151
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Crystal structure of human nuclear pore complex component NUP43. FEBS Lett 2015; 589:3247-53. [DOI: 10.1016/j.febslet.2015.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 08/29/2015] [Accepted: 09/08/2015] [Indexed: 01/10/2023]
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152
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Banerjee S, Barraud P. Functions of double-stranded RNA-binding domains in nucleocytoplasmic transport. RNA Biol 2015; 11:1226-32. [PMID: 25584639 DOI: 10.4161/15476286.2014.972856] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The double-stranded RNA-binding domain (dsRBD) is a small protein domain found in eukaryotic, prokaryotic and viral proteins, whose central property is to bind to double-stranded RNA (dsRNA). Aside from this major function, recent examples of dsRBDs involved in the regulation of the sub-cellular localization of proteins, suggest that the participation of dsRBDs in nucleocytoplasmic trafficking is likely to represent a widespread auxiliary function of this type of RNA-binding domain. Overall, dsRBDs from proteins involved in many different biological processes have been reported to be implicated in nuclear import and export, as well as cytoplasmic, nuclear and nucleolar retention. Interestingly, the function of dsRBDs in nucleocytoplasmic trafficking is often regulated by their dsRNA-binding capacity, which can either enhance or impair the transport from one compartment to another. Here, we present and discuss the emerging function of dsRBDs in nucleocytoplasmic transport.
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Affiliation(s)
- Silpi Banerjee
- a Department of Chromosome Biology; Max F. Perutz Laboratories ; University of Vienna ; Vienna , Austria
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153
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Gebhardt A, Habjan M, Benda C, Meiler A, Haas DA, Hein MY, Mann A, Mann M, Habermann B, Pichlmair A. mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3. Nat Commun 2015; 6:8192. [PMID: 26382858 PMCID: PMC4595607 DOI: 10.1038/ncomms9192] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/28/2015] [Indexed: 02/07/2023] Open
Abstract
The flow of genetic information from DNA to protein requires polymerase-II-transcribed RNA characterized by the presence of a 5'-cap. The cap-binding complex (CBC), consisting of the nuclear cap-binding protein (NCBP) 2 and its adaptor NCBP1, is believed to bind all capped RNA and to be necessary for its processing and intracellular localization. Here we show that NCBP1, but not NCBP2, is required for cell viability and poly(A) RNA export. We identify C17orf85 (here named NCBP3) as a cap-binding protein that together with NCBP1 forms an alternative CBC in higher eukaryotes. NCBP3 binds mRNA, associates with components of the mRNA processing machinery and contributes to poly(A) RNA export. Loss of NCBP3 can be compensated by NCBP2 under steady-state conditions. However, NCBP3 becomes pivotal under stress conditions, such as virus infection. We propose the existence of an alternative CBC involving NCBP1 and NCBP3 that plays a key role in mRNA biogenesis.
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Affiliation(s)
- Anna Gebhardt
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Matthias Habjan
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Christian Benda
- Department of Structural Cell Biology, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Arno Meiler
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Darya A Haas
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Marco Y Hein
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Angelika Mann
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Bianca Habermann
- Bioinformatics Core Facility, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
| | - Andreas Pichlmair
- Innate Immunity Laboratory, Max-Planck Institute of Biochemistry, Martinsried, Munich D-82152, Germany
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154
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Cadmium induces the activation of cell wall integrity pathway in budding yeast. Chem Biol Interact 2015; 240:316-23. [PMID: 26362500 DOI: 10.1016/j.cbi.2015.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 08/07/2015] [Accepted: 09/02/2015] [Indexed: 11/20/2022]
Abstract
MAP kinases are important signaling molecules regulating cell survival, proliferation and differentiation, and can be activated by cadmium stress. In this study, we demonstrate that cadmium induces phosphorylation of the yeast cell wall integrity (CWI) pathway_MAP kinase Slt2, and this cadmium-induced CWI activation is mediated by the cell surface sensor Mid2 through the GEF Rom1, the central regulator Rho1 and Bck1. Nevertheless, cadmium stress does not affect the subcellular localization of Slt2 proteins. In addition, this cadmium-induced CWI activation is independent on the calcium/calcineurin signaling and the high osmolarity glycerol (HOG) signaling pathways in yeast cells. Furthermore, we tested the cadmium sensitivity of 42 paired double-gene deletion mutants between six CWI components and seven components of the HOG pathway. Our results indicate that the CWI pathway is epistatic to the HOG pathway in cadmium sensitivity. However, gene deletion mutations for the Swi4/Swi6 transcription factor complex show synergistic effects with mutations of HOG components in cadmium sensitivity.
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155
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Bauer NC, Doetsch PW, Corbett AH. Mechanisms Regulating Protein Localization. Traffic 2015; 16:1039-61. [PMID: 26172624 DOI: 10.1111/tra.12310] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Revised: 07/08/2015] [Accepted: 07/08/2015] [Indexed: 12/23/2022]
Abstract
Cellular functions are dictated by protein content and activity. There are numerous strategies to regulate proteins varying from modulating gene expression to post-translational modifications. One commonly used mode of regulation in eukaryotes is targeted localization. By specifically redirecting the localization of a pool of existing protein, cells can achieve rapid changes in local protein function. Eukaryotic cells have evolved elegant targeting pathways to direct proteins to the appropriate cellular location or locations. Here, we provide a general overview of these localization pathways, with a focus on nuclear and mitochondrial transport, and present a survey of the evolutionarily conserved regulatory strategies identified thus far. We end with a description of several specific examples of proteins that exploit localization as an important mode of regulation.
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Affiliation(s)
- Nicholas C Bauer
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Graduate Program in Biochemistry, Cell, and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Current address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
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156
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Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S, Mayo DJ, Perriches T, Rundlet EJ, Jeon YE, Collins LN, Huber FM, Lin DH, Paduch M, Koide A, Lu V, Fischer J, Hurt E, Koide S, Kossiakoff AA, Hoelz A. Architecture of the fungal nuclear pore inner ring complex. Science 2015; 350:56-64. [PMID: 26316600 DOI: 10.1126/science.aac9176] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/12/2015] [Indexed: 12/20/2022]
Abstract
The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kilodalton inner ring complex (IRC), which forms the central transport channel and diffusion barrier of the NPC, revealing its interaction network and equimolar stoichiometry. The Nsp1•Nup49•Nup57 channel nucleoporin heterotrimer (CNT) attaches to the IRC solely through the adaptor nucleoporin Nic96. The CNT•Nic96 structure reveals that Nic96 functions as an assembly sensor that recognizes the three-dimensional architecture of the CNT, thereby mediating the incorporation of a defined CNT state into the NPC. We propose that the IRC adopts a relatively rigid scaffold that recruits the CNT to primarily form the diffusion barrier of the NPC, rather than enabling channel dilation.
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Affiliation(s)
- Tobias Stuwe
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Christopher J Bley
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Karsten Thierbach
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Stefan Petrovic
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Sandra Schilbach
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Daniel J Mayo
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Thibaud Perriches
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Emily J Rundlet
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Young E Jeon
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Leslie N Collins
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ferdinand M Huber
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Daniel H Lin
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Vincent Lu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Jessica Fischer
- Biochemistry Center of Heidelberg University, 69120 Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center of Heidelberg University, 69120 Heidelberg, Germany
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - André Hoelz
- California Institute of Technology, Division of Chemistry and Chemical Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA.
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157
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Dickmanns A, Kehlenbach RH, Fahrenkrog B. Nuclear Pore Complexes and Nucleocytoplasmic Transport: From Structure to Function to Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 320:171-233. [PMID: 26614874 DOI: 10.1016/bs.ircmb.2015.07.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nucleocytoplasmic transport is an essential cellular activity and occurs via nuclear pore complexes (NPCs) that reside in the double membrane of the nuclear envelope. Significant progress has been made during the past few years in unravelling the ultrastructural organization of NPCs and their constituents, the nucleoporins, by cryo-electron tomography and X-ray crystallography. Mass spectrometry and genomic approaches have provided deeper insight into the specific regulation and fine tuning of individual nuclear transport pathways. Recent research has also focused on the roles nucleoporins play in health and disease, some of which go beyond nucleocytoplasmic transport. Here we review emerging results aimed at understanding NPC architecture and nucleocytoplasmic transport at the atomic level, elucidating the specific function individual nucleoporins play in nuclear trafficking, and finally lighting up the contribution of nucleoporins and nuclear transport receptors in human diseases, such as cancer and certain genetic disorders.
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Affiliation(s)
- Achim Dickmanns
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ralph H Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Georg-August-University of Göttingen, Göttingen, Germany
| | - Birthe Fahrenkrog
- Institute of Molecular Biology and Medicine, Université Libre de Bruxelles, Charleroi, Belgium
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158
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Honda T, Nakajima K. Proper Level of Cytosolic Disabled-1, Which Is Regulated by Dual Nuclear Translocation Pathways, Is Important for Cortical Neuronal Migration. Cereb Cortex 2015. [PMID: 26209842 DOI: 10.1093/cercor/bhv162] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Disabled-1 (Dab1) is an essential intracellular protein in the Reelin pathway. It has a nuclear localization signal (NLS; hereafter referred to as "NLS1") and 2 nuclear export signals, and shuttles between the nucleus and the cytoplasm. In this study, we found that Dab1 has an additional unidentified NLS, and that the Dab1 NLS1 mutant could translocate to the nucleus in an unconventional ATP/temperature-dependent and cytoplasmic factor/RanGTP gradient-independent manner. Additional mutations in the NLS1 mutant revealed that K(67) and K(69) are important for the nuclear transport. Furthermore, an excess of the intracellular domain of the Reelin receptors inhibited the nuclear translocation of Dab1. An in utero electroporation study showed that a large amount of Dab1 in the cytoplasm in migrating neurons inhibited the migration, and that forced transport of Dab1 into the nucleus attenuated this inhibitory effect. In addition, rescue experiments using yotari, an autosomal recessive mutant of dab1, revealed that cells expressing Dab1 NLS1 mutant tend to distribute at more superficial positions than those expressing wild-type Dab1. Taken together, these findings suggest that Dab1 has at least 2 NLSs, and that the regulation of the subcellular localization of Dab1 is important for the proper migration of excitatory neurons.
