943837 PMCID: PMC4142618 DOI: 10.1091/mbc.e14-04-0865] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nup50 is a mobile nucleoporin with a pronounced presence both at the nuclear pore complex and in the nucleoplasm that can move between these different localizations. The dynamic behavior of Nup50 in both locations is dependent on active transcription by RNA polymerase II. The nuclear pore complex (NPC) plays a critical role in gene expression by mediating import of transcription regulators into the nucleus and export of RNA transcripts to the cytoplasm. Emerging evidence suggests that in addition to mediating transport, a subset of nucleoporins (Nups) engage in transcriptional activation and elongation at genomic loci that are not associated with NPCs. The underlying mechanism and regulation of Nup mobility on and off nuclear pores remain unclear. Here we show that Nup50 is a mobile Nup with a pronounced presence both at the NPC and in the nucleoplasm that can move between these different localizations. Strikingly, the dynamic behavior of Nup50 in both locations is dependent on active transcription by RNA polymerase II and requires the N-terminal half of the protein, which contains importin α– and Nup153-binding domains. However, Nup50 dynamics are independent of importin α, Nup153, and Nup98, even though the latter two proteins also exhibit transcription-dependent mobility. Of interest, depletion of Nup50 from C2C12 myoblasts does not affect cell proliferation but inhibits differentiation into myotubes. Taken together, our results suggest a transport-independent role for Nup50 in chromatin biology that occurs away from the NPC.
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Affiliation(s)
- Abigail L Buchwalter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Yun Liang
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
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29
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Arjomand A, Baker MA, Li C, Buckle AM, Jans DA, Loveland KL, Miyamoto Y. The α-importome of mammalian germ cell maturation provides novel insights for importin biology. FASEB J 2014; 28:3480-93. [PMID: 24790034 DOI: 10.1096/fj.13-244913] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Importin α proteins function as adaptors to connect a cargo protein and importin β1 in the classical nuclear import pathway. Here we measure for the first time the stoichiometry of importins α2, α3, α4, and β1 in primary cells corresponding to 2 successive stages of rat spermatogenesis: meiotic spermatocytes and haploid round spermatids. Importin α2 levels were more than 2-fold higher in spermatocytes than in spermatids, while importins α4 and β1 levels did not differ significantly. We performed a comprehensive proteomics analysis to identify binding proteins in spermatocytes and spermatids using recombinant importin α2 and α4 proteins. Among the 100 candidate partners, 42 contained a strong classical nuclear localization signal (cNLS; score of>6 by cNLS Mapper), while 8 nuclear proteins lacked any cNLS. In addition, we developed a new strategy to predict which cargoes bind to importin α through the conserved C-terminal acidic domain (ARM repeats 9-10), and provided functional validation of a predicted importin α C-terminal binding segment in Senataxin and Smarca4. Evaluation of this set of candidate binding partners from spermatogenic cells using several bioinformatics approaches provides new evidence that individual importin αs may serve unique and nonredundant roles in mediating cellular differentiation.
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Affiliation(s)
- Arash Arjomand
- Department of Biochemistry and Molecular Biology and Australian Research Council Centre of Excellence in Biotechnology and Development, Canberra, Australian Capital Territory, Australia; and
| | - Mark A Baker
- Australian Research Council Centre of Excellence in Biotechnology and Development, Canberra, Australian Capital Territory, Australia; and Priority Research Centre in Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Chen Li
- Department of Biochemistry and Molecular Biology and
| | | | - David A Jans
- Department of Biochemistry and Molecular Biology and Australian Research Council Centre of Excellence in Biotechnology and Development, Canberra, Australian Capital Territory, Australia; and
| | - Kate L Loveland
- Department of Biochemistry and Molecular Biology and Department of Anatomy and Developmental Biology, School of Biological Sciences, Monash University, Clayton, Victoria, Australia; Australian Research Council Centre of Excellence in Biotechnology and Development, Canberra, Australian Capital Territory, Australia; and
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30
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Hügel S, Depping R, Dittmar G, Rother F, Cabot R, Sury MD, Hartmann E, Bader M. Identification of importin α 7 specific transport cargoes using a proteomic screening approach. Mol Cell Proteomics 2014; 13:1286-98. [PMID: 24623588 DOI: 10.1074/mcp.m112.026856] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The importin α:β complex is responsible for the nuclear import of proteins bearing classical nuclear localization signals. In mammals, several importin α subtypes are known to exist that are suggested to have individual functions. Importin α 7 was shown to play a crucial role in early embryonic development in mice. Embryos from importin α 7-depleted females stop at the two-cell stage and show disturbed zygotic genome activation. As there is evidence that individual importin α subtypes possess cargo specificities, we hypothesized that importin α 7 binds a unique set of intracellular proteins. With the use of a collection of in vitro and in vivo binding assays, importin α 7 interaction partners were identified that differed from proteins found to bind to importin α 2 and 3. One of the proteins preferentially binding importin α 7 was the maternal effect protein Brg1. However, Brg1 was localized in oocyte nuclei in importin α 7-deficient embryos, albeit in reduced amounts, suggesting additional modes of nuclear translocation of this factor. An additional SILAC-based screening approach identified Ash2l, Chd3, Mcm3, and Smarcc1, whose nuclear import seems to be disturbed in importin α 7-deficient fibroblasts.
