1
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Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell 2022; 185:361-378.e25. [PMID: 34982960 PMCID: PMC8928745 DOI: 10.1016/j.cell.2021.12.015] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/26/2021] [Accepted: 12/13/2021] [Indexed: 02/06/2023]
Abstract
Nuclear pore complexes (NPCs) mediate the nucleocytoplasmic transport of macromolecules. Here we provide a structure of the isolated yeast NPC in which the inner ring is resolved by cryo-EM at sub-nanometer resolution to show how flexible connectors tie together different structural and functional layers. These connectors may be targets for phosphorylation and regulated disassembly in cells with an open mitosis. Moreover, some nucleoporin pairs and transport factors have similar interaction motifs, which suggests an evolutionary and mechanistic link between assembly and transport. We provide evidence for three major NPC variants that may foreshadow functional specializations at the nuclear periphery. Cryo-electron tomography extended these studies, providing a model of the in situ NPC with a radially expanded inner ring. Our comprehensive model reveals features of the nuclear basket and central transporter, suggests a role for the lumenal Pom152 ring in restricting dilation, and highlights structural plasticity that may be required for transport.
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Affiliation(s)
- Christopher W Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.
| | - Digvijay Singh
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Christna Ouch
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, San Francisco, San Francisco, CA 94158, USA
| | - Ilona Nudelman
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | | | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Fei Fang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Junjie Wang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Daniel Salzberg
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Kangkang Song
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Chen Xu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sergey Suslov
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | | | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA.
| | - Elizabeth Villa
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA.
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Vuković LD, Chen P, Mishra S, White KH, Gigley JP, Levy DL. Nuclear Transport Factor 2 (NTF2) suppresses WM983B metastatic melanoma by modifying cell migration, metastasis, and gene expression. Sci Rep 2021; 11:23586. [PMID: 34880267 PMCID: PMC8654834 DOI: 10.1038/s41598-021-02803-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/23/2021] [Indexed: 12/19/2022] Open
Abstract
While changes in nuclear structure and organization are frequently observed in cancer cells, relatively little is known about how nuclear architecture impacts cancer progression and pathology. To begin to address this question, we studied Nuclear Transport Factor 2 (NTF2) because its levels decrease during melanoma progression. We show that increasing NTF2 expression in WM983B metastatic melanoma cells reduces cell proliferation and motility while increasing apoptosis. We also demonstrate that increasing NTF2 expression in these cells significantly inhibits metastasis and prolongs survival of mice. NTF2 levels affect the expression and nuclear positioning of a number of genes associated with cell proliferation and migration, and increasing NTF2 expression leads to changes in nuclear size, nuclear lamin A levels, and chromatin organization. Thus, ectopic expression of NTF2 in WM983B metastatic melanoma abrogates phenotypes associated with advanced stage cancer both in vitro and in vivo, concomitantly altering nuclear and chromatin structure and generating a gene expression profile with characteristics of primary melanoma. We propose that NTF2 is a melanoma tumor suppressor and could be a novel therapeutic target to improve health outcomes of melanoma patients.
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Affiliation(s)
- Lidija D Vuković
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY, 82071, USA
| | - Pan Chen
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY, 82071, USA
| | - Sampada Mishra
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY, 82071, USA
| | - Karen H White
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY, 82071, USA
| | - Jason P Gigley
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY, 82071, USA
| | - Daniel L Levy
- Department of Molecular Biology, University of Wyoming, 1000 E. University Avenue, Laramie, WY, 82071, USA.
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3
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Schuller AP, Wojtynek M, Mankus D, Tatli M, Kronenberg-Tenga R, Regmi SG, Dip PV, Lytton-Jean AKR, Brignole EJ, Dasso M, Weis K, Medalia O, Schwartz TU. The cellular environment shapes the nuclear pore complex architecture. Nature 2021; 598:667-671. [PMID: 34646014 PMCID: PMC8550940 DOI: 10.1038/s41586-021-03985-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/01/2021] [Indexed: 12/04/2022]
Abstract
Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE)1-3. These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel4-6. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture.
