1
|
Srivastava LK, Ehrlicher AJ. Sensing the squeeze: nuclear mechanotransduction in health and disease. Nucleus 2024; 15:2374854. [PMID: 38951951 PMCID: PMC11221475 DOI: 10.1080/19491034.2024.2374854] [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: 02/23/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024] Open
Abstract
The nucleus not only is a repository for DNA but also a center of cellular and nuclear mechanotransduction. From nuclear deformation to the interplay between mechanosensing components and genetic control, the nucleus is poised at the nexus of mechanical forces and cellular function. Understanding the stresses acting on the nucleus, its mechanical properties, and their effects on gene expression is therefore crucial to appreciate its mechanosensitive function. In this review, we examine many elements of nuclear mechanotransduction, and discuss the repercussions on the health of cells and states of illness. By describing the processes that underlie nuclear mechanosensation and analyzing its effects on gene regulation, the review endeavors to open new avenues for studying nuclear mechanics in physiology and diseases.
Collapse
Affiliation(s)
| | - Allen J. Ehrlicher
- Department of Bioengineering, McGill University, Montreal, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
- Centre for Structural Biology, McGill University, Montreal, Canada
- Department of Mechanical Engineering, McGill University, Montreal, Canada
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Canada
| |
Collapse
|
2
|
Patel MK, Chakrabarti B, Panwar AS. Emergence of selectivity and specificity in a coarse-grained model of the nuclear pore complex with sequence-agnostic FG-Nups. Phys Chem Chem Phys 2023; 25:32824-32836. [PMID: 38018404 DOI: 10.1039/d3cp03746k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The role of hydrophobicity of phenylalanine-glycine nucleoporins (FG-Nups) in determining the transport of receptor-bound cargo across the nuclear pore complex (NPC) is investigated using Langevin dynamics simulations. A coarse-grained, minimal model of the NPC, comprising a cylindrical pore and hydrophobic-hydrophilic random copolymers for FG-Nups was employed. Karyopherin-bound receptor-cargo complexes (Kaps) were modeled as rigid, coarse-grained spheres without (inert) and with (patchy) FG-binding hydrophobic domains. With a sequence-agnostic description of FG-Nups and the absence of any anisotropies associated with either NPC or cargo, the model described tracer transport only as a function of FG-Nup hydrophobicity, f. The simulations showed the emergence of two important features of cargo transport, namely, NPC selectivity and specificity. NPC selectivity to patchy tracers emerged due to hydrophobic Kap-FG interactions and despite the sequence-agnostic description of FG-Nups. Furthermore, NPC selectivity was observed only in a specific range of FG-hydrophobic fraction, 0.05 ≤ f ≤ 0.20, resulting in specificity of NPC transport with respect to f. Significantly, this range corresponded to the number fraction of FG-repeats observed in both S. cerevisiae and H. sapiens NPCs. This established the central role of the FG-hydrophobic fraction in determining NPC transport, and provided a biophysical basis for conservation of the FG-Nup hydrophobic fraction across evolutionarily distant NPCs. Specificity in NPC transport emerged from the formation of a hydrogel-like network inside the pore with a characteristic mesh size dependent on f. This network rejected cargo for f > 0.2 based on size exclusion, which resulted in enhanced translocation probability for 0.05 ≤ f ≤ 0.20. Extended brush configurations outside the pore resulted in entropic repulsion and exclusion of inert cargo in this range. Thus, our minimal NPC model exhibited a hybrid cargo translocation mechanism, with aspects of both virtual gate and selective-phase models, in this range of FG-hydrophobic fraction.
Collapse
Affiliation(s)
- Manoj K Patel
- Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | | | - Ajay S Panwar
- Department of Metallurgical Engineering and Materials Science, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| |
Collapse
|
3
|
Jörgensen AM, Steinbring C, Stengel D, To D, Schmid P, Bernkop-Schnürch A. Self-Emulsifying Drug Delivery Systems (SEDDS) Containing Reverse Micelles: Advanced Oral Formulations for Therapeutic Peptides. Adv Healthc Mater 2023; 12:e2302034. [PMID: 37696266 DOI: 10.1002/adhm.202302034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/05/2023] [Indexed: 09/13/2023]
Abstract
Alternative methods to hydrophobic ion pairing for the formation of lipophilic complexes of peptide drugs to incorporate them in lipid-based nanocarriers such as self-emulsifying drug delivery systems (SEDDS) for oral administration are highly on demand. Such an alternative might be reverse micelles. Within this study, SEDDS containing dry reverse micelles (dRMsPMB ) formed with an anionic (sodium docusate; AOT), cationic (dimethyl-dioctadecyl-ammonium bromide; DODAB), amphoteric (soy lecithin; SL), or non-ionic (polysorbate 85; P85) surfactant loaded with the model peptide drug polymyxin B (PMB) are developed. They are characterized regarding size, payload, release kinetics, cellular uptake, and peptide activity. SEDDS exhibit sizes from 22.2 ± 1.7 (AOT-SEDDS-dRMsPMB ) to 61.7 ± 3.2 nm (P85-SEDDS-dRMsPMB ) with payloads up to 2% that are approximately sevenfold higher than those obtained via hydrophobic ion pairing. Within 6 h P85-SEDDS-dRMsPMB and AOT-SEDDS-dRMsPMB show no release of PMB in aqueous medium, whereas DODAB-SEDDS-dRMsPMB and SL-SEDDS-dRMsPMB show a sustained release. DODAB-SEDDS-dRMsPMB improves uptake by Caco-2 cells most efficiently reaching even ≈100% within 4 h followed by AOT-SEDDS-dRMsPMB with ≈20% and P85-/SL-SEDDS-dRMsPMB with ≈5%. The peptide drug maintains its antimicrobial activity in all SEDDS-dRMsPMB . According to these results, SEDDS containing dRMs might be a game changing strategy for oral peptide drug delivery.
Collapse
Affiliation(s)
- Arne Matteo Jörgensen
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, Innsbruck, 6020, Austria
| | - Christian Steinbring
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, Innsbruck, 6020, Austria
| | - Daniel Stengel
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, Innsbruck, 6020, Austria
| | - Dennis To
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, Innsbruck, 6020, Austria
| | - Pascal Schmid
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, Innsbruck, 6020, Austria
| | - Andreas Bernkop-Schnürch
- Department of Pharmaceutical Technology, University of Innsbruck, Institute of Pharmacy, Center for Chemistry and Biomedicine, Innrain 80-82, Innsbruck, 6020, Austria
| |
Collapse
|
4
|
Neves RPD, Chagoyen M, Martinez-Lorente A, Iñiguez C, Calatrava A, Calabuig J, Iborra FJ. Each Cellular Compartment Has a Characteristic Protein Reactive Cysteine Ratio Determining Its Sensitivity to Oxidation. Antioxidants (Basel) 2023; 12:1274. [PMID: 37372004 DOI: 10.3390/antiox12061274] [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: 03/29/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Signaling and detoxification of Reactive Oxygen Species (ROS) are important patho-physiologcal processes. Despite this, we lack comprehensive information on individual cells and cellular structures and functions affected by ROS, which is essential to build quantitative models of the effects of ROS. The thiol groups from cysteines (Cys) in proteins play a major role in redox defense, signaling, and protein function. In this study, we show that the proteins in each subcellular compartment contain a characteristic Cys amount. Using a fluorescent assay for -SH in thiolate form and amino groups in proteins, we show that the thiolate content correlates with ROS sensitivity and signaling properties of each compartment. The highest absolute thiolate concentration was found in the nucleolus, followed by the nucleoplasm and cytoplasm whereas protein thiolate groups per protein showed an inverse pattern. In the nucleoplasm, protein reactive thiols concentrated in SC35 speckles, SMN, and the IBODY that accumulated oxidized RNA. Our findings have important functional consequences, and explain differential sensitivity to ROS.
