1
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Tang G, Huang S, Luo J, Wu Y, Zheng S, Tong R, Zhong L, Shi J. Advances in research on potential inhibitors of multiple myeloma. Eur J Med Chem 2023; 262:115875. [PMID: 37879169 DOI: 10.1016/j.ejmech.2023.115875] [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: 08/31/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Multiple myeloma (MM) is a common hematological malignancy. Although recent clinical applications of immunomodulatory drugs, proteasome inhibitors and CD38-targeting antibodies have significantly improved the outcome of MM patient with increased survival, the incidence of drug resistance and severe treatment-related complications is gradually on the rise. This review article summarizes the characteristics and clinical investigations of several MM drugs in clinical trials, including their structures, mechanisms of action, structure-activity relationships, and clinical study progress. Furthermore, the application potentials of the drugs that have not yet entered clinical trials are also reviewed. The review also outlines the future directions of MM drug development.
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Affiliation(s)
- Guoyuan Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shan Huang
- Cancer Center, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Ji Luo
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Yingmiao Wu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Shuai Zheng
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
| | - Rongsheng Tong
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China.
| | - Ling Zhong
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center for Medical Genetics, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610044, China.
| | - Jianyou Shi
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China.
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2
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Fichtman B, Harel A. The magnified view: from ancient trinkets to single nuclear pore complexes. FEBS Lett 2023; 597:2590-2596. [PMID: 37777820 DOI: 10.1002/1873-3468.14746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 10/02/2023]
Abstract
A journey from the earliest known use of lenses and magnifying glasses in ancient times, through the development of microscopes and towards modern electron microscopy techniques. The evolving technology and improved microscopes enabled the discovery of intracellular organelles, the nucleus and nuclear pore complexes (NPCs). Current advances have led to composite three-dimensional models showing NPC structure in unprecedented detail but relying on the averaging of many images. A complementary approach is field emission scanning electron microscopy providing topographic surface images that are easily and intuitively interpreted by our brain. Recent advances in this technique have made it possible to expose nuclei from human cells and to focus on individual NPCs and their architectural features.
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Affiliation(s)
- Boris Fichtman
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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3
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Li X, Huang Z, Liao Z, Liu A, Huo S. Transformable nanodrugs for overcoming the biological barriers in the tumor environment during drug delivery. NANOSCALE 2023; 15:8532-8547. [PMID: 37114478 DOI: 10.1039/d2nr06621a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Drug delivery systems have been studied massively with explosive growth in the last few decades. However, challenges such as biological barriers are still obstructing the delivery efficiency of nanomedicines. Reports have shown that the physicochemical properties, such as the morphologies of nanodrugs, could highly affect their biodistribution and bioavailability. Therefore, transformable nanodrugs that take advantage of different sizes and shapes allow for overcoming multiple biological barriers, providing promising prospects for drug delivery. This review aims to present an overview of the most recent developments of transformable nanodrugs in this emerging field. First, the design principles and transformation mechanisms which serve as guidelines for smart nanodrugs are summarized. Afterward, their applications in overcoming biological barriers, including the bloodstream, intratumoral pressure, cellular membrane, endosomal wrapping, and nuclear membrane, are highlighted. Finally, discussions on the current developments and future perspectives of transformable nanodrugs are given.
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Affiliation(s)
- Xuejian Li
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zhenkun Huang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zhihuan Liao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Aijie Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Shuaidong Huo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
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4
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Tai L, Yin G, Sun F, Zhu Y. Cryo-electron microscopy reveals the structure of the nuclear pore complex. J Mol Biol 2023; 435:168051. [PMID: 36933820 DOI: 10.1016/j.jmb.2023.168051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
The nuclear pore complex (NPC) is a giant protein assembly that penetrates the double layers of the nuclear membrane. The overall structure of the NPC has approximately eightfold symmetry and is formed by approximately 30 nucleoporins. The great size and complexity of the NPC have hindered the study of its structure for many years until recent breakthroughs were achieved by integrating the latest high-resolution cryo-electron microscopy (cryo-EM), the emerging artificial intelligence-based modeling and all other available structural information from crystallography and mass spectrometry. Here, we review our latest knowledge of the NPC architecture and the history of its structural study from in vitro to in situ with progressively improved resolutions by cryo-EM, with a particular focus on the latest subnanometer-resolution structural studies. The future directions for structural studies of NPCs are also discussed.
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Affiliation(s)
- Linhua Tai
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Yin
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong 510005, China.
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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5
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Tai L, Zhu Y, Ren H, Huang X, Zhang C, Sun F. 8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI. Protein Cell 2022; 13:760-777. [PMID: 35015240 PMCID: PMC9233733 DOI: 10.1007/s13238-021-00895-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/16/2021] [Indexed: 11/27/2022] Open
Abstract
The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the outer rings containing nuclear ring (NR) and cytoplasmic ring (CR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the outer rings, including the Y complexes and flanking components. In this most comprehensive and accurate model of outer rings to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. In addition to two copies of Y complexes, each asymmetric subunit in CR contains five copies of Nup358, two copies of the Nup214 complex, two copies of Nup205 and one copy of newly identified Nup93, while that in NR contains one copy of Nup205, one copy of ELYS and one copy of Nup93. These in-depth structural features represent a great advance in understanding the assembly of NPCs.
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Affiliation(s)
- Linhua Tai
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China
| | - He Ren
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaojun Huang
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chuanmao Zhang
- The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China.
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, 510005, China.
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6
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Balasubramanian SK, Azmi AS, Maciejewski J. Selective inhibition of nuclear export: a promising approach in the shifting treatment paradigms for hematological neoplasms. Leukemia 2022; 36:601-612. [PMID: 35091658 PMCID: PMC8885406 DOI: 10.1038/s41375-021-01483-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/04/2021] [Accepted: 11/16/2021] [Indexed: 12/12/2022]
Abstract
Novel targeted therapeutics alone or in rational combinations are likely to dominate the future management of various hematological neoplasms. However, the challenges currently faced are the molecular heterogeneity in driver lesions and genetic plasticity leading to multiple resistance pathways. Thus, progress has overall been gradual. For example, despite the advent of targeted agents against actionable drivers like FLT3 in acute myeloid leukemia (AML), the prognosis remains suboptimal in newly diagnosed and dismal in the relapsed/refractory (R/R) setting, due to other molecular abnormalities contributing to inherent and acquired treatment resistance. Nuclear export inhibitors are of keen interest because they can inhibit several active tumorigenic processes simultaneously and also synergize with other targeted drugs and chemotherapy. XPO1 (or CRM1, chromosome maintenance region 1) is one of the most studied exportins involved in transporting critical cargoes, including tumor suppressor proteins like p27, p53, and RB1. Apart from the TSP cargo transport and its role in drug resistance, XPO1 inhibition results in retention of master transcription factors essential for cell differentiation, cell survival, and autophagy, rendering cells more susceptible to the effects of other antineoplastic agents, including targeted therapies. This review will dissect the role of XPO1 inhibition in hematological neoplasms, focusing on mechanistic insights gleaned mainly from work with SINE compounds. Future potential combinatorial strategies will be discussed.
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Affiliation(s)
| | - Asfar S Azmi
- Department of Oncology, Wayne State University School of Medicine, Detroit, USA
| | - Jaroslaw Maciejewski
- Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, USA.
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7
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Raices M, D'Angelo MA. Structure, Maintenance, and Regulation of Nuclear Pore Complexes: The Gatekeepers of the Eukaryotic Genome. Cold Spring Harb Perspect Biol 2022; 14:a040691. [PMID: 34312247 PMCID: PMC8789946 DOI: 10.1101/cshperspect.a040691] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, the genetic material is segregated inside the nucleus. This compartmentalization of the genome requires a transport system that allows cells to move molecules across the nuclear envelope, the membrane-based barrier that surrounds the chromosomes. Nuclear pore complexes (NPCs) are the central component of the nuclear transport machinery. These large protein channels penetrate the nuclear envelope, creating a passage between the nucleus and the cytoplasm through which nucleocytoplasmic molecule exchange occurs. NPCs are one of the largest protein assemblies of eukaryotic cells and, in addition to their critical function in nuclear transport, these structures also play key roles in many cellular processes in a transport-independent manner. Here we will review the current knowledge of the NPC structure, the cellular mechanisms that regulate their formation and maintenance, and we will provide a brief description of a variety of processes that NPCs regulate.
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Affiliation(s)
- Marcela Raices
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
| | - Maximiliano A D'Angelo
- Cell and Molecular Biology of Cancer Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA
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8
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Matsuda A, Mofrad MRK. Free energy calculations shed light on the nuclear pore complex's selective barrier nature. Biophys J 2021; 120:3628-3640. [PMID: 34339633 PMCID: PMC8456294 DOI: 10.1016/j.bpj.2021.07.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/27/2021] [Accepted: 07/27/2021] [Indexed: 12/27/2022] Open
Abstract
The nuclear pore complex (NPC) is the exclusive gateway for traffic control across the nuclear envelope. Although smaller cargoes (less than 5-9 nm in size) can freely diffuse through the NPC, the passage of larger cargoes is restricted to those accompanied by nuclear transport receptors (NTRs). This selective barrier nature of the NPC is putatively associated with the intrinsically disordered, phenylalanine-glycine repeat-domains containing nucleoporins, termed FG-Nups. The precise mechanism underlying how FG-Nups carry out such an exquisite task at high throughputs has, however, remained elusive and the subject of various hypotheses. From the thermodynamics perspective, free energy analysis can be a way to determine cargo's transportability because the traffic through the NPC must be in the direction of reducing the free energy. In this study, we developed a computational model to evaluate the free energy composed of the conformational entropy of FG-Nups and the energetic gain associated with binding interactions between FG-Nups and NTRs and investigated whether these physical features can be the basis of NPC's selectivity. Our results showed that the reduction in conformational entropy by inserting a cargo into the NPC increased the free energy by an amount substantially greater than the thermal energy (≫kBT), whereas the free energy change was negligible (
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Affiliation(s)
- Atsushi Matsuda
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California.