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Affiliation(s)
- Anthony P. Schuller
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Matthias Wojtynek
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland ,grid.5801.c0000 0001 2156 2780Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - David Mankus
- grid.116068.80000 0001 2341 2786Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Meltem Tatli
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Rafael Kronenberg-Tenga
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Saroj G. Regmi
- grid.94365.3d0000 0001 2297 5165Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD USA
| | - Phat V. Dip
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786MIT.nano, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Abigail K. R. Lytton-Jean
- grid.116068.80000 0001 2341 2786Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Edward J. Brignole
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA ,grid.116068.80000 0001 2341 2786MIT.nano, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Mary Dasso
- grid.94365.3d0000 0001 2297 5165Division of Molecular and Cellular Biology, National Institute of Child Health and Human Development, NIH, Bethesda, MD USA
| | - Karsten Weis
- grid.5801.c0000 0001 2156 2780Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ohad Medalia
- grid.7400.30000 0004 1937 0650Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Thomas U. Schwartz
- grid.116068.80000 0001 2341 2786Department of Biology, Massachusetts Institute of Technology, Cambridge, MA USA
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4
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Jevtić P, Mukherjee RN, Chen P, Levy DL. Altering the levels of nuclear import factors in early Xenopus laevis embryos affects later development. PLoS One 2019; 14:e0215740. [PMID: 31009515 PMCID: PMC6476522 DOI: 10.1371/journal.pone.0215740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/08/2019] [Indexed: 11/19/2022] Open
Abstract
More than just a container for DNA, the nuclear envelope carries out a wide variety of critical and highly regulated cellular functions. One of these functions is nuclear import, and in this study we investigate how altering the levels of nuclear transport factors impacts developmental progression and organismal size. During early Xenopus laevis embryogenesis, the timing of a key developmental event, the midblastula transition (MBT), is sensitive to nuclear import factor levels. How might altering nuclear import factors and MBT timing in the early embryo affect downstream development of the organism? We microinjected X. laevis two-cell embryos with mRNA to increase levels of importin α or NTF2, resulting in differential amounts of nuclear import factors in the two halves of the embryo. Compared to controls, these embryos exhibited delayed gastrulation, curved neural plates, and bent tadpoles with different sized eyes. Furthermore, embryos microinjected with NTF2 developed into smaller froglets compared to control microinjected embryos. We propose that altering nuclear import factors and nuclear size affects MBT timing, cell size, and cell number, subsequently disrupting later development. Thus, altering nuclear import factors early in development can affect function and size at the organismal level.
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Affiliation(s)
- Predrag Jevtić
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, United States of America
| | - Richik N. Mukherjee
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, United States of America
| | - Pan Chen
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, United States of America
| | - Daniel L. Levy
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming, United States of America
- * E-mail:
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5
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Preston CC, Storm EC, Leonard RJ, Faustino RS. Emerging roles for nucleoporins in reproductive cellular physiology 1. Can J Physiol Pharmacol 2018; 97:257-264. [PMID: 30388388 DOI: 10.1139/cjpp-2018-0436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Nucleoporins are a specialized subset of nuclear proteins that comprise the nuclear pore complex and regulate nucleocytoplasmic transport. Recent demonstrations of roles for individual nucleoporins in multiple paradigms of differentiation via mechanisms independent of nuclear trafficking represent conceptual advances in understanding the contributions of nucleoporins to cellular development. Among these, a functional role for nucleoporins in reproductive fitness and gametogenesis has been identified, supported by robust models and clinical studies that leverage the power of next generation sequencing technology to identify reproductive-disease-associated mutations in specific nucleoporins. Proper nucleoporin function manifests in different ways during oogenesis and spermatogenesis. However, nonhuman models of gametogenesis may not recapitulate human mechanisms, which may confound translational interpretation and relevance. To circumvent these limitations, identification of reproductive pathologies in patients, combined with next generation sequencing approaches and advanced in silico tools, offers a powerful approach to investigate the potential function of nucleoporins in human reproduction. Ultimately, elucidating the role of nucleoporins in reproductive biology will provide opportunities for predictive, diagnostic, and therapeutic strategies to address reproductive disorders.
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Affiliation(s)
- Claudia C Preston
- a Genetics and Genomics, Sanford Research, 2301 E. 60th Street N., Sioux Falls, SD 57104, USA
| | - Emily C Storm
- a Genetics and Genomics, Sanford Research, 2301 E. 60th Street N., Sioux Falls, SD 57104, USA
| | - Riley J Leonard
- a Genetics and Genomics, Sanford Research, 2301 E. 60th Street N., Sioux Falls, SD 57104, USA
| | - Randolph S Faustino
- a Genetics and Genomics, Sanford Research, 2301 E. 60th Street N., Sioux Falls, SD 57104, USA.,b Department of Pediatrics, Sanford School of Medicine of the University of South Dakota, 1400 W. 22nd Street, Sioux Falls, SD 57105, USA
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6
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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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7
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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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8
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Kodiha M, Crampton N, Shrivastava S, Umar R, Stochaj U. Traffic control at the nuclear pore. Nucleus 2014. [DOI: 10.4161/nucl.11444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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9
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Faustino RS, Maddaford TG, Pierce GN. Mitogen activated protein kinase at the nuclear pore complex. J Cell Mol Med 2011; 15:928-37. [PMID: 20497490 PMCID: PMC3922677 DOI: 10.1111/j.1582-4934.2010.01093.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 03/19/2010] [Indexed: 01/09/2023] Open
Abstract
Mitogen activated protein (MAP) kinases control eukaryotic proliferation, and import of kinases into the nucleus through the nuclear pore complex (NPC) can influence gene expression to affect cellular growth, cell viability and homeostatic function. The NPC is a critical regulatory checkpoint for nucleocytoplasmic traffic that regulates gene expression and cell growth, and MAP kinases may be physically associated with the NPC to modulate transport. In the present study, highly enriched NPC fractions were isolated and investigated for associated kinases and/or activity. Endogenous kinase activity was identified within the NPC fraction, which phosphorylated a 30 kD nuclear pore protein. Phosphomodification of this nucleoporin, here termed Nup30, was inhibited by apigenin and PD-98059, two MAP kinase antagonists as well as with SB-202190, a pharmacological blocker of p38. Furthermore, high throughput profiling of enriched NPCs revealed constitutive presence of all members of the MAP kinase family, extracellular regulated kinases (ERK), p38 and Jun N-terminal kinase. The NPC thus contains a spectrum of associated MAP kinases that suggests an intimate role for ERK and p38 in regulation of nuclear pore function.