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Affiliation(s)
- Stefanie Hügel
- Max Delbrück Center of Molecular Medicine, 13125 Berlin, Germany
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31
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Dahan-Pasternak N, Nasereddin A, Kolevzon N, Pe'er M, Wong W, Shinder V, Turnbull L, Whitchurch CB, Elbaum M, Gilberger TW, Yavin E, Baum J, Dzikowski R. PfSec13 is an unusual chromatin-associated nucleoporin of Plasmodium falciparum that is essential for parasite proliferation in human erythrocytes. J Cell Sci 2013; 126:3055-69. [PMID: 23687383 DOI: 10.1242/jcs.122119] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Plasmodium falciparum, the deadliest form of human malaria, the nuclear periphery has drawn much attention due to its role as a sub-nuclear compartment involved in virulence gene expression. Recent data have implicated components of the nuclear envelope in regulating gene expression in several eukaryotes. Special attention has been given to nucleoporins that compose the nuclear pore complex (NPC). However, very little is known about components of the nuclear envelope in Plasmodium parasites. Here we characterize PfSec13, an unusual nucleoporin of P. falciparum, which shows unique structural similarities suggesting that it is a fusion between Sec13 and Nup145C of yeast. Using super resolution fluorescence microscopy (3D-SIM) and in vivo imaging, we show that the dynamic localization of PfSec13 during parasites' intra-erythrocytic development corresponds with that of the NPCs and that these dynamics are associated with microtubules rather than with F-actin. In addition, PfSec13 does not co-localize with the heterochormatin markers HP1 and H3K9me3, suggesting euchromatic location of the NPCs. The proteins associated with PfSec13 indicate that this unusual Nup is involved in several cellular processes. Indeed, ultrastructural and chromatin immunoprecipitation analyses revealed that, in addition to the NPCs, PfSec13 is found in the nucleoplasm where it is associated with chromatin. Finally, we used peptide nucleic acids (PNA) to downregulate PfSec13 and show that it is essential for parasite proliferation in human erythrocytes.
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Affiliation(s)
- Noa Dahan-Pasternak
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel-Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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32
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Building a nuclear envelope at the end of mitosis: coordinating membrane reorganization, nuclear pore complex assembly, and chromatin de-condensation. Chromosoma 2012; 121:539-54. [PMID: 23104094 PMCID: PMC3501164 DOI: 10.1007/s00412-012-0388-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/04/2012] [Accepted: 10/04/2012] [Indexed: 12/01/2022]
Abstract
The metazoan nucleus is disassembled and re-built at every mitotic cell division. The nuclear envelope, including nuclear pore complexes, breaks down at the beginning of mitosis to accommodate the capture of massively condensed chromosomes by the spindle apparatus. At the end of mitosis, a nuclear envelope is newly formed around each set of segregating and de-condensing chromatin. We review the current understanding of the membrane restructuring events involved in the formation of the nuclear membrane sheets of the envelope, the mechanisms governing nuclear pore complex assembly and integration in the nascent nuclear membranes, and the regulated coordination of these events with chromatin de-condensation.
