1
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Nuclear Transporting Factor 2 as a Novel Biomarker of Head and Neck Squamous Cell Carcinoma and Associated with T/B Cell Receptor Signaling Pathway. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2885323. [PMID: 35155672 PMCID: PMC8837431 DOI: 10.1155/2022/2885323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/06/2022] [Indexed: 12/27/2022]
Abstract
Objective This study is aimed at exploring the role of nuclear transporting factor 2 (NUTF2) in head and neck squamous cell carcinoma (HNSCC) based on The Cancer Genome Atlas (TCGA) database. Methods We obtained 528 HNSCC patients' clinical data from TCGA and performed expression level analysis of NUTF2. Gene Sets Enrichment Analysis (GSEA) was conducted to identify NUTF2-associated regulatory mechanisms in HNSCC. In addition, several other tools were used to enrich the regulatory network. Results We found that NUTF2 was significantly upregulated (P < 0.001) in HNSCC. We then observed that higher NUTF2 is associated with poorer overall survival and disease-free survival. Further, by using Cox analyses, we determined high NUTF2 as an independent risk factor of predicting poorer overall survival. Tumor immune infiltration analysis revealed a significantly negative correlation between NUTF2 expression and the level of tumor infiltrated CD8+ T cell and B cell, suggesting that NUTF2 may be involved in the immune regulation of HNSCC. Gene sets related to T/B cell receptor signaling pathways were differentially enriched based on the NUTF2 expression phenotype. KEGG pathways were used to show that NUTF2 may affect proliferation, differentiation, and immune response of T/B cell through regulating PI3K/AKT, NFκB, MAPK, and Calcium signaling pathways. Conclusion NUTF2 might be a valuable biomarker for HNSCC and correlated with T/B cell receptor signaling pathway.
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2
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McBride JM, Tlusty T. Slowest-first protein translation scheme: Structural asymmetry and co-translational folding. Biophys J 2021; 120:5466-5477. [PMID: 34813729 PMCID: PMC8715247 DOI: 10.1016/j.bpj.2021.11.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/30/2021] [Accepted: 11/17/2021] [Indexed: 11/19/2022] Open
Abstract
Proteins are translated from the N to the C terminus, raising the basic question of how this innate directionality affects their evolution. To explore this question, we analyze 16,200 structures from the Protein Data Bank (PDB). We find remarkable enrichment of α helices at the C terminus and β strands at the N terminus. Furthermore, this α-β asymmetry correlates with sequence length and contact order, both determinants of folding rate, hinting at possible links to co-translational folding (CTF). Hence, we propose the "slowest-first" scheme, whereby protein sequences evolved structural asymmetry to accelerate CTF: the slowest of the cooperatively folding segments are positioned near the N terminus so they have more time to fold during translation. A phenomenological model predicts that CTF can be accelerated by asymmetry in folding rate, up to double the rate, when folding time is commensurate with translation time; analysis of the PDB predicts that structural asymmetry is indeed maximal in this regime. This correspondence is greater in prokaryotes, which generally require faster protein production. Altogether, this indicates that accelerating CTF is a substantial evolutionary force whose interplay with stability and functionality is encoded in secondary structure asymmetry.
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Affiliation(s)
- John M McBride
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, South Korea.
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, South Korea; Departments of Physics and Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea.
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3
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Shen Q, Tian T, Xiong Q, Ellis Fisher PD, Xiong Y, Melia TJ, Lusk CP, Lin C. DNA-Origami NanoTrap for Studying the Selective Barriers Formed by Phenylalanine-Glycine-Rich Nucleoporins. J Am Chem Soc 2021; 143:12294-12303. [PMID: 34324340 DOI: 10.1021/jacs.1c05550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA nanotechnology provides a versatile and powerful tool to dissect the structure-function relationship of biomolecular machines like the nuclear pore complex (NPC), an enormous protein assembly that controls molecular traffic between the nucleus and cytoplasm. To understand how the intrinsically disordered, Phe-Gly-rich nucleoporins (FG-nups) within the NPC establish a selective barrier to macromolecules, we built a DNA-origami NanoTrap. The NanoTrap comprises precisely arranged FG-nups in an NPC-like channel, which sits on a baseplate that captures macromolecules that pass through the FG network. Using this biomimetic construct, we determined that the FG-motif type, grafting density, and spatial arrangement are critical determinants of an effective diffusion barrier. Further, we observed that diffusion barriers formed with cohesive FG interactions dominate in mixed-FG-nup scenarios. Finally, we demonstrated that the nuclear transport receptor, Ntf2, can selectively transport model cargo through NanoTraps composed of FxFG but not GLFG Nups. Our NanoTrap thus recapitulates the NPC's fundamental biological activities, providing a valuable tool for studying nuclear transport.
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Affiliation(s)
- Qi Shen
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Taoran Tian
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qiancheng Xiong
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Patrick D Ellis Fisher
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Thomas J Melia
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - C Patrick Lusk
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States.,Nanobiology Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
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4
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Jevtić P, Schibler AC, Wesley CC, Pegoraro G, Misteli T, Levy DL. The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity. EMBO Rep 2019; 20:embr.201847283. [PMID: 31085625 DOI: 10.15252/embr.201847283] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
How intracellular organelles acquire their characteristic sizes is a fundamental question in cell biology. Given stereotypical changes in nuclear size in cancer, it is important to understand the mechanisms that control nuclear size in human cells. Using a high-throughput imaging RNAi screen, we identify and mechanistically characterize ELYS, a nucleoporin required for post-mitotic nuclear pore complex (NPC) assembly, as a determinant of nuclear size in mammalian cells. ELYS knockdown results in small nuclei, reduced nuclear lamin B2 localization, lower NPC density, and decreased nuclear import. Increasing nuclear import by importin α overexpression rescues nuclear size and lamin B2 import, while inhibiting importin α/β-mediated nuclear import decreases nuclear size. Conversely, ELYS overexpression increases nuclear size, enriches nuclear lamin B2 at the nuclear periphery, and elevates NPC density and nuclear import. Consistent with these observations, knockdown or inhibition of exportin 1 increases nuclear size. Thus, we identify ELYS as a novel positive effector of mammalian nuclear size and propose that nuclear size is sensitive to NPC density and nuclear import capacity.
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Affiliation(s)
- Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | | | - Chase C Wesley
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Gianluca Pegoraro
- High Throughput Imaging Facility (HiTIF), National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tom Misteli
- National Cancer Institute, NIH, Bethesda, MD, USA
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
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5
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Enzyme-catalysed [6+4] cycloadditions in the biosynthesis of natural products. Nature 2019; 568:122-126. [PMID: 30867595 DOI: 10.1038/s41586-019-1021-x] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/07/2019] [Indexed: 01/01/2023]
Abstract
Pericyclic reactions are powerful transformations for the construction of carbon-carbon and carbon-heteroatom bonds in organic synthesis. Their role in biosynthesis is increasingly apparent, and mechanisms by which pericyclases can catalyse reactions are of major interest1. [4+2] cycloadditions (Diels-Alder reactions) have been widely used in organic synthesis2 for the formation of six-membered rings and are now well-established in biosynthesis3-6. [6+4] and other 'higher-order' cycloadditions were predicted7 in 1965, and are now increasingly common in the laboratory despite challenges arising from the generation of a highly strained ten-membered ring system8,9. However, although enzyme-catalysed [6+4] cycloadditions have been proposed10-12, they have not been proven to occur. Here we demonstrate a group of enzymes that catalyse a pericyclic [6+4] cycloaddition, which is a crucial step in the biosynthesis of streptoseomycin-type natural products. This type of pericyclase catalyses [6+4] and [4+2] cycloadditions through a single ambimodal transition state, which is consistent with previous proposals11,12. The [6+4] product is transformed to a less stable [4+2] adduct via a facile Cope rearrangement, and the [4+2] adduct is converted into the natural product enzymatically. Crystal structures of three pericyclases, computational simulations of potential energies and molecular dynamics, and site-directed mutagenesis establish the mechanism of this transformation. This work shows how enzymes are able to catalyse concerted pericyclic reactions involving ambimodal transition states.
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6
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Duan Z, Xu H, Ji X, Zhao J, Xu H, Hu Y, Deng S, Hu S, Liu X. Importin α5 negatively regulates importin β1-mediated nuclear import of Newcastle disease virus matrix protein and viral replication and pathogenicity in chicken fibroblasts. Virulence 2018. [PMID: 29532715 PMCID: PMC5955436 DOI: 10.1080/21505594.2018.1449507] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The matrix (M) protein of Newcastle disease virus (NDV) is demonstrated to localize in the nucleus via intrinsic nuclear localization signal (NLS), but cellular proteins involved in the nuclear import of NDV M protein and the role of M's nuclear localization in the replication and pathogenicity of NDV remain unclear. In this study, importin β1 was screened to interact with NDV M protein by yeast two-hybrid screening. This interaction was subsequently confirmed by co-immunoprecipitation and pull-down assays. In vitro binding studies indicated that the NLS region of M protein and the amino acids 336–433 of importin β1 that belonged to the RanGTP binding region were important for binding. Importantly, a recombinant virus with M/NLS mutation resulted in a pathotype change of NDV and attenuated viral replication and pathogenicity in chicken fibroblasts and SPF chickens. In agreement with the binding data, nuclear import of NDV M protein in digitonin-permeabilized HeLa cells required both importin β1 and RanGTP. Interestingly, importin α5 was verified to interact with M protein through binding importin β1. However, importin β1 or importin α5 depletion by siRNA resulted in different results, which showed the obviously cytoplasmic or nuclear accumulation of M protein and the remarkably decreased or increased replication ability and pathogenicity of NDV in chicken fibroblasts, respectively. Our findings therefore demonstrate for the first time the nuclear import mechanism of NDV M protein and the negative regulation role of importin α5 in importin β1-mediated nuclear import of M protein and the replication and pathogenicity of a paramyxovirus.