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Affiliation(s)
- Randolph S Faustino
- Institute of Cardiovascular Sciences, St Boniface Hospital Research Centre, and Department of Physiology, Faculty of Medicine, University of ManitobaWinnipeg, Canada
| | - Thane G Maddaford
- Institute of Cardiovascular Sciences, St Boniface Hospital Research Centre, and Department of Physiology, Faculty of Medicine, University of ManitobaWinnipeg, Canada
| | - Grant N Pierce
- Institute of Cardiovascular Sciences, St Boniface Hospital Research Centre, and Department of Physiology, Faculty of Medicine, University of ManitobaWinnipeg, Canada
- Faculty of Pharmacy, University of ManitobaWinnipeg, Canada
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10
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Mitchell JM, Mansfeld J, Capitanio J, Kutay U, Wozniak RW. Pom121 links two essential subcomplexes of the nuclear pore complex core to the membrane. ACTA ACUST UNITED AC 2010; 191:505-21. [PMID: 20974814 PMCID: PMC3003318 DOI: 10.1083/jcb.201007098] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pom121 anchors core structures of the NPC to the membrane through its binding to the β-propeller domains of Nup155 and Nup160. Nuclear pore complexes (NPCs) control the movement of molecules across the nuclear envelope (NE). We investigated the molecular interactions that exist at the interface between the NPC scaffold and the pore membrane. We show that key players mediating these interactions in mammalian cells are the nucleoporins Nup155 and Nup160. Nup155 depletion massively alters NE structure, causing a dramatic decrease in NPC numbers and the improper targeting of membrane proteins to the inner nuclear membrane. The role of Nup155 in assembly is likely closely linked to events at the membrane as we show that Nup155 interacts with pore membrane proteins Pom121 and NDC1. Furthermore, we demonstrate that the N terminus of Pom121 directly binds the β-propeller regions of Nup155 and Nup160. We propose a model in which the interactions of Pom121 with Nup155 and Nup160 are predicted to assist in the formation of the nuclear pore and the anchoring of the NPC to the pore membrane.
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Affiliation(s)
- Jana M Mitchell
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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11
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Levy DL, Heald R. Nuclear size is regulated by importin α and Ntf2 in Xenopus. Cell 2010; 143:288-98. [PMID: 20946986 PMCID: PMC2966892 DOI: 10.1016/j.cell.2010.09.012] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 07/06/2010] [Accepted: 09/07/2010] [Indexed: 01/14/2023]
Abstract
The size of the nucleus varies among different cell types, species, and disease states, but mechanisms of nuclear size regulation are poorly understood. We investigated nuclear scaling in the pseudotetraploid frog Xenopus laevis and its smaller diploid relative Xenopus tropicalis, which contains smaller cells and nuclei. Nuclear scaling was recapitulated in vitro using egg extracts, demonstrating that titratable cytoplasmic factors determine nuclear size to a greater extent than DNA content. Nuclear import rates correlated with nuclear size, and varying the concentrations of two transport factors, importin α and Ntf2, was sufficient to account for nuclear scaling between the two species. Both factors modulated lamin B3 import, with importin α increasing overall import rates and Ntf2 reducing import based on cargo size. Importin α also contributes to nuclear size changes during early X. laevis development. Thus, nuclear transport mechanisms are physiological regulators of both interspecies and developmental nuclear scaling.
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Affiliation(s)
- Daniel L Levy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3200, USA
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12
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Tartakoff AM, Tao T. Comparative and evolutionary aspects of macromolecular translocation across membranes. Int J Biochem Cell Biol 2009; 42:214-29. [PMID: 19643202 DOI: 10.1016/j.biocel.2009.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 01/10/2023]
Abstract
Membrane barriers preserve the integrity of organelles of eukaryotic cells, yet the genesis and ongoing functions of the same organelles requires that their limiting membranes allow import and export of selected macromolecules. Multiple distinct mechanisms are used for this purpose, only some of which have been traced to prokaryotes. Some can accommodate both monomeric and also large heterooligomeric cargoes. The best characterized of these is nucleocytoplasmic transport. This synthesis compares the unidirectional and bidirectional mechanisms of macromolecular transport of the endoplasmic reticulum, mitochondria, peroxisomes and the nucleus, calls attention to the powerful experimental approaches which have been used for their elucidation, discusses their regulation and evolutionary origins, and highlights relatively unexplored areas.
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Affiliation(s)
- Alan M Tartakoff
- Department of Pathology & Cell Biology Program, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
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13
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14
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Duricka D, Ullman KS. Analysis of RNA export using Xenopus oocytes. CURRENT PROTOCOLS IN CELL BIOLOGY 2008; Chapter 11:Unit 11.14. [PMID: 18228305 DOI: 10.1002/0471143030.cb1114s10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This unit describes a procedure for monitoring RNA export in Xenopus oocytes. The technique involves synthesizing labeled RNA in vitro and microinjecting the RNA into oocyte nuclei. Following incubation the oocytes are dissected into nuclear and cytoplasmic fractions. These samples are then processed for RNA analysis, allowing the extent of export to be quantitatively assessed.