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33
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Makise M, Mackay DR, Elgort S, Shankaran SS, Adam SA, Ullman KS. The Nup153-Nup50 protein interface and its role in nuclear import. J Biol Chem 2012; 287:38515-22. [PMID: 23007389 DOI: 10.1074/jbc.m112.378893] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Interactions between Nup50 and soluble transport factors underlie the efficiency of certain nucleocytoplasmic transport pathways. The platform on which these interactions take place is important to building a complete understanding of nucleocytoplasmic trafficking. Nup153 is the nucleoporin that provides this scaffold for Nup50. Here, we have delineated requirements for the interaction between Nup153 and Nup50, revealing a dual interface. An interaction between Nup50 and a region in the unique N-terminal region of Nup153 is critical for the nuclear pore localization of Nup50. A second site of interaction is at the distal tail of Nup153 and is dependent on importin α. Both of these interactions involve the N-terminal domain of Nup50. The configuration of the Nup153-Nup50 partnership suggests that the Nup153 scaffold provides not just a means of pore targeting for Nup50 but also serves to provide a local environment that facilitates bringing Nup50 and importin α together, as well as other soluble factors involved in transport. Consistent with this, disruption of the Nup153-Nup50 interface decreases efficiency of nuclear import.
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Affiliation(s)
- Masaki Makise
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah 84112, USA
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34
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Expression profiling of attenuated mitochondrial function identifies retrograde signals in Drosophila. G3-GENES GENOMES GENETICS 2012; 2:843-51. [PMID: 22908033 PMCID: PMC3411240 DOI: 10.1534/g3.112.002584] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/18/2012] [Indexed: 01/12/2023]
Abstract
Mitochondria are able to modulate cell state and fate during normal and pathophysiologic conditions through a nuclear-mediated mechanism collectively termed as a retrograde response. Our previous studies in Drosophila melanogaster have clearly established that progress through the cell cycle is precisely regulated by the intrinsic activity of the mitochondrion by specific signaling cascades mounted by the cell. As a means to further our understanding of how mitochondrial energy status affects nuclear control of basic cell decisions, we have employed Affymetrix microarray-based transcriptional profiling of Drosophila S2 cells knocked down for the gene encoding subunit Va of the complex IV of the mitochondrial electron transport chain. The profiling data identify transcriptional upregulation of glycolytic genes, and metabolic studies confirm this increase in glycolysis. The data provide a model of the shift of metabolism from a predominately oxidative state toward a predominately aerobic glycolytic state mediated through transcriptional control. The transcriptional changes alter many signaling systems, including p53, insulin, hypoxia-induced factor α, and conserved mitochondrial retrograde responses. This rich dataset provides many novel targets for further understanding the mechanism whereby the mitochondrion manages energy substrate disposition and directs cellular fate decisions.
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35
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Chatel G, Fahrenkrog B. Dynamics and diverse functions of nuclear pore complex proteins. Nucleus 2012; 3:162-71. [PMID: 22555605 DOI: 10.4161/nucl.19674] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nuclear pore complexes (NPCs) are best known for their central role in controlling the molecular trafficking between the cytoplasm and the nucleus. NPCs are assembled from about 30 different proteins and a growing body of evidence suggests that these nucleoporins are not only acting in the context of NPCs, but also in the nucleoplasm and cytoplasm. In this context it is well accepted that a set of nucleoporins are important regulators of a variety of mitotic processes, including kinetochore assembly, spindle checkpoint control and cytokinesis, whereas others associate with chromatin and administer gene expression. However, the functional importance of nucleoporins go far beyond these roles and this review will provide an overview of the latest insights into the versatility of metazoan nucleoporins with an emphasis on their roles in cell migration, cellular signaling and tissue-specific activities.
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Affiliation(s)
- Guillaume Chatel
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
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36
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Ao Z, Jayappa KD, Wang B, Zheng Y, Wang X, Peng J, Yao X. Contribution of host nucleoporin 62 in HIV-1 integrase chromatin association and viral DNA integration. J Biol Chem 2012; 287:10544-10555. [PMID: 22308026 DOI: 10.1074/jbc.m111.317057] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
HIV-1 integration is promoted by viral integrase (IN) and its cellular cofactors. The lens epithelium-derived growth factor (LEDGF/p75), an IN interacting cellular cofactor, has been shown to play an important role in HIV-1 chromatin targeting and integration. However, whether other cellular cofactors are also involved in viral replication steps is still elusive. Here, we show that nucleoporin 62 (Nup62) is a chromatin-bound protein and can specifically interact with HIV-1 IN in both soluble nuclear extract and chromatin-bound fractions. The knockdown of Nup62 by shRNA reduced the association of IN with host chromatin and significantly impaired viral integration and replication in HIV-1-susceptible cells. Furthermore, the expression of the IN-binding region of Nup62 in CD4(+) T cells significantly inhibited HIV-1 infection. Taken together, these results indicate that the cellular Nup62 is specifically recruited by HIV-1 IN and contribute to an efficient viral DNA integration.