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Affiliation(s)
- Takao Honda
- Department of Anatomy, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kazunori Nakajima
- Department of Anatomy, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
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159
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Maturana JL, Niechi I, Silva E, Huerta H, Cataldo R, Härtel S, Barros LF, Galindo M, Tapia JC. Transactivation activity and nucleocytoplasmic transport of β-catenin are independently regulated by its C-terminal end. Gene 2015; 573:115-22. [PMID: 26187068 DOI: 10.1016/j.gene.2015.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/11/2015] [Indexed: 11/20/2022]
Abstract
The key protein in the canonical Wnt pathway is β-catenin, which is phosphorylated both in absence and presence of Wnt signals by different kinases. Upon activation in the cytoplasm, β-catenin can enter into the nucleus to transactivate target gene expression, many of which are cancer-related genes. The mechanism governing β-catenin's nucleocytoplasmic transport has been recently unvealed, although phosphorylation at its C-terminal end and its functional consequences are not completely understood. Serine 646 of β-catenin is a putative CK2 phosphorylation site and lies in a region which has been proposed to be important for its nucleocytoplasmic transport and transactivation activity. This residue was mutated to aspartic acid mimicking CK2-phosphorylation and its effects on β-catenin activity as well as localization were explored. β-Catenin S6464D did not show significant differences in both transcriptional activity and nuclear localization compared to the wild-type form, but displayed a characteristic granular nuclear pattern. Three-dimensional models of nuclei were constructed which showed differences in number and volume of granules, being those from β-catenin S646D more and smaller than the wild-type form. FRAP microscopy was used to compare nuclear export of both proteins which showed a slightly higher but not significant retention of β-catenin S646D. Altogether, these results show that C-terminal phosphorylation of β-catenin seems to be related with its nucleocytoplasmic transport but not transactivation activity.
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Affiliation(s)
- J L Maturana
- Program of Cellular and Molecular Biology, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - I Niechi
- Program of Cellular and Molecular Biology, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - E Silva
- Program of Cellular and Molecular Biology, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - H Huerta
- Program of Cellular and Molecular Biology, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - R Cataldo
- Program of Cellular and Molecular Biology, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - S Härtel
- Laboratory for Scientific Image Analysis (SCIAN-Lab), ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - L F Barros
- Centro de Estudios Cientificos, Valdivia, Chile
| | - M Galindo
- Program of Cellular and Molecular Biology, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile
| | - J C Tapia
- Program of Cellular and Molecular Biology, ICBM, Faculty of Medicine, University of Chile, Santiago, Chile.
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160
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Kralt A, Jagalur NB, van den Boom V, Lokareddy RK, Steen A, Cingolani G, Fornerod M, Veenhoff LM. Conservation of inner nuclear membrane targeting sequences in mammalian Pom121 and yeast Heh2 membrane proteins. Mol Biol Cell 2015; 26:3301-12. [PMID: 26179916 PMCID: PMC4569319 DOI: 10.1091/mbc.e15-03-0184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/08/2015] [Indexed: 12/23/2022] Open
Abstract
This study examines whether active transport to the inner nuclear membrane, as shown for yeast membrane proteins Heh1 and Heh2, is conserved in metazoans. In support of this, the nuclear localization signal of metazoan Pom121 shares biochemical, structural, and functional properties with those of Heh1 and Heh2, and a Heh2-derived reporter protein targets to the inner membrane in Hek293T cells. Endoplasmic reticulum–synthesized membrane proteins traffic through the nuclear pore complex (NPC) en route to the inner nuclear membrane (INM). Although many membrane proteins pass the NPC by simple diffusion, two yeast proteins, ScSrc1/ScHeh1 and ScHeh2, are actively imported. In these proteins, a nuclear localization signal (NLS) and an intrinsically disordered linker encode the sorting signal for recruiting the transport factors for FG-Nup and RanGTP-dependent transport through the NPC. Here we address whether a similar import mechanism applies in metazoans. We show that the (putative) NLSs of metazoan HsSun2, MmLem2, HsLBR, and HsLap2β are not sufficient to drive nuclear accumulation of a membrane protein in yeast, but the NLS from RnPom121 is. This NLS of Pom121 adapts a similar fold as the NLS of Heh2 when transport factor bound and rescues the subcellular localization and synthetic sickness of Heh2ΔNLS mutants. Consistent with the conservation of these NLSs, the NLS and linker of Heh2 support INM localization in HEK293T cells. The conserved features of the NLSs of ScHeh1, ScHeh2, and RnPom121 and the effective sorting of Heh2-derived reporters in human cells suggest that active import is conserved but confined to a small subset of INM proteins.
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Affiliation(s)
- Annemarie Kralt
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Netherlands
| | - Noorjahan B Jagalur
- Departments of Biochemistry and Pediatric Oncology, Erasmus MC/Sophia, 3015 CN Rotterdam, Netherlands
| | - Vincent van den Boom
- Department of Experimental Hematology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, Netherlands
| | - Ravi K Lokareddy
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Netherlands
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Maarten Fornerod
- Departments of Biochemistry and Pediatric Oncology, Erasmus MC/Sophia, 3015 CN Rotterdam, Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, Netherlands )
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161
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Abstract
Mechanistic target of rapamycin (mTOR) is a central component of the essential signaling pathway that regulates cell growth and proliferation by controlling anabolic processes in cells. mTOR exists in two distinct mTOR complexes known as mTORC1 and mTORC2 that reside mostly in cytoplasm. In our study, the biochemical characterization of mTOR led to discovery of its novel localization on nuclear envelope where it associates with a critical regulator of nuclear import Ran Binding Protein 2 (RanBP2). We show that association of mTOR with RanBP2 is dependent on the mTOR kinase activity that regulates the nuclear import of ribosomal proteins. The mTOR kinase inhibitors within thirty minutes caused a substantial decrease of ribosomal proteins in the nuclear but not cytoplasmic fraction. Detection of a nuclear accumulation of the GFP-tagged ribosomal protein rpL7a also indicated its dependence on the mTOR kinase activity. The nuclear abundance of ribosomal proteins was not affected by inhibition of mTOR Complex 1 (mTORC1) by rapamycin or deficiency of mTORC2, suggesting a distinctive role of the nuclear envelope mTOR complex in the nuclear import. Thus, we identified that mTOR in association with RanBP2 mediates the active nuclear import of ribosomal proteins.
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162
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Parodi A, Corbo C, Cevenini A, Molinaro R, Palomba R, Pandolfi L, Agostini M, Salvatore F, Tasciotti E. Enabling cytoplasmic delivery and organelle targeting by surface modification of nanocarriers. Nanomedicine (Lond) 2015; 10:1923-40. [PMID: 26139126 PMCID: PMC5561781 DOI: 10.2217/nnm.15.39] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Nanocarriers are designed to specifically accumulate in diseased tissues. In this context, targeting of intracellular compartments was shown to enhance the efficacy of many drugs and to offer new and more effective therapeutic approaches. This is especially true for therapies based on biologicals that must be encapsulated to favor cell internalization, and to avoid intracellular endosomal sequestration and degradation of the payload. In this review, we discuss specific surface modifications designed to achieve cell cytoplasm delivery and to improve targeting of major organelles; we also discuss the therapeutic applications of these approaches. Last, we describe some integrated strategies designed to sequentially overcome the biological barriers that separate the site of administration from the cell cytoplasm, which is the drug's site of action.
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Affiliation(s)
- Alessandro Parodi
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave., Houston, TX 77030, USA
- Fondazione IRCCS SDN, Via Gianturco 113, 80143 Naples, Italy
| | - Claudia Corbo
- Fondazione IRCCS SDN, Via Gianturco 113, 80143 Naples, Italy
| | - Armando Cevenini
- Department of Molecular Medicine & Medical Biotechnology, University of Naples “Federico II”, Via Sergio Pansini 5, Naples 80131, Italy
- CEINGE, Biotecnologie Avanzate s.c.a.r.l., Via G. Salvatore 486, 80145 Naples, Italy
| | - Roberto Molinaro
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave., Houston, TX 77030, USA
- Clinica Chirurgica I, Dipartimento di Scienze Chirurgiche Oncologiche e Gastroeterologiche, Università di Padova, Via Giustiniani 2, 35128 Padova, Italy
| | - Roberto Palomba
- Fondazione IRCCS SDN, Via Gianturco 113, 80143 Naples, Italy
| | - Laura Pandolfi
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave., Houston, TX 77030, USA
- College of Materials Science & Optoelectronic Technology, University of Chinese Academy of Science, 19A Yuquanlu, Beijing, China
| | - Marco Agostini
- Clinica Chirurgica I, Dipartimento di Scienze Chirurgiche Oncologiche e Gastroeterologiche, Università di Padova, Via Giustiniani 2, 35128 Padova, Italy
| | - Francesco Salvatore
- Fondazione IRCCS SDN, Via Gianturco 113, 80143 Naples, Italy
- CEINGE, Biotecnologie Avanzate s.c.a.r.l., Via G. Salvatore 486, 80145 Naples, Italy
| | - Ennio Tasciotti
- Department of Nanomedicine, Houston Methodist Research Institute, 6670 Bertner Ave., Houston, TX 77030, USA
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163
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Pausch P, Singh U, Ahmed YL, Pillet B, Murat G, Altegoer F, Stier G, Thoms M, Hurt E, Sinning I, Bange G, Kressler D. Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones. Nat Commun 2015; 6:7494. [PMID: 26112308 PMCID: PMC4491177 DOI: 10.1038/ncomms8494] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 05/14/2015] [Indexed: 12/11/2022] Open
Abstract
Exponentially growing yeast cells produce every minute >160,000 ribosomal proteins. Owing to their difficult physicochemical properties, the synthesis of assembly-competent ribosomal proteins represents a major challenge. Recent evidence highlights that dedicated chaperone proteins recognize the N-terminal regions of ribosomal proteins and promote their soluble expression and delivery to the assembly site. Here we explore the intuitive possibility that ribosomal proteins are captured by dedicated chaperones in a co-translational manner. Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients (Rpl3, Rpl5, Rpl10 and Rps3). X-ray crystallography reveals how the N-terminal, rRNA-binding residues of Rpl10 are shielded by Sqt1's WD-repeat β-propeller, providing mechanistic insight into the incorporation of Rpl10 into pre-60S subunits. Co-translational capturing of nascent ribosomal proteins by dedicated chaperones constitutes an elegant mechanism to prevent unspecific interactions and aggregation of ribosomal proteins on their road to incorporation. The synthesis of ribosomes requires the orderly assembly of many proteins and large RNA molecules, a process that involves several assembly factors. Here the authors show that dedicated chaperones capture the N termini of specific nascent ribosomal proteins to promote folding and assembly into maturing ribosomes.