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9
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Hoogenboom BW, Hough LE, Lemke EA, Lim RYH, Onck PR, Zilman A. Physics of the Nuclear Pore Complex: Theory, Modeling and Experiment. PHYSICS REPORTS 2021; 921:1-53. [PMID: 35892075 PMCID: PMC9306291 DOI: 10.1016/j.physrep.2021.03.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The hallmark of eukaryotic cells is the nucleus that contains the genome, enclosed by a physical barrier known as the nuclear envelope (NE). On the one hand, this compartmentalization endows the eukaryotic cells with high regulatory complexity and flexibility. On the other hand, it poses a tremendous logistic and energetic problem of transporting millions of molecules per second across the nuclear envelope, to facilitate their biological function in all compartments of the cell. Therefore, eukaryotes have evolved a molecular "nanomachine" known as the Nuclear Pore Complex (NPC). Embedded in the nuclear envelope, NPCs control and regulate all the bi-directional transport between the cell nucleus and the cytoplasm. NPCs combine high molecular specificity of transport with high throughput and speed, and are highly robust with respect to molecular noise and structural perturbations. Remarkably, the functional mechanisms of NPC transport are highly conserved among eukaryotes, from yeast to humans, despite significant differences in the molecular components among various species. The NPC is the largest macromolecular complex in the cell. Yet, despite its significant complexity, it has become clear that its principles of operation can be largely understood based on fundamental physical concepts, as have emerged from a combination of experimental methods of molecular cell biology, biophysics, nanoscience and theoretical and computational modeling. Indeed, many aspects of NPC function can be recapitulated in artificial mimics with a drastically reduced complexity compared to biological pores. We review the current physical understanding of the NPC architecture and function, with the focus on the critical analysis of experimental studies in cells and artificial NPC mimics through the lens of theoretical and computational models. We also discuss the connections between the emerging concepts of NPC operation and other areas of biophysics and bionanotechnology.
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Affiliation(s)
- Bart W. Hoogenboom
- London Centre for Nanotechnology and Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Loren E. Hough
- Department of Physics and BioFrontiers Institute, University of Colorado, Boulder CO 80309, United States of America
| | - Edward A. Lemke
- Biocenter Mainz, Departments of Biology and Chemistry, Johannes Gutenberg University and Institute of Molecular Biology, 55128 Mainz, Germany
| | - Roderick Y. H. Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Patrick R. Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Anton Zilman
- Department of Physics and Institute for Biomedical Engineering (IBME), University of Toronto, Toronto, ON M5S 1A7, Canada
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10
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Park JH, Ryu SJ, Kim BJ, Cho HJ, Park CH, Choi HJC, Jang EJ, Yang EJ, Hwang JA, Woo SH, Lee JH, Park JH, Choi KM, Kwon YY, Lee CK, Park JT, Cho SC, Lee YI, Lee SB, Han JA, Cho KA, Kim MS, Hwang D, Lee YS, Park SC. Disruption of nucleocytoplasmic trafficking as a cellular senescence driver. Exp Mol Med 2021; 53:1092-1108. [PMID: 34188179 PMCID: PMC8257587 DOI: 10.1038/s12276-021-00643-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/20/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
Senescent cells exhibit a reduced response to intrinsic and extrinsic stimuli. This diminished reaction may be explained by the disrupted transmission of nuclear signals. However, this hypothesis requires more evidence before it can be accepted as a mechanism of cellular senescence. A proteomic analysis of the cytoplasmic and nuclear fractions obtained from young and senescent cells revealed disruption of nucleocytoplasmic trafficking (NCT) as an essential feature of replicative senescence (RS) at the global level. Blocking NCT either chemically or genetically induced the acquisition of an RS-like senescence phenotype, named nuclear barrier-induced senescence (NBIS). A transcriptome analysis revealed that, among various types of cellular senescence, NBIS exhibited a gene expression pattern most similar to that of RS. Core proteomic and transcriptomic patterns common to both RS and NBIS included upregulation of the endocytosis-lysosome network and downregulation of NCT in senescent cells, patterns also observed in an aging yeast model. These results imply coordinated aging-dependent reduction in the transmission of extrinsic signals to the nucleus and in the nucleus-to-cytoplasm supply of proteins/RNAs. We further showed that the aging-associated decrease in Sp1 transcription factor expression was critical for the downregulation of NCT. Our results suggest that NBIS is a modality of cellular senescence that may represent the nature of physiological aging in eukaryotes.
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Affiliation(s)
- Ji-Hwan Park
- grid.249967.70000 0004 0636 3099Korea Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, 34141 Republic of Korea
| | - Sung Jin Ryu
- grid.419666.a0000 0001 1945 5898Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon, 16677 Republic of Korea ,Present Address: UBLBio Corporation, Suwon, 16679 Republic of Korea
| | - Byung Ju Kim
- grid.417736.00000 0004 0438 6721Present Address: Well Aging Research Center, Division of Biotechnology, DGIST, Daegu, 42988 Republic of Korea ,Present Address: UBLBio Corporation, Suwon, 16679 Republic of Korea
| | - Hyun-Ji Cho
- grid.417736.00000 0004 0438 6721Present Address: Well Aging Research Center, Division of Biotechnology, DGIST, Daegu, 42988 Republic of Korea
| | - Chi Hyun Park
- grid.412010.60000 0001 0707 9039Department of Computer Science and Engineering, Kangwon National University, Chuncheon, 24341 Republic of Korea
| | - Hyo Jei Claudia Choi
- grid.419666.a0000 0001 1945 5898Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon, 16677 Republic of Korea
| | - Eun-Jin Jang
- grid.417736.00000 0004 0438 6721Present Address: Well Aging Research Center, Division of Biotechnology, DGIST, Daegu, 42988 Republic of Korea
| | - Eun Jae Yang
- grid.417736.00000 0004 0438 6721Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - Jeong-A Hwang
- grid.417736.00000 0004 0438 6721Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - Seung-Hwa Woo
- grid.417736.00000 0004 0438 6721Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - Jun Hyung Lee
- grid.417736.00000 0004 0438 6721Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - Ji Hwan Park
- grid.417736.00000 0004 0438 6721Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - Kyung-Mi Choi
- grid.222754.40000 0001 0840 2678Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841 Republic of Korea
| | - Young-Yon Kwon
- grid.222754.40000 0001 0840 2678Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841 Republic of Korea
| | - Cheol-Koo Lee
- grid.222754.40000 0001 0840 2678Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841 Republic of Korea
| | - Joon Tae Park
- grid.412977.e0000 0004 0532 7395Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, 22012 Republic of Korea
| | - Sung Chun Cho
- grid.417736.00000 0004 0438 6721Present Address: Well Aging Research Center, Division of Biotechnology, DGIST, Daegu, 42988 Republic of Korea
| | - Yun-Il Lee
- grid.417736.00000 0004 0438 6721Present Address: Well Aging Research Center, Division of Biotechnology, DGIST, Daegu, 42988 Republic of Korea
| | - Sung Bae Lee
- grid.417736.00000 0004 0438 6721Department of Brain & Cognitive Science, DGIST, Daegu, 42988 Republic of Korea
| | - Jeong A. Han
- grid.412010.60000 0001 0707 9039Department of Biochemistry and Molecular Biology, Kangwon National University School of Medicine, Chuncheon, 24341 Republic of Korea
| | - Kyung A Cho
- grid.14005.300000 0001 0356 9399Department of Biochemistry, Chonnam National University, Medical School, Gwangju, 61469 Republic of Korea
| | - Min-Sik Kim
- grid.417736.00000 0004 0438 6721Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - Daehee Hwang
- grid.31501.360000 0004 0470 5905Department of Biological Sciences, Seoul National University, Seoul, 08826 Republic of Korea
| | - Young-Sam Lee
- grid.417736.00000 0004 0438 6721Present Address: Well Aging Research Center, Division of Biotechnology, DGIST, Daegu, 42988 Republic of Korea ,grid.417736.00000 0004 0438 6721Department of New Biology, DGIST, Daegu, 42988 Republic of Korea
| | - Sang Chul Park
- grid.417736.00000 0004 0438 6721Present Address: Well Aging Research Center, Division of Biotechnology, DGIST, Daegu, 42988 Republic of Korea ,grid.14005.300000 0001 0356 9399The Future Life & Society Research Center, Advanced Institute of Aging Science, Chonnam National University, Gwangju, 61469 Republic of Korea
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11
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Havrdová M, Urbančič I, Bartoň Tománková K, Malina L, Štrancar J, Bourlinos AB. Self-Targeting of Carbon Dots into the Cell Nucleus: Diverse Mechanisms of Toxicity in NIH/3T3 and L929 Cells. Int J Mol Sci 2021; 22:ijms22115608. [PMID: 34070594 PMCID: PMC8198156 DOI: 10.3390/ijms22115608] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022] Open
Abstract
It is important to understand the nanomaterials intracellular trafficking and distribution and investigate their targeting into the nuclear area in the living cells. In our previous study, we firstly observed penetration of nonmodified positively charged carbon dots decorated with quaternary ammonium groups (QCDs) into the nucleus of mouse NIH/3T3 fibroblasts. Thus, in this work, we focused on deeper study of QCDs distribution inside two healthy mouse NIH/3T3 and L929 cell lines by fluorescence microspectroscopy and performed a comprehensive cytotoxic and DNA damage measurements. Real-time penetration of QCDs across the plasma cell membrane was recorded, concentration dependent uptake was determined and endocytic pathways were characterized. We found out that the QCDs concentration of 200 µg/mL is close to saturation and subsequently, NIH/3T3 had a different cell cycle profile, however, no significant changes in viability (not even in the case with QCDs in the nuclei) and DNA damage. In the case of L929, the presence of QCDs in the nucleus evoked a cellular death. Intranuclear environment of NIH/3T3 cells affected fluorescent properties of QCDs and evoked fluorescence blue shifts. Studying the intracellular interactions with CDs is essential for development of future applications such as DNA sensing, because CDs as DNA probes have not yet been developed.