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Affiliation(s)
- Zhujun Ao
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Kallesh Danappa Jayappa
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Binchen Wang
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Yingfeng Zheng
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Xiaoxia Wang
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Jinyu Peng
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Xiaojian Yao
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada.
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Miyamoto Y, Boag PR, Hime GR, Loveland KL. Regulated nucleocytoplasmic transport during gametogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:616-30. [PMID: 22326858 DOI: 10.1016/j.bbagrm.2012.01.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/23/2012] [Accepted: 01/24/2012] [Indexed: 12/13/2022]
Abstract
Gametogenesis is the process by which sperm or ova are produced in the gonads. It is governed by a tightly controlled series of gene expression events, with some common and others distinct for males and females. Nucleocytoplasmic transport is of central importance to the fidelity of gene regulation that is required to achieve the precisely regulated germ cell differentiation essential for fertility. In this review we discuss the physiological importance for gamete formation of the molecules involved in classical nucleocytoplasmic protein transport, including importins/karyopherins, Ran and nucleoporins. To address what functions/factors are conserved or specialized for these developmental processes between species, we compare knowledge from mice, flies and worms. The present analysis provides evidence of the necessity for and specificity of each nuclear transport factor and for nucleoporins during germ cell differentiation. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Yoichi Miyamoto
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.
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38
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Pumroy RA, Nardozzi JD, Hart DJ, Root MJ, Cingolani G. Nucleoporin Nup50 stabilizes closed conformation of armadillo repeat 10 in importin α5. J Biol Chem 2011; 287:2022-31. [PMID: 22130666 DOI: 10.1074/jbc.m111.315838] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The human genome encodes six isoforms of importin α that show greater than 60% sequence similarity and remarkable substrate specificity. The isoform importin α5 can bind phosphorylated cargos such as STAT1 and Epstein-Barr Virus Nuclear Antigen 1, as well as the influenza virus polymerase subunit PB2. In this work, we have studied the interaction of the nucleoporin Nup50 with importin α5. We show that the first 47 residues of Nup50 bind to the C terminus of importin α5 like a "clip," stabilizing the closed conformation of ARM 10. In vitro, Nup50 binds with high affinity either to empty importin α5 or to a preassembled complex of importin α5 bound to the C-terminal domain of the import cargo PB2, resulting in a trimeric complex. By contrast, PB2 can only bind with high affinity to importin α5 in the absence of Nup50. This suggests that Nup50 primary function may not be to actively displace the import cargo from importin α5 but rather to prevent cargo rebinding in preparation for recycling. This is the first evidence for a nucleoporin modulating the import reaction by directly altering the three-dimensional structure of an import adaptor.
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Affiliation(s)
- Ruth A Pumroy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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39
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Goeres J, Chan PK, Mukhopadhyay D, Zhang H, Raught B, Matunis MJ. The SUMO-specific isopeptidase SENP2 associates dynamically with nuclear pore complexes through interactions with karyopherins and the Nup107-160 nucleoporin subcomplex. Mol Biol Cell 2011; 22:4868-82. [PMID: 22031293 PMCID: PMC3237629 DOI: 10.1091/mbc.e10-12-0953] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We determined that the small, ubiquitin-related modifier–specific isopeptidase, SENP2, is dynamically associated with nuclear pore complexes (NPCs). This association is determined by the activities of three N-terminal signals in SENP2: a high-affinity nuclear localization sequence, an Nup107-160–binding element, and a nuclear export signal. NPC association, and its potential regulation, affects SENP2 accessibility to substrates. The association of small, ubiquitin-related modifier–specific isopeptidases (also known as sentrin-specific proteases, or SENPs) with nuclear pore complexes (NPCs) is conserved in eukaryotic organisms ranging from yeast to mammals. However, the functional significance of this association remains poorly understood, particularly in mammalian cells. In this study, we have characterized the molecular basis for interactions between SENP2 and NPCs in human cells. Using fluorescence recovery after photobleaching, we demonstrate that SENP2, although concentrated at the nuclear basket, is dynamically associated with NPCs. This association is mediated by multiple targeting elements within the N-terminus of SENP2 that function cooperatively to mediate NPC localization. One of these elements consists of a high-affinity nuclear localization signal that mediates indirect tethering to FG-repeat–containing nucleoporins through karyopherins. A second element mediates interactions with the Nup107-160 nucleoporin subcomplex. A third element consists of a nuclear export signal. Collectively, our findings reveal that SENP2 is tethered to NPCs through a complex interplay of interactions with nuclear import and export receptors and nucleoporins. Disruption of these interactions enhances SENP2 substrate accessibility, suggesting an important regulatory node in the SUMO pathway.