Collapse
Affiliation(s)
- Ricardo Pires das Neves
- Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-517 Coimbra, Portugal
- IIIUC-Institute of Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Mónica Chagoyen
- Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Madrid, Spain
| | - Antonio Martinez-Lorente
- Unidad de Investigación, Innovación y Docencia Médica, Hospital Universitario Vinalopó, 03293 Elx, Spain
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), 46020 Valencia, Spain
- Department of Biotecnology, University of Alicante, 03690 Alicante, Spain
| | - Carlos Iñiguez
- Department of Biotecnology, University of Alicante, 03690 Alicante, Spain
| | - Ana Calatrava
- Department of Pathology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain
| | | | - Francisco J Iborra
- Instituto de Biomedicina de Valencia, CSIC, Jaime Roig 11, 46010 Valencia, Spain
- Centro de Investigación Príncipe Felipe (CIPF), Primo Yufera 3, 46012 Valencia, Spain
| |
Collapse
|
5
|
Ewerling A, Maissl V, Wickstead B, May-Simera HL. Neofunctionalization of ciliary BBS proteins to nuclear roles is likely a frequent innovation across eukaryotes. iScience 2023; 26:106410. [PMID: 37034981 PMCID: PMC10074162 DOI: 10.1016/j.isci.2023.106410] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/20/2022] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The eukaryotic BBSome is a transport complex within cilia and assembled by chaperonin-like BBS proteins. Recent work indicates nuclear functions for BBS proteins in mammals, but it is unclear how common these are in extant proteins or when they evolved. We screened for BBS orthologues across a diverse set of eukaryotes, consolidated nuclear association via signal sequence predictions and permutation analysis, and validated nuclear localization in mammalian cells via fractionation and immunocytochemistry. BBS proteins are-with exceptions-conserved as a set in ciliated species. Predictions highlight five most likely nuclear proteins and suggest that nuclear roles evolved independently of nuclear access during mitosis. Nuclear localization was confirmed in human cells. These findings suggest that nuclear BBS functions are potentially not restricted to mammals, but may be a common frequently co-opted eukaryotic feature. Understanding the functional spectrum of BBS proteins will help elucidating their role in gene regulation, development, and disease.
Collapse
Affiliation(s)
- Alexander Ewerling
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Vanessa Maissl
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Bill Wickstead
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Helen Louise May-Simera
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-University Mainz, Mainz, Germany
| |
Collapse
|
6
|
van der Zanden SY, Jongsma MLM, Neefjes ACM, Berlin I, Neefjes J. Maintaining soluble protein homeostasis between nuclear and cytoplasmic compartments across mitosis. Trends Cell Biol 2023; 33:18-29. [PMID: 35778326 DOI: 10.1016/j.tcb.2022.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/23/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022]
Abstract
The nuclear envelope (NE) is central to the architecture of eukaryotic cells, both as a physical barrier separating the nucleus from the cytoplasm and as gatekeeper of selective transport between them. However, in open mitosis, the NE fragments to allow for spindle formation and segregation of chromosomes, resulting in intermixing of nuclear and cytoplasmic soluble fractions. Recent studies have shed new light on the mechanisms driving reinstatement of soluble proteome homeostasis following NE reformation in daughter cells. Here, we provide an overview of how mitotic cells confront this challenge to ensure continuity of basic cellular functions across generations and elaborate on the implications for the proteasome - a macromolecular machine that functions in both cytoplasmic and nuclear compartments.
Collapse
Affiliation(s)
- Sabina Y van der Zanden
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Marlieke L M Jongsma
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Anna C M Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Yoo TY, Mitchison TJ. O-GlcNAc modification of nuclear pore complexes accelerates bidirectional transport. J Cell Biol 2021; 220:212033. [PMID: 33909044 PMCID: PMC8091080 DOI: 10.1083/jcb.202010141] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/28/2021] [Accepted: 03/17/2021] [Indexed: 01/09/2023] Open
Abstract
Macromolecular transport across the nuclear envelope depends on facilitated diffusion through nuclear pore complexes (NPCs). The interior of NPCs contains a permeability barrier made of phenylalanine-glycine (FG) repeat domains that selectively facilitates the permeation of cargoes bound to nuclear transport receptors (NTRs). FG-repeat domains in NPCs are a major site of O-linked N-acetylglucosamine (O-GlcNAc) modification, but the functional role of this modification in nucleocytoplasmic transport is unclear. We developed high-throughput assays based on optogenetic probes to quantify the kinetics of nuclear import and export in living human cells. We found that increasing O-GlcNAc modification of the NPC accelerated NTR-facilitated transport of proteins in both directions, and decreasing modification slowed transport. Superresolution imaging revealed strong enrichment of O-GlcNAc at the FG-repeat barrier. O-GlcNAc modification also accelerated passive permeation of a small, inert protein through NPCs. We conclude that O-GlcNAc modification accelerates nucleocytoplasmic transport by enhancing the nonspecific permeability of the FG-repeat barrier, perhaps by steric inhibition of interactions between FG repeats.
Collapse
Affiliation(s)
- Tae Yeon Yoo
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Timothy J Mitchison
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA
| |
Collapse
|
9
|
Moonlighting nuclear pore proteins: tissue-specific nucleoporin function in health and disease. Histochem Cell Biol 2018; 150:593-605. [PMID: 30361777 DOI: 10.1007/s00418-018-1748-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2018] [Indexed: 12/14/2022]
Abstract
The nuclear pore complex is the main transportation hub for exchange between the cytoplasm and the nucleus. It is built from nucleoporins that form distinct subcomplexes to establish this huge protein complex in the nuclear envelope. Malfunctioning of nucleoporins is well known in human malignancies, such as gene fusions of NUP214 and NUP98 in hematological neoplasms and overexpression of NUP88 in a variety of human cancers. In the past decade, the incremental utilization of next-generation sequencing has unraveled mutations in nucleoporin genes in the context of an increasing number of hereditary diseases, often in a tissue-specific manner. It emerges that, on one hand, the central nervous system and the heart are particularly sensitive to mutations in nucleoporin genes. On the other hand, nucleoporins forming the scaffold structure of the nuclear pore complex are eminently mutation-prone. These novel and exciting associations between nucleoporins and human diseases emphasize the need to shed light on these unanticipated tissue-specific roles of nucleoporins that may go well beyond their role in nucleocytoplasmic transport. In this review, the current insights into altered nucleoporin function associated with human hereditary disorders will be discussed.
Collapse
|
10
|
Selection and Identification of Skeletal-Muscle-Targeted RNA Aptamers. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:199-214. [PMID: 29499933 PMCID: PMC5862129 DOI: 10.1016/j.omtn.2017.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/06/2017] [Accepted: 12/06/2017] [Indexed: 01/16/2023]
Abstract
Oligonucleotide gene therapy has shown great promise for the treatment of muscular dystrophies. Nevertheless, the selective delivery to affected muscles has shown to be challenging because of their high representation in the body and the high complexity of their cell membranes. Current trials show loss of therapeutic molecules to non-target tissues leading to lower target efficacy. Therefore, strategies that increase uptake efficiency would be particularly compelling. To address this need, we applied a cell-internalization SELEX (Systematic Evolution of Ligands by Exponential Enrichment) approach and identified a skeletal muscle-specific RNA aptamer. A01B RNA aptamer preferentially internalizes in skeletal muscle cells and exhibits decreased affinity for off-target cells. Moreover, this in vitro selected aptamer retained its functionality in vivo, suggesting a potential new approach for targeting skeletal muscles. Ultimately, this will aid in the development of targeted oligonucleotide therapies against muscular dystrophies.