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Affiliation(s)
- Markéta Havrdová
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 511/8, 779 00 Olomouc, Czech Republic
- Correspondence: ; Tel.: +420-58-563-4384
| | - Iztok Urbančič
- Laboratory of Biophysics, Condensed Matter Physics Department, “Jozef Stefan” Institute, Jamova 39, 1000 Ljubljana, Slovenia; (I.U.); (J.Š.)
| | - Kateřina Bartoň Tománková
- Department of Medical Biophysics, Faculty of Medicine and Dentistry, Institute of Translation Medicine, Palacký University in Olomouc, Hněvotínská 3, 775 15 Olomouc, Czech Republic; (K.B.T.); (L.M.)
| | - Lukáš Malina
- Department of Medical Biophysics, Faculty of Medicine and Dentistry, Institute of Translation Medicine, Palacký University in Olomouc, Hněvotínská 3, 775 15 Olomouc, Czech Republic; (K.B.T.); (L.M.)
| | - Janez Štrancar
- Laboratory of Biophysics, Condensed Matter Physics Department, “Jozef Stefan” Institute, Jamova 39, 1000 Ljubljana, Slovenia; (I.U.); (J.Š.)
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12
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Diez L, Wegmann S. Nuclear Transport Deficits in Tau-Related Neurodegenerative Diseases. Front Neurol 2020; 11:1056. [PMID: 33101165 PMCID: PMC7546323 DOI: 10.3389/fneur.2020.01056] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Tau is a cytosolic microtubule binding protein that is highly abundant in the axons of the central nervous system. However, alternative functions of tau also in other cellular compartments are suggested, for example, in the nucleus, where interactions of tau with specific nuclear entities such as DNA, the nucleolus, and the nuclear envelope have been reported. We would like to review the current knowledge about tau-nucleus interactions and lay out possible neurotoxic mechanisms that are based on the (pathological) interactions of tau with the nucleus.
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Affiliation(s)
- Lisa Diez
- German Center for Neurodegenerative Diseases, Berlin, Germany
| | - Susanne Wegmann
- German Center for Neurodegenerative Diseases, Berlin, Germany
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13
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Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis. Cell Res 2020; 30:520-531. [PMID: 32376910 PMCID: PMC7264146 DOI: 10.1038/s41422-020-0319-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
The nuclear pore complex (NPC) exhibits structural plasticity and has only been characterized at local resolutions of up to 15 Å for the cytoplasmic ring (CR). Here we present a single-particle cryo-electron microscopy (cryo-EM) structure of the CR from Xenopus laevis NPC at average resolutions of 5.5–7.9 Å, with local resolutions reaching 4.5 Å. Improved resolutions allow identification and placement of secondary structural elements in the majority of the CR components. The two Y complexes in each CR subunit interact with each other and associate with those from flanking subunits, forming a circular scaffold. Within each CR subunit, the Nup358-containing region wraps around the stems of both Y complexes, likely stabilizing the scaffold. Nup205 connects the short arms of the two Y complexes and associates with the stem of a neighboring Y complex. The Nup214-containing region uses an extended coiled-coil to link Nup85 of the two Y complexes and protrudes into the axial pore of the NPC. These previously uncharacterized structural features reveal insights into NPC assembly.
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14
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Mudumbi KC, Czapiewski R, Ruba A, Junod SL, Li Y, Luo W, Ngo C, Ospina V, Schirmer EC, Yang W. Nucleoplasmic signals promote directed transmembrane protein import simultaneously via multiple channels of nuclear pores. Nat Commun 2020; 11:2184. [PMID: 32366843 PMCID: PMC7198523 DOI: 10.1038/s41467-020-16033-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 04/09/2020] [Indexed: 02/07/2023] Open
Abstract
Roughly 10% of eukaryotic transmembrane proteins are found on the nuclear membrane, yet how such proteins target and translocate to the nucleus remains in dispute. Most models propose transport through the nuclear pore complexes, but a central outstanding question is whether transit occurs through their central or peripheral channels. Using live-cell high-speed super-resolution single-molecule microscopy we could distinguish protein translocation through the central and peripheral channels, finding that most inner nuclear membrane proteins use only the peripheral channels, but some apparently extend intrinsically disordered domains containing nuclear localization signals into the central channel for directed nuclear transport. These nucleoplasmic signals are critical for central channel transport as their mutation blocks use of the central channels; however, the mutated proteins can still complete their translocation using only the peripheral channels, albeit at a reduced rate. Such proteins can still translocate using only the peripheral channels when central channel is blocked, but blocking the peripheral channels blocks translocation through both channels. This suggests that peripheral channel transport is the default mechanism that was adapted in evolution to include aspects of receptor-mediated central channel transport for directed trafficking of certain membrane proteins.
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Affiliation(s)
- Krishna C Mudumbi
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA.
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Biology Institute, Yale University, West Haven, CT, 06516, USA.
| | - Rafal Czapiewski
- The Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Andrew Ruba
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Yichen Li
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Wangxi Luo
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Christina Ngo
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Valentina Ospina
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA
| | - Eric C Schirmer
- The Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK.
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, 19122, USA.
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15
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Rout MP, Sali A. Principles for Integrative Structural Biology Studies. Cell 2020; 177:1384-1403. [PMID: 31150619 DOI: 10.1016/j.cell.2019.05.016] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/24/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022]
Abstract
Integrative structure determination is a powerful approach to modeling the structures of biological systems based on data produced by multiple experimental and theoretical methods, with implications for our understanding of cellular biology and drug discovery. This Primer introduces the theory and methods of integrative approaches, emphasizing the kinds of data that can be effectively included in developing models and using the nuclear pore complex as an example to illustrate the practice and challenges involved. These guidelines are intended to aid the researcher in understanding and applying integrative structural methods to systems of their interest and thus take advantage of this rapidly evolving field.
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Affiliation(s)
- Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall, 1700 4th Street, Suite 503B, University of California, San Francisco, San Francisco, CA 94158, USA.
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16
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Casting a Wider Net: Differentiating between Inner Nuclear Envelope and Outer Nuclear Envelope Transmembrane Proteins. Int J Mol Sci 2019; 20:ijms20215248. [PMID: 31652739 PMCID: PMC6862087 DOI: 10.3390/ijms20215248] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/11/2022] Open
Abstract
The nuclear envelope (NE) surrounds the nucleus with a double membrane in eukaryotic cells. The double membranes are embedded with proteins that are synthesized on the endoplasmic reticulum and often destined specifically for either the outer nuclear membrane (ONM) or the inner nuclear membrane (INM). These nuclear envelope transmembrane proteins (NETs) play important roles in cellular function and participate in transcription, epigenetics, splicing, DNA replication, genome architecture, nuclear structure, nuclear stability, nuclear organization, and nuclear positioning. These vital functions are dependent upon both the correct localization and relative concentrations of NETs on the appropriate membrane of the NE. It is, therefore, important to understand the distribution and abundance of NETs on the NE. This review will evaluate the current tools and methodologies available to address this important topic.