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Affiliation(s)
- Jacqueline Goeres
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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40
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Merkle T. Nucleo-cytoplasmic transport of proteins and RNA in plants. PLANT CELL REPORTS 2011; 30:153-76. [PMID: 20960203 PMCID: PMC3020307 DOI: 10.1007/s00299-010-0928-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 09/30/2010] [Indexed: 05/19/2023]
Abstract
Transport of macromolecules between the nucleus and the cytoplasm is an essential necessity in eukaryotic cells, since the nuclear envelope separates transcription from translation. In the past few years, an increasing number of components of the plant nuclear transport machinery have been characterised. This progress, although far from being completed, confirmed that the general characteristics of nuclear transport are conserved between plants and other organisms. However, plant-specific components were also identified. Interestingly, several mutants in genes encoding components of the plant nuclear transport machinery were investigated, revealing differential sensitivity of plant-specific pathways to impaired nuclear transport. These findings attracted attention towards plant-specific cargoes that are transported over the nuclear envelope, unravelling connections between nuclear transport and components of signalling and developmental pathways. The current state of research in plants is summarised in comparison to yeast and vertebrate systems, and special emphasis is given to plant nuclear transport mutants.
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Affiliation(s)
- Thomas Merkle
- Faculty of Biology, Institute for Genome Research and Systems Biology, University of Bielefeld, 33594 Bielefeld, Germany.
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41
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Arib G, Akhtar A. Multiple facets of nuclear periphery in gene expression control. Curr Opin Cell Biol 2011; 23:346-53. [PMID: 21242077 DOI: 10.1016/j.ceb.2010.12.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Revised: 12/17/2010] [Accepted: 12/20/2010] [Indexed: 01/26/2023]
Abstract
Nuclear pore complexes play a central role in controlling the traffic between the nucleus and the cytoplasm. Progress during the last decade has highlighted nuclear periphery components as novel players in chromatin organization, gene regulation, and genome stability. For instance, lamins associate with repressive chromatin while nuclear pores tend to associate with active chromatin. Interestingly, nucleoporins (Nups) act not only at the nuclear periphery but also in the nucleoplasm. Here we provide an overview of the latest findings and discuss the functional importance of nucleoporin association with specific genes, their role in transcriptional memory, the coupling of transcription and mRNA export, and genome integrity.
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Affiliation(s)
- Ghislaine Arib
- Max-Planck-Institute of Immunobiology und Epigenetics, Stübeweg 51,79108 Freiburg im Breisgau, Germany
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42
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Tamura K, Fukao Y, Iwamoto M, Haraguchi T, Hara-Nishimura I. Identification and characterization of nuclear pore complex components in Arabidopsis thaliana. THE PLANT CELL 2010; 22:4084-97. [PMID: 21189294 PMCID: PMC3027183 DOI: 10.1105/tpc.110.079947] [Citation(s) in RCA: 220] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/19/2010] [Accepted: 12/02/2010] [Indexed: 05/17/2023]
Abstract
The nuclear pore complex (NPC) facilitates nucleocytoplasmic transport, a crucial process for various cellular activities. The NPC comprises ~30 nucleoporins and is well characterized in vertebrates and yeast. However, only eight plant nucleoporins have been identified, and little information is available about the complete molecular structure of plant NPCs. In this study, an interactive proteomic approach was used to identify Arabidopsis thaliana nucleoporins. A series of five cycles of interactive proteomic analysis was performed using green fluorescent protein (GFP)-tagged nucleoporins. The identified nucleoporins were then cloned and subcellular localization analyses were performed. We found that the plant NPC contains at least 30 nucleoporins, 22 of which had not been previously annotated. Surprisingly, plant nucleoporins shared a similar domain organization to their vertebrate (human) and yeast (Saccharomyces cerevisiae) counterparts. Moreover, the plant nucleoporins exhibited higher sequence homology to vertebrate nucleoporins than to yeast nucleoporins. Plant NPCs lacked seven components (NUCLEOPORIN358 [Nup358], Nup188, Nup153, Nup45, Nup37, NUCLEAR DIVISION CYCLE1, and PORE MEMBRANE PROTEIN OF 121 kD) that were present in vertebrate NPCs. However, plants possessed a nucleoporin, Nup136/Nup1, that contained Phe-Gly repeats, and sequence analysis failed to identify a vertebrate homolog for this protein. Interestingly, Nup136-GFP showed greater mobility on the nuclear envelope than did other nucleoporins, and a Nup136/Nup1 deficiency caused various defects in plant development. These findings provide valuable new information about plant NPC structure and function.