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Affiliation(s)
- D Duricka
- University of Utah, Salt Lake City, Utah, USA
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15
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Perez-Terzic C, Faustino RS, Boorsma BJ, Arrell DK, Niederländer NJ, Behfar A, Terzic A. Stem cells transform into a cardiac phenotype with remodeling of the nuclear transport machinery. ACTA ACUST UNITED AC 2007; 4 Suppl 1:S68-76. [PMID: 17230218 DOI: 10.1038/ncpcardio0763] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 11/03/2006] [Indexed: 01/08/2023]
Abstract
Nuclear transport of transcription factors is a critical step in stem cell commitment to a tissue-specific lineage. While it is recognized that nuclear pores are gatekeepers of nucleocytoplasmic exchange, it is unknown how the nuclear transport machinery becomes competent to support genetic reprogramming and cell differentiation. Here, we report the dynamics of nuclear transport factor expression and nuclear pore microanatomy during cardiac differentiation of embryonic stem cells. Cardiac progeny derived from pluripotent stem cells displayed a distinct proteomic profile characterized by the emergence of cardiac-specific proteins. This profile correlated with the nuclear translocation of cardiac transcription factors. The nuclear transport genes, including nucleoporins, importins, exportins, transportins, and Ran-related factors, were globally downregulated at the genomic level, streamlining the differentiation program underlying stem cell-derived cardiogenesis. Establishment of the cardiac molecular phenotype was associated with an increased density of nuclear pores spanning the nuclear envelope. At nanoscale resolution, individual nuclear pores exhibited conformational changes resulting in the expansion of the pore diameter and an augmented probability of conduit occupancy. Thus, embryonic stem cells undergo adaptive remodeling of the nuclear transport infrastructure associated with nuclear translocation of cardiac transcription factors and execution of the cardiogenic program, underscoring the plasticity of the nucleocytoplasmic trafficking machinery in accommodating differentiation requirements.
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Affiliation(s)
- Carmen Perez-Terzic
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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Shahin V, Albermann L, Schillers H, Kastrup L, Schäfer C, Ludwig Y, Stock C, Oberleithner H. Steroids dilate nuclear pores imaged with atomic force microscopy. J Cell Physiol 2005; 202:591-601. [PMID: 15316931 DOI: 10.1002/jcp.20152] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Macromolecules that act in the cell nucleus must overcome the nuclear envelope (NE). This barrier between cytosol and the nucleus is perforated by nuclear pore complexes (NPCs) that serve as translocation machineries. We visualized the translocation process at the NE surface, applying a nanotechnical approach using atomic force microscopy (AFM). In order to initiate protein targeting to NPCs, dexamethasone (dex) was injected into Xenopus laevis oocytes. Dex is a synthetic steroid of great therapeutic relevance that specifically binds to glucocorticoid receptors and thus triggers an intracellular signal cascade involving the cell nucleus. Ninety and 180 sec after dex injection cell nuclei were isolated, the NEs spread on glass and scanned with AFM. With single molecule resolution we observed that dex initiated proteins (DIPs) first bind to NPC-free areas of the outer nuclear membrane. This causes NPCs to dilate. Then, in a second step, DIPs attach directly to NPCs and enter the dilated central channels. DIPs accumulation and NPC conformational changes were blocked by RU486, a specific glucocorticoid receptor antagonist. In conclusion, dex exposure induces NPC dilation. NPCs change conformation already prior to transport. The NPC dilation signal is most likely transmitted through NPC associated filaments or yet unknown structures in the NE outer membrane. NPC dilation could have significant impact on nuclear targeting of therapeutic macromolecules.
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Affiliation(s)
- Victor Shahin
- Nanolab, Institute of Physiology II, University of Münster, Münster, Germany.
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17
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Perez-Terzic C, Behfar A, Méry A, van Deursen JMA, Terzic A, Pucéat M. Structural adaptation of the nuclear pore complex in stem cell-derived cardiomyocytes. Circ Res 2003; 92:444-52. [PMID: 12600892 DOI: 10.1161/01.res.0000059415.25070.54] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Macromolecules are transported in and out of the nucleus through nuclear pores. It is poorly understood how these megadalton conduits support nucleocytoplasmic traffic during genetic reprogramming associated with cell commitment to a specific lineage. Murine embryonic stem cells were differentiated into cardiomyocytes within embryoid bodies, and contracting cells expressing myocardial-specific proteins were isolated from the mesodermal layer. Compared with postmitotic cardiac cells from heart muscle, these proliferative and differentiating stem cell-derived cardiomyocytes demonstrated a significantly lower density of nuclear pores. At nanoscale resolution, the pore channel was commonly unoccupied in heart muscle-isolated cardiac cells, yet a dense material, presumably the central transporter, protruded toward the cytosolic face of the nuclear pore complex in stem cell-derived cardiomyocytes. Stem cell-derived cardiac cells distributed the nuclear transport factor Ran in the nucleus, decreased the number of spare nuclear pore complexes from the cytosolic annulate lamellae reservoir, and expressed a set of nucleoporins, NUP214, NUP358, NUP153, and p62, involved in nuclear transport. Stem cell-derived cardiomyocytes secured transport of nuclear constitutive proteins, cardiogenic transcription factors, and cell cycle regulators, including the prototypic histone H1, myocyte enhancer binding factor 2, and p53. Thus, differentiating stem cell-derived cardiomyocytes undergo structural adaptation and mobilize nuclear transport regulators in support of nucleocytoplasmic communication during commitment to mature cardiac lineage.