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Affiliation(s)
- Zhiqiang Duan
- a Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education , Guizhou University , Guiyang , China.,b College of Animal Science , Guizhou University , Guiyang , China
| | - Haixu Xu
- c Key Laboratory of Animal Infectious Diseases of Ministry of Agriculture , Yangzhou University , Yangzhou , China
| | - Xinqin Ji
- a Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education , Guizhou University , Guiyang , China.,b College of Animal Science , Guizhou University , Guiyang , China
| | - Jiafu Zhao
- a Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education , Guizhou University , Guiyang , China.,b College of Animal Science , Guizhou University , Guiyang , China
| | - Houqiang Xu
- a Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education , Guizhou University , Guiyang , China.,b College of Animal Science , Guizhou University , Guiyang , China
| | - Yan Hu
- b College of Animal Science , Guizhou University , Guiyang , China
| | - Shanshan Deng
- b College of Animal Science , Guizhou University , Guiyang , China
| | - Shunlin Hu
- c Key Laboratory of Animal Infectious Diseases of Ministry of Agriculture , Yangzhou University , Yangzhou , China
| | - Xiufan Liu
- c Key Laboratory of Animal Infectious Diseases of Ministry of Agriculture , Yangzhou University , Yangzhou , China
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7
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Duan Z, Zhao J, Xu H, Xu H, Ji X, Chen X, Xiong J. Characterization of the nuclear import pathway for BLM protein. Arch Biochem Biophys 2017; 634:57-68. [PMID: 29017749 DOI: 10.1016/j.abb.2017.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/18/2017] [Accepted: 09/29/2017] [Indexed: 01/13/2023]
Abstract
Numerous studies have shown that nuclear localization of BLM protein, a member of the RecQ helicases, mediated by nuclear localization signal (NLS) is critical for DNA recombination, replication and transcription, but the mechanism by which BLM protein is imported into the nucleus remains unknown. In this study, the nuclear import pathway for BLM was investigated. We found that nuclear import of BLM was inhibited by two dominant-negative mutants of importin β1 and NTF2/E42K, which lacks the ability to bind Ran and RanGDP, respectively, but was not inhibited by the Ran/Q69L, which is deficient in GTP hydrolysis. Further studies revealed that nuclear import of BLM was reconstituted using importin β1, RanGDP and NTF2 in digitonin-permeabilized HeLa cells. Moreover, BLM had direct binding to importin β1 through its NLS domain with the 14-16 HEAT repeats of importin β1. Furthermore, importin β1, Ran or NTF2 depletion by siRNA disrupted the accumulation of BLM protein in the nucleus. These results showed that BLM enters the nucleus via the importin β1, RanGDP and NTF2 dependent pathway, demonstrating for the first time the nuclear trafficking mechanism of a DNA helicase.
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Affiliation(s)
- Zhiqiang Duan
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jiafu Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; College of Animal Science, Guizhou University, Guiyang 550025, China.
| | - Haixu Xu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Xinqin Ji
- College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; College of Animal Science, Guizhou University, Guiyang 550025, China
| | - Jianming Xiong
- College of Animal Science, Guizhou University, Guiyang 550025, China
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8
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Jovanovic-Talisman T, Zilman A. Protein Transport by the Nuclear Pore Complex: Simple Biophysics of a Complex Biomachine. Biophys J 2017; 113:6-14. [PMID: 28700925 DOI: 10.1016/j.bpj.2017.05.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 05/01/2017] [Accepted: 05/08/2017] [Indexed: 01/07/2023] Open
Abstract
In eukaryotic cells, transport of molecules between the nucleus and the cytoplasm is facilitated by highly selective and efficient biomachines known as nuclear pore complexes (NPCs). The structural details of NPCs vary across species, with many of their constituent proteins exhibiting relatively low sequence conservation; yet the NPC as a whole retains its general architecture and mechanism of action in all eukaryotes from yeast to humans. This functional conservation in the absence of precise molecular conservation suggests that many aspects of the NPC transport mechanism may be understood based on general biophysical considerations. Accordingly, some aspects of NPC function have been recapitulated in artificial nanochannel mimics, even though they lack certain molecular elements of the endogenous NPC. Herein, we review biophysical aspects of NPC architecture and function and cover recent progress in the field. We also review recent advances in man-made molecular filters inspired by NPCs, and their applications in nanotechnology. We conclude the review with an outlook on outstanding questions in the field and biomedical aspects of NPC transport.
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Affiliation(s)
- Tijana Jovanovic-Talisman
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, California.
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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9
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Zahn R, Osmanović D, Ehret S, Araya Callis C, Frey S, Stewart M, You C, Görlich D, Hoogenboom BW, Richter RP. A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies. eLife 2016; 5. [PMID: 27058170 PMCID: PMC4874776 DOI: 10.7554/elife.14119] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/07/2016] [Indexed: 11/13/2022] Open
Abstract
The permeability barrier of nuclear pore complexes (NPCs) controls bulk nucleocytoplasmic exchange. It consists of nucleoporin domains rich in phenylalanine-glycine motifs (FG domains). As a bottom-up nanoscale model for the permeability barrier, we have used planar films produced with three different end-grafted FG domains, and quantitatively analyzed the binding of two different nuclear transport receptors (NTRs), NTF2 and Importin β, together with the concomitant film thickness changes. NTR binding caused only moderate changes in film thickness; the binding isotherms showed negative cooperativity and could all be mapped onto a single master curve. This universal NTR binding behavior - a key element for the transport selectivity of the NPC - was quantitatively reproduced by a physical model that treats FG domains as regular, flexible polymers, and NTRs as spherical colloids with a homogeneous surface, ignoring the detailed arrangement of interaction sites along FG domains and on the NTR surface.
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Affiliation(s)
- Raphael Zahn
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain
| | - Dino Osmanović
- London Centre for Nanotechnology, University College London, London, United Kingdom.,Department of Physics and Astronomy, University College London, London, United Kingdom.,Department of Physics, Bar-Ilan University, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Severin Ehret
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain
| | | | - Steffen Frey
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Murray Stewart
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Changjiang You
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, United Kingdom.,Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Ralf P Richter
- Biosurfaces Lab, CIC biomaGUNE, San Sebastian, Spain.,Laboratory of Interdisciplinary Physics, University Grenoble Alpes - CNRS, Grenoble, France.,Max-Planck-Institute for Intelligent Systems, Stuttgart, Germany
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10
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Vuković LD, Jevtić P, Zhang Z, Stohr BA, Levy DL. Nuclear size is sensitive to NTF2 protein levels in a manner dependent on Ran binding. J Cell Sci 2016; 129:1115-27. [PMID: 26823604 DOI: 10.1242/jcs.181263] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/20/2016] [Indexed: 12/20/2022] Open
Abstract
Altered nuclear size is associated with many cancers, and determining whether cancer-associated changes in nuclear size contribute to carcinogenesis necessitates an understanding of mechanisms of nuclear size regulation. Although nuclear import rates generally positively correlate with nuclear size, NTF2 levels negatively affect nuclear size, despite the role of NTF2 (also known as NUTF2) in nuclear recycling of the import factor Ran. We show that binding of Ran to NTF2 is required for NTF2 to inhibit nuclear expansion and import of large cargo molecules in Xenopus laevis egg and embryo extracts, consistent with our observation that NTF2 reduces the diameter of the nuclear pore complex (NPC) in a Ran-binding-dependent manner. Furthermore, we demonstrate that ectopic NTF2 expression in Xenopus embryos and mammalian tissue culture cells alters nuclear size. Finally, we show that increases in nuclear size during melanoma progression correlate with reduced NTF2 expression, and increasing NTF2 levels in melanoma cells is sufficient to reduce nuclear size. These results show a conserved capacity for NTF2 to impact on nuclear size, and we propose that NTF2 might be a new cancer biomarker.
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Affiliation(s)
- Lidija D Vuković
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Zhaojie Zhang
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Bradley A Stohr
- Department of Pathology, University of California, San Francisco, CA 94143, USA
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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11
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Vuković LD, Jevtić P, Edens LJ, Levy DL. New Insights into Mechanisms and Functions of Nuclear Size Regulation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 322:1-59. [PMID: 26940517 DOI: 10.1016/bs.ircmb.2015.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nuclear size is generally maintained within a defined range in a given cell type. Changes in cell size that occur during cell growth, development, and differentiation are accompanied by dynamic nuclear size adjustments in order to establish appropriate nuclear-to-cytoplasmic volume relationships. It has long been recognized that aberrations in nuclear size are associated with certain disease states, most notably cancer. Nuclear size and morphology must impact nuclear and cellular functions. Understanding these functional implications requires an understanding of the mechanisms that control nuclear size. In this review, we first provide a general overview of the diverse cellular structures and activities that contribute to nuclear size control, including structural components of the nucleus, effects of DNA amount and chromatin compaction, signaling, and transport pathways that impinge on the nucleus, extranuclear structures, and cell cycle state. We then detail some of the key mechanistic findings about nuclear size regulation that have been gleaned from a variety of model organisms. Lastly, we review studies that have implicated nuclear size in the regulation of cell and nuclear function and speculate on the potential functional significance of nuclear size in chromatin organization, gene expression, nuclear mechanics, and disease. With many fundamental cell biological questions remaining to be answered, the field of nuclear size regulation is still wide open.
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Affiliation(s)
- Lidija D Vuković
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Lisa J Edens
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, Laramie, WY, United States of America.