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17
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Frey S, Rees R, Schünemann J, Ng SC, Fünfgeld K, Huyton T, Görlich D. Surface Properties Determining Passage Rates of Proteins through Nuclear Pores. Cell 2019; 174:202-217.e9. [PMID: 29958108 DOI: 10.1016/j.cell.2018.05.045] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 02/18/2018] [Accepted: 05/21/2018] [Indexed: 10/28/2022]
Abstract
Nuclear pore complexes (NPCs) conduct nucleocytoplasmic transport through an FG domain-controlled barrier. We now explore how surface-features of a mobile species determine its NPC passage rate. Negative charges and lysines impede passage. Hydrophobic residues, certain polar residues (Cys, His), and, surprisingly, charged arginines have striking translocation-promoting effects. Favorable cation-π interactions between arginines and FG-phenylalanines may explain this apparent paradox. Application of these principles to redesign the surface of GFP resulted in variants that show a wide span of transit rates, ranging from 35-fold slower than wild-type to ∼500 times faster, with the latter outpacing even naturally occurring nuclear transport receptors (NTRs). The structure of a fast and particularly FG-specific GFPNTR variant illustrates how NTRs can expose multiple regions for binding hydrophobic FG motifs while evading non-specific aggregation. Finally, we document that even for NTR-mediated transport, the surface-properties of the "passively carried" cargo can strikingly affect the translocation rate.
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Affiliation(s)
- Steffen Frey
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Renate Rees
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Jürgen Schünemann
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sheung Chun Ng
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Kevser Fünfgeld
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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18
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Abstract
The nuclear pore complex (NPC) serves as the sole bidirectional gateway of macromolecules in and out of the nucleus. Owing to its size and complexity (∼1,000 protein subunits, ∼110 MDa in humans), the NPC has remained one of the foremost challenges for structure determination. Structural studies have now provided atomic-resolution crystal structures of most nucleoporins. The acquisition of these structures, combined with biochemical reconstitution experiments, cross-linking mass spectrometry, and cryo-electron tomography, has facilitated the determination of the near-atomic overall architecture of the symmetric core of the human, fungal, and algal NPCs. Here, we discuss the insights gained from these new advances and outstanding issues regarding NPC structure and function. The powerful combination of bottom-up and top-down approaches toward determining the structure of the NPC offers a paradigm for uncovering the architectures of other complex biological machines to near-atomic resolution.
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Affiliation(s)
- Daniel H Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
| | - André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA;
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19
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Eftekharzadeh B, Daigle JG, Kapinos LE, Coyne A, Schiantarelli J, Carlomagno Y, Cook C, Miller SJ, Dujardin S, Amaral AS, Grima JC, Bennett RE, Tepper K, DeTure M, Vanderburg CR, Corjuc BT, DeVos SL, Gonzalez JA, Chew J, Vidensky S, Gage FH, Mertens J, Troncoso J, Mandelkow E, Salvatella X, Lim RYH, Petrucelli L, Wegmann S, Rothstein JD, Hyman BT. Tau Protein Disrupts Nucleocytoplasmic Transport in Alzheimer's Disease. Neuron 2018; 99:925-940.e7. [PMID: 30189209 PMCID: PMC6240334 DOI: 10.1016/j.neuron.2018.07.039] [Citation(s) in RCA: 262] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/14/2018] [Accepted: 07/20/2018] [Indexed: 10/28/2022]
Abstract
Tau is the major constituent of neurofibrillary tangles in Alzheimer's disease (AD), but the mechanism underlying tau-associated neural damage remains unclear. Here, we show that tau can directly interact with nucleoporins of the nuclear pore complex (NPC) and affect their structural and functional integrity. Pathological tau impairs nuclear import and export in tau-overexpressing transgenic mice and in human AD brain tissue. Furthermore, the nucleoporin Nup98 accumulates in the cell bodies of some tangle-bearing neurons and can facilitate tau aggregation in vitro. These data support the hypothesis that tau can directly interact with NPC components, leading to their mislocalization and consequent disruption of NPC function. This raises the possibility that NPC dysfunction contributes to tau-induced neurotoxicity in AD and tauopathies.
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Affiliation(s)
- Bahareh Eftekharzadeh
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - J Gavin Daigle
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | | | - Alyssa Coyne
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Julia Schiantarelli
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Yari Carlomagno
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Casey Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Sean J Miller
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Simon Dujardin
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ana S Amaral
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jonathan C Grima
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Rachel E Bennett
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Katharina Tepper
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Michael DeTure
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| | - Charles R Vanderburg
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Bianca T Corjuc
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sarah L DeVos
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jose Antonio Gonzalez
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jeannie Chew
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Svetlana Vidensky
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jerome Mertens
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Juan Troncoso
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| | - Eckhard Mandelkow
- German Center for Neurodegenerative Diseases (DZNE) and CAESAR Research Center, 53175 Bonn, Germany
| | | | | | | | - Susanne Wegmann
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jeffrey D Rothstein
- Brain Science Institute, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
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20
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Cheng Y, Li C, Mu R, Li Y, Xing T, Chen B, Huang C. Dynamically Long-Term Imaging of Cellular RNA by Fluorescent Carbon Dots with Surface Isoquinoline Moieties and Amines. Anal Chem 2018; 90:11358-11365. [DOI: 10.1021/acs.analchem.8b02301] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yunying Cheng
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Chunmei Li
- College of Pharmaceutical Science, Southwest University, Chongqing 400716, P. R. China
| | - Ruizhu Mu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Yuanfang Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Tiantian Xing
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Binbin Chen
- College of Pharmaceutical Science, Southwest University, Chongqing 400716, P. R. China
| | - Chengzhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
- College of Pharmaceutical Science, Southwest University, Chongqing 400716, P. R. China
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21
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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: 81] [Impact Index Per Article: 13.5] [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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22
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Jong YJI, Harmon SK, O'Malley KL. GPCR signalling from within the cell. Br J Pharmacol 2017; 175:4026-4035. [PMID: 28872669 DOI: 10.1111/bph.14023] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/08/2017] [Accepted: 08/17/2017] [Indexed: 12/22/2022] Open
Abstract
Traditionally, signal transduction from GPCRs is thought to emanate from the cell surface where receptor interactions with external stimuli can be transformed into a broad range of cellular responses. However, emergent data show that numerous GPCRs are also associated with various intracellular membranes where they may couple to different signalling systems, display unique desensitization patterns and/or exhibit distinct patterns of subcellular distribution. Although many GPCRs can be activated at the cell surface and subsequently endocytosed and transported to a unique intracellular site, other intracellular GPCRs can be activated in situ either via de novo ligand synthesis, diffusion of permeable ligands or active transport of nonpermeable ligands. Current findings reinforce the notion that intracellular GPCRs play a dynamic role in various biological functions including learning and memory, contractility and angiogenesis. As new intracellular GPCR roles are defined, the need to selectively tailor agonists and/or antagonists to both intracellular and cell surface receptors may lead to the development of more effective therapeutic tools. LINKED ARTICLES This article is part of a themed section on Molecular Pharmacology of GPCRs. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.21/issuetoc.
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Affiliation(s)
- Yuh-Jiin I Jong
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Steven K Harmon
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen L O'Malley
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
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23
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Abstract
Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.
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Affiliation(s)
- Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; ,
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; , .,Howard Hughes Medical Institute, Pasadena, California 91125
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24
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Ma J, Kelich JM, Junod SL, Yang W. Super-resolution mapping of scaffold nucleoporins in the nuclear pore complex. J Cell Sci 2017; 130:1299-1306. [PMID: 28202688 DOI: 10.1242/jcs.193912] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 02/09/2017] [Indexed: 01/22/2023] Open
Abstract
The nuclear pore complex (NPC), composed of ∼30 different nucleoporins (Nups), is one of the largest supramolecular structures in eukaryotic cells. Its octagonal ring scaffold perforates the nuclear envelope and features a unique molecular machinery that regulates nucleocytoplasmic transport. However, the precise copy number and the spatial location of each Nup in the native NPC remain obscure due to the inherent difficulty of counting and localizing proteins inside of the sub-micrometer supramolecular complex. Here, we combined super-resolution single-point edge-excitation subdiffraction (SPEED) microscopy and nanobody-specific labeling to reveal the spatial distribution of scaffold Nups within three separate layers in the native NPC with a precision of ∼3 nm. Our data reveal both the radial and axial spatial distributions for Pom121, Nup37 and Nup35 and provide evidence for their copy numbers of 8, 32 and 16, respectively, per NPC. This approach can help pave the path for mapping the entirety of Nups in native NPCs and also other structural components of macromolecular complexes.
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Affiliation(s)
- Jiong Ma
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA.,Department of Optical Science and Engineering, Fudan University, 220 Handan Road, Shanghai, 200433, PR China
| | - Joseph M Kelich
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Samuel L Junod
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
| | - Weidong Yang
- Department of Biology, Temple University, 1900 N. 12th Street, Philadelphia, PA, 19122, USA
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25
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Sagulenko E, Nouwens A, Webb RI, Green K, Yee B, Morgan G, Leis A, Lee KC, Butler MK, Chia N, Pham UTP, Lindgreen S, Catchpole R, Poole AM, Fuerst JA. Nuclear Pore-Like Structures in a Compartmentalized Bacterium. PLoS One 2017; 12:e0169432. [PMID: 28146565 PMCID: PMC5287468 DOI: 10.1371/journal.pone.0169432] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/02/2016] [Indexed: 01/02/2023] Open
Abstract
Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence.