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Affiliation(s)
- Kentaro Tamura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoichiro Fukao
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0101, Japan
| | - Masaaki Iwamoto
- Kobe Advanced ICT Research Center, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Tokuko Haraguchi
- Kobe Advanced ICT Research Center, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Ikuko Hara-Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
- Address correspondence to
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43
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Lott K, Cingolani G. The importin β binding domain as a master regulator of nucleocytoplasmic transport. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:1578-92. [PMID: 21029753 DOI: 10.1016/j.bbamcr.2010.10.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 10/11/2010] [Accepted: 10/19/2010] [Indexed: 12/16/2022]
Abstract
Specific and efficient recognition of import cargoes is essential to ensure nucleocytoplasmic transport. To this end, the prototypical karyopherin importin β associates with import cargoes directly or, more commonly, through import adaptors, such as importin α and snurportin. Adaptor proteins bind the nuclear localization sequence (NLS) of import cargoes while recruiting importin β via an N-terminal importin β binding (IBB) domain. The use of adaptors greatly expands and amplifies the repertoire of cellular cargoes that importin β can efficiently import into the cell nucleus and allows for fine regulation of nuclear import. Accordingly, the IBB domain is a dedicated NLS, unique to adaptor proteins that functions as a molecular liaison between importin β and import cargoes. This review provides an overview of the molecular role played by the IBB domain in orchestrating nucleocytoplasmic transport. Recent work has determined that the IBB domain has specialized functions at every step of the import and export pathway. Unexpectedly, this stretch of ~40 amino acids plays an essential role in regulating processes such as formation of the import complex, docking and translocation through the nuclear pore complex (NPC), release of import cargoes into the cell nucleus and finally recycling of import adaptors and importin β into the cytoplasm. Thus, the IBB domain is a master regulator of nucleocytoplasmic transport, whose complex molecular function is only recently beginning to emerge. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.
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Affiliation(s)
- Kaylen Lott
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
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44
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Oka M, Asally M, Yasuda Y, Ogawa Y, Tachibana T, Yoneda Y. The mobile FG nucleoporin Nup98 is a cofactor for Crm1-dependent protein export. Mol Biol Cell 2010; 21:1885-96. [PMID: 20375145 PMCID: PMC2877646 DOI: 10.1091/mbc.e09-12-1041] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 03/26/2010] [Accepted: 03/29/2010] [Indexed: 12/18/2022] Open
Abstract
Nup98 is a mobile nucleoporin that forms distinct dots in the nucleus, and, although a role for Nup98 in nuclear transport has been suggested, its precise function remains unclear. Here, we show that Nup98 plays an important role in Crm1-mediated nuclear protein export. Nuclear, but not cytoplasmic, dots of EGFP-tagged Nup98 disappeared rapidly after cell treatment with leptomycin B, a specific inhibitor of the nuclear export receptor, Crm1. Mutational analysis demonstrated that Nup98 physically and functionally interacts with Crm1 in a RanGTP-dependent manner through its N-terminal phenylalanine-glycine (FG) repeat region. Moreover, the activity of the Nup98-Crm1 complex was modulated by RanBP3, a known cofactor for Crm1-mediated nuclear export. Finally, cytoplasmic microinjection of anti-Nup98 inhibited the Crm1-dependent nuclear export of proteins, concomitant with the accumulation of anti-Nup98 in the nucleus. These results clearly demonstrate that Nup98 functions as a novel shuttling cofactor for Crm1-mediated nuclear export in conjunction with RanBP3.