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12
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Promiscuous binding of Karyopherinβ1 modulates FG nucleoporin barrier function and expedites NTF2 transport kinetics. Biophys J 2015; 108:918-927. [PMID: 25692596 PMCID: PMC4336380 DOI: 10.1016/j.bpj.2014.12.041] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/05/2014] [Accepted: 12/19/2014] [Indexed: 12/22/2022] Open
Abstract
The transport channel of nuclear pore complexes (NPCs) contains a high density of intrinsically disordered proteins that are rich in phenylalanine-glycine (FG)-repeat motifs (FG Nups). The FG Nups interact promiscuously with various nuclear transport receptors (NTRs), such as karyopherins (Kaps), that mediate the trafficking of nucleocytoplasmic cargoes while also generating a selectively permeable barrier against other macromolecules. Although the binding of NTRs to FG Nups increases molecular crowding in the NPC transport channel, it is unclear how this impacts FG Nup barrier function or the movement of other molecules, such as the Ran importer NTF2. Here, we use surface plasmon resonance to evaluate FG Nup conformation, binding equilibria, and interaction kinetics associated with the multivalent binding of NTF2 and karyopherinβ1 (Kapβ1) to Nsp1p molecular brushes. NTF2 and Kapβ1 show different long- and short-lived binding characteristics that emerge from varying degrees of molecular retention and FG repeat binding avidity within the Nsp1p brush. Physiological concentrations of NTF2 produce a collapse of Nsp1p brushes, whereas Kapβ1 binding generates brush extension. However, the presence of prebound Kapβ1 inhibits Nsp1p brush collapse during NTF2 binding, which is dominated by weak, short-lived interactions that derive from steric hindrance and diminished avidity with Nsp1p. This suggests that binding promiscuity confers kinetic advantages to NTF2 by expediting its facilitated diffusion and reinforces the proposal that Kapβ1 contributes to the integral barrier function of the NPC.
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13
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Sakin V, Richter SM, Hsiao HH, Urlaub H, Melchior F. Sumoylation of the GTPase Ran by the RanBP2 SUMO E3 Ligase Complex. J Biol Chem 2015; 290:23589-602. [PMID: 26251516 DOI: 10.1074/jbc.m115.660118] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/20/2022] Open
Abstract
The SUMO E3 ligase complex RanBP2/RanGAP1*SUMO1/Ubc9 localizes at cytoplasmic nuclear pore complex (NPC) filaments and is a docking site in nucleocytoplasmic transport. RanBP2 has four Ran binding domains (RBDs), two of which flank RanBP2's E3 ligase region. We thus wondered whether the small GTPase Ran is a target for RanBP2-dependent sumoylation. Indeed, Ran is sumoylated both by a reconstituted and the endogenous RanBP2 complex in semi-permeabilized cells. Generic inhibition of SUMO isopeptidases or depletion of the SUMO isopeptidase SENP1 enhances sumoylation of Ran in semi-permeabilized cells. As Ran is typically associated with transport receptors, we tested the influence of Crm1, Imp β, Transportin, and NTF2 on Ran sumoylation. Surprisingly, all inhibited Ran sumoylation. Mapping Ran sumoylation sites revealed that transport receptors may simply block access of the E2-conjugating enzyme Ubc9, however the acceptor lysines are perfectly accessible in Ran/NTF2 complexes. Isothermal titration calorimetry revealed that NTF2 prevents sumoylation by reducing RanGDP's affinity to RanBP2's RBDs to undetectable levels. Taken together, our findings indicate that RanGDP and not RanGTP is the physiological target for the RanBP2 SUMO E3 ligase complex. Recognition requires interaction of Ran with RanBP2's RBDs, which is prevented by the transport factor NTF2.
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Affiliation(s)
- Volkan Sakin
- From the Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ, ZMBH Alliance, Heidelberg, Germany
| | - Sebastian M Richter
- From the Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ, ZMBH Alliance, Heidelberg, Germany
| | - He-Hsuan Hsiao
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, and
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany, and Department of Clinical Chemistry, University Medical Center, 37075 Göttingen, Germany
| | - Frauke Melchior
- From the Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ, ZMBH Alliance, Heidelberg, Germany,
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Jiang L, Wu J, Fan S, Li W, Dong L, Cheng Q, Xu P, Zhang S. Isolation and Characterization of a Novel Pathogenesis-Related Protein Gene (GmPRP) with Induced Expression in Soybean (Glycine max) during Infection with Phytophthora sojae. PLoS One 2015; 10:e0129932. [PMID: 26114301 PMCID: PMC4482714 DOI: 10.1371/journal.pone.0129932] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/14/2015] [Indexed: 01/08/2023] Open
Abstract
Pathogenesis-related proteins (PR proteins) play crucial roles in the plant defense system. A novel PRP gene was isolated from highly resistant soybean infected with Phytophthora sojae (P. sojae) and was named GmPRP (GenBank accession number: KM506762). The amino acid sequences of GmPRP showed identities of 74%, 73%, 72% and 69% with PRP proteins from Vitis vinifera, Populus trichocarpa, Citrus sinensis and Theobroma cacao, respectively. Quantitative real-time reverse transcription PCR (qRT-PCR) data showed that the expression of GmPRP was highest in roots, followed by the stems and leaves. GmPRP expression was upregulated in soybean leaves infected with P. sojae. Similarly, GmPRP expression also responded to defense/stress signaling molecules, including salicylic acid (SA), ethylene (ET), abscisic acid (ABA) and jasmonic acid (JA). GmPRP was localized in the cell plasma membrane and cytoplasm. Recombinant GmPRP protein exhibited ribonuclease activity and significant inhibition of hyphal growth of P. sojae 1 in vitro. Overexpression of the GmPRP gene in T2 transgenic tobacco and T2 soybean plants resulted in enhanced resistance to Phytophthora nicotianae (P. nicotianae) and P. sojae race 1, respectively. These results indicated that the GmPRP protein played an important role in the defense of soybean against P. sojae infection.
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Affiliation(s)
- Liangyu Jiang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People’s Republic of China
| | - Junjiang Wu
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Collaborative Innovation Center of Grain Production Capacity Improvement in Heilongjiang Province, Harbin, 150086, Heilongjiang, People’s Republic of China
| | - Sujie Fan
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People’s Republic of China
| | - Wenbin Li
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People’s Republic of China
| | - Lidong Dong
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People’s Republic of China
| | - Qun Cheng
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People’s Republic of China
| | - Pengfei Xu
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People’s Republic of China
| | - Shuzhen Zhang
- Soybean Research Institute, Key Laboratory of Soybean Biology of Chinese Education Ministry, Northeast Agricultural University, Harbin, 150030, Heilongjiang, People’s Republic of China
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15
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Disruption of the ran system by cysteine oxidation of the nucleotide exchange factor RCC1. Mol Cell Biol 2014; 35:566-81. [PMID: 25452301 DOI: 10.1128/mcb.01133-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transport regulation by the Ran GTPase requires its nuclear localization and GTP loading by the chromatin-associated exchange factor RCC1. These reactions generate Ran protein and Ran nucleotide gradients between the nucleus and the cytoplasm. Cellular stress disrupts the Ran gradients, but the specific mechanisms underlying this disruption have not been elucidated. We used biochemical approaches to determine how oxidative stress disrupts the Ran system. RCC1 exchange activity was reduced by diamide-induced oxidative stress and restored with dithiothreitol. Using mass spectrometry, we found that multiple solvent-exposed cysteines in RCC1 are oxidized in cells treated with diamide. The cysteines oxidized in RCC1 included Cys93, which is solvent exposed and unique because it becomes buried upon contact with Ran. A Cys93Ser substitution dramatically reduced exchange activity through an effect on RCC1 binding to RanGDP. Diamide treatment reduced the size of the mobile fraction of RCC1-green fluorescent protein in cells and inhibited nuclear import in digitonin-permeabilized cell assays. The Ran protein gradient was also disrupted by UV-induced stress but without affecting RCC1 exchange activity. Our data suggest that stress can disrupt the Ran gradients through RCC1-dependent and RCC1-independent mechanisms, possibly dependent on the particular stress condition.
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16
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Tamura K, Hara-Nishimura I. The molecular architecture of the plant nuclear pore complex. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:823-32. [PMID: 22987840 DOI: 10.1093/jxb/ers258] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The nucleus contains the cell's genetic material, which directs cellular activity via gene regulation. The physical barrier of the nuclear envelope needs to be permeable to a variety of macromolecules and signals. The most prominent gateways for the transport of macromolecules are the nuclear pore complexes (NPCs). The NPC is the largest multiprotein complex in the cell, and is composed of multiple copies of ~30 different proteins called nucleoporins. Although much progress has been made in dissecting the NPC structure in vertebrates and yeast, the molecular architecture and physiological function of nucleoporins in plants remain poorly understood. In this review, we summarize the current knowledge regarding the plant NPC proteome and address structural and functional aspects of plant nucleoporins, which support the fundamental cellular machinery.