Collapse
|
11
|
Yang J, Kopeček J. Design of smart HPMA copolymer-based nanomedicines. J Control Release 2016; 240:9-23. [DOI: 10.1016/j.jconrel.2015.10.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 09/29/2015] [Accepted: 10/01/2015] [Indexed: 01/13/2023]
|
12
|
Tauchert MJ, Hémonnot C, Neumann P, Köster S, Ficner R, Dickmanns A. Impact of the crystallization condition on importin-β conformation. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:705-17. [DOI: 10.1107/s2059798316004940] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/23/2016] [Indexed: 11/10/2022]
Abstract
In eukaryotic cells, the exchange of macromolecules between the nucleus and cytoplasm is highly selective and requires specialized soluble transport factors. Many of them belong to the importin-β superfamily, the members of which share an overall superhelical structure owing to the tandem arrangement of a specific motif, the HEAT repeat. This structural organization leads to great intrinsic flexibility, which in turn is a prerequisite for the interaction with a variety of proteins and for its transport function. During the passage from the aqueous cytosol into the nucleus, the receptor passes the gated channel of the nuclear pore complex filled with a protein meshwork of unknown organization, which seems to be highly selective owing to the presence of FG-repeats, which are peptides with hydrophobic patches. Here, the structural changes of free importin-β from a single organism, crystallized in polar (salt) or apolar (PEG) buffer conditions, are reported. This allowed analysis of the structural changes, which are attributable to the surrounding milieu and are not affected by bound interaction partners. The importin-β structures obtained exhibit significant conformational changes and suggest an influence of the polarity of the environment, resulting in an extended conformation in the PEG condition. The significance of this observation is supported by SAXS experiments and the analysis of other crystal structures of importin-β deposited in the Protein Data Bank.
Collapse
|
13
|
Vovk A, Gu C, Opferman MG, Kapinos LE, Lim RY, Coalson RD, Jasnow D, Zilman A. Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex. eLife 2016; 5. [PMID: 27198189 PMCID: PMC4874778 DOI: 10.7554/elife.10785] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 03/24/2016] [Indexed: 12/13/2022] Open
Abstract
Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function. DOI:http://dx.doi.org/10.7554/eLife.10785.001 Animal, plant and fungal cells contain a structure called the nucleus, inside which the genetic material of the cell is stored. For the cell to work properly, certain proteins and other molecules need to be able to enter and exit the nucleus. This transport is carried out by pore-like molecular “devices” known as Nuclear Pore Complexes, whose architecture and mode of operation are unique among cellular transporters. Nuclear Pore Complexes are charged with a daunting task of deciding which of the hundreds of molecules it conducts per second should go through and which should not. Small molecules can pass freely through Nuclear Pore Complexes. However, larger molecules can only pass through the pore efficiently if they are bound to specialized transport proteins that interact with the proteins – called FG nucleoporins – that line the pore. A unique feature of the FG nucleoporins is that, unlike typical proteins, they do not have a defined three-dimensional structure. Instead, they form a soft and pliable lining inside the Nuclear Pore Complex passageway. Exactly how interacting with transport proteins affects the structure and spatial arrangements of the FG nucleoporins in a way that allows them to control transport is not well understood. This is in part because existing experimental techniques are unable to study the structures of the FG nucleoporins in enough detail to track how they change during transport. The complexity and the diversity of the FG nucleoporins also make them difficult to model in detail. Vovk, Gu et al. have developed a theoretical model that is based on just three basic physical properties of the FG nucleoporins – their flexibility, their ability to interact with each other, and their binding with the transport proteins. Future work can refine the model by incorporating further molecular details about the interactions between FG nucleoporins and transport proteins. The predictions made by this simple model agree well with experimental results in a wide range of situations – from single molecules to complex spatial assemblies. They also explain why some of the experimental results appear to contradict each other and suggest how several outstanding controversies in the field can be reconciled. Because the model invokes only fundamental physical principles of FG nucleoporin assemblies, it shows that some of their general properties do not depend on the exact conditions. In particular, this might shed light on why Nuclear Pore Complexes in different organisms perform essentially the same function, although the details of their molecular structure may differ. This also suggests how the FG nucleoporins can be manipulated to build artificial devices based on the same principles. DOI:http://dx.doi.org/10.7554/eLife.10785.002
Collapse
Affiliation(s)
- Andrei Vovk
- Department of Physics, University of Toronto, Toronto, Canada
| | - Chad Gu
- Department of Physics, University of Toronto, Toronto, Canada
| | - Michael G Opferman
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, United States
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Roderick Yh Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Rob D Coalson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, United States
| | - David Jasnow
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, United States
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Canada.,Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Canada
| |
Collapse
|
14
|
Energetics of Transport through the Nuclear Pore Complex. PLoS One 2016; 11:e0148876. [PMID: 26894898 PMCID: PMC4764519 DOI: 10.1371/journal.pone.0148876] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/25/2016] [Indexed: 01/30/2023] Open
Abstract
Molecular transport across the nuclear envelope in eukaryotic cells is solely controlled by the nuclear pore complex (NPC). The NPC provides two types of nucleocytoplasmic transport: passive diffusion of small molecules and active chaperon-mediated translocation of large molecules. It has been shown that the interaction between intrinsically disordered proteins that line the central channel of the NPC and the transporting cargoes is the determining factor, but the exact mechanism of transport is yet unknown. Here, we use coarse-grained molecular dynamics simulations to quantify the energy barrier that has to be overcome for molecules to pass through the NPC. We focus on two aspects of transport. First, the passive transport of model cargo molecules with different sizes is studied and the size selectivity feature of the NPC is investigated. Our results show that the transport probability of cargoes is significantly reduced when they are larger than ∼5 nm in diameter. Secondly, we show that incorporating hydrophobic binding spots on the surface of the cargo effectively decreases the energy barrier of the pore. Finally, a simple transport model is proposed which characterizes the energy barrier of the NPC as a function of diameter and hydrophobicity of the transporting particles.
Collapse
|
15
|
Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex. PLoS Biol 2016; 14:e1002365. [PMID: 26891179 PMCID: PMC4758718 DOI: 10.1371/journal.pbio.1002365] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/23/2015] [Indexed: 02/08/2023] Open
Abstract
The nuclear pore complex (NPC) is responsible for nucleocytoplasmic transport and constitutes a hub for control of gene expression. The components of NPCs from several eukaryotic lineages have been determined, but only the yeast and vertebrate NPCs have been extensively characterized at the quaternary level. Significantly, recent evidence indicates that compositional similarity does not necessarily correspond to homologous architecture between NPCs from different taxa. To address this, we describe the interactome of the trypanosome NPC, a representative, highly divergent eukaryote. We identify numerous new NPC components and report an exhaustive interactome, allowing assignment of trypanosome nucleoporins to discrete NPC substructures. Remarkably, despite retaining similar protein composition, there are exceptional architectural dissimilarities between opisthokont (yeast and vertebrates) and excavate (trypanosomes) NPCs. Whilst elements of the inner core are conserved, numerous peripheral structures are highly divergent, perhaps reflecting requirements to interface with divergent nuclear and cytoplasmic functions. Moreover, the trypanosome NPC has almost complete nucleocytoplasmic symmetry, in contrast to the opisthokont NPC; this may reflect divergence in RNA export processes at the NPC cytoplasmic face, as we find evidence supporting Ran-dependent mRNA export in trypanosomes, similar to protein transport. We propose a model of stepwise acquisition of nucleocytoplasmic mechanistic complexity and demonstrate that detailed dissection of macromolecular complexes provides fuller understanding of evolutionary processes. Dissection of the nuclear pore complex—an ancient eukaryotic molecular machine—exposes a fundamental divergence in structure and function between yeast and humans versus trypanosomes and provides insights into the evolution of the nucleus. Much of the core architecture of the eukaryotic cell was established over one billion years ago. Significantly, many cellular systems possess lineage-specific features, and architectural and compositional variation of complexes and pathways that are likely keyed to specific functional adaptations. The nuclear pore complex (NPC) contributes to many processes, including nucleocytoplasmic transport, interactions with the nuclear lamina, and mRNA processing. We exploited trypanosome parasites to investigate NPC evolution and conservation at the level of protein–protein interactions and composition. We unambiguously assigned NPC components to specific substructures and found that the NPC structural scaffold is generally conserved, albeit with lineage-specific elements. However, there is significant variation in pore membrane proteins and an absence of critical components involved in mRNA export in fungi and animals (opisthokonts). This is reflected by the completely symmetric localization of all trypanosome nucleoporins, with the exception of the nuclear basket. This architecture is highly distinct from opisthokonts. We also identify features that suggest a Ran-dependent system for mRNA export in trypanosomes, a system that may presage distinct mechanisms of protein and mRNA transport in animals and fungi. Our study highlights that shared composition of macromolecular assemblies does not necessarily equate to shared architecture. Identification of lineage-specific features within the trypanosome NPC significantly advances our understanding of mechanisms of nuclear transport, gene expression, and evolution of the nucleus.