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Affiliation(s)
- Carmen Perez-Terzic
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, Mayo Foundation, Rochester, Minn, USA
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18
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Steggerda SM, Paschal BM. Regulation of nuclear import and export by the GTPase Ran. INTERNATIONAL REVIEW OF CYTOLOGY 2002; 217:41-91. [PMID: 12019565 DOI: 10.1016/s0074-7696(02)17012-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This review focuses on the control of nuclear import and export pathways by the small GTPase Ran. Transport of signal-containing cargo substrates is mediated by receptors that bind to the cargo proteins and RNAs and deliver them to the appropriate cellular compartment. Ran is an evolutionarily conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. We describe the identification and characterization of the RanGTPase and its binding partners: the guanine nucleotide exchange factor, RanGEF; the GTPase activating protein, RanGAP; the soluble import and export receptors; Ran-binding domain-(RBD) containing proteins; and NTF2 and related factors.
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Affiliation(s)
- Susanne M Steggerda
- Center for Cell Signaling and Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville 22908, USA
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19
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Fahrenkrog B, Aebi U. The vertebrate nuclear pore complex: from structure to function. Results Probl Cell Differ 2002; 35:25-48. [PMID: 11791407 DOI: 10.1007/978-3-540-44603-3_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- Birthe Fahrenkrog
- M.E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
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20
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21
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Fahrenkrog B, Stoffler D, Aebi U. Nuclear pore complex architecture and functional dynamics. Curr Top Microbiol Immunol 2001; 259:95-117. [PMID: 11417129 DOI: 10.1007/978-3-642-56597-7_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- B Fahrenkrog
- Biozentrum, M.E. Müller Institute for Structural Biology, University of Basel, 4056 Basel, Switzerland
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22
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Stewart M, Baker RP, Bayliss R, Clayton L, Grant RP, Littlewood T, Matsuura Y. Molecular mechanism of translocation through nuclear pore complexes during nuclear protein import. FEBS Lett 2001; 498:145-9. [PMID: 11412846 DOI: 10.1016/s0014-5793(01)02489-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The trafficking of macromolecules between cytoplasm and nucleus through nuclear pore complexes is mediated by specific carrier molecules such as members of the importin-beta family. Nuclear pore proteins (nucleoporins) frequently contain sequence repeats based on FG cores and carriers appear to move their cargo through the pores by hopping between successive FG cores. A major question is why some macromolecules are transported while others are not. This selectivity may be generated by the ability to bind FG repeats, a local concentration of carrier-cargo complexes near the entrance to the pore channel, and steric hindrance produced by high concentrations of nucleoporins in the channel.
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Affiliation(s)
- M Stewart
- MRC Laboratory of Molecular Biology, Hills Rd., CB2 2QH, Cambridge, UK.
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23
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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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25
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Quimby BB, Lamitina T, L'Hernault SW, Corbett AH. The mechanism of ran import into the nucleus by nuclear transport factor 2. J Biol Chem 2000; 275:28575-82. [PMID: 10889207 DOI: 10.1074/jbc.m005055200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The small GTPase Ran is essential for virtually all nucleocytoplasmic transport events. It is hypothesized that Ran drives vectorial transport of macromolecules into and out of the nucleus via the establishment of a Ran gradient between the cytoplasm and nucleoplasm. Although Ran shuttles between the nucleus and cytoplasm, it is concentrated in the nucleus at steady state. We show that nuclear transport factor 2 (NTF2) is required to concentrate Ran in the nucleus in the budding yeast, Saccharomyces cerevisiae. To analyze the mechanism of Ran import into the nucleus by NTF2, we use mutants in a variety of nuclear transport factors along with biochemical analyses of NTF2 complexes. We find that Ran remains concentrated in the nucleus when importin-mediated protein import is disrupted and demonstrate that NTF2 does not form a stable complex with the transport receptor, importin-beta. Consistent with a critical role for NTF2 in establishing and maintaining the Ran gradient, we show that NTF2 is required for early embryogenesis in Caenorhabditis elegans. Our data distinguish between two possible mechanisms for Ran import by NTF2 and demonstrate that Ran import is independent from importin-beta-mediated protein import.