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Affiliation(s)
- Patrick Pausch
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg D-35043, Germany
| | - Ujjwala Singh
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Yasar Luqman Ahmed
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Benjamin Pillet
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Guillaume Murat
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Florian Altegoer
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg D-35043, Germany
| | - Gunter Stier
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Matthias Thoms
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, Heidelberg D-61920, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße, Marburg D-35043, Germany
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
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164
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Lokareddy RK, Hapsari RA, van Rheenen M, Pumroy RA, Bhardwaj A, Steen A, Veenhoff LM, Cingolani G. Distinctive Properties of the Nuclear Localization Signals of Inner Nuclear Membrane Proteins Heh1 and Heh2. Structure 2015; 23:1305-1316. [PMID: 26051712 DOI: 10.1016/j.str.2015.04.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/23/2015] [Accepted: 04/23/2015] [Indexed: 01/13/2023]
Abstract
Targeting of ER-synthesized membrane proteins to the inner nuclear membrane (INM) has long been explained by the diffusion-retention model. However, several INM proteins contain non-classical nuclear localization signal (NLS) sequences, which, in a few instances, have been shown to promote importin α/β- and Ran-dependent translocation to the INM. Here, using structural and biochemical methods, we show that yeast INM proteins Heh2 and Src1/Heh1 contain bipartite import sequences that associate intimately with the minor NLS-binding pocket of yeast importin α and unlike classical NLSs efficiently displace the IBB domain in the absence of importin β. In vivo, the intimate interactions at the minor NLS-binding pocket make the h2NLS highly efficient at recruiting importin α at the ER and drive INM localization of endogenous Heh2. Thus, h1/h2NLSs delineate a novel class of super-potent, IBB-like membrane protein NLSs, distinct from classical NLSs found in soluble cargos and of general interest in biology.
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Affiliation(s)
- Ravi K Lokareddy
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10 Street, Philadelphia, PA 19107, USA
| | - Rizqiya A Hapsari
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.,Zernike Institute for Advanced Materials, Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Mathilde van Rheenen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Ruth A Pumroy
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10 Street, Philadelphia, PA 19107, USA
| | - Anshul Bhardwaj
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10 Street, Philadelphia, PA 19107, USA
| | - Anton Steen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Gino Cingolani
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10 Street, Philadelphia, PA 19107, USA
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165
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Gao W, Lu C, Chen L, Keohavong P. Overexpression of CRM1: A Characteristic Feature in a Transformed Phenotype of Lung Carcinogenesis and a Molecular Target for Lung Cancer Adjuvant Therapy. J Thorac Oncol 2015; 10:815-825. [PMID: 25629636 DOI: 10.1097/jto.0000000000000485] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Our previous study showed that chromosome region maintenance 1 (CRM1), a nuclear export receptor for various cancer-associated "cargo" proteins, was important in regulating lung carcinogenesis in response to a tobacco carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). The objectives of this study are to comprehensively evaluate the significance of CRM1 in lung cancer development and investigate the therapeutic potential of targeting CRM1 for lung cancer treatment using both in vitro and in vivo models. We showed that CRM1 was overexpressed not only in lung tumor tissues from both lung cancer patients and mice treated with NNK but also in NNK-transformed BEAS-2B human bronchial epithelial cells. Furthermore, stable overexpression of CRM1 in BEAS-2B cells by plasmid vector transfection led to malignant cellular transformation. Moreover, a decreased CRM1 expression level in A549 cells by short hairpin siRNA transfection led to a decreased tumorigenic activity both in vitro and in nude mice, suggesting the potential to target CRM1 for lung cancer treatment. Indeed, we showed that the cytotoxic effects of cisplatin on A549 cells with CRM1 down-regulated by short hairpin siRNA were significantly increased, compared with A549 cells, and the cytotoxic effects of cisplatin became further enhanced when the drug was used in combination with leptomycin B, a CRM1 inhibitor, in both in vitro and in vivo models. Cancer target genes were significantly involved in these processes. These data suggest that CRM1 plays an important role in lung carcinogenesis and provides a novel target for lung cancer adjuvant therapy.
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MESH Headings
- Adenocarcinoma/chemistry
- Adenocarcinoma/genetics
- Adult
- Aged
- Aged, 80 and over
- Animals
- Antibiotics, Antineoplastic/pharmacology
- Antineoplastic Agents/pharmacology
- Carcinoma, Non-Small-Cell Lung/chemistry
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Squamous Cell/chemistry
- Carcinoma, Squamous Cell/genetics
- Cell Cycle Checkpoints/drug effects
- Cell Survival/drug effects
- Cell Transformation, Neoplastic/drug effects
- Cells, Cultured
- Cisplatin/pharmacology
- Cyclin-Dependent Kinase Inhibitor p21/metabolism
- Fatty Acids, Unsaturated/pharmacology
- Female
- Gene Expression/drug effects
- Gene Silencing
- Humans
- Inhibitor of Apoptosis Proteins/metabolism
- Karyopherins/analysis
- Karyopherins/genetics
- Karyopherins/metabolism
- Lung/chemistry
- Lung Neoplasms/chemistry
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Male
- Mice
- Mice, Nude
- Middle Aged
- Nitrosamines/pharmacology
- Phosphorylation
- Poly (ADP-Ribose) Polymerase-1
- Poly(ADP-ribose) Polymerases/metabolism
- RNA, Messenger/metabolism
- Receptors, Cytoplasmic and Nuclear/analysis
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Smoking
- Survivin
- Transfection
- Tumor Stem Cell Assay
- Tumor Suppressor Protein p53/metabolism
- Exportin 1 Protein
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Affiliation(s)
- Weimin Gao
- Department of Environmental Toxicology, The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX.
| | - Chuanwen Lu
- Department of Environmental Toxicology, The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX
| | - Lixia Chen
- Department of Environmental Toxicology, The Institute of Environmental and Human Health, Texas Tech University, Lubbock, TX
| | - Phouthone Keohavong
- Department Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
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166
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De la Fuente IM. Elements of the cellular metabolic structure. Front Mol Biosci 2015; 2:16. [PMID: 25988183 PMCID: PMC4428431 DOI: 10.3389/fmolb.2015.00016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/12/2015] [Indexed: 12/19/2022] Open
Abstract
A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra,” Consejo Superior de Investigaciones CientíficasGranada, Spain
- Department of Mathematics, University of the Basque Country, UPV/Euskal Herriko UnibertsitateaLeioa, Spain
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167
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Fischer U, Schäuble N, Schütz S, Altvater M, Chang Y, Boulos Faza M, Panse VG. A non-canonical mechanism for Crm1-export cargo complex assembly. eLife 2015; 4:e05745. [PMID: 25895666 PMCID: PMC4402694 DOI: 10.7554/elife.05745] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 03/26/2015] [Indexed: 01/19/2023] Open
Abstract
The transport receptor Crm1 mediates the export of diverse cargos containing leucine-rich nuclear export signals (NESs) through complex formation with RanGTP. To ensure efficient cargo release in the cytoplasm, NESs have evolved to display low affinity for Crm1. However, mechanisms that overcome low affinity to assemble Crm1-export complexes in the nucleus remain poorly understood. In this study, we reveal a new type of RanGTP-binding protein, Slx9, which facilitates Crm1 recruitment to the 40S pre-ribosome-associated NES-containing adaptor Rio2. In vitro, Slx9 binds Rio2 and RanGTP, forming a complex. This complex directly loads Crm1, unveiling a non-canonical stepwise mechanism to assemble a Crm1-export complex. A mutation in Slx9 that impairs Crm1-export complex assembly inhibits 40S pre-ribosome export. Thus, Slx9 functions as a scaffold to optimally present RanGTP and the NES to Crm1, therefore, triggering 40S pre-ribosome export. This mechanism could represent one solution to the paradox of weak binding events underlying rapid Crm1-mediated export.
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Affiliation(s)
- Ute Fischer
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Nico Schäuble
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Sabina Schütz
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
- Molecular Life Science, Graduate School, Zurich, Switzerland
| | - Martin Altvater
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
- Molecular Life Science, Graduate School, Zurich, Switzerland
| | - Yiming Chang
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Marius Boulos Faza
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Vikram Govind Panse
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
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168
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Abstract
The human genome encodes seven isoforms of importin α which are grouped into three subfamilies known as α1, α2 and α3. All isoforms share a fundamentally conserved architecture that consists of an N-terminal, autoinhibitory, importin-β-binding (IBB) domain and a C-terminal Arm (Armadillo)-core that associates with nuclear localization signal (NLS) cargoes. Despite striking similarity in amino acid sequence and 3D structure, importin-α isoforms display remarkable substrate specificity in vivo. In the present review, we look at key differences among importin-α isoforms and provide a comprehensive inventory of known viral and cellular cargoes that have been shown to associate preferentially with specific isoforms. We illustrate how the diversification of the adaptor importin α into seven isoforms expands the dynamic range and regulatory control of nucleocytoplasmic transport, offering unexpected opportunities for pharmacological intervention. The emerging view of importin α is that of a key signalling molecule, with isoforms that confer preferential nuclear entry and spatiotemporal specificity on viral and cellular cargoes directly linked to human diseases.