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Affiliation(s)
- Kentaro Tamura
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, Japan
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17
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Lin CY, Chen YC, Lo YS, Yang JM. Inferring homologous protein-protein interactions through pair position specific scoring matrix. BMC Bioinformatics 2013; 14 Suppl 2:S11. [PMID: 23367879 PMCID: PMC3549806 DOI: 10.1186/1471-2105-14-s2-s11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background The protein-protein interaction (PPI) is one of the most important features to understand biological processes. For a PPI, the physical domain-domain interaction (DDI) plays the key role for biology functions. In the post-genomic era, to rapidly identify homologous PPIs for analyzing the contact residue pairs of their interfaces within DDIs on a genomic scale is essential to determine PPI networks and the PPI interface evolution across multiple species. Results In this study, we proposed "pair Position Specific Scoring Matrix (pairPSSM)" to identify homologous PPIs. The pairPSSM can successfully distinguish the true protein complexes from unreasonable protein pairs with about 90% accuracy. For the test set including 1,122 representative heterodimers and 2,708,746 non-interacting protein pairs, the mean average precision and mean false positive rate of pairPSSM were 0.42 and 0.31, respectively. Moreover, we applied pairPSSM to identify ~450,000 homologous PPIs with their interacting domains and residues in seven common organisms (e.g. Homo sapiens, Mus musculus, Saccharomyces cerevisiae and Escherichia coli). Conclusions Our pairPSSM is able to provide statistical significance of residue pairs using evolutionary profiles and a scoring system for inferring homologous PPIs. According to our best knowledge, the pairPSSM is the first method for searching homologous PPIs across multiple species using pair position specific scoring matrix and a 3D dimer as the template to map interacting domain pairs of these PPIs. We believe that pairPSSM is able to provide valuable insights for the PPI evolution and networks across multiple species.
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Affiliation(s)
- Chun-Yu Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
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18
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Zhao Q, Meier I. Identification and characterization of the Arabidopsis FG-repeat nucleoporin Nup62. PLANT SIGNALING & BEHAVIOR 2011; 6:330-4. [PMID: 21673506 PMCID: PMC3142410 DOI: 10.4161/psb.6.3.13402] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 08/24/2010] [Indexed: 05/03/2023]
Abstract
Ran is a multifunctional small GTPase that is involved in nucleocytoplasmic transport, mitotic spindle assembly, and nuclear envelope reformation. Nuclear transport factor 2 (NTF2) facilitates nuclear import of Ran. It binds FxFG repeat-containing domains of the nucleoporins Nup62 (vertebrate) and Nsp1p (yeast). Here, we have identified Arabidopsis Nup62 through its sequence similarity to mammalian Nup62 and yeast Nsp1p. A GFP¬AtNup62 fusion protein is associated with the nuclear envelope in transgenic Arabidopsis plants and interacts in planta with AtNTF2a, one of the two Arabidopsis NTF2 homologs. Overexpression-based co-suppression of AtNup62 leads to severely dwarfed, early-flowering plants, suggesting an important function for Nup62 in plants.
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Affiliation(s)
- Qiao Zhao
- Department of Plant Cellular and Molecular Biology Plant Bio Technology Center, The Ohio State University, Columbus, OH, USA
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19
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He HJ, Wang Q, Zheng WW, Wang JX, Song QS, Zhao XF. Function of nuclear transport factor 2 and Ran in the 20E signal transduction pathway in the cotton bollworm, Helicoverpa armigera. BMC Cell Biol 2010; 11:1. [PMID: 20044931 PMCID: PMC2830935 DOI: 10.1186/1471-2121-11-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2009] [Accepted: 01/02/2010] [Indexed: 01/02/2023] Open
Abstract
Background Nuclear transport factor 2 and small GTPase Ran participate in the nucleo-cytoplasm transport of macromolecules, but their function in the 20-hydroxyecdysone (20E) signal transduction pathway are not well known. Results A 703 bp encoding Ntf2 and a 1233 bp encoding Ran full-length cDNAs were cloned from Helicoverpa armigera, and named Ha-Ntf2 and Ha-Ran, respectively. Northern blot and immunoblotting revealed that Ha-Ntf2 had an obviously higher expression levels in the head-thorax and integument of the metamorphically committed larvae. In contrast, the expression of Ha-Ran did not show obvious variation at various developmental stages in four tissues by immunoblotting analysis, except in the midgut, which showed increased expression from 5th-36 h (molting) to 6th-48 h. Both expressions of Ha-Ntf2 and Ha-Ran could be upregulated by 20E in vitro. Immunohistochemistry revealed that Ha-Ntf2 and Ha-Ran were primarily localized in the nucleus of various tissues. Protein binding assay and co-immunoprecipitation indicated that Ha-Ntf2 and Ha-Ran can combine with each other in vitro and in vivo. Knock down of Ha-Ntf2 or Ha-Ran by RNAi resulted in the suppression of other 20E regulated genes including EcR-B1, USP1, E75B, BR-CZ2, HHR3 and Ha-eIF5c. In addition, the knockdown of Ha-Ntf2 resulted in Ha-Ran being prevented in the cytoplasm. The nuclear location of the ecdysone receptor b1 (EcR-B1) was also blocked after the knockdown of Ha-Ntf2 and Ha-Ran. Conclusion These evidences suggested that Ha-Ntf2 and Ha-Ran participated in the 20E signal transduction pathway by regulating the location of EcR-B1.
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Affiliation(s)
- Hong-Juan He
- School of Life Sciences, Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, Shandong University, Jinan 250100, Shandong, PR China
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20
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Kahms M, Lehrich P, Hüve J, Sanetra N, Peters R. Binding site distribution of nuclear transport receptors and transport complexes in single nuclear pore complexes. Traffic 2009; 10:1228-42. [PMID: 19548985 DOI: 10.1111/j.1600-0854.2009.00947.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Transport through the nuclear pore complex (NPC) involves a large channel and an abundance of binding sites for nuclear transport receptors (NTRs). However, the mechanistically important distribution of NTR-binding sites along the channel is vividly debated. In this study, we visualized binding site distributions directly by two complementary optical super-resolution methods, single-molecule microscopy and 4Pi microscopy. First, we analyzed the distribution of RanGDP because this important nuclear transport substrate has two types of binding sites at the NPC, direct and indirect, NTR-mediated sites. We found that the direct binding sites had a maximum at approximately -30 nm with regard to the NPC center, whereas the indirect transport-relevant binding sites peaked at approximately -10 nm. The 20 nm-shift could be only resolved by 4Pi microscopy because of a two to threefold improved localization precision as compared with single-molecule microscopy. Then we analyzed the distribution of the NTR Kapbeta1 and a Kapbeta1-based transport complex and found them to have also binding maxima at approximately -10 nm. These observations support transport models in which NTR binding sites are distributed all along the transport channel and argue against models in which the cytoplasmic entrance of the channel is surrounded by a large cloud of binding sites.
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Affiliation(s)
- Martin Kahms
- Institute of Medical Physics and Biophysics, and Center for Nanotechnology (CeNTech), University of Münster, 48149 Münster, Germany
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21
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Jovanovic-Talisman T, Tetenbaum-Novatt J, McKenney AS, Zilman A, Peters R, Rout MP, Chait BT. Artificial nanopores that mimic the transport selectivity of the nuclear pore complex. Nature 2008; 457:1023-7. [PMID: 19098896 DOI: 10.1038/nature07600] [Citation(s) in RCA: 217] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 10/29/2008] [Indexed: 11/09/2022]
Abstract
Nuclear pore complexes (NPCs) act as effective and robust gateways between the nucleus and the cytoplasm, selecting for the passage of particular macromolecules across the nuclear envelope. NPCs comprise an elaborate scaffold that defines a approximately 30 nm diameter passageway connecting the nucleus and the cytoplasm. This scaffold anchors proteins termed 'phenylalanine-glycine' (FG)-nucleoporins, the natively disordered domains of which line the passageway and extend into its lumen. Passive diffusion through this lined passageway is hindered in a size-dependent manner. However, transport factors and their cargo-bound complexes overcome this restriction by transient binding to the FG-nucleoporins. To test whether a simple passageway and a lining of transport-factor-binding FG-nucleoporins are sufficient for selective transport, we designed a functionalized membrane that incorporates just these two elements. Here we demonstrate that this membrane functions as a nanoselective filter, efficiently passing transport factors and transport-factor-cargo complexes that specifically bind FG-nucleoporins, while significantly inhibiting the passage of proteins that do not. This inhibition is greatly enhanced when transport factor is present. Determinants of selectivity include the passageway diameter, the length of the nanopore region coated with FG-nucleoporins, the binding strength to FG-nucleoporins, and the antagonistic effect of transport factors on the passage of proteins that do not specifically bind FG-nucleoporins. We show that this artificial system faithfully reproduces key features of trafficking through the NPC, including transport-factor-mediated cargo import.
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Affiliation(s)
- Tijana Jovanovic-Talisman
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
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Van Impe K, Hubert T, De Corte V, Vanloo B, Boucherie C, Vandekerckhove J, Gettemans J. A new role for nuclear transport factor 2 and Ran: nuclear import of CapG. Traffic 2008; 9:695-707. [PMID: 18266911 DOI: 10.1111/j.1600-0854.2008.00720.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The small GTPase Ran plays a central role in nucleocytoplasmic transport. Nuclear transport of Ran itself depends on nuclear transport factor 2 (NTF2). Here, we report that NTF2 and Ran control nuclear import of the filamentous actin capping protein CapG. In digitonin-permeabilized cells, neither GTPgammaS nor the GTP hydrolysis-deficient Ran mutant RanQ69L affect transit of CapG to the nucleus in the presence of cytosol. Obstruction of nucleoporins prevents nuclear transport of CapG, and we show that CapG binds to nucleoporin62. In addition, CapG interacts with NTF2, associates with Ran and is furthermore able to bind the NTF2-Ran complex. NTF2-Ran interaction is required for CapG nuclear import. This is corroborated by a NTF2 mutant with reduced affinity for Ran and a Ran mutant that does not bind NTF2, both of which prevent CapG import. Thus, a ubiquitously expressed protein shuttles to the nucleus through direct association with NTF2 and Ran. The role of NTF2 may therefore not be solely confined to sustaining the Ran gradient in cells.