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Affiliation(s)
- B B Quimby
- Department of Biochemistry, Emory University School of Medicine and the Department of Biology, Emory University, Atlanta, Georgia 30322, USA
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26
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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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27
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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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28
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Allen TD, Cronshaw JM, Bagley S, Kiseleva E, Goldberg MW. The nuclear pore complex: mediator of translocation between nucleus and cytoplasm. J Cell Sci 2000; 113 ( Pt 10):1651-9. [PMID: 10769196 DOI: 10.1242/jcs.113.10.1651] [Citation(s) in RCA: 195] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enclosure of nuclear contents in eukaryotes means that cells require sites in the boundary that mediate exchange of material between nucleus and cytoplasm. These sites, termed nuclear pore complexes (NPCs), number 100–200 in yeast, a few thousand in mammalian cells and approximately 50 million in the giant nuclei of amphibian oocytes. NPCs are large (125 MDa) macromolecular complexes that comprise 50–100 different proteins in vertebrates. In spite of their size and complex structure, NPCs undergo complete breakdown and reformation at cell division. Transport through NPCs can be rapid (estimated at several hundred molecules/pore/second) and accommodates both passive diffusion of relatively small molecules, and active transport of complexes up to several megadaltons in molecular mass. Each pore can facilitate both import and export. The two processes apparently involve multiple pathways for different cargoes, and their transport signals, transport receptors and adapters, and the molecules (and their regulators) that underpin the transport mechanisms. Over the past few years there has been an increasing interest in the pore complex: structural studies have been followed by elucidation of the biochemical aspects of nuclear import, and subsequent investigations into nuclear export. The current challenge is to understand the interactions between the structural elements of the pore complex and the mechanisms that drive the physical processes of translocation through it.
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Affiliation(s)
- T D Allen
- CRC Structural Cell Biology Group, Paterson Institute, Christie Hospital, Manchester, M20 4BX, UK
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29
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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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30
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Steggerda SM, Black BE, Paschal BM. Monoclonal antibodies to NTF2 inhibit nuclear protein import by preventing nuclear translocation of the GTPase Ran. Mol Biol Cell 2000; 11:703-19. [PMID: 10679025 PMCID: PMC14804 DOI: 10.1091/mbc.11.2.703] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [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) is a soluble transport protein originally identified by its ability to stimulate nuclear localization signal (NLS)-dependent protein import in digitonin-permeabilized cells. NTF2 has been shown to bind nuclear pore complex proteins and the GDP form of Ran in vitro. Recently, it has been reported that NTF2 can stimulate the accumulation of Ran in digitonin-permeabilized cells. Evidence that NTF2 directly mediates Ran import or that NTF2 is required to maintain the nuclear concentration of Ran in living cells has not been obtained. Here we show that cytoplasmic injection of anti-NTF2 mAbs resulted in a dramatic relocalization of Ran to the cytoplasm. This provides the first evidence that NTF2 regulates the distribution of Ran in vivo. Moreover, anti-NTF2 mAbs inhibited nuclear import of both Ran and NLS-containing protein in vitro, suggesting that NTF2 stimulates NLS-dependent protein import by driving the nuclear accumulation of Ran. We also show that biotinylated NTF2-streptavidin microinjected into the cytoplasm accumulated at the nuclear envelope, indicating that NTF2 can target a binding partner to the nuclear pore complex. Taken together, our data show that NTF2 is an essential regulator of the Ran distribution in living cells and that NTF2-mediated Ran nuclear import is required for NLS-dependent protein import.
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Affiliation(s)
- S M Steggerda
- Center for Cell Signaling, Department of Biochemistry and Molecular Genetics, and Cell and Molecular Biology Program, University of Virginia Health Sciences Center, Charlottesville, Virginia, 22908, USA
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31
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Affiliation(s)
- S Nakielny
- Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia 19104-6148, USA
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32
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Bayliss R, Ribbeck K, Akin D, Kent HM, Feldherr CM, Görlich D, Stewart M. Interaction between NTF2 and xFxFG-containing nucleoporins is required to mediate nuclear import of RanGDP. J Mol Biol 1999; 293:579-93. [PMID: 10543952 DOI: 10.1006/jmbi.1999.3166] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nuclear transport factor 2 (NTF2) is a small, homodimeric protein that binds to both RanGDP and xFxFG repeat-containing nucleoporins, such as yeast Nsp1p and vertebrate p62. NTF2 is required for efficient nuclear protein import and has been shown to mediate the nuclear import of RanGDP. We have used the crystal structures of rat NTF2 and its complex with RanGDP to design a mutant, W7A-NTF2, in which the affinity for xFxFG-repeat nucleoporins is reduced while wild-type binding to RanGDP is retained. The 2.5 A resolution crystal structure of W7A-NTF2 is virtually superimposable upon the wild-type protein structure, indicating that the mutation had not introduced a more general conformational change. Therefore, our data suggest that the exposed side-chain of residue 7 is crucial to the interaction between NTF2 and xFxFG repeat-containing nucleoporins. Consistent with its reduced affinity for xFxFG nucleoporins, fluorescently labelled W7A-NTF2 binds less strongly to the nuclear envelope of permeabilized cultured cells than wild-type NTF2 and, when microinjected into Xenopus oocytes, colloidal gold coated with W7A-NTF2 binds less strongly to the central channel of nuclear pore complexes than wild-type NTF2-coated gold. Significantly, W7A-NTF2 only weakly stimulated the nuclear import of fluorescein-labelled RanGDP, providing direct evidence that an interaction between NTF2 and xFxFG repeat-containing nucleoporins is required to mediate the nuclear import of RanGDP.