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169
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Christodoulou A, Yokoyama H. Purification of nuclear localization signal-containing proteins and its application to investigation of the mechanisms of the cell division cycle. Small GTPases 2015; 6:20-7. [PMID: 25862163 PMCID: PMC4601338 DOI: 10.4161/21541248.2014.978162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The GTP bound form of the Ran GTPase (RanGTP) in the nucleus promotes nuclear import of the proteins bearing nuclear localization signals (NLS). When nuclear envelopes break down during mitosis, RanGTP is locally produced around chromosomes and drives the assembly of the spindle early in mitosis and the nuclear envelope (NE) later. RanGTP binds to the heterodimeric nuclear transport receptor importin α/β and releases NLS proteins from the receptor. Liberated NLS proteins around chromosomes have been shown to play distinct, essential roles in spindle and NE assembly. Here we provide a highly specific protocol to purify NLS proteins from crude cell lysates. The pure NLS fraction is an excellent resource to investigate the NLS protein function and identify new mitotic regulators, uncovering fundamental mechanisms of the cell division cycle. It takes 2–3 days to obtain the NLS fraction.
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170
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Daugherty MD, Malik HS. How a virus blocks a cellular emergency access lane to the nucleus, STAT! Cell Host Microbe 2015; 16:150-152. [PMID: 25121743 DOI: 10.1016/j.chom.2014.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Early in viral infection, the STAT1 transcription factor is rapidly transported into the nucleus using a nonconventional import mechanism to establish an antiviral state. In this issue, Xu et al. (2014) show how the Ebola virus VP24 protein precisely blocks specialized STAT1 import while leaving other cellular import processes intact.
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Affiliation(s)
- Matthew D Daugherty
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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171
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Xu W, Edwards MR, Borek DM, Feagins AR, Mittal A, Alinger JB, Berry KN, Yen B, Hamilton J, Brett TJ, Pappu RV, Leung DW, Basler CF, Amarasinghe GK. Ebola virus VP24 targets a unique NLS binding site on karyopherin alpha 5 to selectively compete with nuclear import of phosphorylated STAT1. Cell Host Microbe 2015; 16:187-200. [PMID: 25121748 DOI: 10.1016/j.chom.2014.07.008] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/10/2014] [Accepted: 07/18/2014] [Indexed: 01/05/2023]
Abstract
During antiviral defense, interferon (IFN) signaling triggers nuclear transport of tyrosine-phosphorylated STAT1 (PY-STAT1), which occurs via a subset of karyopherin alpha (KPNA) nuclear transporters. Many viruses, including Ebola virus, actively antagonize STAT1 signaling to counteract the antiviral effects of IFN. Ebola virus VP24 protein (eVP24) binds KPNA to inhibit PY-STAT1 nuclear transport and render cells refractory to IFNs. We describe the structure of human KPNA5 C terminus in complex with eVP24. In the complex, eVP24 recognizes a unique nonclassical nuclear localization signal (NLS) binding site on KPNA5 that is necessary for efficient PY-STAT1 nuclear transport. eVP24 binds KPNA5 with very high affinity to effectively compete with and inhibit PY-STAT1 nuclear transport. In contrast, eVP24 binding does not affect the transport of classical NLS cargo. Thus, eVP24 counters cell-intrinsic innate immunity by selectively targeting PY-STAT1 nuclear import while leaving the transport of other cargo that may be required for viral replication unaffected.
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Affiliation(s)
- Wei Xu
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Megan R Edwards
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dominika M Borek
- Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Alicia R Feagins
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anuradha Mittal
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University, St. Louis, MO 63110, USA
| | - Joshua B Alinger
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Kayla N Berry
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Benjamin Yen
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jennifer Hamilton
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tom J Brett
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University, St. Louis, MO 63110, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Christopher F Basler
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO 63110, USA.
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172
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Mott HR, Owen D. Structures of Ras superfamily effector complexes: What have we learnt in two decades? Crit Rev Biochem Mol Biol 2015; 50:85-133. [PMID: 25830673 DOI: 10.3109/10409238.2014.999191] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The Ras superfamily small G proteins are master regulators of a diverse range of cellular processes and act via downstream effector molecules. The first structure of a small G protein-effector complex, that of Rap1A with c-Raf1, was published 20 years ago. Since then, the structures of more than 60 small G proteins in complex with their effectors have been published. These effectors utilize a diverse array of structural motifs to interact with the G protein fold, which we have divided into four structural classes: intermolecular β-sheets, helical pairs, other interactions, and pleckstrin homology (PH) domains. These classes and their representative structures are discussed and a contact analysis of the interactions is presented, which highlights the common effector-binding regions between and within the small G protein families.
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Affiliation(s)
- Helen R Mott
- Department of Biochemistry, University of Cambridge , Cambridge , UK
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173
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Kelley K, Knockenhauer KE, Kabachinski G, Schwartz TU. Atomic structure of the Y complex of the nuclear pore. Nat Struct Mol Biol 2015; 22:425-431. [PMID: 25822992 PMCID: PMC4424061 DOI: 10.1038/nsmb.2998] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/05/2015] [Indexed: 01/08/2023]
Abstract
The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. Here we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved core of the Y complex has six rather than seven members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.
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Affiliation(s)
- Kotaro Kelley
- Department of Biology, Massachusetts Institute of Technology Cambridge, MA USA
| | | | - Greg Kabachinski
- Department of Biology, Massachusetts Institute of Technology Cambridge, MA USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology Cambridge, MA USA
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174
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Khorashad JS, Eiring AM, Mason CC, Gantz KC, Bowler AD, Redwine HM, Yu F, Kraft IL, Pomicter AD, Reynolds KR, Iovino AJ, Zabriskie MS, Heaton WL, Tantravahi SK, Kauffman M, Shacham S, Chenchik A, Bonneau K, Ullman KS, O'Hare T, Deininger MW. shRNA library screening identifies nucleocytoplasmic transport as a mediator of BCR-ABL1 kinase-independent resistance. Blood 2015; 125:1772-81. [PMID: 25573989 PMCID: PMC4357584 DOI: 10.1182/blood-2014-08-588855] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/23/2014] [Indexed: 12/26/2022] Open
Abstract
The mechanisms underlying tyrosine kinase inhibitor (TKI) resistance in chronic myeloid leukemia (CML) patients lacking explanatory BCR-ABL1 kinase domain mutations are incompletely understood. To identify mechanisms of TKI resistance that are independent of BCR-ABL1 kinase activity, we introduced a lentiviral short hairpin RNA (shRNA) library targeting ∼5000 cell signaling genes into K562(R), a CML cell line with BCR-ABL1 kinase-independent TKI resistance expressing exclusively native BCR-ABL1. A customized algorithm identified genes whose shRNA-mediated knockdown markedly impaired growth of K562(R) cells compared with TKI-sensitive controls. Among the top candidates were 2 components of the nucleocytoplasmic transport complex, RAN and XPO1 (CRM1). shRNA-mediated RAN inhibition or treatment of cells with the XPO1 inhibitor, KPT-330 (Selinexor), increased the imatinib sensitivity of CML cell lines with kinase-independent TKI resistance. Inhibition of either RAN or XPO1 impaired colony formation of CD34(+) cells from newly diagnosed and TKI-resistant CML patients in the presence of imatinib, without effects on CD34(+) cells from normal cord blood or from a patient harboring the BCR-ABL1(T315I) mutant. These data implicate RAN in BCR-ABL1 kinase-independent imatinib resistance and show that shRNA library screens are useful to identify alternative pathways critical to drug resistance in CML.
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MESH Headings
- Active Transport, Cell Nucleus/genetics
- Benzamides/pharmacology
- Cell Line, Tumor
- Cell Survival
- Drug Resistance, Neoplasm/genetics
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Gene Knockdown Techniques
- Gene Library
- Humans
- Hydrazines/pharmacology
- Imatinib Mesylate
- K562 Cells
- Karyopherins/antagonists & inhibitors
- Karyopherins/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Mutation
- Piperazines/pharmacology
- Protein Kinase Inhibitors/pharmacology
- Pyrimidines/pharmacology
- RNA, Small Interfering/genetics
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/genetics
- Signal Transduction
- Triazoles/pharmacology
- Tumor Stem Cell Assay
- ran GTP-Binding Protein/antagonists & inhibitors
- ran GTP-Binding Protein/genetics
- Exportin 1 Protein
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Affiliation(s)
| | - Anna M Eiring
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | - Clinton C Mason
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | - Kevin C Gantz
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | - Amber D Bowler
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | - Hannah M Redwine
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | - Fan Yu
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT; Beijing Tsinghua Chang Gung Hospital, Tsinghua University, Beijing, China
| | - Ira L Kraft
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | | | | | - Anthony J Iovino
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | | | - William L Heaton
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT
| | - Srinivas K Tantravahi
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT; Division of Hematology and Hematologic Malignancies, The University of Utah, Salt Lake City, UT
| | | | | | | | | | | | - Thomas O'Hare
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT; Division of Hematology and Hematologic Malignancies, The University of Utah, Salt Lake City, UT
| | - Michael W Deininger
- Huntsman Cancer Institute, The University of Utah, Salt Lake City, UT; Division of Hematology and Hematologic Malignancies, The University of Utah, Salt Lake City, UT
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175
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Song J, Kose S, Watanabe A, Son SY, Choi S, Hong H, Yamashita E, Park IY, Imamoto N, Lee SJ. Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70s. ACTA ACUST UNITED AC 2015; 71:473-83. [PMID: 25760597 DOI: 10.1107/s1399004714026881] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/08/2014] [Indexed: 11/10/2022]
Abstract
Hikeshi is a nuclear transport receptor required for cell survival after stress. It mediates heat-shock-induced nuclear import of 70 kDa heat-shock proteins (Hsp70s) through interactions with FG-nucleoporins (FG-Nups), which are proteins in nuclear pore complexes (NPCs). Here, the crystal structure of human Hikeshi is presented at 1.8 Å resolution. Hikeshi forms an asymmetric homodimer that is responsible for the interaction with Hsp70s. The asymmetry of Hikeshi arises from the distinct conformation of the C-terminal domain (CTD) and the flexibility of the linker regions of each monomer. Structure-guided mutational analyses showed that both the flexible linker region and the CTD are important for nuclear import of Hsp70. Pull-down assays revealed that only full-length Hsp70s can interact with Hikeshi. The N-terminal domain (NTD) consists of a jelly-roll/β-sandwich fold structure which contains hydrophobic pockets involved in FG-Nup recognition. A unique extended loop (E-loop) in the NTD is likely to regulate the interactions of Hikeshi with FG-Nups. The crystal structure of Hikeshi explains how Hikeshi participates in the regulation of nuclear import through the recognition of FG-Nups and which part of Hikeshi affects its binding to Hsp70. This study is the first to yield structural insight into this highly unique import receptor.