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Affiliation(s)
- Masahiro Oka
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
- Department of Biochemistry, Graduate School of Medicine, Osaka University, and
- Japan Science and Technology Corporation (JST), Core Research for Evolution Science and Technology (CREST), Osaka University, Suita, Osaka 565-0871, Japan; and
| | - Munehiro Asally
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
| | - Yoshinari Yasuda
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
| | - Yutaka Ogawa
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
| | - Taro Tachibana
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, Osaka 558-8585, Japan
| | - Yoshihiro Yoneda
- *Biomolecular Dynamics Group, Graduate School of Frontier Biosciences
- Department of Biochemistry, Graduate School of Medicine, Osaka University, and
- Japan Science and Technology Corporation (JST), Core Research for Evolution Science and Technology (CREST), Osaka University, Suita, Osaka 565-0871, Japan; and
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45
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Chumakov SP, Prassolov VS. Organization and regulation of nucleocytoplasmic transport. Mol Biol 2010; 44:186-201. [PMID: 32214470 PMCID: PMC7088953 DOI: 10.1134/s0026893310020020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 11/03/2009] [Indexed: 01/05/2023]
Abstract
Separation of DNA replication and transcription, which occur in the nucleus, from protein synthesis, which occurs in the cytoplasm, allows a more precise regulation of these processes. Selective exchange of macromolecules between the two compartments is mediated by proteins of the nuclear pore complex (NPC). Receptor proteins of the karyopherin family interact with NPC components and transfer their cargos between the nucleus and cytoplasm. Nucleocytoplasmic transport pathways are regulated at multiple levels by modulating the expression or function of individual cargoes, transport receptors, or the transport channel. The regulatory levels have increasingly broad effects on the transport pathways and affect a wide range of processes from gene expression to development and differentiation.
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Affiliation(s)
- S P Chumakov
- 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,2Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195 USA
| | - V S Prassolov
- 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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46
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Broggini-Tenzer A, Hollenstein A, Pianowski Z, Wampfler A, Furmanova P, Winssinger N, Pruschy M. Substrate screening identifies a novel target sequence for the proteasomal activity regulated by ionizing radiation. Proteomics 2010; 10:304-14. [PMID: 19957288 DOI: 10.1002/pmic.200900162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The screening for treatment-induced enzyme activities offers the opportunity to discover important regulatory mechanisms and the identification of potential targets for anti-cancer therapies. A novel screening technique was applied to screen substrate peptide sequences for proteolytic activities up- or down-regulated by ionizing radiation in tumor cells. One specific substrate sequence was cleaved in control cell extracts but to a smaller extent in irradiated cell extracts and investigated in detail. Based on protease-class-specific inhibitory studies and cleavage site analysis a potent warhead-inhibitor was synthesized and used to identify the proteasome as the protease of interest. The investigated sequence shows high homology to a regulatory site of nucleoporin 50, an element of the nuclear pore complex, and site specific cleavage of nucleoporin 50 was determined in vitro suggesting a novel link between the ionizing radiation-regulated proteasome and nuclear protein shuttling.
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Affiliation(s)
- Angela Broggini-Tenzer
- Laboratory for Molecular Radiobiology, University Hospital Zurich, CH-8091 Zürich, Switzerland
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47
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Kosako H, Imamoto N. Phosphorylation of nucleoporins: signal transduction-mediated regulation of their interaction with nuclear transport receptors. Nucleus 2010; 1:309-13. [PMID: 21327077 DOI: 10.4161/nucl.1.4.11744] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/01/2010] [Accepted: 01/26/2010] [Indexed: 11/19/2022] Open
Abstract
The nuclear pore complex (NPC) is composed of ∼30 unique proteins, collectively referred to as nucleoporins or Nups. While metazoan Nups are known to be phosphorylated during mitosis to cause disassembly of the NPC, what is less clear is whether Nups are phosphorylated and regulated by extracellular stimuli in interphase cells. Our multi-step phosphoproteomic approach revealed a number of physiologically relevant extracellular signal-regulated kinase (ERK) targets, including Nups containing FG repeats (FG Nups) that provide binding sites for nuclear transport receptors (NTRs) during the NPC passage. The phosphorylation of FG Nups by ERK does not affect the overall architecture of the NPC but directly inhibits their interactions with NTRs and regulates the permeability barrier properties of the NPC. Such regulation at the levels of transport machinery is expected to have a broad impact on cellular physiology through the spatiotemporal control of signaling events. Until recently, many studies have focused on cellular signaling-mediated phosphorylation of individual cargo proteins, such as transcription factors. An understanding of the effects of signaling pathways on nucleocytoplasmic transport machinery is only beginning to emerge.
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Affiliation(s)
- Hidetaka Kosako
- Division of Disease Proteomics; Institute for Enzyme Research; The University of Tokushima; Tokushima, Japan.