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Affiliation(s)
- Evgeny Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard I. Webb
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Kathryn Green
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin Yee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Garry Morgan
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew Leis
- CSIRO - Livestock Industries, Australian Animal Health Laboratory, Biosecurity Microscopy Facility (ABMF), Geelong, Victoria, Australia
| | - Kuo-Chang Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Margaret K. Butler
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Chia
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Uyen Thi Phuong Pham
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Stinus Lindgreen
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ryan Catchpole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
| | - Anthony M. Poole
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- Allan Wilson Centre, University of Canterbury, Christchurch, New Zealand
- Bioinformatics Institute, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John A. Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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26
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Lopez-Denman AJ, Mackenzie JM. The IMPORTance of the Nucleus during Flavivirus Replication. Viruses 2017; 9:v9010014. [PMID: 28106839 PMCID: PMC5294983 DOI: 10.3390/v9010014] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/10/2017] [Accepted: 01/12/2017] [Indexed: 12/24/2022] Open
Abstract
Flaviviruses are a large group of arboviruses of significant medical concern worldwide. With outbreaks a common occurrence, the need for efficient viral control is required more than ever. It is well understood that flaviviruses modulate the composition and structure of membranes in the cytoplasm that are crucial for efficient replication and evading immune detection. As the flavivirus genome consists of positive sense RNA, replication can occur wholly within the cytoplasm. What is becoming more evident is that some viral proteins also have the ability to translocate to the nucleus, with potential roles in replication and immune system perturbation. In this review, we discuss the current understanding of flavivirus nuclear localisation, and the function it has during flavivirus infection. We also describe-while closely related-the functional differences between similar viral proteins in their nuclear translocation.
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Affiliation(s)
- Adam J Lopez-Denman
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne 3086, Australia.
| | - Jason M Mackenzie
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia.
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27
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Sergin I, Jong YJI, Harmon SK, Kumar V, O'Malley KL. Sequences within the C Terminus of the Metabotropic Glutamate Receptor 5 (mGluR5) Are Responsible for Inner Nuclear Membrane Localization. J Biol Chem 2017; 292:3637-3655. [PMID: 28096465 DOI: 10.1074/jbc.m116.757724] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 01/12/2017] [Indexed: 12/19/2022] Open
Abstract
Traditionally, G-protein-coupled receptors (GPCR) are thought to be located on the cell surface where they transmit extracellular signals to the cytoplasm. However, recent studies indicate that some GPCRs are also localized to various subcellular compartments such as the nucleus where they appear required for various biological functions. For example, the metabotropic glutamate receptor 5 (mGluR5) is concentrated at the inner nuclear membrane (INM) where it mediates Ca2+ changes in the nucleoplasm by coupling with Gq/11 Here, we identified a region within the C-terminal domain (amino acids 852-876) that is necessary and sufficient for INM localization of the receptor. Because these sequences do not correspond to known nuclear localization signal motifs, they represent a new motif for INM trafficking. mGluR5 is also trafficked to the plasma membrane where it undergoes re-cycling/degradation in a separate receptor pool, one that does not interact with the nuclear mGluR5 pool. Finally, our data suggest that once at the INM, mGluR5 is stably retained via interactions with chromatin. Thus, mGluR5 is perfectly positioned to regulate nucleoplasmic Ca2+in situ.
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Affiliation(s)
- Ismail Sergin
- From the Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Yuh-Jiin I Jong
- From the Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Steven K Harmon
- From the Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Vikas Kumar
- From the Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Karen L O'Malley
- From the Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri 63110
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28
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Beck M, Hurt E. The nuclear pore complex: understanding its function through structural insight. Nat Rev Mol Cell Biol 2016; 18:73-89. [PMID: 27999437 DOI: 10.1038/nrm.2016.147] [Citation(s) in RCA: 429] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. They are large macromolecular assemblies with a complex composition and diverse functions. Apart from facilitating nucleocytoplasmic transport, NPCs are involved in chromatin organization, the regulation of gene expression and DNA repair. Understanding the molecular mechanisms underlying these functions has been hampered by a lack of structural knowledge about the NPC. The recent convergence of crystallographic and biochemical in vitro analysis of nucleoporins (NUPs), the components of the NPC, with cryo-electron microscopic imaging of the entire NPC in situ has provided first pseudo-atomic view of its central core and revealed that an unexpected network of short linear motifs is an important spatial organization principle. These breakthroughs have transformed the way we understand NPC structure, and they provide an important base for functional investigations, including the elucidation of the molecular mechanisms underlying clinically manifested mutations of the nucleocytoplasmic transport system.
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Affiliation(s)
- Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstrasse 1, Heidelberg D-69117, Germany
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, INF328, Heidelberg D-69120, Germany
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29
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Hoelz A, Glavy JS, Beck M. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up. Nat Struct Mol Biol 2016; 23:624-30. [PMID: 27273515 DOI: 10.1038/nsmb.3244] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/13/2016] [Indexed: 01/16/2023]
Abstract
Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, owing to its sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom-up approaches rely on biochemical interaction studies and crystal-structure determination of NPC components, top-down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, thereby bridging the resolution gap from the higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function.
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Affiliation(s)
- André Hoelz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Joseph S Glavy
- Department of Chemistry, Chemical Biology and Biomedical Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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30
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Abstract
O-GlcNAc-ylation is the post-translational addition of an O-linked β-N-acetylglucosamine to the serine and threonine residues of thousands of proteins in eukaryotic cells. Specifically, half of the thirty different types of protein components in the nuclear pore complex (NPC) are modified by O-GlcNAc, of which the majority are intrinsically disordered nucleoporins (Nups) containing multiple phenylalanine-glycine (FG) repeats. Moreover, these FG-Nups form a strict selectivity barrier with a high density of O-GlcNAc in the NPC to mediate bidirectional trafficking between the cytoplasm and nucleus. However, the roles that O-GlcNAc plays in the structure and function of the NPC remain obscure. In this review paper, we will discuss the current knowledge of O-GlcNAc-ylated Nups, highlight some new techniques used to probe O-GlcNAc's roles in the nuclear pore, and finally propose a new model for the effect of O-GlcNAc on the NPC's permeability.
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Affiliation(s)
- Andrew Ruba
- Department of Biology, Temple University, Philadelphia, PA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA
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31
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Schwartz TU. The Structure Inventory of the Nuclear Pore Complex. J Mol Biol 2016; 428:1986-2000. [PMID: 27016207 DOI: 10.1016/j.jmb.2016.03.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/18/2022]
Abstract
The nuclear pore complex (NPC) is the principal gateway for molecular exchange between nucleus and cytoplasm across the nuclear envelope. Due to its sheer size of estimated 50-112MDa and its complex buildup from about 500-1000 individual proteins, it is a difficult object to study for structural biologists. Here, I review the extensive ensemble of high-resolution structures of the building blocks of the NPC. Concurrent with the increase in size and complexity, these latest, large structures and assemblies can now be used as the basis for hybrid approaches, primarily in combination with cryo-electron microscopic analysis, generating the first structure-based assembly models of the NPC. Going forward, the structures will be critically important for a detailed analysis of the NPC, including function, evolution, and assembly.
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Affiliation(s)
- Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
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32
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Murphy RF. Building cell models and simulations from microscope images. Methods 2016; 96:33-39. [PMID: 26484733 PMCID: PMC4766043 DOI: 10.1016/j.ymeth.2015.10.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 01/13/2023] Open
Abstract
The use of fluorescence microscopy has undergone a major revolution over the past twenty years, both with the development of dramatic new technologies and with the widespread adoption of image analysis and machine learning methods. Many open source software tools provide the ability to use these methods in a wide range of studies, and many molecular and cellular phenotypes can now be automatically distinguished. This article presents the next major challenge in microscopy automation, the creation of accurate models of cell organization directly from images, and reviews the progress that has been made towards this challenge.
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Affiliation(s)
- Robert F Murphy
- Computational Biology Department, Center for Bioimage Informatics, and Departments of Biological Sciences, Biomedical Engineering and Machine Learning, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA, USA; Freiburg Institute for Advanced Studies and Faculty of Biology, Albert Ludwig University of Freiburg, Germany.
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33
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Asakawa H, Yang HJ, Hiraoka Y, Haraguchi T. Virtual Nuclear Envelope Breakdown and Its Regulators in Fission Yeast Meiosis. Front Cell Dev Biol 2016; 4:5. [PMID: 26870731 PMCID: PMC4735346 DOI: 10.3389/fcell.2016.00005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/15/2016] [Indexed: 11/24/2022] Open
Abstract
Ran, a small GTPase, is required for the spindle formation and nuclear envelope (NE) formation. After NE breakdown (NEBD) during mitosis in metazoan cells, the Ran-GTP gradient across the NE is lost and Ran-GTP becomes concentrated around chromatin, thus affecting the stability of microtubules and promoting the assembly of spindle microtubules and segregation of chromosomes. Mitosis in which chromosomes are segregated subsequent to NEBD is called “open mitosis.” In contrast, many fungi undergo a process termed “closed mitosis” in which chromosome segregation and spindle formation occur without NEBD. Although the fission yeast Schizosaccharomyces pombe undergoes a closed mitosis, it exhibits a short period during meiosis (anaphase of the second meiosis; called “anaphase II”) when nuclear and cytoplasmic proteins are mixed in the presence of intact NE and nuclear pore complexes (NPC). This “virtual” nuclear envelope breakdown (vNEBD) involves changes in the localization of RanGAP1, an activator of Ran-GTP hydrolysis. Recently, Nup132, a component of the structural core Nup107-160 subcomplex of the NPC, has been shown to be involved in the maintenance of the nuclear cytoplasmic barrier in yeast meiosis. In this review, we highlight the possible roles of RanGAP1 and Nup132 in vNEBD and discuss the biological significance of vNEBD in S. pombe meiosis.