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Affiliation(s)
- R Bayliss
- MRC Laboratory of Molecular Biology, Hills Rd, Cambridge, CB2 2QH, England
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33
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Yaseen NR, Blobel G. GTP hydrolysis links initiation and termination of nuclear import on the nucleoporin nup358. J Biol Chem 1999; 274:26493-502. [PMID: 10473610 DOI: 10.1074/jbc.274.37.26493] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Binding of GTP-bound Ran (RanGTP) to karyopherin beta1 (Kapbeta1) releases import cargo into the nucleus. Using an ultrastructural, biochemical, and functional approach, we have studied the mechanism by which Kapbeta1.RanGTP is recycled at the nuclear pore complex for repeated rounds of import. In vitro, Kapbeta1 bound to the RanBP1-homologous (RBH) domains of Nup358 in the presence of either RanGTP or RanGDP, forming trimeric complexes. The Kapbeta1.RanGTP. RBH complex resisted dissociation by RanBP1 and GTP hydrolysis by Ran GTPase activating protein 1. Ran-dependent binding of gold-conjugated Kapbeta1 to the cytoplasmic fibers of the nuclear pore complex in digitonin-permeabilized cells and RanBP1 competition confirmed the in vitro binding data. Interaction of karyopherin alpha and a classical nuclear localization sequence peptide with the Kapbeta1.RanGTP.RBH complex stimulated GTP hydrolysis by Ran GTPase activating protein 1 both in vitro and in permeabilized cells. This GTP hydrolysis was required for reinitiation of import of a nuclear localization sequence-bearing substrate in permeabilized cells. These data suggest that GTP hydrolysis on the RBH domains of Nup358 couples the termination of one cycle of nuclear import with the initiation of the next.
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Affiliation(s)
- N R Yaseen
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10021, USA
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34
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Abstract
The evolutionary changes that occur in signal-mediated nuclear transport would be expected to reflect an increasing need to regulate nucleocytoplasmic exchanges as the complexity of organisms increases. This could involve changes in both the composition and structure of the pore complex, as well as the cytosolic factors that mediate transport. In this regard, we investigated the transport process in amoebae (Amoeba proteus and Chaos carolinensis), primitive cells that would be expected to have less stringent regulatory requirements than more complex organisms. Colloidal gold particles, coated with bovine serum albumin (BSA) conjugated with simple (large T) nuclear localization signals (NLSs), bipartite (nucleoplasmin) NLSs or mutant NLSs, were used to assay nuclear import. It was found that in amoebae (1) the diameter of the particles that are able to enter the nucleoplasm is significantly less than in vertebrate cells, (2) the simple NLS is more effective in mediating nuclear import than the bipartite NLS, and (3) the nucleoporins do not appear to be glycosylated. Evidence was also obtained suggesting that, in amoebae, the simple NLS can mediate nuclear export.
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Affiliation(s)
- C M Feldherr
- Dept of Anatomy and Cell Biology, University of Florida, College of Medicine, Gainesville, FL 32610, USA.
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35
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Hu W, Jans DA. Efficiency of importin alpha/beta-mediated nuclear localization sequence recognition and nuclear import. Differential role of NTF2. J Biol Chem 1999; 274:15820-7. [PMID: 10336485 DOI: 10.1074/jbc.274.22.15820] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Little quantitative, kinetic information is available with respect to the process of nuclear import of conventional nuclear localization sequence (NLS)-containing proteins, which initially involves recognition and docking at the nuclear pore by importin alpha/beta. This study compares the binding and nuclear import properties of mouse (m) and yeast (y) importin (IMP) subunits with respect to the NLSs from the SV40 large tumor antigen (T-ag), and the Xenopus laevis phosphoprotein N1N2. m- and y-IMPalpha recognized both NLSs, with y-IMPalpha exhibiting higher affinity. m-IMPbeta greatly enhanced the binding of m-IMPalpha to the T-ag and N1N2 NLSs, but y-IMPbeta did not significantly affect the affinity of y-IMPalpha for the T-ag NLS. In contrast, y-IMPbeta enhanced y-IMPalpha binding to the NLS of N1N2, but to a lesser extent than the enhancement of m-IMPalpha binding by m-IMPbeta. NLS-dependent nuclear import was reconstituted in vitro using the different importin subunits together with the transport factors Ran and NTF2. Whereas T-ag NLS-mediated nuclear import did not exhibit an absolute requirement for NTF2, N1N2 NLS-mediated transport strictly required NTF2. High levels of NTF2 inhibited nuclear accumulation conferred by both NLSs. We conclude that different NLSs possess distinct nuclear import properties due to differences in recognition by importin and requirements for NTF2.