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Affiliation(s)
- Katrien Van Impe
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium
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23
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Abstract
In eukaryotic cells, segregation of DNA replication and RNA biogenesis in the nucleus and protein synthesis in the cytoplasm poses the requirement of transporting thousands of macromolecules between the two cellular compartments. Transport between nucleus and cytoplasm is mediated by soluble receptors that recognize specific cargoes and carry them through the nuclear pore complex (NPC), the sole gateway between the two compartments at interphase. Nucleocytoplasmic transport is specific not only in terms of cargo recognition, but also in terms of directionality, with nuclear proteins imported into the nucleus and RNAs exported from it. How is directionality achieved? How can the receptors be both specific and versatile in recognizing a multitude of cargoes? And how can their interaction with NPCs allow fast translocation? We describe the molecular mechanisms underlying nucleocytoplasmic transport as they have been revealed by structural studies of the receptors and regulators in different steps of transport cycles.
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Affiliation(s)
- Atlanta Cook
- European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.
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24
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Süel KE, Cansizoglu AE, Chook YM. Atomic resolution structures in nuclear transport. Methods 2006; 39:342-55. [PMID: 16938467 PMCID: PMC3471385 DOI: 10.1016/j.ymeth.2006.06.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Accepted: 06/28/2006] [Indexed: 11/17/2022] Open
Abstract
There are currently at least 53 structures of components of nuclear transport in the Protein Databank. In addition to providing critical insights into molecular mechanisms of nuclear transport, these atomic resolution structures provide a large body of information that could guide biochemical and cell biological analyses involving nuclear transport proteins. This paper catalogs 53 crystal and NMR structures of nuclear transport proteins, with the emphasis on providing information useful for mutagenesis and overexpression of recombinant proteins.
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Affiliation(s)
| | | | - Yuh Min Chook
- Corresponding author. Fax: +1 214 645 6166. (Y.M. Chook)
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25
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Isgro TA, Schulten K. Association of nuclear pore FG-repeat domains to NTF2 import and export complexes. J Mol Biol 2006; 366:330-45. [PMID: 17161424 DOI: 10.1016/j.jmb.2006.11.048] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 11/08/2006] [Accepted: 11/14/2006] [Indexed: 01/12/2023]
Abstract
Transport into and out of the nucleus is regulated by the nuclear pore complex. Vital to this regulation are nuclear pore proteins with FG sequence repeats, which have been shown to be crucial for cell viability and which interact with nuclear transport receptors. Here we use molecular dynamics simulations to investigate the binding of FG-repeat peptides to the surface of NTF2, the Ran importer. The simulations, covering over 254 ns, agree with previous X-ray, mutational, NMR, and computational data in identifying four binding spots. They also serve to provide an all-atom view of binding at each spot, whereas FG-repeat binding has been only directly observed at a single spot. Furthermore, the simulations identify two novel binding spots in addition to the four others. All six binding spots broadly form a stripe across the surface of NTF2. The resulting regularity and proximity of binding spots on the surface may be necessary for identification of the transport receptor by the FG-repeats in the nuclear pore complex and for the successful transit of NTF2 through the pore.
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Affiliation(s)
- Timothy A Isgro
- Department of Physics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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26
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Zhao Q, Leung S, Corbett AH, Meier I. Identification and characterization of the Arabidopsis orthologs of nuclear transport factor 2, the nuclear import factor of ran. PLANT PHYSIOLOGY 2006; 140:869-78. [PMID: 16428596 PMCID: PMC1400580 DOI: 10.1104/pp.105.075499] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 01/09/2006] [Accepted: 01/09/2006] [Indexed: 05/06/2023]
Abstract
Ran is a multifunctional small GTPase that is involved in nucleocytoplasmic transport, mitotic spindle assembly, and nuclear envelope formation. Nuclear import of Ran relies on a small RanGDP-binding protein, Nuclear Transport Factor 2 (NTF2). Three proteins are expressed in Arabidopsis (Arabidopsis thaliana) that show significant sequence similarity to human and yeast (Saccharomyces cerevisiae) NTF2. Here, we demonstrate that two of them, AtNTF2a and AtNTF2b, can functionally replace the essential NTF2 gene in yeast. Consistent with this finding, both AtNTF2a and AtNTF2b interact with yeast and Arabidopsis Ran. The third NTF2-related protein, AtNTL, does not functionally replace NTF2 in yeast. Similar to yeast NTF2-green fluorescent protein (GFP), AtNTF2a-GFP and AtNTF2b-GFP accumulate at the nuclear rim. The AtNTF2a E38K and E91K mutants, which fail to bind Ran, are not functional in yeast, indicating conservation of the requirement for these key amino acids in plants and yeast. AtNTF2a overexpression, but not AtNTF2aE38K overexpression, blocks nuclear import of a plant transcription factor in Nicotiana benthamiana leaves, indicating that excess AtNTF2a disrupts nuclear import in a Ran-binding-dependent manner. On the basis of these results, we propose that AtNTF2a and AtNTF2b function in Ran import in Arabidopsis and that nuclear import of Ran is functionally conserved in plants.
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Affiliation(s)
- Qiao Zhao
- Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, Columbus, 43210, USA
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27
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Lévesque L, Bor YC, Matzat LH, Jin L, Berberoglu S, Rekosh D, Hammarskjöld ML, Paschal BM. Mutations in tap uncouple RNA export activity from translocation through the nuclear pore complex. Mol Biol Cell 2005; 17:931-43. [PMID: 16314397 PMCID: PMC1356601 DOI: 10.1091/mbc.e04-07-0634] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Interactions between transport receptors and phenylalanine-glycine (FG) repeats on nucleoporins drive the translocation of receptor-cargo complexes through nuclear pores. Tap, a transport receptor that mediates nuclear export of cellular mRNAs, contains a UBA-like and NTF2-like folds that can associate directly with FG repeats. In addition, two nuclear export sequences (NESs) within the NTF2-like region can also interact with nucleoporins. The Tap-RNA complex was shown to bind to three nucleoporins, Nup98, p62, and RanBP2, and these interactions were enhanced by Nxt1. Mutations in the Tap-UBA region abolished interactions with all three nucleoporins, whereas the effect of point mutations within the NTF2-like domain of Tap known to disrupt Nxt1 binding or nucleoporin binding were nucleoporin dependent. A mutation in any of these Tap domains was sufficient to reduce RNA export but was not sufficient to disrupt Tap interaction with the NPC in vivo or its nucleocytoplasmic shuttling. However, shuttling activity was reduced or abolished by combined mutations within the UBA and either the Nxt1-binding domain or NESs. These data suggest that Tap requires both the UBA- and NTF2-like domains to mediate the export of RNA cargo, but can move through the pores independently of these domains when free of RNA cargo.
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Affiliation(s)
- Lyne Lévesque
- Department of Cell and Developmental Biology, University of Illinois in Urbana-Champaign, Urbana, IL 61801, USA.
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28
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Cushman I, Bowman BR, Sowa ME, Lichtarge O, Quiocho FA, Moore MS. Computational and biochemical identification of a nuclear pore complex binding site on the nuclear transport carrier NTF2. J Mol Biol 2004; 344:303-10. [PMID: 15522285 DOI: 10.1016/j.jmb.2004.09.043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2004] [Revised: 09/18/2004] [Accepted: 09/20/2004] [Indexed: 10/26/2022]
Abstract
Nuclear transport carriers interact with proteins of the nuclear pore complex (NPC) to transport their cargo across the nuclear envelope. One such carrier is nuclear transport factor 2 (NTF2), whose import cargo is the small GTPase Ran. A domain highly homologous to the small NTF2 protein (14kDa) is also found in a number of additional proteins, which together make up the NTF2 domain containing superfamily of proteins. Using structural, computational and biochemical analysis we have identified a functional site that is present throughout this superfamily, and our results indicate that this site functions as an NPC binding site in NTF2. Previously we showed that a D23A mutant of NTF2 exhibits increased affinity for the NPC. The mechanism of this mutation, however, was unknown as this region of NTF2 had not been implicated in binding to NPC proteins. Here we show that the D23A mutation in NTF2 does not result in gross structural changes affecting other known NPC binding sites. Instead, the D23 residue is located in an evolutionarily important region in the NTF2 domain containing superfamily, that in NTF2, is involved in binding to the NPC.
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Affiliation(s)
- Ian Cushman
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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29
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Abstract
In optical single transporter recording, membranes are firmly attached to flat solid substrates containing small wells or test compartments (TC). Transport of fluorescent molecules through TC-spanning membrane patches is induced by solution change and recorded by confocal microscopy. Previously, track-etched membrane filters were used to create solid substrates containing populations of randomly distributed TCs. In this study the possibilities offered by orderly TC arrays as created by laser microdrilling were explored. A theoretical framework was developed taking the convolution of membrane transport, solution change, and diffusion into account. The optical properties of orderly TC arrays were studied and the kinetics of solution change measured. Export and import through the nuclear pore complex (NPC) was analyzed in isolated envelopes of Xenopus oocyte nuclei. In accordance with previous reports nuclear transport receptor NTF2, which binds directly to NPC proteins, was found to be translocated much faster than "inert" molecules of similar size. Unexpectedly, NXT1, a homolog of NTF2 reportedly unable to bind to NPC proteins directly, was translocated as fast as NTF2. Thus, microstructured TC arrays were shown to provide optical single transporter recording with a new basis.