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Affiliation(s)
- Haruhiko Asakawa
- Graduate School of Frontier Biosciences, Osaka University Suita, Japan
| | - Hui-Ju Yang
- Graduate School of Frontier Biosciences, Osaka University Suita, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; Cell Biology Group, Advanced ICT Research Institute Kobe, National Institute of Information and Communications TechnologyKobe, Japan; Graduate School of Science, Department of Biology, Osaka UniversityToyonaka, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka UniversitySuita, Japan; Cell Biology Group, Advanced ICT Research Institute Kobe, National Institute of Information and Communications TechnologyKobe, Japan; Graduate School of Science, Department of Biology, Osaka UniversityToyonaka, Japan
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34
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Structure Determination of the Nuclear Pore Complex with Three-Dimensional Cryo electron Microscopy. J Mol Biol 2016; 428:2001-10. [PMID: 26791760 PMCID: PMC4898182 DOI: 10.1016/j.jmb.2016.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/02/2015] [Accepted: 01/06/2016] [Indexed: 11/21/2022]
Abstract
Determining the structure of the nuclear pore complex (NPC) imposes an enormous challenge due to its size, intricate composition and membrane-embedded nature. In vertebrates, about 1000 protein building blocks assemble into a 110-MDa complex that fuses the inner and outer membranes of a cell's nucleus. Here, we review the recent progress in understanding the in situ architecture of the NPC with a specific focus on approaches using three-dimensional cryo electron microscopy. We discuss technological benefits and limitations and give an outlook toward obtaining a high-resolution structure of the NPC. Overview over three-dimensional electron microscopic analysis of the nuclear pore complex. Review of recent integrative structural biology studies of the nuclear pore complex scaffold architecture.
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35
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Popken J, Schmid VJ, Strauss A, Guengoer T, Wolf E, Zakhartchenko V. Stage-dependent remodeling of the nuclear envelope and lamina during rabbit early embryonic development. J Reprod Dev 2015; 62:127-35. [PMID: 26640117 PMCID: PMC4848569 DOI: 10.1262/jrd.2015-100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Utilizing 3D structured illumination microscopy, we investigated the quality and quantity of nuclear
invaginations and the distribution of nuclear pores during rabbit early embryonic development and identified
the exact time point of nucleoporin 153 (NUP153) association with chromatin during mitosis. Contrary to bovine
early embryonic nuclei, featuring almost exclusively nuclear invaginations containing a small volume of
cytoplasm, nuclei in rabbit early embryonic stages show additionally numerous invaginations containing a large
volume of cytoplasm. Small-volume invaginations frequently emanated from large-volume nuclear invaginations
but not vice versa, indicating a different underlying mechanism. Large- and small-volume
nuclear envelope invaginations required the presence of chromatin, as they were restricted to
chromatin-positive areas. The chromatin-free contact areas between nucleolar precursor bodies (NPBs) and
large-volume invaginations were free of nuclear pores. Small-volume invaginations were not in contact with
NPBs. The number of invaginations and isolated intranuclear vesicles per nucleus peaked at the 4-cell stage.
At this stage, the nuclear surface showed highly concentrated clusters of nuclear pores surrounded by areas
free of nuclear pores. Isolated intranuclear lamina vesicles were usually NUP153 negative. Cytoplasmic,
randomly distributed NUP153-positive clusters were highly abundant at the zygote stage and decreased in number
until they were almost absent at the 8-cell stage and later. These large NUP153 clusters may represent a
maternally provided NUP153 deposit, but they were not visible as clusters during mitosis. Major genome
activation at the 8- to 16-cell stage may mark the switch from a necessity for a deposit to on-demand
production. NUP153 association with chromatin is initiated during metaphase before the initiation of the
regeneration of the lamina. To our knowledge, the present study demonstrates for the first time major
remodeling of the nuclear envelope and its underlying lamina during rabbit preimplantation development.
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Affiliation(s)
- Jens Popken
- Division of Anthropology and Human Genetics, Biocenter, LMU Munich, D-82152 Planegg-Martinsried, Germany
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36
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Kralt A, Jagalur NB, van den Boom V, Lokareddy RK, Steen A, Cingolani G, Fornerod M, Veenhoff LM. Conservation of inner nuclear membrane targeting sequences in mammalian Pom121 and yeast Heh2 membrane proteins. Mol Biol Cell 2015; 26:3301-12. [PMID: 26179916 PMCID: PMC4569319 DOI: 10.1091/mbc.e15-03-0184] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/08/2015] [Indexed: 12/23/2022] Open
Abstract
This study examines whether active transport to the inner nuclear membrane, as shown for yeast membrane proteins Heh1 and Heh2, is conserved in metazoans. In support of this, the nuclear localization signal of metazoan Pom121 shares biochemical, structural, and functional properties with those of Heh1 and Heh2, and a Heh2-derived reporter protein targets to the inner membrane in Hek293T cells. Endoplasmic reticulum–synthesized membrane proteins traffic through the nuclear pore complex (NPC) en route to the inner nuclear membrane (INM). Although many membrane proteins pass the NPC by simple diffusion, two yeast proteins, ScSrc1/ScHeh1 and ScHeh2, are actively imported. In these proteins, a nuclear localization signal (NLS) and an intrinsically disordered linker encode the sorting signal for recruiting the transport factors for FG-Nup and RanGTP-dependent transport through the NPC. Here we address whether a similar import mechanism applies in metazoans. We show that the (putative) NLSs of metazoan HsSun2, MmLem2, HsLBR, and HsLap2β are not sufficient to drive nuclear accumulation of a membrane protein in yeast, but the NLS from RnPom121 is. This NLS of Pom121 adapts a similar fold as the NLS of Heh2 when transport factor bound and rescues the subcellular localization and synthetic sickness of Heh2ΔNLS mutants. Consistent with the conservation of these NLSs, the NLS and linker of Heh2 support INM localization in HEK293T cells. The conserved features of the NLSs of ScHeh1, ScHeh2, and RnPom121 and the effective sorting of Heh2-derived reporters in human cells suggest that active import is conserved but confined to a small subset of INM proteins.
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Affiliation(s)
- Annemarie Kralt
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Netherlands
| | - Noorjahan B Jagalur
- Departments of Biochemistry and Pediatric Oncology, Erasmus MC/Sophia, 3015 CN Rotterdam, Netherlands
| | - Vincent van den Boom
- Department of Experimental Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, Netherlands
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Netherlands
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Maarten Fornerod
- Departments of Biochemistry and Pediatric Oncology, Erasmus MC/Sophia, 3015 CN Rotterdam, Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Netherlands )
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Liu Y, Miao Q, Zou P, Liu L, Wang X, An L, Zhang X, Qian X, Luo S, Liang G. Enzyme-Controlled Intracellular Self-Assembly of (18)F Nanoparticles for Enhanced MicroPET Imaging of Tumor. Am J Cancer Res 2015. [PMID: 26199645 PMCID: PMC4508496 DOI: 10.7150/thno.11758] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Herein, we report the development of a new "smart" radioactive probe (i.e., 1) which can undergo furin-controlled condensation and self-assembly of radioactive nanoparticles (i.e., 1-NPs) in tumor cells and its application for enhanced microPET imaging of tumors in nude mice co-injected with its cold analog (i.e., 1-Cold). Furin-controlled condensation of 1-Cold and self-assembly of its nanoparticles (i.e., 1-Cold-NPs) in vitro were validated and characterized with HPLC, mass spectra, SEM, and TEM analyses. Cell uptake studies showed that both 1 and 1-Cold have good cell permeability. TEM images of 1-Cold-treated MDA-MB-468 cells directly uncovered that the intracellular 1-Cold-NPs were at/near the location of furin (i.e., Golgi bodies). MTT results indicated that 50 µM 1-Cold did not impose cytotoxicity to MDA-MB-468 cells up to 12 hours. MicroPET imaging of MDA-MB-468 tumor-bearing mice indicated that mice co-injected with 1 and 1-Cold showed higher uptake and longer attenuation of the radioactivity in tumors than those mice only injected with same dosage of 1. Tumor uptake ratios of 1 between these two groups of mice reached the maximum of 8.2 folds at 240 min post injection. Biodistribution study indicated that the uptake ratios of 1 in kidneys between these two groups continuously increased and reached 81.9 folds at 240 min post injection, suggesting the formation of radioactive NPs (i.e., 1-NPs) in MDA-MB-468 tumors of mice co-injected with 1 and 1-Cold. And the nanoparticles were slowly digested and secreted from the tumors, accumulating in the kidneys. Our ''smart'' probe (i.e., 1), together with the strategy of co-injection, might help researchers trace the biomarkers of interest within a longer time window.