Collapse
|
16
|
Honcharenko M, Bestas B, Jezowska M, Wojtczak BA, Moreno PMD, Romanowska J, Bächle SM, Darzynkiewicz E, Jemielity J, Smith CIE, Strömberg R. Synthetic m3G-CAP attachment necessitates a minimum trinucleotide constituent to be recognised as a nuclear import signal. RSC Adv 2016. [DOI: 10.1039/c6ra09568b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Minimal requirement for Snurportin based nuclear uptake is the inclusion of a trinucleotide sequence between the m3G-CAP and the artificial linker.
Collapse
|
17
|
Zhong J, Li L, Zhu X, Guan S, Yang Q, Zhou Z, Zhang Z, Huang Y. A smart polymeric platform for multistage nucleus-targeted anticancer drug delivery. Biomaterials 2015; 65:43-55. [PMID: 26142775 DOI: 10.1016/j.biomaterials.2015.06.042] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/14/2015] [Accepted: 06/18/2015] [Indexed: 11/30/2022]
Abstract
Tumor cell nucleus-targeted delivery of antitumor agents is of great interest in cancer therapy, since the nucleus is one of the most frequent targets of drug action. Here we report a smart polymeric conjugate platform, which utilizes stimulus-responsive strategies to achieve multistage nuclear drug delivery upon systemic administration. The conjugates composed of a backbone based on N-(2-hydroxypropyl) methacrylamide (HPMA) copolymer and detachable nucleus transport sub-units that sensitive to lysosomal enzyme. The sub-units possess a biforked structure with one end conjugated with the model drug, H1 peptide, and the other end conjugated with a novel pH-responsive targeting peptide (R8NLS) that combining the strength of cell penetrating peptide and nuclear localization sequence. The conjugates exhibited prolonged circulation time and excellent tumor homing ability. And the activation of R8NLS in acidic tumor microenvironment facilitated tissue penetration and cellular internalization. Once internalized into the cell, the sub-units were unleashed for nuclear transport through nuclear pore complex. The unique features resulted in 50-fold increase of nuclear drug accumulation relative to the original polymer-drug conjugates in vitro, and excellent in vivo nuclear drug delivery efficiency. Our report provides a strategy in systemic nuclear drug delivery by combining the microenvironment-responsive structure and detachable sub-units.
Collapse
Affiliation(s)
- Jiaju Zhong
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, NO. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Lian Li
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, NO. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Xi Zhu
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, NO. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Shan Guan
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, NO. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Qingqing Yang
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, NO. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Zhou Zhou
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, NO. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Zhirong Zhang
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, NO. 17, Block 3, South Renmin Road, Chengdu 610041, PR China
| | - Yuan Huang
- Key Laboratory of Drug Targeting and Drug Delivery System (Ministry of Education), West China School of Pharmacy, Sichuan University, NO. 17, Block 3, South Renmin Road, Chengdu 610041, PR China.
| |
Collapse
|
18
|
Probing the disordered domain of the nuclear pore complex through coarse-grained molecular dynamics simulations. Biophys J 2015; 107:1393-402. [PMID: 25229147 DOI: 10.1016/j.bpj.2014.07.060] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 07/11/2014] [Accepted: 07/22/2014] [Indexed: 01/27/2023] Open
Abstract
The distribution of disordered proteins (FG-nups) that line the transport channel of the nuclear pore complex (NPC) is investigated by means of coarse-grained molecular dynamics simulations. A one-bead-per-amino-acid model is presented that accounts for the hydrophobic/hydrophilic and electrostatic interactions between different amino acids, polarity of the solvent, and screening of free ions. The results indicate that the interaction of the FG-nups forms a high-density, doughnut-like distribution inside the NPC, which is rich in FG-repeats. We show that the obtained distribution is encoded in the amino-acid sequence of the FG-nups and is driven by both electrostatic and hydrophobic interactions. To explore the relation between structure and function, we have systematically removed different combinations of FG-nups from the pore to simulate inviable and viable NPCs that were previously studied experimentally. The obtained density distributions show that the maximum density of the FG-nups inside the pore does not exceed 185 mg/mL in the inviable NPCs, whereas for the wild-type and viable NPCs, this value increases to 300 mg/mL. Interestingly, this maximum density is not correlated to the total mass of the FG-nups, but depends sensitively on the specific combination of essential Nups located in the central plane of the NPC.
Collapse
|
19
|
Tran EJ, King MC, Corbett AH. Macromolecular transport between the nucleus and the cytoplasm: Advances in mechanism and emerging links to disease. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:2784-2795. [PMID: 25116306 PMCID: PMC4161953 DOI: 10.1016/j.bbamcr.2014.08.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/01/2014] [Accepted: 08/02/2014] [Indexed: 01/08/2023]
Abstract
Transport of macromolecules between the cytoplasm and the nucleus is critical for the function of all eukaryotic cells. Large macromolecular channels termed nuclear pore complexes that span the nuclear envelope mediate the bidirectional transport of cargoes between the nucleus and cytoplasm. However, the influence of macromolecular trafficking extends past the nuclear pore complex to transcription and RNA processing within the nucleus and signaling pathways that reach into the cytoplasm and beyond. At the Mechanisms of Nuclear Transport biennial meeting held from October 18 to 23, 2013 in Woods Hole, MA, researchers in the field met to report on their recent findings. The work presented highlighted significant advances in understanding nucleocytoplasmic trafficking including how transport receptors and cargoes pass through the nuclear pore complex, the many signaling pathways that impinge on transport pathways, interplay between the nuclear envelope, nuclear pore complexes, and transport pathways, and numerous links between transport pathways and human disease. The goal of this review is to highlight newly emerging themes in nuclear transport and underscore the major questions that are likely to be the focus of future research in the field.
Collapse
Affiliation(s)
- Elizabeth J Tran
- Department of Biochemistry, Purdue University, 175 S. University Street, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN 47907, USA.
| | - Megan C King
- Department of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, 4117 Rollins Research Center, 1510 Clifton Road, NE, Atlanta, GA 30322, USA.
| |
Collapse
|
20
|
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.
Collapse
Affiliation(s)
- Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, USA.
| |
Collapse
|
21
|
Atkinson CE, Mattheyses AL, Kampmann M, Simon SM. Conserved spatial organization of FG domains in the nuclear pore complex. Biophys J 2013; 104:37-50. [PMID: 23332057 DOI: 10.1016/j.bpj.2012.11.3823] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/31/2012] [Accepted: 11/02/2012] [Indexed: 10/27/2022] Open
Abstract
Selective transport through the nuclear pore complex (NPC) requires nucleoporins containing natively unfolded phenylalanine-glycine (FG) domains. Several differing models for their dynamics within the pore have been proposed. We characterize the behavior of the FG nucleoporins in vivo using polarized fluorescence microscopy. Using nucleoporins tagged with green fluorescent protein along their FG domains, we show that some of these proteins are ordered, indicating an overall orientational organization within the NPC. This orientational ordering of the FG domains depends on their specific context within the NPC, but is independent of active transport and cargo load. For most nups, behavior does not depend on the FG motifs. These data support a model whereby local geometry constrains the orientational organization of the FG nups. Intriguingly, homologous yeast and mammalian proteins show conserved behavior, suggesting functional relevance. Our findings have implications for mechanistic models of NPC transport.
Collapse
Affiliation(s)
- Claire E Atkinson
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York, USA
| | | | | | | |
Collapse
|
22
|
Abstract
This article focuses on drug targeting to specific cellular organelles for therapeutic purposes. Drugs can be delivered to all major organelles of the cell (cytosol, endosome/lysosome, nucleus, nucleolus, mitochondria, endoplasmic reticulum, Golgi apparatus, peroxisomes and proteasomes) where they exert specific effects in those particular subcellular compartments. Delivery can be achieved by chemical (e.g., polymeric) or biological (e.g., signal sequences) means. Unidirectional targeting to individual organelles has proven to be immensely successful for drug therapy. Newer technologies that accommodate multiple signals (e.g., protein switch and virus-like delivery systems) mimic nature and allow for a more sophisticated approach to drug delivery. Harnessing different methods of targeting multiple organelles in a cell will lead to better drug delivery and improvements in disease therapy.