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48
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Kalverda B, Pickersgill H, Shloma VV, Fornerod M. Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 2010; 140:360-71. [PMID: 20144760 DOI: 10.1016/j.cell.2010.01.011] [Citation(s) in RCA: 326] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 05/18/2009] [Accepted: 12/31/2009] [Indexed: 10/19/2022]
Abstract
Nuclear pore complexes (NPCs) mediate transport across the nuclear envelope. In yeast, they also interact with active genes, attracting or retaining them at the nuclear periphery. In higher eukaryotes, some NPC components (nucleoporins) are also found in the nucleoplasm, with a so far unknown function. We have functionally characterized nucleoporin-chromatin interactions specifically at the NPC or within the nucleoplasm in Drosophila. We analyzed genomic interactions of full-length nucleoporins Nup98, Nup50, and Nup62 and nucleoplasmic and NPC-tethered forms of Nup98. We found that nucleoporins predominantly interacted with transcriptionally active genes inside the nucleoplasm, in particular those involved in developmental regulation and the cell cycle. A smaller set of nonactive genes interacted with the NPC. Genes strongly interacting with nucleoplasmic Nup98 were downregulated upon Nup98 depletion and activated on nucleoplasmic Nup98 overexpression. Thus, nucleoporins stimulate developmental and cell-cycle gene expression away from the NPC by interacting with these genes inside the nucleoplasm.
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Affiliation(s)
- Bernike Kalverda
- Division of Gene Regulation, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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49
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Spatial distribution and mobility of the Ran GTPase in live interphase cells. Biophys J 2010; 97:2164-78. [PMID: 19843449 DOI: 10.1016/j.bpj.2009.07.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 07/14/2009] [Accepted: 07/30/2009] [Indexed: 12/30/2022] Open
Abstract
The GTPase Ran is a key regulator of molecular transport through nuclear pore complex (NPC) channels. To analyze the role of Ran in its nuclear transport function, we used several quantitative fluorescence techniques to follow the distribution and dynamics of an enhanced yellow fluorescent protein (EYFP)-Ran in HeLa cells. The diffusion coefficient of the majority of EYFP-Ran molecules throughout the cells corresponded to an unbound state, revealing the remarkably dynamic Ran regulation. Although we observed no significant immobile Ran populations in cells, approximately 10% of the cytoplasmic EYFP-Ran and 30% of the nuclear EYFP-Ran exhibited low mobility indicative of molecular interactions. The high fraction of slow nuclear EYFP-Ran reflects the expected numerous interactions of nuclear RanGTP with nuclear transport receptors. However, it is not high enough to support retention mechanisms as the main cause for the observed nuclear accumulation of Ran. The highest cellular concentration of EYFP-Ran was detected at the nuclear envelope, corresponding to approximately 200 endogenous Ran molecules for each NPC, and exceeding the currently estimated NPC channel transport capacity. Together with the relatively long residence time of EYFP-Ran at the nuclear envelope (33 +/- 14 ms), these observations suggest that only a fraction of the Ran concentrated at NPCs transits through NPC channels.
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50
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Ogawa Y, Miyamoto Y, Asally M, Oka M, Yasuda Y, Yoneda Y. Two isoforms of Npap60 (Nup50) differentially regulate nuclear protein import. Mol Biol Cell 2009; 21:630-8. [PMID: 20016008 PMCID: PMC2820426 DOI: 10.1091/mbc.e09-05-0374] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Npap60 (Nup50) is a nucleoporin that binds directly to importin α. In humans, there are two Npap60 isoforms: the long (Npap60L) and short (Npap60S) forms. Our results demonstrate that Npap60S stabilizes the binding of importin α to classical NLS-cargo, whereas Npap60L promotes the release of NLS-cargo from importin α. Npap60 (Nup50) is a nucleoporin that binds directly to importin α. In humans, there are two Npap60 isoforms: the long (Npap60L) and short (Npap60S) forms. In this study, we provide both in vitro and in vivo evidence that Npap60L and Npap60S function differently in nuclear protein import. In vitro binding assays revealed that Npap60S stabilizes the binding of importin α to classical NLS-cargo, whereas Npap60L promotes the release of NLS-cargo from importin α. In vivo time-lapse experiments showed that when the Npap60 protein level is controlled, allowing CAS to efficiently promote the dissociation of the Npap60/importin α complex, Npap60S and Npap60L suppress and accelerate the nuclear import of NLS-cargo, respectively. These results demonstrate that Npap60L and Npap60S have opposing functions and suggest that Npap60L and Npap60S levels must be carefully controlled for efficient nuclear import of classical NLS-cargo in humans. This study provides novel evidence that nucleoporin expression levels regulate nuclear import efficiency.
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Affiliation(s)
- Yutaka Ogawa
- Department of Frontier Biosciences, Graduate School of Frontier Biosciences, and Department of Biochemistry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
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