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Flather D, Semler BL. Picornaviruses and nuclear functions: targeting a cellular compartment distinct from the replication site of a positive-strand RNA virus. Front Microbiol 2015; 6:594. [PMID: 26150805 PMCID: PMC4471892 DOI: 10.3389/fmicb.2015.00594] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 05/29/2015] [Indexed: 11/13/2022] Open
Abstract
The compartmentalization of DNA replication and gene transcription in the nucleus and protein production in the cytoplasm is a defining feature of eukaryotic cells. The nucleus functions to maintain the integrity of the nuclear genome of the cell and to control gene expression based on intracellular and environmental signals received through the cytoplasm. The spatial separation of the major processes that lead to the expression of protein-coding genes establishes the necessity of a transport network to allow biomolecules to translocate between these two regions of the cell. The nucleocytoplasmic transport network is therefore essential for regulating normal cellular functioning. The Picornaviridae virus family is one of many viral families that disrupt the nucleocytoplasmic trafficking of cells to promote viral replication. Picornaviruses contain positive-sense, single-stranded RNA genomes and replicate in the cytoplasm of infected cells. As a result of the limited coding capacity of these viruses, cellular proteins are required by these intracellular parasites for both translation and genomic RNA replication. Being of messenger RNA polarity, a picornavirus genome can immediately be translated upon entering the cell cytoplasm. However, the replication of viral RNA requires the activity of RNA-binding proteins, many of which function in host gene expression, and are consequently localized to the nucleus. As a result, picornaviruses disrupt nucleocytoplasmic trafficking to exploit protein functions normally localized to a different cellular compartment from which they translate their genome to facilitate efficient replication. Furthermore, picornavirus proteins are also known to enter the nucleus of infected cells to limit host-cell transcription and down-regulate innate antiviral responses. The interactions of picornavirus proteins and host-cell nuclei are extensive, required for a productive infection, and are the focus of this review.
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Affiliation(s)
- Dylan Flather
- Department of Microbiology and Molecular Genetics, Center for Virus Research, School of Medicine, University of California, Irvine Irvine, CA, USA
| | - Bert L Semler
- Department of Microbiology and Molecular Genetics, Center for Virus Research, School of Medicine, University of California, Irvine Irvine, CA, USA
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Popken J, Graf A, Krebs S, Blum H, Schmid VJ, Strauss A, Guengoer T, Zakhartchenko V, Wolf E, Cremer T. Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications. PLoS One 2015; 10:e0124619. [PMID: 25932910 PMCID: PMC4416817 DOI: 10.1371/journal.pone.0124619] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 03/17/2015] [Indexed: 11/19/2022] Open
Abstract
The present study demonstrates a major remodeling of the nuclear envelope and its underlying lamina during bovine preimplantation development. Up to the onset of major embryonic genome activation (MGA) at the 8-cell stage nuclei showed a non-uniform distribution of nuclear pore complexes (NPCs). NPCs were exclusively present at sites where DNA contacted the nuclear lamina. Extended regions of the lamina, which were not contacted by DNA, lacked NPCs. In post-MGA nuclei the whole lamina was contacted rather uniformly by DNA. Accordingly, NPCs became uniformly distributed throughout the entire nuclear envelope. These findings shed new light on the conditions which control the integration of NPCs into the nuclear envelope. The switch from maternal to embryonic production of mRNAs was accompanied by multiple invaginations covered with NPCs, which may serve the increased demands of mRNA export and protein import. Other invaginations, as well as interior nuclear segments and vesicles without contact to the nuclear envelope, were exclusively positive for lamin B. Since the abundance of these invaginations and vesicles increased in concert with a massive nuclear volume reduction, we suggest that they reflect a mechanism for fitting the nuclear envelope and its lamina to a shrinking nuclear size during bovine preimplantation development. In addition, a deposit of extranuclear clusters of NUP153 (a marker for NPCs) without associated lamin B was frequently observed from the zygote stage up to MGA. Corresponding RNA-Seq data revealed deposits of spliced, maternally provided NUP153 mRNA and little unspliced, newly synthesized RNA prior to MGA, which increased strongly at the initiation of embryonic expression of NUP153 at MGA.
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Affiliation(s)
- Jens Popken
- Division of Anthropology and Human Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
- * E-mail: (JP); (EW); (TC)
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | | | - Axel Strauss
- Division of Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
| | - Tuna Guengoer
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
| | - Valeri Zakhartchenko
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
- * E-mail: (JP); (EW); (TC)
| | - Thomas Cremer
- Division of Anthropology and Human Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
- * E-mail: (JP); (EW); (TC)
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40
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Popken P, Ghavami A, Onck PR, Poolman B, Veenhoff LM. Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex. Mol Biol Cell 2015; 26:1386-94. [PMID: 25631821 PMCID: PMC4454183 DOI: 10.1091/mbc.e14-07-1175] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The permeability of the baker's yeast nuclear pore complex for multidomain proteins of different sizes, both soluble and transmembrane, was measured. The permeability for soluble proteins correlated with models of the disordered phase of wild-type and mutant NPCs generated using a one bead per amino acid molecular dynamics model. Nuclear pore complexes (NPCs) allow selective import and export while forming a barrier for untargeted proteins. Using fluorescence microscopy, we measured in vivo the permeability of the Saccharomyces cerevisiae NPC for multidomain proteins of different sizes and found that soluble proteins of 150 kDa and membrane proteins with an extralumenal domain of 90 kDa were still partly localized in the nucleus on a time scale of hours. The NPCs thus form only a weak barrier for the majority of yeast proteins, given their monomeric size. Using FGΔ-mutant strains, we showed that specific combinations of Nups, especially with Nup100, but not the total mass of FG-nups per pore, were important for forming the barrier. Models of the disordered phase of wild-type and mutant NPCs were generated using a one bead per amino acid molecular dynamics model. The permeability measurements correlated with the density predictions from coarse-grained molecular dynamics simulations in the center of the NPC. The combined in vivo and computational approach provides a framework for elucidating the structural and functional properties of the permeability barrier of nuclear pore complexes.
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Affiliation(s)
- Petra Popken
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Netherlands Zernike Institute for Advanced Materials and Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Ali Ghavami
- Zernike Institute for Advanced Materials and
| | | | - Bert Poolman
- Zernike Institute for Advanced Materials and Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Netherlands
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Protein quality control at the inner nuclear membrane. Nature 2014; 516:410-3. [PMID: 25519137 DOI: 10.1038/nature14096] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 11/20/2014] [Indexed: 02/05/2023]
Abstract
The nuclear envelope is a double membrane that separates the nucleus from the cytoplasm. The inner nuclear membrane (INM) functions in essential nuclear processes including chromatin organization and regulation of gene expression. The outer nuclear membrane is continuous with the endoplasmic reticulum and is the site of membrane protein synthesis. Protein homeostasis in this compartment is ensured by endoplasmic-reticulum-associated protein degradation (ERAD) pathways that in yeast involve the integral membrane E3 ubiquitin ligases Hrd1 and Doa10 operating with the E2 ubiquitin-conjugating enzymes Ubc6 and Ubc7 (refs 2, 3). However, little is known about protein quality control at the INM. Here we describe a protein degradation pathway at the INM in yeast (Saccharomyces cerevisiae) mediated by the Asi complex consisting of the RING domain proteins Asi1 and Asi3 (ref. 4). We report that the Asi complex functions together with the ubiquitin-conjugating enzymes Ubc6 and Ubc7 to degrade soluble and integral membrane proteins. Genetic evidence suggests that the Asi ubiquitin ligase defines a pathway distinct from, but complementary to, ERAD. Using unbiased screening with a novel genome-wide yeast library based on a tandem fluorescent protein timer, we identify more than 50 substrates of the Asi, Hrd1 and Doa10 E3 ubiquitin ligases. We show that the Asi ubiquitin ligase is involved in degradation of mislocalized integral membrane proteins, thus acting to maintain and safeguard the identity of the INM.
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Meinema AC, Poolman B, Veenhoff LM. The transport of integral membrane proteins across the nuclear pore complex. Nucleus 2014; 3:322-9. [DOI: 10.4161/nucl.20439] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Silver and gold nanoparticles exposure to in vitro cultured retina--studies on nanoparticle internalization, apoptosis, oxidative stress, glial- and microglial activity. PLoS One 2014; 9:e105359. [PMID: 25144684 PMCID: PMC4140780 DOI: 10.1371/journal.pone.0105359] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 07/22/2014] [Indexed: 11/19/2022] Open
Abstract
The complex network of neuronal cells in the retina makes it a potential target of neuronal toxicity – a risk factor for visual loss. With growing use of nanoparticles (NPs) in commercial and medical applications, including ophthalmology, there is a need for reliable models for early prediction of NP toxicity in the eye and retina. Metal NPs, such as gold and silver, gain much of attention in the ophthalmology community due to their potential to cross the barriers of the eye. Here, NP uptake and signs of toxicity were investigated after exposure to 20 and 80 nm Ag- and AuNPs, using an in vitro tissue culture model of the mouse retina. The model offers long-term preservation of retinal cell types, numbers and morphology and is a controlled system for delivery of NPs, using serum-free defined culture medium. AgNO3-treatment was used as control for toxicity caused by silver ions. These end-points were studied; gross morphological organization, glial activity, microglial activity, level of apoptosis and oxidative stress, which are all well described as signs of insult to neural tissue. TEM analysis demonstrated cellular- and nuclear uptake of all NP types in all neuronal layers of the retina. Htx-eosin staining showed morphological disruption of the normal complex layered retinal structure, vacuole formation and pyknotic cells after exposure to all Ag- and AuNPs. Significantly higher numbers of apoptotic cells as well as an increased number of oxidative stressed cells demonstrated NP-related neuronal toxicity. NPs also caused increased glial staining and microglial cell activation, typical hallmarks of neural tissue insult. This study demonstrates that low concentrations of 20 and 80 nm sized Ag- and AuNPs have adverse effects on the retina, using an organotypic retina culture model. Our results motivate careful assessment of candidate NP, metallic or-non-metallic, to be used in neural systems for therapeutic approaches.