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Affiliation(s)
- Nikolai I Kiskin
- Institut für Medizinische Physik und Biophysik, Westfälische Wilhelms-Universität, D-48149 Münster, Germany
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Yamada M, Mattaj IW, Yoneda Y. An ATP-dependent activity that releases RanGDP from NTF2. J Biol Chem 2004; 279:36228-34. [PMID: 15155737 DOI: 10.1074/jbc.m403101200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The small GTPase Ran functions in several critical processes in eukaryotic cells including nuclear transport, nuclear envelope formation, and spindle formation. A RanGDP-binding protein, NTF2, facilitates translocation of RanGDP through the nuclear pore complex and also acts to stabilize RanGDP against nucleotide exchange. Here, we identify a novel activity that stimulates release of GDP from Ran in the presence of NTF2. Hydrolyzable ATP enhances the GDP dissociation activity, and this enhancement is inhibited by nonhydrolyzable ATP analogues. In contrast, neither hydrolyzable ATP nor nonhydrolyzable ATP analogues affect GDP dissociation from Ran catalyzed by recombinant RCC1 or inhibition of GDP dissociation from Ran by recombinant NTF2. The ATP-dependent RanGDP dissociation activity therefore has the properties of a RanGDP dissociation inhibitor (GDI) displacement factor (RanGDF) where the GDI is NTF2. A protein phosphatase inhibitor mixture stimulates the RanGDF activity, suggesting the activity is regulated by phosphorylation. We propose that the ATP-dependent NTF2 releasing factor may have a role in the RanGDP/GTP cycle.
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Affiliation(s)
- Masami Yamada
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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31
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Morrison J, Yang JC, Stewart M, Neuhaus D. Solution NMR Study of the Interaction Between NTF2 and Nucleoporin FxFG Repeats. J Mol Biol 2003; 333:587-603. [PMID: 14556747 DOI: 10.1016/j.jmb.2003.08.050] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Interactions with nucleoporins containing FxFG repeat cores are crucial for the nuclear import of RanGDP mediated by nuclear transport factor 2 (NTF2). We describe here a solution NMR-based study that identifies primary and secondary FxFG-binding sites on NTF2 and accounts for a range of observations on the rate of NTF2 nuclear trafficking. We used three complementary NMR methods, namely amide group chemical shift titrations, NOE and cross-saturation measurements, to show that the major FxFG-binding site on the dimeric rat NTF2 (rNTF2) molecule is centred on Trp7 and is formed by residues from both NTF2 chains. A secondary FxFG-binding site is located at the rNTF2 hydrophobic cavity and these two sites, together with a surface hydrophobic cluster centred on Trp112, merge into an elongated hydrophobic stripe on the rNTF2 surface. The primary site centred on Trp7 is lost in the rNTF2-W7A mutant that has been shown to bind FxFG nucleoporins with greatly reduced affinity, whereas the secondary site at the rNTF2 hydrophobic cavity is retained. The interface between NTF2 and FxFG nucleoporins detected by NMR is more extensive than that detected by X-ray crystallography, and the presence of a secondary site at the NTF2 hydrophobic cavity accounts for the unexpectedly rapid nuclear import of rNTF2-W7R recently observed by others. The structure of the binding interfaces on these transport factors provides a rationale for the specificity of their interactions with nucleoporins that, combined with their weak binding constants, facilitates rapid translocation through NPCs during nuclear trafficking.
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Affiliation(s)
- Jonathan Morrison
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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32
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Bayliss R, Littlewood T, Strawn LA, Wente SR, Stewart M. GLFG and FxFG nucleoporins bind to overlapping sites on importin-beta. J Biol Chem 2002; 277:50597-606. [PMID: 12372823 DOI: 10.1074/jbc.m209037200] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interaction between nuclear pore proteins (nucleoporins) and transport factors is crucial for the translocation of macromolecules through nuclear pores. Many nucleoporins contain FG sequence repeats, and previous studies have demonstrated interactions between repeats containing FxFG or GLFG cores and transport factors. The crystal structure of residues 1-442 of importin-beta bound to a GLFG peptide indicates that this repeat core binds to the same primary site as FxFG cores. Importin-beta-I178D shows reduced binding to both FxFG and GLFG repeats, consistent with both binding to an overlapping site in the hydrophobic groove between the A-helices of HEAT repeats 5 and 6. Moreover, FxFG repeats can displace importin-beta or its S. cerevisiae homologue, Kap95, bound to GLFG repeats. Addition of soluble GLFG repeats decreases the rate of nuclear protein import in digitonin-permeabilized HeLa cells, indicating that this interaction has a role in the translocation of carrier-cargo complexes through nuclear pores. The binding of GLFG and FxFG repeats to overlapping sites on importin-beta indicates that functional differences between different repeats probably arise from differences in their spatial organization.
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Affiliation(s)
- Richard Bayliss
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
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33
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Feldherr C, Akin D, Littlewood T, Stewart M. The molecular mechanism of translocation through the nuclear pore complex is highly conserved. J Cell Sci 2002; 115:2997-3005. [PMID: 12082159 DOI: 10.1242/jcs.115.14.2997] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this report we investigated the activity of vertebrate nuclear transport factors in a primitive organism, Amoeba proteus, to better understand evolutionary changes in the transport mechanisms of organisms expected to have different requirements for nucleocytoplasmic exchange. It was initially determined that FxFG-containing nucleoporins and Ran, both of which are essential for nuclear import in vertebrates, as well as yeast, are also present and functional in amoebae. This suggests that there are fundamental similarities in the transport process; however, there are also significant differences. Transport substrates containing either the hnRNP A1 M9 shuttling signal (a GST/GFP/M9 fusion protein) or the classical bipartite NLS (colloidal gold coated with BSA-bipartite NLS conjugates), both of which are effectively transported in vertebrate cells, are excluded from the nucleus when microinjected into amoebae. However, when these substrates are injected along with transportin or importin α/β, respectively, the vertebrate receptors for these signals, they readily accumulate in the nucleoplasm. These results indicate that although the molecular recognition of substrates is not well conserved between vertebrates and amoebae, vertebrate transport receptors are functional in A. proteus, showing that the translocation machinery is highly conserved. Since selected nuclear import pathways can be investigated in the absence of competing endogenous transport, A. proteus might provide a useful in vivo system for investigating specific molecular interactions involved in trafficking.
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Affiliation(s)
- Carl Feldherr
- Department of Anatomy and Cell Biology, University of Florida, College of Medicine, Gainesville 32610, USA.
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34
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Bayliss R, Leung SW, Baker RP, Quimby B, Corbett AH, Stewart M. Structural basis for the interaction between NTF2 and nucleoporin FxFG repeats. EMBO J 2002; 21:2843-53. [PMID: 12065398 PMCID: PMC126060 DOI: 10.1093/emboj/cdf305] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Interactions with nucleoporins containing FxFG-repeat cores are crucial for the nuclear import of RanGDP mediated by nuclear transport factor 2 (NTF2). We describe here the 1.9 A resolution crystal structure of yeast NTF2-N77Y bound to a FxFG-nucleoporin core, which provides a basis for understanding this interaction and its role in nuclear trafficking. The two identical FxFG binding sites on the dimeric molecule are formed by residues from each chain of NTF2. Engineered mutants at the interaction interface reduce the binding of NTF2 to nuclear pores and cause reduced growth rates and Ran mislocalization when substituted for the wild-type protein in yeast. Comparison with the crystal structure of FG-nucleoporin cores bound to importin-beta and TAP/p15 identified a number of common features of their binding sites. The structure of the binding interfaces on these transport factors provides a rationale for the specificity of their interactions with nucleoporins that, combined with their weak binding constants, facilitates rapid translocation through NPCs during nuclear trafficking.
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Affiliation(s)
- Richard Bayliss
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK and
Department of Biochemistry, Emory University School of Medicine, Rollins Research Center, Atlanta, GA 30322-3050, USA Present address: EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany Present address: Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, MD 20892-5431, USA Corresponding author e-mail:
| | - Sara W. Leung
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK and
Department of Biochemistry, Emory University School of Medicine, Rollins Research Center, Atlanta, GA 30322-3050, USA Present address: EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany Present address: Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, MD 20892-5431, USA Corresponding author e-mail:
| | | | - B.Booth Quimby
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK and
Department of Biochemistry, Emory University School of Medicine, Rollins Research Center, Atlanta, GA 30322-3050, USA Present address: EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany Present address: Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, MD 20892-5431, USA Corresponding author e-mail:
| | - Anita H. Corbett
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK and
Department of Biochemistry, Emory University School of Medicine, Rollins Research Center, Atlanta, GA 30322-3050, USA Present address: EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany Present address: Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, MD 20892-5431, USA Corresponding author e-mail:
| | - Murray Stewart
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK and
Department of Biochemistry, Emory University School of Medicine, Rollins Research Center, Atlanta, GA 30322-3050, USA Present address: EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany Present address: Laboratory of Gene Regulation and Development, NICHD, National Institutes of Health, Bethesda, MD 20892-5431, USA Corresponding author e-mail:
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35
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Affiliation(s)
- F Ralf Bischoff
- Division for Molecular Biology of Mitosis, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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36
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Chaillan-Huntington C, Butler PJ, Huntington JA, Akin D, Feldherr C, Stewart M. NTF2 monomer-dimer equilibrium. J Mol Biol 2001; 314:465-77. [PMID: 11846560 DOI: 10.1006/jmbi.2001.5136] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nuclear transport factor 2 (NTF2) mediates nuclear import of RanGDP, a central component of many nuclear trafficking pathways. NTF2 is a homodimer and each chain has independent binding sites for RanGDP and nuclear pore proteins (nucleoporins) that contain FxFG sequence repeats. We show here that the monomer-dimer dissociation constant for NTF2 obtained by sedimentation equilibrium ultracentrifugation is in the micromolar range, indicating that a substantial proportion of cellular NTF2 may be monomeric. To investigate the functional significance of NTF2 dimerization, we engineered a series of point mutations at the dimerization interface and one of these (M118E) remained monomeric below concentrations of 150 microM. CD spectra and X-ray crystallography showed that M118E-NTF2 preserved the wild-type NTF2 fold, although its thermal stability was 20 deg. C lower than that of the wild-type. M118E-NTF2 bound both RanGDP and FxFG nucleoporins less strongly, suggesting that dissociation of the NTF2 dimer could facilitate RanGDP release and thus nucleotide exchange after it had been transported into the nucleus. Moreover, colloidal gold coated with M118E-NTF2 showed reduced binding to Xenopus oocyte nuclear pores. Overall, our results indicate that dimer formation is important for NTF2 function and give insight into the formation of heterodimers by mRNA export factors such as TAP1 and NXT1 that contain NTF2-homology domains.