Collapse
|
23
|
Lee S, Wang PY, Jeong Y, Mangelsdorf DJ, Anderson RGW, Michaely P. Sterol-dependent nuclear import of ORP1S promotes LXR regulated trans-activation of apoE. Exp Cell Res 2012; 318:2128-42. [PMID: 22728266 DOI: 10.1016/j.yexcr.2012.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 05/30/2012] [Accepted: 06/08/2012] [Indexed: 01/30/2023]
Abstract
Oxysterol binding protein related protein 1S (ORP1S) is a member of a family of sterol transport proteins. Here we present evidence that ORP1S translocates from the cytoplasm to the nucleus in response to sterol binding. The sterols that best promote nuclear import of ORP1S also activate the liver X receptor (LXR) transcription factors and we show that ORP1S binds to LXRs, promotes binding of LXRs to LXR response elements (LXREs) and specifically enhances LXR-dependent transcription via the ME.1 and ME.2 enhancer elements of the apoE gene. We propose that ORP1S is a cytoplasmic sterol sensor, which transports sterols to the nucleus and promotes LXR-dependent gene transcription through select enhancer elements.
Collapse
Affiliation(s)
- Sungsoo Lee
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, United States.
| | | | | | | | | | | |
Collapse
|
24
|
Domain topology of nucleoporin Nup98 within the nuclear pore complex. J Struct Biol 2011; 177:81-9. [PMID: 22100335 DOI: 10.1016/j.jsb.2011.11.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 11/22/2022]
Abstract
Nuclear pore complexes (NPCs) facilitate selective transport of macromolecules across the nuclear envelope in interphase eukaryotic cells. NPCs are composed of roughly 30 different proteins (nucleoporins) of which about one third are characterized by the presence of phenylalanine-glycine (FG) repeat domains that allow the association of soluble nuclear transport receptors with the NPC. Two types of FG (FG/FxFG and FG/GLFG) domains are found in nucleoporins and Nup98 is the sole vertebrate nucleoporin harboring the GLFG-type repeats. By immuno-electron microscopy using isolated nuclei from Xenopus oocytes we show here the localization of distinct domains of Nup98. We examined the localization of the C- and N-terminal domain of Nup98 by immunogold-labeling using domain-specific antibodies against Nup98 and by expressing epitope tagged versions of Nup98. Our studies revealed that anchorage of Nup98 to NPCs through its C-terminal autoproteolytic domain occurs in the center of the NPC, whereas its N-terminal GLFG domain is more flexible and is detected at multiple locations within the NPC. Additionally, we have confirmed the central localization of Nup98 within the NPC using super resolution structured illumination fluorescence microscopy (SIM) to position Nup98 domains relative to markers of cytoplasmic filaments and the nuclear basket. Our data support the notion that Nup98 is a major determinant of the permeability barrier of NPCs.
Collapse
|
25
|
Rémillard-Labrosse G, Lippé R. In vitro nuclear egress of herpes simplex virus type 1 capsids. Methods 2011; 55:153-9. [PMID: 21824520 DOI: 10.1016/j.ymeth.2011.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 07/18/2011] [Accepted: 07/20/2011] [Indexed: 11/24/2022] Open
Abstract
During their life cycles, viruses typically undergo many transport events throughout the cell. These events depend on a variety of both viral and host proteins and are often not fully understood. Such studies are often complicated by asynchronous infections and the concurrent presence of various viral intermediates in the cells, making it difficult to molecularly define each step. In the case of the herpes simplex virus type 1, the etiological agent of cold sores and many other illnesses, the viral particles undergo an intricate series of transport steps during its life cycle. Upon entry by fusion with a cellular membrane, they travel to the host cell nucleus where the virus replicates and assembles new viral particles. These particles then travel across the two nuclear envelopes and transit through the trans-Golgi network before finally being transported to and released at the cell surface. Though viral components and some host proteins modulating these numerous transport events have been identified, the details of these processes remain to be elucidated. To specifically address how the virus escapes the nucleus, we set up an in vitro model that reproduces the unconventional route used by herpes simplex type 1 virus to leave nuclei. This has not only allowed us to clarify the route of capsid egress of the virus but is now useful to define it at the molecular level.
Collapse
Affiliation(s)
- Gaudeline Rémillard-Labrosse
- Department of Pathology and Cell Biology, University of Montreal, PO Box 6128, Succursale Centre-Ville, Montreal, Quebec, Canada H3C 3J7
| | | |
Collapse
|
26
|
Nucleocytoplasmic mRNP export is an integral part of mRNP biogenesis. Chromosoma 2010; 120:23-38. [PMID: 21079985 PMCID: PMC3028071 DOI: 10.1007/s00412-010-0298-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 10/27/2010] [Accepted: 10/27/2010] [Indexed: 01/16/2023]
Abstract
Nucleocytoplasmic export and biogenesis of mRNPs are closely coupled. At the gene, concomitant with synthesis of the pre-mRNA, the transcription machinery, hnRNP proteins, processing, quality control and export machineries cooperate to release processed and export competent mRNPs. After diffusion through the interchromatin space, the mRNPs are translocated through the nuclear pore complex and released into the cytoplasm. At the nuclear pore complex, defined compositional and conformational changes are triggered, but specific cotranscriptionally added components are retained in the mRNP and subsequently influence the cytoplasmic fate of the mRNP. Processes taking place at the gene locus and at the nuclear pore complex are crucial for integrating export as an essential part of gene expression. Spatial, temporal and structural aspects of these events have been highlighted in analyses of the Balbiani ring genes.
Collapse
|
27
|
Kapon R, Naim B, Zbaida D, Nevo R, Tsabari O, Reich Z. Permeating the nuclear pore complex. Nucleus 2010; 1:475-80. [PMID: 21327089 PMCID: PMC3027049 DOI: 10.4161/nucl.1.6.13112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 06/22/2010] [Accepted: 07/22/2010] [Indexed: 11/19/2022] Open
Abstract
The extensive and multifaceted traffic between nucleus and cytoplasm is handled by a single type of macromolecular assembly called the nuclear pore complex (NPC). While being readily accessible to ions and metabolites, the NPC imposes stringent selectivity on the passage of proteins and RNA, tightly regulating their traffic between the two major cellular compartments. Here we discuss how shuttling carriers, which mediate the transport of macromolecules through NPCs, cross its permeability barrier. We also discuss the co-existence of receptor-mediated macromolecular transport with the passive diffusion of small molecules in the context of the various models suggested for the permeability barrier of the NPC. Finally, we speculate on how nuclear transport receptors negotiate the dependence of their NPC-permeating abilities on hydrophobic interactions with the necessity of avoiding these promiscuous interactions in the cytoplasm and nucleus.
Collapse
Affiliation(s)
- Ruti Kapon
- Department of Biological Chemistry; Weizmann Institute of Science; Rehovot Israel
| | - Bracha Naim
- Department of Biological Chemistry; Weizmann Institute of Science; Rehovot Israel
| | - David Zbaida
- Department of Materials and Interfaces; Weizmann Institute of Science; Rehovot Israel
| | - Reinat Nevo
- Department of Biological Chemistry; Weizmann Institute of Science; Rehovot Israel
| | - Onie Tsabari
- Department of Biological Chemistry; Weizmann Institute of Science; Rehovot Israel
| | - Ziv Reich
- Department of Biological Chemistry; Weizmann Institute of Science; Rehovot Israel
| |
Collapse
|
28
|
Fichtman B, Ramos C, Rasala B, Harel A, Forbes DJ. Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis. Mol Biol Cell 2010; 21:4197-211. [PMID: 20926687 PMCID: PMC2993748 DOI: 10.1091/mbc.e10-04-0309] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.