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Affiliation(s)
- Jinsue Song
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Shingo Kose
- Cellular Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ai Watanabe
- Cellular Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Se Young Son
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Saehae Choi
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Hyerim Hong
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, 3-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Il Yeong Park
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Soo Jae Lee
- College of Pharmacy, Chungbuk National University, 48 Gaeshin-dong, Heungduk-gu, Cheongju, Chungbuk 361-763, Republic of Korea
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176
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Jang AR, Moravcevic K, Saez L, Young MW, Sehgal A. Drosophila TIM binds importin α1, and acts as an adapter to transport PER to the nucleus. PLoS Genet 2015; 11:e1004974. [PMID: 25674790 PMCID: PMC4335507 DOI: 10.1371/journal.pgen.1004974] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 12/23/2014] [Indexed: 02/07/2023] Open
Abstract
Regulated nuclear entry of clock proteins is a conserved feature of eukaryotic circadian clocks and serves to separate the phase of mRNA activation from mRNA repression in the molecular feedback loop. In Drosophila, nuclear entry of the clock proteins, PERIOD (PER) and TIMELESS (TIM), is tightly controlled, and impairments of this process produce profound behavioral phenotypes. We report here that nuclear entry of PER-TIM in clock cells, and consequently behavioral rhythms, require a specific member of a classic nuclear import pathway, Importin α1 (IMPα1). In addition to IMPα1, rhythmic behavior and nuclear expression of PER-TIM require a specific nuclear pore protein, Nup153, and Ran-GTPase. IMPα1 can also drive rapid and efficient nuclear expression of TIM and PER in cultured cells, although the effect on PER is mediated by TIM. Mapping of interaction domains between IMPα1 and TIM/PER suggests that TIM is the primary cargo for the importin machinery. This is supported by attenuated interaction of IMPα1 with TIM carrying a mutation previously shown to prevent nuclear entry of TIM and PER. TIM is detected at the nuclear envelope, and computational modeling suggests that it contains HEAT-ARM repeats typically found in karyopherins, consistent with its role as a co-transporter for PER. These findings suggest that although PER is the major timekeeper of the clock, TIM is the primary target of nuclear import mechanisms. Thus, the circadian clock uses specific components of the importin pathway with a novel twist in that TIM serves a karyopherin-like role for PER. In Drosophila, circadian rhythms are driven by a negative feedback loop that includes the key regulators, period (per) and timeless (tim). To generate this feedback loop, PER and TIM proteins first accumulate in the cytoplasm and then translocate to the nucleus where PER represses transcription. Thus, the nuclear import of PER-TIM proteins is a critical step to separate the phases of activation and repression of mRNA synthesis. In this study, we discovered that a member of the nuclear import machinery, importin α1 is an essential component of this feedback loop. Flies lacking importin α1 (IMPα1) display arrhythmic behavior and cytoplasmic expression of both PER and TIM at all times. In cultured S2 cells, IMPα1 expression directly facilitates nuclear import of TIM, but the effect on PER appears to be indirect. TIM expression is detected at the nuclear envelope and it interacts with other components of the nuclear transport machinery, which we show are also required for nuclear expression of TIM-PER and for behavioral rhythms. Our results thus suggest that TIM functions to link PER to the nuclear import machinery through IMPα1. Altogether, this study provides the mechanistic basis of a crucial step in the circadian clock mechanism.
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Affiliation(s)
- A. Reum Jang
- Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katarina Moravcevic
- Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Lino Saez
- Laboratory of Genetics, The Rockefeller University, New York, New York, United States of America
| | - Michael W. Young
- Laboratory of Genetics, The Rockefeller University, New York, New York, United States of America
| | - Amita Sehgal
- Howard Hughes Medical Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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177
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Molecular determinants for nuclear import of influenza A PB2 by importin α isoforms 3 and 7. Structure 2015; 23:374-84. [PMID: 25599645 DOI: 10.1016/j.str.2014.11.015] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/14/2014] [Accepted: 11/18/2014] [Indexed: 11/23/2022]
Abstract
Influenza A virus polymerase subunit PB2 is a major virulence determinant implicated in pathogenicity and host adaptation. During cross-species virus transfer from avian to mammalian cells, PB2 switches specificity from importin α3 to α7. This specificity is not recapitulated in vitro, where PB2 binds all importin α isoforms with comparably high affinity. In this study, we investigated the structure, conformational dynamics, and autoinhibition of importin α isoforms 1, 3, and 7 in complex with PB2. Our data suggest that association of PB2 with α3 and α7 is favored by reduced autoinhibition of these isoforms and by the unique structure of the nuclear localization signal (NLS) domain of PB2. We propose that by recruiting importin α3 or α7 in the absence of importin β, PB2 reduces the complexity of adaptor-mediated import to a pseudo-bimolecular reaction, thereby acquiring a kinetic advantage over classical NLS cargos, which form an import complex only when importin α and β are simultaneously available.
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178
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Schmidt HB, Görlich D. Nup98 FG domains from diverse species spontaneously phase-separate into particles with nuclear pore-like permselectivity. eLife 2015; 4. [PMID: 25562883 PMCID: PMC4283134 DOI: 10.7554/elife.04251] [Citation(s) in RCA: 247] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/20/2014] [Indexed: 01/28/2023] Open
Abstract
Nuclear pore complexes (NPCs) conduct massive transport mediated by shuttling nuclear transport receptors (NTRs), while keeping nuclear and cytoplasmic contents separated. The NPC barrier in Xenopus relies primarily on the intrinsically disordered FG domain of Nup98. We now observed that Nup98 FG domains of mammals, lancelets, insects, nematodes, fungi, plants, amoebas, ciliates, and excavates spontaneously and rapidly phase-separate from dilute (submicromolar) aqueous solutions into characteristic 'FG particles'. This required neither sophisticated experimental conditions nor auxiliary eukaryotic factors. Instead, it occurred already during FG domain expression in bacteria. All Nup98 FG phases rejected inert macromolecules and yet allowed far larger NTR cargo complexes to rapidly enter. They even recapitulated the observations that large cargo-domains counteract NPC passage of NTR⋅cargo complexes, while cargo shielding and increased NTR⋅cargo surface-ratios override this inhibition. Their exquisite NPC-typical sorting selectivity and strong intrinsic assembly propensity suggest that Nup98 FG phases can form in authentic NPCs and indeed account for the permeability properties of the pore.
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Affiliation(s)
- Hermann Broder Schmidt
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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179
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Wirthmueller L, Roth C, Fabro G, Caillaud MC, Rallapalli G, Asai S, Sklenar J, Jones AME, Wiermer M, Jones JDG, Banfield MJ. Probing formation of cargo/importin-α transport complexes in plant cells using a pathogen effector. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:40-52. [PMID: 25284001 PMCID: PMC4350430 DOI: 10.1111/tpj.12691] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/26/2014] [Accepted: 09/29/2014] [Indexed: 05/17/2023]
Abstract
Importin-αs are essential adapter proteins that recruit cytoplasmic proteins destined for active nuclear import to the nuclear transport machinery. Cargo proteins interact with the importin-α armadillo repeat domain via nuclear localization sequences (NLSs), short amino acids motifs enriched in Lys and Arg residues. Plant genomes typically encode several importin-α paralogs that can have both specific and partially redundant functions. Although some cargos are preferentially imported by a distinct importin-α it remains unknown how this specificity is generated and to what extent cargos compete for binding to nuclear transport receptors. Here we report that the effector protein HaRxL106 from the oomycete pathogen Hyaloperonospora arabidopsidis co-opts the host cell's nuclear import machinery. We use HaRxL106 as a probe to determine redundant and specific functions of importin-α paralogs from Arabidopsis thaliana. A crystal structure of the importin-α3/MOS6 armadillo repeat domain suggests that five of the six Arabidopsis importin-αs expressed in rosette leaves have an almost identical NLS-binding site. Comparison of the importin-α binding affinities of HaRxL106 and other cargos in vitro and in plant cells suggests that relatively small affinity differences in vitro affect the rate of transport complex formation in vivo. Our results suggest that cargo affinity for importin-α, sequence variation at the importin-α NLS-binding sites and tissue-specific expression levels of importin-αs determine formation of cargo/importin-α transport complexes in plant cells.