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37
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Quimby BB, Leung SW, Bayliss R, Harreman MT, Thirumala G, Stewart M, Corbett AH. Functional analysis of the hydrophobic patch on nuclear transport factor 2 involved in interactions with the nuclear pore in vivo. J Biol Chem 2001; 276:38820-9. [PMID: 11489893 DOI: 10.1074/jbc.m105054200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nuclear transport factor 2 (NTF2) is a small homodimeric protein that interacts simultaneously with both RanGDP and FxFG nucleoporins. The interaction between NTF2 and Ran is essential for the import of Ran into the nucleus. Here we use mutational analysis to dissect the in vivo role of the interaction between NTF2 and nucleoporins. We identify a series of surface residues that form a hydrophobic patch on NTF2, which when mutated disrupt the NTF2-nucleoporin interaction. Analysis of these mutants in vivo demonstrates that the strength of this interaction can be significantly reduced without affecting cell viability. However, cells cease to be viable if the interaction between NTF2 and nucleoporins is abolished completely, indicating that this interaction is essential for the function of NTF2 in vivo. In addition, we have isolated a dominant negative mutant of NTF2, N77Y, which has increased affinity for nucleoporins. Overexpression of the N77Y protein blocks nuclear protein import and concentrates Ran at the nuclear rim. These data support a mechanism in which NTF2 interacts transiently with FxFG nucleoporins to translocate through the pore and import RanGDP into the nucleus.
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Affiliation(s)
- B B Quimby
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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38
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Abstract
The Ran GTPase plays a key role in nucleocytoplasmic transport. In its GTP-bound form, it directly interacts with members of the importin β family of nuclear transport receptors and modulates their association with cargo. Work in cell-free higher-eukaryote systems has demonstrated additional roles for Ran in spindle and nuclear envelope formation during mitosis. However, until recently, no Ran-target proteins in these cellular processes were known. Several groups have now identified importin β as one important target of Ran during mitotic spindle formation. This finding suggests that Ran uses the same effectors to regulate different cellular processes.
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Affiliation(s)
- M Künzler
- Biochemie-Zentrum Heidelberg (BZH), Im Neuenheimer Feld 328, 4. OG, Heidelberg 69120, Germany.
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39
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Marfatia KA, Harreman MT, Fanara P, Vertino PM, Corbett AH. Identification and characterization of the human MOG1 gene. Gene 2001; 266:45-56. [PMID: 11290418 DOI: 10.1016/s0378-1119(01)00364-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Many of the proteins that mediate transport into and out of the nucleus have been structurally and functionally conserved throughout evolution. Here we describe the sequence and characterization of the human MOG1 gene. The MOG1 gene was originally identified in Saccharomyces cerevisiae as a multi-copy suppressor of conditional alleles of the yeast nuclear transport factor, GSP1 (scRan) (Oki and Nishimoto (1998) Proc. Natl. Acad. Sci. USA 95, 15388-15393). A search of the expressed sequence tag database identified a putative human protein that is 29% identical and 47% similar to the yeast protein. Our experiments demonstrate that the human MOG1 message is expressed in a variety of tissue samples. Several experiments indicate that the human MOG1 protein binds to both yeast and human Ran suggesting functional conservation between the yeast and human MOG1 proteins. Furthermore, hMOG1a, like scMOG1, is localized throughout the cell but is concentrated within the nucleus. Consistent with these findings, hMOG1a can partially complement the growth defect present in yeast MOG1 deletion cells. Taken together, our findings suggest that MOG1 is an evolutionarily conserved Ran binding protein that could play a role in regulating nuclear protein trafficking.
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Affiliation(s)
- K A Marfatia
- Department of Biochemistry, Emory University School of Medicine , Atlanta, GA 30322, USA
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40
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Black BE, Holaska JM, Lévesque L, Ossareh-Nazari B, Gwizdek C, Dargemont C, Paschal BM. NXT1 is necessary for the terminal step of Crm1-mediated nuclear export. J Cell Biol 2001; 152:141-55. [PMID: 11149927 PMCID: PMC2193657 DOI: 10.1083/jcb.152.1.141] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2000] [Accepted: 11/14/2000] [Indexed: 11/22/2022] Open
Abstract
Soluble factors are required to mediate nuclear export of protein and RNA through the nuclear pore complex (NPC). These soluble factors include receptors that bind directly to the transport substrate and regulators that determine the assembly state of receptor-substrate complexes. We recently reported the identification of NXT1, an NTF2-related export factor that stimulates nuclear protein export in permeabilized cells and undergoes nucleocytoplasmic shuttling in vivo (Black, B.E., L. Lévesque, J.M. Holaska, T.C. Wood, and B.M. Paschal. 1999. Mol. Cell. Biol. 19:8616-8624). Here, we describe the molecular characterization of NXT1 in the context of the Crm1-dependent export pathway. We find that NXT1 binds directly to Crm1, and that the interaction is sensitive to the presence of Ran-GTP. Moreover, mutations in NXT1 that reduce binding to Crm1 inhibit the activity of NXT1 in nuclear export assays. We show that recombinant Crm1 and Ran are sufficient to reconstitute nuclear translocation of a Rev reporter protein from the nucleolus to an antibody accessible site on the cytoplasmic side of the NPC. Further progress on the export pathway, including the terminal step of Crm1 and Rev reporter protein release, requires NXT1. We propose that NXT1 engages with the export complex in the nucleoplasm, and that it facilitates delivery of the export complex to a site on the cytoplasmic side of NPC where the receptor and substrate are released into the cytoplasm.
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Affiliation(s)
- Ben E. Black
- Center for Cell Signaling, Department of Biochemistry and Molecular Genetics, Cell and Molecular Biology Program, University of Virginia, Charlottesville, Virginia 22908
| | - James M. Holaska
- Center for Cell Signaling, Department of Biochemistry and Molecular Genetics, Cell and Molecular Biology Program, University of Virginia, Charlottesville, Virginia 22908
| | - Lyne Lévesque
- Center for Cell Signaling, Department of Biochemistry and Molecular Genetics, Cell and Molecular Biology Program, University of Virginia, Charlottesville, Virginia 22908
| | - Batool Ossareh-Nazari
- Nucleocytoplasmic Transport Group, Institut Jacques Monod, UMR 7592, 75251 Paris Cedex 05, France
| | - Carol Gwizdek
- Nucleocytoplasmic Transport Group, Institut Jacques Monod, UMR 7592, 75251 Paris Cedex 05, France
| | - Catherine Dargemont
- Nucleocytoplasmic Transport Group, Institut Jacques Monod, UMR 7592, 75251 Paris Cedex 05, France
| | - Bryce M. Paschal
- Center for Cell Signaling, Department of Biochemistry and Molecular Genetics, Cell and Molecular Biology Program, University of Virginia, Charlottesville, Virginia 22908
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41
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Lane CM, Cushman I, Moore MS. Selective disruption of nuclear import by a functional mutant nuclear transport carrier. J Cell Biol 2000; 151:321-32. [PMID: 11038179 PMCID: PMC2192641 DOI: 10.1083/jcb.151.2.321] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
p10/NTF2 is a nuclear transport carrier that mediates the uptake of cytoplasmic RanGDP into the nucleus. We constructed a point mutant of p10, D23A, that exhibited unexpected behavior both in digitonin-permeabilized and microinjected mammalian cells. D23A p10 was markedly more efficient than wild-type (wt) p10 at supporting Ran import, but simultaneously acted as a dominant-negative inhibitor of classical nuclear localization sequence (cNLS)-mediated nuclear import supported by karyopherins (Kaps) alpha and beta1. Binding studies indicated that these two nuclear transport carriers of different classes, p10 and Kap-beta1, compete for identical and/or overlapping binding sites at the nuclear pore complex (NPC) and that D23A p10 has an increased affinity relative to wt p10 and Kap-beta1 for these shared binding sites. Because of this increased affinity, D23A p10 is able to import its own cargo (RanGDP) more efficiently than wt p10, but Kap-beta1 can no longer compete efficiently for shared NPC docking sites, thus the import of cNLS cargo is inhibited. The competition of different nuclear carriers for shared NPC docking sites observed here predicts a dynamic equilibrium between multiple nuclear transport pathways inside the cell that could be easily shifted by a transient modification of one of the carriers.