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Affiliation(s)
- W Hu
- Nuclear Signalling Laboratory, Division for Biochemistry and Molecular Biology, John Curtin School of Medical Research, Canberra, ACT 2601, Australia
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36
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Ullman KS, Shah S, Powers MA, Forbes DJ. The nucleoporin nup153 plays a critical role in multiple types of nuclear export. Mol Biol Cell 1999; 10:649-64. [PMID: 10069809 PMCID: PMC25193 DOI: 10.1091/mbc.10.3.649] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The fundamental process of nucleocytoplasmic transport takes place through the nuclear pore. Peripheral pore structures are presumably poised to interact with transport receptors and their cargo as these receptor complexes first encounter the pore. One such peripheral structure likely to play an important role in nuclear export is the basket structure located on the nuclear side of the pore. At present, Nup153 is the only nucleoporin known to localize to the surface of this basket, suggesting that Nup153 is potentially one of the first pore components an RNA or protein encounters during export. In this study, anti-Nup153 antibodies were used to probe the role of Nup153 in nuclear export in Xenopus oocytes. We found that Nup153 antibodies block three major classes of RNA export, that of snRNA, mRNA, and 5S rRNA. Nup153 antibodies also block the NES protein export pathway, specifically the export of the HIV Rev protein, as well as Rev-dependent RNA export. Not all export was blocked; Nup153 antibodies did not impede the export of tRNA or the recycling of importin beta to the cytoplasm. The specific antibodies used here also did not affect nuclear import, whether mediated by importin alpha/beta or by transportin. Overall, the results indicate that Nup153 is crucial to multiple classes of RNA and protein export, being involved at a vital juncture point in their export pathways. This juncture point appears to be one that is bypassed by tRNA during its export. We asked whether a physical interaction between RNA and Nup153 could be observed, using homoribopolymers as sequence-independent probes for interaction. Nup153, unlike four other nucleoporins including Nup98, associated strongly with poly(G) and significantly with poly(U). Thus, Nup153 is unique among the nucleoporins tested in its ability to interact with RNA and must do so either directly or indirectly through an adaptor protein. These results suggest a unique mechanistic role for Nup153 in the export of multiple cargos.
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Affiliation(s)
- K S Ullman
- Department of Biology, University of California at San Diego, La Jolla, California 92093-0347, USA.
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37
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Hurt E, Hannus S, Schmelzl B, Lau D, Tollervey D, Simos G. A novel in vivo assay reveals inhibition of ribosomal nuclear export in ran-cycle and nucleoporin mutants. J Biophys Biochem Cytol 1999; 144:389-401. [PMID: 9971735 PMCID: PMC2132911 DOI: 10.1083/jcb.144.3.389] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To identify components involved in the nuclear export of ribosomes in yeast, we developed an in vivo assay exploiting a green fluorescent protein (GFP)-tagged version of ribosomal protein L25. After its import into the nucleolus, L25-GFP assembles with 60S ribosomal subunits that are subsequently exported into the cytoplasm. In wild-type cells, GFP-labeled ribosomes are only detected by fluorescence in the cytoplasm. However, thermosensitive rna1-1 (Ran-GAP), prp20-1 (Ran-GEF), and nucleoporin nup49 and nsp1 mutants are impaired in ribosomal export as revealed by nuclear accumulation of L25-GFP. Furthermore, overexpression of dominant-negative RanGTP (Gsp1-G21V) and the tRNA exportin Los1p inhibits ribosomal export. The pattern of subnuclear accumulation of L25-GFP observed in different mutants is not identical, suggesting that transport can be blocked at different steps. Thus, nuclear export of ribosomes requires the nuclear/cytoplasmic Ran-cycle and distinct nucleoporins. This assay can be used to identify soluble transport factors required for nuclear exit of ribosomes.
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Affiliation(s)
- E Hurt
- Biochemie-Zentrum Heidelberg, D-69120 Heidelberg, Germany
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Stewart M, Kent HM, McCoy AJ. The structure of the Q69L mutant of GDP-Ran shows a major conformational change in the switch II loop that accounts for its failure to bind nuclear transport factor 2 (NTF2). J Mol Biol 1998; 284:1517-27. [PMID: 9878368 DOI: 10.1006/jmbi.1998.2204] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report the 2.3 A resolution X-ray crystal structure of the GDP-bound form of the RanQ69L mutant that is used extensively in studies of nucleocytoplasmic transport and cell-cycle progression. When the structure of GDP-RanQ69L from monoclinic crystals with P21 symmetry was compared with the structure of wild-type Ran obtained from monoclinic crystals, the Q69L mutant showed a large conformational change in residues 68-74, which are in the switch II region of the molecule which changes conformation in response to nucleotide state and which forms the major interaction interface with nuclear transport factor 2 (NTF2, sometimes called p10). This conformational change alters the positions of key residues such as Lys71, Phe72 and Arg76 that are crucial for the interaction of GDP-Ran with NTF2 and indeed, solution binding studies were unable to detect any interaction between NTF2 and GDP-RanQ69L under conditions where GDP-Ran bound effectively. This interaction between NTF2 and GDP-Ran is required for efficient nuclear protein import and may function between the docking and translocation steps of the pathway.
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Affiliation(s)
- M Stewart
- MRC Laboratory of Molecular Biology, Hills Rd., Cambridge, CB2 2QH,
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Affiliation(s)
- M S Moore
- Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
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Feldherr CM. Macromolecular exchanges between the nucleus and cytoplasm. J Cell Biochem 1998; 72 Suppl 30-31:214-219. [DOI: 10.1002/(sici)1097-4644(1998)72:30/31+<214::aid-jcb26>3.0.co;2-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/1998] [Accepted: 09/04/1998] [Indexed: 11/11/2022]
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