Collapse
Affiliation(s)
- Boris Fichtman
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0347, USA
| | | | | | | | | |
Collapse
|
29
|
Fiserova J, Richards SA, Wente SR, Goldberg MW. Facilitated transport and diffusion take distinct spatial routes through the nuclear pore complex. J Cell Sci 2010; 123:2773-80. [PMID: 20647373 DOI: 10.1242/jcs.070730] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transport across the nuclear envelope is regulated by nuclear pore complexes (NPCs). Much is understood about the factors that shuttle and control the movement of cargos through the NPC, but less has been resolved about the translocation process itself. Various models predict how cargos move through the channel; however, direct observation of the process is missing. Therefore, we have developed methods to accurately determine cargo positions within the NPC. Cargos were instantly trapped in transit by high-pressure freezing, optimally preserved by low-temperature fixation and then localized by immunoelectron microscopy. A statistical modelling approach was used to identify cargo distribution. We found import cargos localized surprisingly close to the edge of the channel, whereas mRNA export factors were at the very centre of the NPC. On the other hand, diffusion of GFP was randomly distributed. Thus, we suggest that spatially distinguished pathways exist within the NPC. Deletion of specific FG domains of particular NPC proteins resulted in collapse of the peripheral localization and transport defects specific to a certain karyopherin pathway. This further confirms that constraints on the route of travel are biochemical rather than structural and that the peripheral route of travel is essential for facilitated import.
Collapse
Affiliation(s)
- Jindriska Fiserova
- Department of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK
| | | | | | | |
Collapse
|
30
|
Yamada J, Phillips JL, Patel S, Goldfien G, Calestagne-Morelli A, Huang H, Reza R, Acheson J, Krishnan VV, Newsam S, Gopinathan A, Lau EY, Colvin ME, Uversky VN, Rexach MF. A bimodal distribution of two distinct categories of intrinsically disordered structures with separate functions in FG nucleoporins. Mol Cell Proteomics 2010; 9:2205-24. [PMID: 20368288 DOI: 10.1074/mcp.m000035-mcp201] [Citation(s) in RCA: 247] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nuclear pore complexes (NPCs) gate the only conduits for nucleocytoplasmic transport in eukaryotes. Their gate is formed by nucleoporins containing large intrinsically disordered domains with multiple phenylalanine-glycine repeats (FG domains). In combination, these are hypothesized to form a structurally and chemically homogeneous network of random coils at the NPC center, which sorts macromolecules by size and hydrophobicity. Instead, we found that FG domains are structurally and chemically heterogeneous. They adopt distinct categories of intrinsically disordered structures in non-random distributions. Some adopt globular, collapsed coil configurations and are characterized by a low charge content. Others are highly charged and adopt more dynamic, extended coil conformations. Interestingly, several FG nucleoporins feature both types of structures in a bimodal distribution along their polypeptide chain. This distribution functionally correlates with the attractive or repulsive character of their interactions with collapsed coil FG domains displaying cohesion toward one another and extended coil FG domains displaying repulsion. Topologically, these bipartite FG domains may resemble sticky molten globules connected to the tip of relaxed or extended coils. Within the NPC, the crowding of FG nucleoporins and the segregation of their disordered structures based on their topology, dimensions, and cohesive character could force the FG domains to form a tubular gate structure or transporter at the NPC center featuring two separate zones of traffic with distinct physicochemical properties.
Collapse
Affiliation(s)
- Justin Yamada
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Abstract
Eukaryotic cells have developed a series of highly controlled processes of transport between the nucleus and cytoplasm. The present review focuses on the latest advances in our understanding of nucleocytoplasmic exchange of molecules in yeast, a widely studied model organism in the field. It concentrates on the role of individual proteins such as nucleoporins and karyopherins in the translocation process and relates this to how the organization of the nuclear pore complex effectively facilitates the bidirectional transport between the two compartments.
Collapse
|
32
|
Flexible gates: dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic transport. EUKARYOTIC CELL 2009; 8:1814-27. [PMID: 19801417 DOI: 10.1128/ec.00225-09] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The nuclear envelope is a physical barrier between the nucleus and cytoplasm and, as such, separates the mechanisms of transcription from translation. This compartmentalization of eukaryotic cells allows spatial regulation of gene expression; however, it also necessitates a mechanism for transport between the nucleus and cytoplasm. Macromolecular trafficking of protein and RNA occurs exclusively through nuclear pore complexes (NPCs), specialized channels spanning the nuclear envelope. A novel family of NPC proteins, the FG-nucleoporins (FG-Nups), coordinates and potentially regulates NPC translocation. The extensive repeats of phenylalanine-glycine (FG) in each FG-Nup directly bind to shuttling transport receptors moving through the NPC. In addition, FG-Nups are essential components of the nuclear permeability barrier. In this review, we discuss the structural features, cellular functions, and evolutionary conservation of the FG-Nups.
Collapse
|
33
|
Peters R. Functionalization of a nanopore: the nuclear pore complex paradigm. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1793:1533-9. [PMID: 19596381 PMCID: PMC2756448 DOI: 10.1016/j.bbamcr.2009.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 06/26/2009] [Accepted: 06/30/2009] [Indexed: 10/20/2022]
Abstract
Biological cells maintain a myriad of nanopores which, although relying on the same basic small-hole principle, serve a large variety of functions. Here we consider how the nuclear pore complex (NPC), a large nanopore mediating the traffic between genetic material and protein synthesizing apparatus, is functionalized to carry out a set of transport functions. A major parameter of NPC functionalization is a lining of it external and internal surfaces with so-called phenylalanine glycine (FG) proteins. FG proteins integrate a multitude of transport factor binding sites into intrinsically disordered domains. This surprising finding has given rise to a number of transport models assigning direct gating functions to FG proteins. However, recent data suggest that the properties of FG proteins cannot be properly assessed by considering only the purified, transport-factor-stripped NPC. At physiological conditions transport factors may shape FG proteins in a way allotting an essential role to surface diffusion, reconciling tight binding with efficient transport. Thus, NPC studies are revealing both general traits and novel aspects of nanopore functionalization. In addition, they inspire artificial molecule sorters for proteomic and pharmaceutical applications.
Collapse
Affiliation(s)
- Reiner Peters
- The Rockefeller University, Laboratory for mass spectrometry and gaseous ion chemistry, 1230 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
34
|
Mohr D, Frey S, Fischer T, Güttler T, Görlich D. Characterisation of the passive permeability barrier of nuclear pore complexes. EMBO J 2009; 28:2541-53. [PMID: 19680228 PMCID: PMC2728435 DOI: 10.1038/emboj.2009.200] [Citation(s) in RCA: 274] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Accepted: 06/09/2009] [Indexed: 12/27/2022] Open
Abstract
Nuclear pore complexes (NPCs) restrict uncontrolled nucleocytoplasmic fluxes of inert macromolecules but permit facilitated translocation of nuclear transport receptors and their cargo complexes. We probed the passive barrier of NPCs and observed sieve-like properties with a dominating mesh or channel radius of 2.6 nm, which is narrower than proposed earlier. A small fraction of diffusion channels has a wider opening, explaining the very slow passage of larger molecules. The observed dominant passive diameter approximates the distance of adjacent hydrophobic clusters of FG repeats, supporting the model that the barrier is made of FG repeat domains cross-linked with a spacing of an FG repeat unit length. Wheat germ agglutinin and the dominant-negative importin beta(45-462) fragment were previously regarded as selective inhibitors of facilitated NPC passage. We now observed that they do not distinguish between the passive and the facilitated mode. Instead, their inhibitory effect correlates with the size of the NPC-passing molecule. They have little effect on small species, inhibit the passage of green fluorescent protein-sized objects >10-fold and virtually block the translocation of larger ones. This suggests that passive and facilitated NPC passage proceed through one and the same permeability barrier.