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Affiliation(s)
- C M Lane
- Baylor College of Medicine, Department of Molecular and Cellular Biology, Houston, Texas 77030, USA
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42
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Sweitzer TD, Love DC, Hanover JA. Regulation of nuclear import and export. CURRENT TOPICS IN CELLULAR REGULATION 2000; 36:77-94. [PMID: 10842747 DOI: 10.1016/s0070-2137(01)80003-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- T D Sweitzer
- Laboratory of Cell Biochemistry and Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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43
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Bayliss R, Kent HM, Corbett AH, Stewart M. Crystallization and initial X-ray diffraction characterization of complexes of FxFG nucleoporin repeats with nuclear transport factors. J Struct Biol 2000; 131:240-7. [PMID: 11052897 DOI: 10.1006/jsbi.2000.4297] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
NTF2 and importin-beta are transport factors that mediate nuclear protein import and which interact with nuclear pore proteins (nucleoporins) during translocation from the cytoplasm to the nucleus through nuclear pore complexes. We employed a native gel electrophoresis method to assess the interaction of nucleoporin constructs that contain FxFG sequence repeats with NTF2 and truncation mutants of importin-beta to determine suitable fragments for crystallization. Based on these data, we obtained crystals of complexes between yeast NTF2 and a construct containing five FxFG nucleoporin repeats from the yeast nucleoporin Nsp1p and between a construct containing residues 1-442 of human importin-beta and the same nucleoporin construct. The yeast NTF2-nucleoporin crystals have trigonal symmetry and diffract past 2.8 A resolution using synchrotron radiation, whereas the importin-beta-nucleoporin complex crystals have P2(1)2(1)2 orthorhombic symmetry and diffract past 3.2 A resolution.
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Affiliation(s)
- R Bayliss
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
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44
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Quimby BB, Wilson CA, Corbett AH. The interaction between Ran and NTF2 is required for cell cycle progression. Mol Biol Cell 2000; 11:2617-29. [PMID: 10930458 PMCID: PMC14944 DOI: 10.1091/mbc.11.8.2617] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The small GTPase Ran is required for the trafficking of macromolecules into and out of the nucleus. Ran also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, Ran is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. Nuclear transport factor 2 (NTF2) has been shown to import RanGDP into the nucleus. Here, we examine the in vivo role of NTF2 in Ran import and the effect that disruption of Ran imported into the nucleus has on the cell cycle. A temperature-sensitive (ts) mutant of Saccharomyces cerevisiae NTF2 that does not bind to Ran is unable to import Ran into the nucleus at the nonpermissive temperature. Moreover, when Ran is inefficiently imported into the nucleus, cells arrest in G(2) in a MAD2 checkpoint-dependent manner. These findings demonstrate that NTF2 is required to transport Ran into the nucleus in vivo. Furthermore, we present data that suggest that depletion of nuclear Ran triggers a spindle-assembly checkpoint-dependent cell cycle arrest.
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Affiliation(s)
- B B Quimby
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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45
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Stewart M. Insights into the molecular mechanism of nuclear trafficking using nuclear transport factor 2 (NTF2). Cell Struct Funct 2000; 25:217-25. [PMID: 11129791 DOI: 10.1247/csf.25.217] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP. The simplicity and specialization of this system, combined with the availability of crystal structures of NTF2, RanGDP and their complex, has facilitated the investigation of the molecular mechanism of its trafficking. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins. Mutants engineered on the basis of structural information together with determination of binding constants have been used to dissect the roles of these interactions in transport. Thus, NTF2 binds to RanGDP sufficiently strongly for the complex to remain intact during transport through NPCs, but the interaction between NTF2 and FxFG nucleoporins is much more transient, which would enable NTF2 to move through the NPC by hopping from one repeat to another. An analogous nucleoporin hopping mechanism may also be used by carrier molecules of the importin-beta family to move through NPCs.
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Affiliation(s)
- M Stewart
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England.
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Bayliss R, Littlewood T, Stewart M. Structural basis for the interaction between FxFG nucleoporin repeats and importin-beta in nuclear trafficking. Cell 2000; 102:99-108. [PMID: 10929717 DOI: 10.1016/s0092-8674(00)00014-3] [Citation(s) in RCA: 367] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We describe the crystal structure of a complex between importin-beta residues 1-442 (Ib442) and five FxFG nucleoporin repeats from Nsp1p. Nucleoporin FxFG cores bind on the convex face of Ib442 to a primary site between the A helices of HEAT repeats 5 and 6, and to a secondary site between HEAT repeats 6 and 7. Mutations at importin-beta Ile178 in the primary FxFG binding site reduce both binding and nuclear protein import, providing direct evidence for the functional significance of the importin-beta-FxFG interaction. The FxFG binding sites on importin-beta do not overlap with the RanGTP binding site. Instead, RanGTP may release importin-beta from FxFG nucleoporins by generating a conformational change that alters the structure of the FxFG binding site.
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Affiliation(s)
- R Bayliss
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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Bayliss R, Corbett AH, Stewart M. The molecular mechanism of transport of macromolecules through nuclear pore complexes. Traffic 2000; 1:448-56. [PMID: 11208130 DOI: 10.1034/j.1600-0854.2000.010602.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Trafficking of macromolecules between nuclear and cytoplasmic compartments takes place through the nuclear pore complexes (NPCs) of the nuclear envelope. Nuclear trafficking involves a complex series of interactions between cargo, soluble transport factors (carriers) and nuclear pore proteins (nucleoporins) that are orchestrated by the Ras-family GTPase Ran. The primary role of Ran is probably to establish directionality and to sort molecules to be transported by controlling the interaction between carriers and cargoes, so that they bind in one compartment but dissociate in the other. Translocation of carriers and cargo-carrier complexes through NPCs requires interactions between the carriers and nucleoporins that contain distinctive tandem sequence repeats based on cores rich in glycine and phenylalanine residues that are separated by hydrophilic linkers. Much recent work has focused on these interactions and, in particular, their specificity, regulation and function. Evidence is accumulating that carriers move through the NPC by distinct but overlapping routes using specific subsets of nucleoporins.
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Affiliation(s)
- R Bayliss
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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Stewart M, Baker RP. 1.9 A resolution crystal structure of the Saccharomyces cerevisiae Ran-binding protein Mog1p. J Mol Biol 2000; 299:213-23. [PMID: 10860733 DOI: 10.1006/jmbi.2000.3733] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 1.9 A resolution X-ray crystal structure of Ran-binding protein Mog1p shows that it has a unique fold based on a six-stranded antiparallel beta-sheet backed on both sides by an extensive alpha-helix. The topology of some elements of Mog1p secondary structure resemble a portion of nuclear transport factor 2 (NTF2), but the hydrophobic cavity and surrounding negatively charged residues that are important in the NTF2-RanGDP interaction are not conserved in Mog1p. In addition to binding RanGTP, Mog1p forms a 1:1 complex with RanGDP and so binds Ran independent of its nucleotide state. Mog1p and NTF2 compete for binding to RanGDP indicating that their binding sites on RanGDP are sufficiently close to prevent both proteins binding simultaneously. Although there may be some overlap between the Mog1p and NTF2 binding sites on RanGDP, these sites are not identical. Sequence analysis of Mog1p homologues from Schizosaccharomyces pombe, human, and Caenorhabditis elegans in the context of the Mog1p crystal structure indicates the presence of a cluster of highly conserved surface residues consistent with an interaction site for Ran.
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Affiliation(s)
- M Stewart
- MRC Laboratory of Molecular Biology, Cambridge, England.
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Chaillan-Huntington C, Braslavsky CV, Kuhlmann J, Stewart M. Dissecting the interactions between NTF2, RanGDP, and the nucleoporin XFXFG repeats. J Biol Chem 2000; 275:5874-9. [PMID: 10681579 DOI: 10.1074/jbc.275.8.5874] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have used a range of complementary biochemical and biophysical methods to investigate the interactions between nuclear transport factor 2 (NTF2), the Ras family GTPase Ran, and XFXFG nucleoporin repeats that are crucial for nuclear trafficking. Microcalorimetry, microtiter plate binding, and fluorescence quenching in solution are all consistent with the binding constant for the NTF2-RanGDP interaction being in the 100 nM range, whereas the interaction between NTF2 and XFXFG repeat-containing nucleoporins such as Nsp1p is in the 1 microM range. Although the accumulation of NTF2 at the nuclear envelope is enhanced by RanGDP, we show that Ran binding does not alter the affinity of NTF2 for nucleoporins nor does the binding of nucleoporins alter the affinity of NTF2 for RanGDP. These results indicate that, instead, Ran increases the binding of NTF2 to nucleoporins by another mechanism, most probably by Ran itself binding to nucleoporins and NTF2 binding to this nuclear pore-associated Ran.
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Affiliation(s)
- C Chaillan-Huntington
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
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Saphire AC, Guan T, Schirmer EC, Nemerow GR, Gerace L. Nuclear import of adenovirus DNA in vitro involves the nuclear protein import pathway and hsc70. J Biol Chem 2000; 275:4298-304. [PMID: 10660598 DOI: 10.1074/jbc.275.6.4298] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adenovirus, a respiratory virus with a double-stranded DNA genome, replicates in the nuclei of mammalian cells. We have developed a cytosol-dependent in vitro assay utilizing adenovirus nucleocapsids to examine the requirements for adenovirus docking to the nuclear pore complex and for DNA import into the nucleus. Our assay reveals that adenovirus DNA import is blocked by a competitive excess of classical protein nuclear localization sequences and other inhibitors of nuclear protein import and indicates that this process is dependent on hsc70. Previous work revealed that the hexon (coat) protein of adenovirus is the only major protein on the surface of the adenovirus nucleocapsid that docks at the nuclear pore complex. This, together with our finding that in vitro nuclear import of hexon is inhibited by an excess of classical nuclear localization sequences, suggests a role for the hexon protein in adenovirus DNA import. However, recombinant transport factors that are sufficient for hexon import in permeabilized cells do not support DNA import, indicating that there are other as yet unidentified factors required for this process.
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Affiliation(s)
- A C Saphire
- Departments of Cell and Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA
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