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Affiliation(s)
- Lennart Wirthmueller
- The Sainsbury LaboratoryNorwich Research Park, Norwich, NR4 7UH, UK
- Department of Biological Chemistry, John Innes CentreNorwich Research Park, Norwich, NR4 7UH, UK
| | - Charlotte Roth
- Department of Plant Cell Biology, Georg-August-UniversityJulia-Lermontowa-Weg 3, 37077, Goettingen, Germany
| | - Georgina Fabro
- The Sainsbury LaboratoryNorwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Shuta Asai
- The Sainsbury LaboratoryNorwich Research Park, Norwich, NR4 7UH, UK
| | - Jan Sklenar
- The Sainsbury LaboratoryNorwich Research Park, Norwich, NR4 7UH, UK
| | | | - Marcel Wiermer
- Department of Plant Cell Biology, Georg-August-UniversityJulia-Lermontowa-Weg 3, 37077, Goettingen, Germany
| | | | - Mark J Banfield
- Department of Biological Chemistry, John Innes CentreNorwich Research Park, Norwich, NR4 7UH, UK
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180
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Nerurkar P, Altvater M, Gerhardy S, Schütz S, Fischer U, Weirich C, Panse VG. Eukaryotic Ribosome Assembly and Nuclear Export. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 319:107-40. [DOI: 10.1016/bs.ircmb.2015.07.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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181
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Khalil H, Loukili N, Regamey A, Cuesta-Marban A, Santori E, Huber M, Widmann C. The caspase-3/p120 RasGAP module generates a NF-κB repressor in response to cellular stress. J Cell Sci 2015. [DOI: 10.1242/jcs.174409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The NF-κB transcription factor is a master regulator of inflammation. Short-term NF-κB activation is generally beneficial. However, sustained NF-κB may be detrimental, directly causing apoptosis of cells or leading to a persistent damaging inflammatory response. NF-κB activity in stressed cells needs therefore to be controlled for homeostasis maintenance. Here we show that fragment N that is produced by the caspase-3/p120 RasGAP sensor in mildly stressed cells is a potent NF-κB inhibitor. Fragment N decreases the transcriptional activity of NF-κB by promoting its export from the nucleus. Cells unable to generate fragment N displayed increased NF-κB activation upon stress. Knock-in mice expressing the uncleavable RasGAP mutant showed exaggerated NF-κB activation when their epidermis was treated with anthralin, a drug used for the treatment of psoriasis. Our study provides biochemical and genetic evidence of the importance of the caspase-3/p120 RasGAP stress-sensing module in the control of stress-induced NF-κB activation.
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Affiliation(s)
- Hadi Khalil
- Department of Physiology, Biology and Medicine Faculty, University of Lausanne, Switzerland
| | - Noureddine Loukili
- Department of Physiology, Biology and Medicine Faculty, University of Lausanne, Switzerland
| | - Alexandre Regamey
- Department of Dermatology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alvaro Cuesta-Marban
- Department of Physiology, Biology and Medicine Faculty, University of Lausanne, Switzerland
| | - Elettra Santori
- Department of Physiology, Biology and Medicine Faculty, University of Lausanne, Switzerland
| | - Marcel Huber
- Department of Dermatology, Lausanne University Hospital, Lausanne, Switzerland
| | - Christian Widmann
- Department of Physiology, Biology and Medicine Faculty, University of Lausanne, Switzerland
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182
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Cautain B, Hill R, de Pedro N, Link W. Components and regulation of nuclear transport processes. FEBS J 2014; 282:445-62. [PMID: 25429850 PMCID: PMC7163960 DOI: 10.1111/febs.13163] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 12/27/2022]
Abstract
The spatial separation of DNA replication and gene transcription in the nucleus and protein translation in the cytoplasm is a uniform principle of eukaryotic cells. This compartmentalization imposes a requirement for a transport network of macromolecules to shuttle these components in and out of the nucleus. This nucleo‐cytoplasmic transport of macromolecules is critical for both cell physiology and pathology. Consequently, investigating its regulation and disease‐associated alterations can reveal novel therapeutic approaches to fight human diseases, such as cancer or viral infection. The characterization of the nuclear pore complex, the identification of transport signals and transport receptors, as well as the characterization of the Ran system (providing the energy source for efficient cargo transport) has greatly facilitated our understanding of the components, mechanisms and regulation of the nucleo‐cytoplasmic transport of proteins in our cells. Here we review this knowledge with a specific emphasis on the selection of disease‐relevant molecular targets for potential therapeutic intervention.
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Affiliation(s)
- Bastien Cautain
- Fundacion MEDINA Parque tecnológico ciencias de la salud, Granada, Spain
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183
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Róna G, Pálinkás HL, Borsos M, Horváth A, Scheer I, Benedek A, Nagy GN, Zagyva I, Vértessy BG. NLS copy-number variation governs efficiency of nuclear import - case study on dUTPases. FEBS J 2014; 281:5463-78. [DOI: 10.1111/febs.13086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 09/10/2014] [Accepted: 09/29/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Gergely Róna
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
| | - Hajnalka L. Pálinkás
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Doctoral School of Multidisciplinary Medical Science; University of Szeged; Hungary
| | - Máté Borsos
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - András Horváth
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - Ildikó Scheer
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
| | - András Benedek
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
| | - Gergely N. Nagy
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
| | - Imre Zagyva
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest Hungary
- Department of Applied Biotechnology and Food Sciences; Budapest University of Technology and Economics; Hungary
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184
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Abstract
SNPs (single nucleotide polymorphisms) on a chromosome 16 locus encompassing FTO, as well as IRX3, 5, 6, FTM and FTL are robustly associated with human obesity. FTO catalyses the Fe(II)- and 2OG-dependent demethylation of RNA and is an AA (amino acid) sensor that couples AA levels to mTORC1 (mammalian target of rapamycin complex 1) signalling, thereby playing a key role in regulating growth and translation. However, the cellular compartment in which FTO primarily resides to perform its biochemical role is unclear. Here, we undertake live cell imaging of GFP (green fluorescent protein)-FTO, and demonstrate that FTO resides in both the nucleus and cytoplasm. We show using ‘FLIP’ (fluorescence loss in photobleaching) that a mobile FTO fraction shuttles between both compartments. We performed a proteomic study and identified XPO2 (Exportin 2), one of a family of proteins that mediates the shuttling of proteins between the nucleus and the cytoplasm, as a binding partner of FTO. Finally, using deletion studies, we show that the N-terminus of FTO is required for its ability to shuttle between the nucleus and cytoplasm. In conclusion, FTO is present in both the nucleus and cytoplasm, with a mobile fraction that shuttles between both cellular compartments, possibly by interaction with XPO2. Exportin interacts with FTO and this interaction might be involved in the nucelocytoplasmic shuttling of FTO in the cell.
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185
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186
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Anderson F, Savulescu AF, Rudolph K, Schipke J, Cohen I, Ibiricu I, Rotem A, Grünewald K, Sodeik B, Harel A. Targeting of viral capsids to nuclear pores in a cell-free reconstitution system. Traffic 2014; 15:1266-81. [PMID: 25131140 DOI: 10.1111/tra.12209] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/13/2014] [Accepted: 08/13/2014] [Indexed: 11/28/2022]
Abstract
Many viruses deliver their genomes into the nucleoplasm for viral transcription and replication. Here, we describe a novel cell-free system to elucidate specific interactions between viruses and nuclear pore complexes (NPCs). Nuclei reconstituted in vitro from egg extracts of Xenopus laevis, an established biochemical system to decipher nuclear functions, were incubated with GFP-tagged capsids of herpes simplex virus, an alphaherpesvirus replicating in the nucleus. Capsid binding to NPCs was analyzed using fluorescence and field emission scanning electron microscopy. Tegument-free capsids or viral capsids exposing inner tegument proteins on their surface bound to nuclei, while capsids inactivated by a high-salt treatment or covered by inner and outer tegument showed less binding. There was little binding of the four different capsid types to nuclei lacking functional NPCs. This novel approach provides a powerful system to elucidate the molecular mechanisms that enable viral structures to engage with NPCs. Furthermore, this assay could be expanded to identify molecular cues triggering viral genome uncoating and nuclear import of viral genomes.
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Affiliation(s)
- Fenja Anderson
- Institute of Virology, OE 5230, Hannover Medical School, Carl-Neuberg-Straße 1, D-30623, Hannover, Germany
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187
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Monecke T, Dickmanns A, Ficner R. Allosteric control of the exportin CRM1 unraveled by crystal structure analysis. FEBS J 2014; 281:4179-94. [PMID: 24823279 PMCID: PMC4231977 DOI: 10.1111/febs.12842] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/02/2014] [Accepted: 05/12/2014] [Indexed: 01/07/2023]
Abstract
Nucleocytoplasmic trafficking in eukaryotic cells is a highly regulated and coordinated process which involves an increasing variety of soluble nuclear transport receptors. Generally, transport receptors specifically bind their cargo and facilitate its transition through nuclear pore complexes, aqueous channels connecting the two compartments. Directionality of such transport events by receptors of the importin β superfamily requires the interaction with the small GTPase Ras-related nuclear antigen (Ran). While importins need RanGTP to release their cargo in the nucleus and thus to terminate import, exportins recruit cargo in the RanGTP-bound state. The exportin chromosome region maintenance 1 (CRM1) is a highly versatile transport receptor that exports a plethora of different protein and RNP cargoes. Moreover, binding of RanGTP and of cargo to CRM1 are highly cooperative events despite the fact that cargo and RanGTP do not interact directly in crystal structures of assembled export complexes. Integrative approaches have recently unraveled the individual steps of the CRM1 transport cycle at a structural level and explained how the HEAT-repeat architecture of CRM1 provides a framework for the key elements to mediate allosteric interactions with RanGTP, Ran binding proteins and cargo. Moreover, during the last decade, CRM1 has become a more and more appreciated target for anti-cancer drugs. Hence, detailed understanding of the flexibility, the regulatory features and the positive binding cooperativity between CRM1, Ran and cargo is a prerequisite for the development of highly effective drugs. Here we review recent structural advances in the characterization of CRM1 and CRM1-containing complexes with a special emphasis on X-ray crystallographic studies.