Collapse
Affiliation(s)
- Dagmar Mohr
- ZMBH, Im Neuenheimer Feld 282, Heidelberg, Germany
| | | | | | | | | |
Collapse
|
35
|
|
36
|
Abstract
Transport through the nuclear pore complex (NPC), a keystone of the eukaryotic building plan, is known to involve a large channel and an abundance of phenylalanine-glycine (FG) protein domains serving as binding sites for soluble nuclear transport receptors and their cargo complexes. However, the conformation of the FG domains in vivo, their arrangement in relation to the transport channel and their function(s) in transport are still vividly debated. Here, we revisit a number of representative transport models-specifically Brownian affinity gating, selective phase gating, reversible FG domain collapse, and reduction of dimensionality (ROD)-in the light of new data obtained by optical single transporter recording, optical superresolution microscopy, artificial nanopores, and many other techniques. The analysis suggests that a properly adapted, simplified version of the ROD model accounts well for the available data. This has implications for nucleocytoplasmic transport in general.
Collapse
Affiliation(s)
- Reiner Peters
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065 , USA.
| |
Collapse
|
37
|
Callahan J, Kopečkov P, Kopeček J. Intracellular trafficking and subcellular distribution of a large array of HPMA copolymers. Biomacromolecules 2009; 10:1704-14. [PMID: 21197960 DOI: 10.1021/bm801514x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The basic physicochemical properties that determine the distribution and fate of synthetic macromolecules in living cells were characterized using fluorescently labeled HPMA (N-(2-hydroxypropyl)methacrylamide) copolymers. Twelve different classes of water-soluble copolymers were created by incorporating eight different functionalized comonomers. These comonomers possessed functional groups with positive or negative charges or contained short hydrophobic peptides. The copolymers were fractionated to create parallel "ladders" consisting of 10 fractions of narrow polydispersity with molecular weights ranging from 10 to 200 kDa. The intracellular distributions were characterized for copolymer solutions microinjected into the cytoplasm of cultured ovarian carcinoma cells. Even the highest molecular weight HPMA copolymers were shown to quickly and evenly diffuse throughout the cytoplasm and remain excluded from membrane-bound organelles, regardless of composition. The exceptions were the strongly cationic copolymers, which demonstrated a pronounced localization to microtubules. For all copolymers, nuclear entry was consistent with passive transport through the nuclear pore complex (NPC). Nuclear uptake was shown to be largely dictated by the molecular weight of the copolymers, however, detailed kinetic analyses showed that nuclear import rates were moderately, but significantly, affected by differences in comonomer composition. HPMA copolymers containing amide-terminated phenylalanine-glycine (FG) sequences, analogous to those found in the NPC channel protein, demonstrated a potential to regulate import to the nuclear compartment. Kinetic analyses showed that 15 kDa copolymers containing GGFG, but not those containing GGLFG, peptide pendant groups altered the size-exclusion characteristics of NPC-mediated nuclear import.
Collapse
Affiliation(s)
- Jon Callahan
- Department of Bioengineering, University of Utah, Salt Lake City, Utah 84112, USA
| | | | | |
Collapse
|
38
|
New strategies for nucleic acid delivery to conquer cellular and nuclear membranes. J Control Release 2008; 132:279-88. [DOI: 10.1016/j.jconrel.2008.06.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 06/23/2008] [Accepted: 06/30/2008] [Indexed: 12/17/2022]
|
39
|
Caspi Y, Zbaida D, Cohen H, Elbaum M. Synthetic mimic of selective transport through the nuclear pore complex. NANO LETTERS 2008; 8:3728-3734. [PMID: 18950236 DOI: 10.1021/nl801975q] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The nuclear pore complex is a large protein channel present universally in eukaryotic cells. It generates an essential macromolecular separation between the nucleus and cytoplasm. The transport mechanism relies on recognition of molecular cargos by receptor proteins, and on specific interaction between the receptors and the pores. We present a chemical mimic of this "receptor-mediated" transport using modified nanoporous membrane filters, polyisopropylacrylamide as the carrier molecule, or receptor, and single-stranded DNA as the cargo. We show that a complex of ssDNA and polyisopropylacrylamide diffuses faster through the modified pores than does the bare ssDNA, in spite of the larger size of the complex. The mobile polymer thus acts as a soluble receptor to usher a macromolecular cargo specifically through the pores.
Collapse
Affiliation(s)
- Yaron Caspi
- Department of Materials and Interfaces, The Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | |
Collapse
|
40
|
Aghdam AG, Vossoughi M, Almzadeh I, Zeinali M. Bioconjugation of Interferon-alpha Molecules to Lysine-Capped Gold Nanoparticles for Further Drug Delivery Applications. J DISPER SCI TECHNOL 2008. [DOI: 10.1080/01932690701815762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
41
|
Zilman A, Di Talia S, Chait BT, Rout MP, Magnasco MO. Efficiency, selectivity, and robustness of nucleocytoplasmic transport. PLoS Comput Biol 2008; 3:e125. [PMID: 17630825 PMCID: PMC1914370 DOI: 10.1371/journal.pcbi.0030125] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 05/17/2007] [Indexed: 01/16/2023] Open
Abstract
All materials enter or exit the cell nucleus through nuclear pore complexes (NPCs), efficient transport devices that combine high selectivity and throughput. NPC-associated proteins containing phenylalanine–glycine repeats (FG nups) have large, flexible, unstructured proteinaceous regions, and line the NPC. A central feature of NPC-mediated transport is the binding of cargo-carrying soluble transport factors to the unstructured regions of FG nups. Here, we model the dynamics of nucleocytoplasmic transport as diffusion in an effective potential resulting from the interaction of the transport factors with the flexible FG nups, using a minimal number of assumptions consistent with the most well-established structural and functional properties of NPC transport. We discuss how specific binding of transport factors to the FG nups facilitates transport, and how this binding and competition between transport factors and other macromolecules for binding sites and space inside the NPC accounts for the high selectivity of transport. We also account for why transport is relatively insensitive to changes in the number and distribution of FG nups in the NPC, providing an explanation for recent experiments where up to half the total mass of the FG nups has been deleted without abolishing transport. Our results suggest strategies for the creation of artificial nanomolecular sorting devices. The DNA at the heart of our cells is contained in the nucleus. This nucleus is surrounded by a barrier in which are buried gatekeepers, termed nuclear pore complexes (NPCs), which allow the quick and efficient passage of certain materials while excluding all others. It has long been known that materials must bind to the NPC to be transported across it, but how this binding translates into selective passage through the NPC has remained a mystery. Here we describe a theory to explain how the NPC works. Our theory accounts for the observed characteristics of NPC–mediated transport, and even suggests strategies for the creation of artificial nanomolecular sorting devices.
Collapse
Affiliation(s)
- Anton Zilman
- Laboratory of Mathematical Physics, The Rockefeller University, New York, New York, United States of America
| | - Stefano Di Talia
- Laboratory of Mathematical Physics, The Rockefeller University, New York, New York, United States of America
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, United States of America
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, United States of America
- * To whom correspondence should be addressed. E-mail: (MPR); (MOM)
| | - Marcelo O Magnasco
- Laboratory of Mathematical Physics, The Rockefeller University, New York, New York, United States of America
- * To whom correspondence should be addressed. E-mail: (MPR); (MOM)
| |
Collapse
|
42
|
Kapon R, Topchik A, Mukamel D, Reich Z. A possible mechanism for self-coordination of bidirectional traffic across nuclear pores. Phys Biol 2008; 5:036001. [DOI: 10.1088/1478-3975/5/3/036001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
43
|
Ragusa A, García I, Penadés S. Nanoparticles as nonviral gene delivery vectors. IEEE Trans Nanobioscience 2008; 6:319-30. [PMID: 18217625 DOI: 10.1109/tnb.2007.908996] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Gene therapy, as therapeutic treatment to genetic or acquired diseases, is attracting much interest in the research community, leading to noteworthy developments over the past two decades. Although this field is still dominated by viral vectors, nonviral vectors have recently received an ever increasing attention in order to overcome the safety problems of their viral counterpart. This review presents the biological aspects involved in the gene delivery process and explores the recent developments and achievements of nonviral gene carriers.