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Goryaynov A, Yang W. Role of molecular charge in nucleocytoplasmic transport. PLoS One 2014; 9:e88792. [PMID: 24558427 PMCID: PMC3928296 DOI: 10.1371/journal.pone.0088792] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 01/12/2014] [Indexed: 12/17/2022] Open
Abstract
Transport of genetic materials and proteins between the nucleus and cytoplasm of eukaryotic cells is mediated by nuclear pore complexes (NPCs). A selective barrier formed by phenylalanine-glycine (FG) nucleoporins (Nups) with net positive charges in the NPC allows for passive diffusion of signal-independent small molecules and transport-receptor facilitated translocation of signal-dependent cargo molecules. Recently, negative surface charge was postulated to be another essential criterion for selective passage through the NPC. However, the charge-driven mechanism in determining the transport kinetics and spatial transport route for either passive diffusion or facilitated translocation remains obscure. Here we employed high-speed single-molecule fluorescence microscopy with an unprecedented spatiotemporal resolution of 9 nm and 400 µs to uncover these mechanistic fundamentals for nuclear transport of charged substrates through native NPCs. We found that electrostatic interaction between negative surface charges on transiting molecules and the positively charged FG Nups, although enhancing their probability of binding to the NPC, never plays a dominant role in determining their nuclear transport mode or spatial transport route. A 3D reconstruction of transport routes revealed that small signal-dependent endogenous cargo protein constructs with high positive surface charges that are destined to the nucleus, rather than repelled from the NPC as suggested in previous models, passively diffused through an axial central channel of the NPC in the absence of transport receptors. Finally, we postulated a comprehensive map of interactions between transiting molecules and FG Nups during nucleocytoplasmic transport by combining the effects of molecular size, signal and surface charge.
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Affiliation(s)
- Alexander Goryaynov
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Bernis C, Swift-Taylor B, Nord M, Carmona S, Chook YM, Forbes DJ. Transportin acts to regulate mitotic assembly events by target binding rather than Ran sequestration. Mol Biol Cell 2014; 25:992-1009. [PMID: 24478460 PMCID: PMC3967982 DOI: 10.1091/mbc.e13-08-0506] [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: 01/01/2023] Open
Abstract
Transportin-specific molecular tools are used to show that the mitotic cell contains importin β and transportin “global positioning system” pathways that are mechanistically parallel. Transportin works to control where the spindle, nuclear membrane, and nuclear pores are formed by directly affecting assembly factor function. The nuclear import receptors importin β and transportin play a different role in mitosis: both act phenotypically as spatial regulators to ensure that mitotic spindle, nuclear membrane, and nuclear pore assembly occur exclusively around chromatin. Importin β is known to act by repressing assembly factors in regions distant from chromatin, whereas RanGTP produced on chromatin frees factors from importin β for localized assembly. The mechanism of transportin regulation was unknown. Diametrically opposed models for transportin action are as follows: 1) indirect action by RanGTP sequestration, thus down-regulating release of assembly factors from importin β, and 2) direct action by transportin binding and inhibiting assembly factors. Experiments in Xenopus assembly extracts with M9M, a superaffinity nuclear localization sequence that displaces cargoes bound by transportin, or TLB, a mutant transportin that can bind cargo and RanGTP simultaneously, support direct inhibition. Consistently, simple addition of M9M to mitotic cytosol induces microtubule aster assembly. ELYS and the nucleoporin 107–160 complex, components of mitotic kinetochores and nuclear pores, are blocked from binding to kinetochores in vitro by transportin, a block reversible by M9M. In vivo, 30% of M9M-transfected cells have spindle/cytokinesis defects. We conclude that the cell contains importin β and transportin “global positioning system”or “GPS” pathways that are mechanistically parallel.
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Affiliation(s)
- Cyril Bernis
- Section of Cell and Developmental Biology, Division of Biological Sciences 0347, University of California-San Diego, La Jolla, CA 92093-0347 Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9041
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Fichtman B, Harel A. Stress and aging at the nuclear gateway. Mech Ageing Dev 2014; 135:24-32. [PMID: 24447784 DOI: 10.1016/j.mad.2014.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/31/2013] [Accepted: 01/06/2014] [Indexed: 12/11/2022]
Abstract
The nuclear pore complex (NPC) is a massive molecular machine embedded in the nuclear envelope and controlling traffic into and out of the cell nucleus. Here, we describe some of the outstanding research questions concerning the NPC, its assembly and functions. We also discuss recent findings that link the NPC and its immediate surroundings to the process of cellular aging. Scaffold and barrier nucleoporins are two major types of protein building blocks that make up the NPC. Surprisingly, these two groups of nucleoporins differ dramatically in their turnover rates. Recent work identifies some of the scaffold nucleoporins as the most extremely long-lived proteins in rat brain. Some of the consequences of these findings and new open questions arising from them are discussed. We also consider the evidence for a perturbed permeability barrier in nuclei from old cells and the alteration of nuclear transport pathways under stress conditions. Finally, we describe the connection between premature aging syndromes and the nuclear lamina, a filamentous protein network which underlies the nuclear envelope.
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Affiliation(s)
- Boris Fichtman
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, 1311502, Israel
| | - Amnon Harel
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, 1311502, Israel.
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48
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Katta SS, Smoyer CJ, Jaspersen SL. Destination: inner nuclear membrane. Trends Cell Biol 2013; 24:221-9. [PMID: 24268652 DOI: 10.1016/j.tcb.2013.10.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 12/25/2022]
Abstract
The inner nuclear membrane (INM) of eukaryotic cells is enriched in proteins that are required for nuclear structure, chromosome organization, DNA repair, and transcriptional control. Mislocalization of INM proteins is observed in a wide spectrum of human diseases; however, the mechanism by which INM proteins reach their final destination is poorly understood. In this review we discuss how investigating INM composition, dissecting targeting pathways of conserved INM proteins in multiple systems and analyzing the nuclear transport of viruses and signaling complexes have broadened our knowledge of INM transport to include both nuclear pore complex-dependent and -independent pathways. The study of these INM targeting pathways is important to understanding nuclear organization and in both normal and diseased cells.
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Affiliation(s)
| | | | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Yang W. Distinct, but not completely separate spatial transport routes in the nuclear pore complex. Nucleus 2013; 4:166-75. [PMID: 23669120 DOI: 10.4161/nucl.24874] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The nuclear pore complex (NPC), which provides the permeable and selective transport path between the nucleus and cytoplasm of eukaryotic cells, allows both the passive diffusion of small molecules in a signal-independent manner and the transport receptor-facilitated translocation of cargo molecules in a signal-dependent manner. However, the spatial and functional relationships between these two transport pathways, which represent critical information for unraveling the fundamental nucleocytoplasmic transport mechanism, remain in dispute. The direct experimental examination of passive and facilitated transport with a high spatiotemporal resolution under real-time trafficking conditions in native NPCs is still difficult. To address this issue and further define these transport mechanisms, we recently developed single-point edge-excitation sub-diffraction (SPEED) microscopy and a deconvolution algorithm to directly map both passive and facilitated transport routes in three dimensions (3D) in native NPCs. Our findings revealed that passive and facilitated transport occur through spatially distinct transport routes. Signal-independent small molecules exhibit a high probability of passively diffusing through an axial central viscous channel, while transport receptors and their cargo complexes preferentially travel through the periphery, around this central channel, after interacting with phenylalanine-glycine (FG) filaments. Strikingly, these two distinct transport zones are not completely separate either spatially or functionally. Instead, their conformations are closely correlated and simultaneously regulated. In this review, we will specifically highlight a detailed procedure for 3D mapping of passive and facilitated transport routes, demonstrate the correlation between these two distinct pathways, and finally, speculate regarding the regulation of the transport pathways driven by the conformational changes of FG filaments in NPCs.
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Affiliation(s)
- Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, USA.
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50
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Abstract
The nuclear pore complex (NPC) is the sole gateway between the nucleus and the cytoplasm. NPCs fuse the inner and outer nuclear membranes to form aqueous translocation channels that allow the free diffusion of small molecules and ions, as well as receptor-mediated transport of large macromolecules. The NPC regulates nucleocytoplasmic transport of macromolecules, utilizing soluble receptors that identify and present cargo to the NPC, in a highly selective manner to maintain cellular functions. The NPC is composed of multiple copies of approximately 30 different proteins, termed nucleoporins, which assemble to form one of the largest multiprotein assemblies in the cell. In this review, we address structural and functional aspects of this fundamental cellular machinery.
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Affiliation(s)
- Einat Grossman
- Department of Life Sciences, Ben Gurion University, Beersheva 84105, Israel
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