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Affiliation(s)
- Thomas Monecke
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August-Universität Göttingen, Germany
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188
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Subbotin RI, Chait BT. A pipeline for determining protein-protein interactions and proximities in the cellular milieu. Mol Cell Proteomics 2014; 13:2824-35. [PMID: 25172955 DOI: 10.1074/mcp.m114.041095] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It remains extraordinarily challenging to elucidate endogenous protein-protein interactions and proximities within the cellular milieu. The dynamic nature and the large range of affinities of these interactions augment the difficulty of this undertaking. Among the most useful tools for extracting such information are those based on affinity capture of target bait proteins in combination with mass spectrometric readout of the co-isolated species. Although highly enabling, the utility of affinity-based methods is generally limited by difficulties in distinguishing specific from nonspecific interactors, preserving and isolating all unique interactions including those that are weak, transient, or rapidly exchanging, and differentiating proximal interactions from those that are more distal. Here, we have devised and optimized a set of methods to address these challenges. The resulting pipeline involves flash-freezing cells in liquid nitrogen to preserve the cellular environment at the moment of freezing; cryomilling to fracture the frozen cells into intact micron chunks to allow for rapid access of a chemical reagent and to stabilize the intact endogenous subcellular assemblies and interactors upon thawing; and utilizing the high reactivity of glutaraldehyde to achieve sufficiently rapid stabilization at low temperatures to preserve native cellular interactions. In the course of this work, we determined that relatively low molar ratios of glutaraldehyde to reactive amines within the cellular milieu were sufficient to preserve even labile and transient interactions. This mild treatment enables efficient and rapid affinity capture of the protein assemblies of interest under nondenaturing conditions, followed by bottom-up MS to identify and quantify the protein constituents. For convenience, we have termed this approach Stabilized Affinity Capture Mass Spectrometry. Here, we demonstrate that Stabilized Affinity Capture Mass Spectrometry allows us to stabilize and elucidate local, distant, and transient protein interactions within complex cellular milieux, many of which are not observed in the absence of chemical stabilization.
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Affiliation(s)
- Roman I Subbotin
- From the ‡The Rockefeller University 1230 York Ave, New York, New York
| | - Brian T Chait
- From the ‡The Rockefeller University 1230 York Ave, New York, New York
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189
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Schütz S, Fischer U, Altvater M, Nerurkar P, Peña C, Gerber M, Chang Y, Caesar S, Schubert OT, Schlenstedt G, Panse VG. A RanGTP-independent mechanism allows ribosomal protein nuclear import for ribosome assembly. eLife 2014; 3:e03473. [PMID: 25144938 PMCID: PMC4161973 DOI: 10.7554/elife.03473] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Within a single generation time a growing yeast cell imports ∼14 million ribosomal proteins (r-proteins) into the nucleus for ribosome production. After import, it is unclear how these intrinsically unstable and aggregation-prone proteins are targeted to the ribosome assembly site in the nucleolus. Here, we report the discovery of a conserved nuclear carrier Tsr2 that coordinates transfer of the r-protein eS26 to the earliest assembling pre-ribosome, the 90S. In vitro studies revealed that Tsr2 efficiently dissociates importin:eS26 complexes via an atypical RanGTP-independent mechanism that terminates the import process. Subsequently, Tsr2 binds the released eS26, shields it from proteolysis, and ensures its safe delivery to the 90S pre-ribosome. We anticipate similar carriers—termed here escortins—to securely connect the nuclear import machinery with pathways that deposit r-proteins onto developing pre-ribosomal particles. DOI:http://dx.doi.org/10.7554/eLife.03473.001 The production of a protein in a cell starts with a region of DNA being transcribed to produce a molecule of messenger RNA. A large molecular machine called ribosome then reads the information in the messenger RNA molecule to produce a protein. Ribosomes themselves are made of RNA and several different proteins called r-proteins. The construction of a ribosome starts with the assembly of a pre-ribosome inside the cell nucleus, and the ribosome is completed in the cytosol of the cell. A yeast cell will divide about 30 times during its lifetime, and before each division event a single yeast cell needs to import about 14 million r-proteins into its nucleus in order to make about 200,000 ribosomes. However, many details of this process are mysterious. In particular, many r-proteins are known to be unstable: meaning that, left to their own devices, r-proteins are highly likely to aggregate, which would prevent them becoming part of a ribosome. Now, Schütz et al. have figured out how a carrier protein called Tsr2 makes sure that an r-protein called eS26 does indeed become part of a ribosome. The human disorder known as Diamond-Blackfan anemia is caused by a mutation in the gene for eS26. The eS26 proteins are ferried to the cell nucleus on specialized transport vehicles. Schütz et al. have now shown that the Tsr2 carrier protein unloads the r-protein from the transport vehicle in the nucleus, and then binds it. This means that the r-protein does not form an aggregate. Finally, the Tsr2 carrier protein transfers the r-protein to the pre-ribosome. This is the first time that a carrier protein that unloads an r-protein cargo from its transport vehicle, to ensure safe delivery to the pre-ribosome, has been identified. DOI:http://dx.doi.org/10.7554/eLife.03473.002
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Affiliation(s)
- Sabina Schütz
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland Molecular Life Science Graduate School, University of Zurich, Zurich, Switzerland
| | - Ute Fischer
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Martin Altvater
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland Molecular Life Science Graduate School, University of Zurich, Zurich, Switzerland
| | - Purnima Nerurkar
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland Molecular Life Science Graduate School, University of Zurich, Zurich, Switzerland
| | - Cohue Peña
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Michaela Gerber
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Yiming Chang
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Stefanie Caesar
- Institute of Medical Biochemistry and Molecular Biology, Universität des Saarlandes, Homburg, Germany
| | - Olga T Schubert
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland Systems Biology Graduate School, Zurich, Zurich, Switzerland
| | - Gabriel Schlenstedt
- Institute of Medical Biochemistry and Molecular Biology, Universität des Saarlandes, Homburg, Germany
| | - Vikram G Panse
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
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190
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Turner JG, Dawson J, Cubitt CL, Baz R, Sullivan DM. Inhibition of CRM1-dependent nuclear export sensitizes malignant cells to cytotoxic and targeted agents. Semin Cancer Biol 2014; 27:62-73. [PMID: 24631834 PMCID: PMC4108511 DOI: 10.1016/j.semcancer.2014.03.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 02/25/2014] [Accepted: 03/01/2014] [Indexed: 10/25/2022]
Abstract
Nuclear-cytoplasmic trafficking of proteins is a significant factor in the development of cancer and drug resistance. Subcellular localization of exported proteins linked to cancer development include those involved in cell growth and proliferation, apoptosis, cell cycle regulation, transformation, angiogenesis, cell adhesion, invasion, and metastasis. Here, we examined the basic mechanisms involved in the export of proteins from the nucleus to the cytoplasm. All proteins over 40kDa use the nuclear pore complex to gain entry or exit from the nucleus, with the primary nuclear export molecule involved in these processes being chromosome region maintenance 1 (CRM1, exportin 1 or XPO1). Proteins exported from the nucleus must possess a hydrophobic nuclear export signal (NES) peptide that binds to a hydrophobic groove containing an active-site Cys528 in the CRM1 protein. CRM1 inhibitors function largely by covalent modification of the active site Cys528 and prevent binding to the cargo protein NES. In the absence of a CRM1 inhibitor, CRM1 binds cooperatively to the NES of the cargo protein and RanGTP, forming a trimer that is actively transported out of the nucleus by facilitated diffusion. Nuclear export can be blocked by CRM1 inhibitors, NES peptide inhibitors or by preventing post-translational modification of cargo proteins. Clinical trials using the classic CRM1 inhibitor leptomycin B proved too toxic for patients; however, a new generation of less toxic small molecule inhibitors is being used in clinical trials in patients with both hematological malignancies and solid tumors. Additional trials are being initiated using small-molecule CRM1 inhibitors in combination with chemotherapeutics such as pegylated liposomal doxorubicin. In this review, we present evidence that combining the new CRM1 inhibitors with other classes of therapeutics may prove effective in the treatment of cancer. Potential combinatorial therapies discussed include the use of CRM1 inhibitors and the addition of alkylating agents (melphalan), anthracyclines (doxorubicin and daunomycin), BRAF inhibitors, platinum drugs (cisplatin and oxaliplatin), proteosome inhibitors (bortezomib and carfilzomib), or tyrosine-kinase inhibitors (imatinib). Also, the sequence of treatment may be important for combination therapy. We found that the most effective treatment regimen involved first priming the cancer cells with the CRM1 inhibitor followed by doxorubicin, bortezomib, carfilzomib, or melphalan. This order sensitized both de novo and acquired drug-resistant cancer cell lines.