Collapse
Affiliation(s)
- Andrea Ragusa
- Laboratory of Glyconanotechnology, IIQ-CSIC, Americo Vespucio 49, 41092 Seville, Spain.
| | | | | |
Collapse
|
44
|
Abstract
The spatial separation between the cytoplasm and the cell nucleus necessitates the continuous exchange of macromolecular cargo across the double-membraned nuclear envelope. Being the only passageway in and out of the nucleus, the nuclear pore complex (NPC) has the principal function of regulating the high throughput of nucleocytoplasmic transport in a highly selective manner so as to maintain cellular order and function. Here, we present a retrospective review of the evidence that has led to the current understanding of both NPC structure and function. Looking towards the future, we contemplate on how various outstanding effects and nanoscopic characteristics ought to be addressed, with the goal of reconciling structure and function into a single unified picture of the NPC.
Collapse
|
45
|
Lim RYH, Ullman KS, Fahrenkrog B. Biology and biophysics of the nuclear pore complex and its components. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 267:299-342. [PMID: 18544502 DOI: 10.1016/s1937-6448(08)00632-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleocytoplasmic exchange of proteins and ribonucleoprotein particles occurs via nuclear pore complexes (NPCs) that reside in the double membrane of the nuclear envelope (NE). Significant progress has been made during the past few years in obtaining better structural resolution of the three-dimensional architecture of NPC with the help of cryo-electron tomography and atomic structures of domains from nuclear pore proteins (nucleoporins). Biophysical and imaging approaches have helped elucidate how nucleoporins act as a selective barrier in nucleocytoplasmic transport. Nucleoporins act not only in trafficking of macromolecules but also in proper microtubule attachment to kinetochores, in the regulation of gene expression and signaling events associated with, for example, innate and adaptive immunity, development and neurodegenerative disorders. Recent research has also been focused on the dynamic processes of NPC assembly and disassembly that occur with each cell cycle. Here we review emerging results aimed at understanding the molecular arrangement of the NPC and how it is achieved, defining the roles of individual nucleoporins both at the NPC and at other sites within the cell, and finally deciphering how the NPC serves as both a barrier and a conduit of active transport.
Collapse
Affiliation(s)
- Roderick Y H Lim
- M.E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
| | | | | |
Collapse
|
46
|
Patel SS, Belmont BJ, Sante JM, Rexach MF. Natively unfolded nucleoporins gate protein diffusion across the nuclear pore complex. Cell 2007; 129:83-96. [PMID: 17418788 DOI: 10.1016/j.cell.2007.01.044] [Citation(s) in RCA: 406] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 11/23/2006] [Accepted: 01/24/2007] [Indexed: 12/24/2022]
Abstract
Nuclear pore complexes (NPCs) form aqueous conduits in the nuclear envelope and gate the diffusion of large proteins between the cytoplasm and nucleoplasm. NPC proteins (nucleoporins) that contain phenylalanine-glycine motifs in filamentous, natively unfolded domains (FG domains) line the diffusion conduit of the NPC, but their role in the size-selective barrier is unclear. We show that deletion of individual FG domains in yeast relaxes the NPC permeability barrier. At the molecular level, the FG domains of five nucleoporins anchored at the NPC center form a cohesive meshwork of filaments through hydrophobic interactions, which involve phenylalanines in FG motifs and are dispersed by aliphatic alcohols. In contrast, the FG domains of four peripherally anchored nucleoporins are generally noncohesive. The results support a two-gate model of NPC architecture featuring a central diffusion gate formed by a meshwork of cohesive FG nucleoporin filaments and a peripheral gate formed by repulsive FG nucleoporin filaments.
Collapse
Affiliation(s)
- Samir S Patel
- MCD Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | | | | |
Collapse
|
47
|
Managing free-energy barriers in nuclear pore transport. J Biol Phys 2006; 32:465-72. [PMID: 19669451 DOI: 10.1007/s10867-006-9029-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Accepted: 11/12/2006] [Indexed: 10/23/2022] Open
Abstract
The Nuclear Pore Complexes (NPC) facilitate highly selective gateways for transport of macromolecules across the Nuclear Envelope (NE). Based on the current accumulated knowledge of the architecture of NPC we have established a minimal physical model of the pore and the transport mechanism. The barrier properties of the NPC model are analyzed by the recently established Wang-Landau Monte Carlo computer simulation technique and the transport properties are extracted by employing Kramers' theory of reaction rates. We show that our physical model can account for a range of characteristics observed for nuclear pore transport.
Collapse
|
48
|
Naim B, Brumfeld V, Kapon R, Kiss V, Nevo R, Reich Z. Passive and facilitated transport in nuclear pore complexes is largely uncoupled. J Biol Chem 2006; 282:3881-8. [PMID: 17164246 DOI: 10.1074/jbc.m608329200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Nuclear pore complexes provide the sole gateway for the exchange of material between nucleus and cytoplasm of interphase eukaryotic cells. They support two modes of transport: passive diffusion of ions, metabolites, and intermediate-sized macromolecules and facilitated, receptor-mediated translocation of proteins, RNA, and ribonucleoprotein complexes. It is generally assumed that both modes of transport occur through a single diffusion channel located within the central pore of the nuclear pore complex. To test this hypothesis, we studied the mutual effects between transporting molecules utilizing either the same or different modes of translocation. We find that the two modes of transport do not interfere with each other, but molecules utilizing a particular mode of transport do hinder motion of others utilizing the same pathway. We therefore conclude that the two modes of transport are largely segregated.
Collapse
Affiliation(s)
- Bracha Naim
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | | | | | |
Collapse
|
49
|
Davis JR, Kakar M, Lim CS. Controlling protein compartmentalization to overcome disease. Pharm Res 2006; 24:17-27. [PMID: 16969692 DOI: 10.1007/s11095-006-9133-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 07/20/2006] [Indexed: 01/08/2023]
Abstract
Over the past decade, considerable progress has been made to improve our understanding of the intracellular transport of proteins. Mechanisms of nuclear import and export involving classical receptors have been studied. Signal sequences required for directing a protein molecule to a specific cellular compartment have been defined. Knowledge of subcellular trafficking of proteins has also increased our understanding of diseases caused due to mislocalization of proteins. A specific protein on deviating from its native cellular compartment may result in disease due to loss of its normal functioning and aberrant activity in the "wrong" compartment. Mislocalization of proteins results in diseases that range from metabolic disorders to cancer. In this review we discuss some of the diseases caused due to mislocalization. We further focus on application of nucleocytoplasmic transport to drug delivery. Various rationales to treat diseases by exploiting intracellular transport machinery have been proposed. Although the pathways for intracellular movement of proteins have been defined, these have not been adequately utilized for management of diseases involving mislocalized proteins. This review stresses the need for designing drug delivery systems utilizing these mechanisms as this area is least exploited but offers great potential.
Collapse
Affiliation(s)
- James R Davis
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah 84108, USA
| | | | | |
Collapse
|
50
|
Abstract
Nucleocytoplasmic transport, the exchange of matter between nucleus and cytoplasm, plays a fundamental role in human and other eukaryotic cells, affecting almost every aspect of health and disease. The only gate for the transport of small and large molecules as well as supramolecular complexes between nucleus and cytoplasm is the nuclear pore complex (NPC). The NPC is not a normal membrane transport protein (transporter). Composed of 500 to 1000 peptide chains, the NPC features a mysterious functional duality. For most molecules, it constitutes a molecular sieve with a blurred cutoff at approx 10 nm, but for molecules binding to phenylalanine-glycine (FG) motifs, the NPC appears to be a channel of approx 50 nm diameter, permitting bidirectional translocation at high speed. To achieve this, the NPC cooperates with soluble factors, the nuclear transport receptors, which shuttle between nuclear contents and cytoplasm. Here, we provide a short introduction to nucleocytoplasmic transport by describing first the structure and composition of the nuclear pore complex. Then, mechanisms of nucleocytoplasmic transport are discussed. Finally, the still essentially unresolved mechanisms by which nuclear transport receptors and transport complexes are translocated through the nuclear pore complex are considered, and a novel translocation model is suggested.
Collapse
Affiliation(s)
- Reiner Peters
- Institute of Medical Physics and Biophysics and Center for Nanotechnology, University of Münster, Germany
| |
Collapse
|