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Affiliation(s)
- Joel G Turner
- Department of Blood and Marrow Transplantation and Chemical Biology and Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jana Dawson
- Department of Blood and Marrow Transplantation and Chemical Biology and Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Christopher L Cubitt
- Translational Research Core Laboratory, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Rachid Baz
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Daniel M Sullivan
- Department of Blood and Marrow Transplantation and Chemical Biology and Molecular Medicine Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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191
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Senapedis WT, Baloglu E, Landesman Y. Clinical translation of nuclear export inhibitors in cancer. Semin Cancer Biol 2014; 27:74-86. [DOI: 10.1016/j.semcancer.2014.04.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/10/2014] [Indexed: 01/18/2023]
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192
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Lu M, Zak J, Chen S, Sanchez-Pulido L, Severson DT, Endicott J, Ponting CP, Schofield CJ, Lu X. A code for RanGDP binding in ankyrin repeats defines a nuclear import pathway. Cell 2014; 157:1130-45. [PMID: 24855949 DOI: 10.1016/j.cell.2014.05.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 01/22/2014] [Accepted: 03/13/2014] [Indexed: 01/23/2023]
Abstract
Regulation of nuclear import is fundamental to eukaryotic biology. The majority of nuclear import pathways are mediated by importin-cargo interactions. Yet not all nuclear proteins interact with importins, necessitating the identification of a general importin-independent nuclear import pathway. Here, we identify a code that determines importin-independent nuclear import of ankyrin repeats (ARs), a structural motif found in over 250 human proteins with diverse functions. AR-containing proteins (ARPs) with a hydrophobic residue at the 13th position of two consecutive ARs bind RanGDP efficiently, and consequently enter the nucleus. This code, experimentally tested in 17 ARPs, predicts the nuclear-cytoplasmic localization of over 150 annotated human ARPs with high accuracy and is acquired by the most common familial melanoma-associated CDKN2A mutation, leading to nuclear accumulation of mutant p16ink4a. The RaDAR (RanGDP/AR) pathway represents a general importin-independent nuclear import pathway and is frequently used by AR-containing transcriptional regulators, especially those regulating NF-κB/p53.
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Affiliation(s)
- Min Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Jaroslav Zak
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Shuo Chen
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Luis Sanchez-Pulido
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - David T Severson
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Jane Endicott
- Northern Institute for Cancer Research, University of Newcastle, Newcastle, NE2 4HH, UK
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
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193
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Iron-rich ferritin in the hypoxia-tolerant rodent Spalax ehrenbergi: a naturally-occurring biomarker confirms the internalization and pathways of intracellular macromolecules. J Struct Biol 2014; 187:254-265. [PMID: 25050761 DOI: 10.1016/j.jsb.2014.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 06/20/2014] [Accepted: 07/11/2014] [Indexed: 02/08/2023]
Abstract
The discovery of pits/caveolae in the plasmalemma advanced the study of macromolecule internalization. "Transcytosis" describes the transport of macromolecular cargo from one front of a polarized cell to the other within membrane-bounded carrier(s), via endocytosis, intracellular trafficking and exocytosis. Clathrin-mediated transcytosis is used extensively by epithelial cells, while caveolae-mediated transcytosis mostly occurs in endothelial cells. The internalization pathways were monitored by various markers, including radioisotopes, nanoparticles, enzymes, immunostains, and fluorophores. We describe an internalization pathway identified using a naturally-occurring biomarker, in vivo assembled ferritin, containing electron-dense iron cores. Iron, an essential trace metal for most living species and iron homeostasis, is crucial for cellular life. Ferritin is a ubiquitous and highly conserved archeoprotein whose main function is to store a reserve iron supply inside the cytoplasm in a non-toxic form. Ferritin is present in all organisms which have a metabolic requirement for iron and in even in organisms whose taxonomic rank is very low. The newborns of the blind mole, Spalax ehrenbergi, are born and live in a hypoxic environment and have significant iron overload in their liver and heart, but their iron metabolism has not been previously studied. These newborns, which are evolutionarily adapted to fluctuations in the environmental oxygen, have a unique ability to sequester transplacental iron and store it in ferritin without any signs of iron toxicity. Using the ferrihydrite cores of ferritin, we were able to monitor the ferritin internalization from portals of its entry into the cytosol of hepatocytes and cardiomyocytes and into the lysosomes.
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194
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Milles S, Lemke EA. Mapping Multivalency and Differential Affinities within Large Intrinsically Disordered Protein Complexes with Segmental Motion Analysis. Angew Chem Int Ed Engl 2014; 53:7364-7. [DOI: 10.1002/anie.201403694] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Sigrid Milles
- Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg (Germany)
| | - Edward A. Lemke
- Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg (Germany)
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195
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Milles S, Lemke EA. Detektion von Mehrbindigkeit und differenziellen Affinitäten in großen, intrinsisch ungeordneten Proteinen mithilfe von Segmentbewegungsanalyse. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403694] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sigrid Milles
- Structural and Computational Biology Unit, EMBL, Meyerhofstraße 1, 69117 Heidelberg (Deutschland)
| | - Edward A. Lemke
- Structural and Computational Biology Unit, EMBL, Meyerhofstraße 1, 69117 Heidelberg (Deutschland)
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196
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Tsirkone VG, Beutels KG, Demeulemeester J, Debyser Z, Christ F, Strelkov SV. Structure of transportin SR2, a karyopherin involved in human disease, in complex with Ran. Acta Crystallogr F Struct Biol Commun 2014; 70:723-9. [PMID: 24915079 PMCID: PMC4051523 DOI: 10.1107/s2053230x14009492] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 04/28/2014] [Indexed: 11/10/2022] Open
Abstract
Transportin SR2 (TRN-SR2) is a β-type karyopherin responsible for the nuclear import of specific cargoes, including serine/arginine-rich splicing factors. The protein has been implicated in a variety of human diseases, including HIV infection, primary biliary cirrhosis and limb-girdle muscular dystrophy 1F. Towards understanding its molecular mechanism, a 2.9 Å resolution crystal structure of human TRN-SR2 complexed with the small GTPase Ran has been determined. TRN-SR2 is composed of 20 α-helical HEAT repeats forming a solenoid-like fold. The first nine repeats form a `cradle' for the binding of RanGTP, revealing similarities but also differences with respect to the related importin 13 complex.
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Affiliation(s)
- Vicky G. Tsirkone
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - Katrien G. Beutels
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - Jonas Demeulemeester
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - Zeger Debyser
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - Frauke Christ
- Laboratory of Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
| | - Sergei V. Strelkov
- Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 bus 822, 3000 Leuven, Belgium
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197
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Kimura M, Imamoto N. Biological significance of the importin-β family-dependent nucleocytoplasmic transport pathways. Traffic 2014; 15:727-48. [PMID: 24766099 DOI: 10.1111/tra.12174] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/22/2014] [Accepted: 04/22/2014] [Indexed: 12/19/2022]
Abstract
Importin-β family proteins (Imp-βs) are nucleocytoplasmic transport receptors (NTRs) that import and export proteins and RNAs through the nuclear pores. The family consists of 14-20 members depending on the biological species, and each member transports a specific group of cargoes. Thus, the Imp-βs mediate multiple, parallel transport pathways that can be regulated separately. In fact, the spatiotemporally differential expressions and the functional regulations of Imp-βs have been reported. Additionally, the biological significance of each pathway has been characterized by linking the function of a member of Imp-βs to a cellular consequence. Connecting these concepts, the regulation of the transport pathways conceivably induces alterations in the cellular physiological states. However, few studies have linked the regulation of an importin-β family NTR to an induced cellular response and the corresponding cargoes, despite the significance of this linkage in comprehending the biological relevance of the transport pathways. This review of recent reports on the regulation and biological functions of the Imp-βs highlights the significance of the transport pathways in physiological contexts and points out the possibility that the identification of yet unknown specific cargoes will reinforce the importance of transport regulation.
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Affiliation(s)
- Makoto Kimura
- Cellular Dynamics Laboratory, RIKEN, Hirosawa 2-1, Wako, Saitama, 351-0198, Japan
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198
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Eisele NB, Labokha AA, Frey S, Görlich D, Richter RP. Cohesiveness tunes assembly and morphology of FG nucleoporin domain meshworks - Implications for nuclear pore permeability. Biophys J 2014; 105:1860-70. [PMID: 24138862 DOI: 10.1016/j.bpj.2013.09.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/25/2013] [Accepted: 09/04/2013] [Indexed: 12/20/2022] Open
Abstract
Nuclear pore complexes control the exchange of macromolecules between the cytoplasm and the nucleus. A selective permeability barrier that arises from a supramolecular assembly of intrinsically unfolded nucleoporin domains rich in phenylalanine-glycine dipeptides (FG domains) fills the nuclear pore. There is increasing evidence that selective transport requires cohesive FG domain interactions. To understand the functional roles of cohesive interactions, we studied monolayers of end-grafted FG domains as a bottom-up nanoscale model system of the permeability barrier. Based on detailed physicochemical analysis of the model films and comparison of the data with polymer theory, we propose that cohesiveness is tuned to promote rapid assembly of the permeability barrier and to generate a stable and compact pore-filling meshwork with a small mesh size. Our results highlight the functional importance of weak interactions, typically a few kBT per chain, and contribute important information to understand the mechanism of size-selective transport.
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Affiliation(s)
- Nico B Eisele
- Biosurfaces Unit, CIC biomaGUNE, San Sebastian, Spain; Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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199
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Zhang J, Dong ZQ, Zhang CD, He Q, Chen XM, Cao MY, Li HQ, Xiao WF, Lu C, Pan MH. Identification of a novel nuclear localization signal of baculovirus late expression factor 11. Virus Res 2014; 184:111-9. [DOI: 10.1016/j.virusres.2014.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/20/2014] [Accepted: 02/26/2014] [Indexed: 10/25/2022]
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200
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Tan DSP, Bedard PL, Kuruvilla J, Siu LL, Razak ARA. Promising SINEs for embargoing nuclear-cytoplasmic export as an anticancer strategy. Cancer Discov 2014; 4:527-37. [PMID: 24743138 DOI: 10.1158/2159-8290.cd-13-1005] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In cancer cells, the nuclear-cytoplasmic transport machinery is frequently disrupted, resulting in mislocalization and loss of function for many key regulatory proteins. In this review, the mechanisms by which tumor cells co-opt the nuclear transport machinery to facilitate carcinogenesis, cell survival, drug resistance, and tumor progression will be elucidated, with a particular focus on the role of the nuclear-cytoplasmic export protein. The recent development of a new generation of selective inhibitors of nuclear export (XPO1 antagonists) and how these novel anticancer drugs may bring us closer to the implementation of this therapeutic strategy in the clinic will be discussed.
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Affiliation(s)
- David S P Tan
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
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