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Davuluri G, Gong W, Yusuff S, Lorent K, Muthumani M, Dolan AC, Pack M. Mutation of the zebrafish nucleoporin elys sensitizes tissue progenitors to replication stress. PLoS Genet 2008; 4:e1000240. [PMID: 18974873 PMCID: PMC2570612 DOI: 10.1371/journal.pgen.1000240] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 09/29/2008] [Indexed: 12/15/2022] Open
Abstract
The recessive lethal mutation flotte lotte (flo) disrupts development of the zebrafish digestive system and other tissues. We show that flo encodes the ortholog of Mel-28/Elys, a highly conserved gene that has been shown to be required for nuclear integrity in worms and nuclear pore complex (NPC) assembly in amphibian and mammalian cells. Maternal elys expression sustains zebrafish flo mutants to larval stages when cells in proliferative tissues that lack nuclear pores undergo cell cycle arrest and apoptosis. p53 mutation rescues apoptosis in the flo retina and optic tectum, but not in the intestine, where the checkpoint kinase Chk2 is activated. Chk2 inhibition and replication stress induced by DNA synthesis inhibitors were lethal to flo larvae. By contrast, flo mutants were not sensitized to agents that cause DNA double strand breaks, thus showing that loss of Elys disrupts responses to selected replication inhibitors. Elys binds Mcm2-7 complexes derived from Xenopus egg extracts. Mutation of elys reduced chromatin binding of Mcm2, but not binding of Mcm3 or Mcm4 in the flo intestine. These in vivo data indicate a role for Elys in Mcm2-chromatin interactions. Furthermore, they support a recently proposed model in which replication origins licensed by excess Mcm2-7 are required for the survival of human cells exposed to replication stress. DNA replication is a complex process that requires activation of cell cycle checkpoints and DNA repair pathways. Genetic analyses in fungi have suggested that nucleoporins, the proteins that make up the nuclear pore complex (NPC), play a role in the cellular response to agents that disrupt cell proliferation or damage DNA. Here we show that mutation of the Elys nucleoporin causes widespread apoptosis in the intestine and other tissues of zebrafish flotte lotte (flo) mutants. Intestinal apoptosis occurs in the absence of the DNA damage marker γH2X, and levels of chromatin bound Mcm2, a component of the DNA replication helicase, were also reduced in flo mutants. These findings suggested that flo intestinal cells cannot repair endogenous replication errors. Consistent with this idea, flo mutants were highly sensitized to treatment with DNA replication inhibitors such as hydroxyurea, UV irradiation, or cisplatin, but not agents that cause DNA double strand breaks, such as γ-irradiation or camptothecin. These data point to a conserved role for nucleoporins in the cellular response to replication stress in eukaryote cells.
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Affiliation(s)
- Gangarao Davuluri
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Weilong Gong
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Shamila Yusuff
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Kristin Lorent
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Manimegalai Muthumani
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Amy C. Dolan
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michael Pack
- Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Cell & Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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52
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Rasala BA, Ramos C, Harel A, Forbes DJ. Capture of AT-rich chromatin by ELYS recruits POM121 and NDC1 to initiate nuclear pore assembly. Mol Biol Cell 2008; 19:3982-96. [PMID: 18596237 DOI: 10.1091/mbc.e08-01-0012] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Assembly of the nuclear pore, gateway to the genome, from its component subunits is a complex process. In higher eukaryotes, nuclear pore assembly begins with the binding of ELYS/MEL-28 to chromatin and recruitment of the large critical Nup107-160 pore subunit. The choreography of steps that follow is largely speculative. Here, we set out to molecularly define early steps in nuclear pore assembly, beginning with chromatin binding. Point mutation analysis indicates that pore assembly is exquisitely sensitive to the change of only two amino acids in the AT-hook motif of ELYS. The dependence on AT-rich chromatin for ELYS binding is borne out by the use of two DNA-binding antibiotics. AT-binding Distamycin A largely blocks nuclear pore assembly, whereas GC-binding Chromomycin A(3) does not. Next, we find that recruitment of vesicles containing the key integral membrane pore proteins POM121 and NDC1 to the forming nucleus is dependent on chromatin-bound ELYS/Nup107-160 complex, whereas recruitment of gp210 vesicles is not. Indeed, we reveal an interaction between the cytoplasmic domain of POM121 and the Nup107-160 complex. Our data thus suggest an order for nuclear pore assembly of 1) AT-rich chromatin sites, 2) ELYS, 3) the Nup107-160 complex, and 4) POM121- and NDC1-containing membrane vesicles and/or sheets, followed by (5) assembly of the bulk of the remaining soluble pore subunits.
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Affiliation(s)
- Beth A Rasala
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0347, USA
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53
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Katsani KR, Karess RE, Dostatni N, Doye V. In vivo dynamics of Drosophila nuclear envelope components. Mol Biol Cell 2008; 19:3652-66. [PMID: 18562695 DOI: 10.1091/mbc.e07-11-1162] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Nuclear pore complexes (NPCs) are multisubunit protein entities embedded into the nuclear envelope (NE). Here, we examine the in vivo dynamics of the essential Drosophila nucleoporin Nup107 and several other NE-associated proteins during NE and NPCs disassembly and reassembly that take place within each mitosis. During both the rapid mitosis of syncytial embryos and the more conventional mitosis of larval neuroblasts, Nup107 is gradually released from the NE, but it remains partially confined to the nuclear (spindle) region up to late prometaphase, in contrast to nucleoporins detected by wheat germ agglutinin and lamins. We provide evidence that in all Drosophila cells, a structure derived from the NE persists throughout metaphase and early anaphase. Finally, we examined the dynamics of the spindle checkpoint proteins Mad2 and Mad1. During mitotic exit, Mad2 and Mad1 are actively imported back from the cytoplasm into the nucleus after the NE and NPCs have reformed, but they reassociate with the NE only later in G1, concomitantly with the recruitment of the basket nucleoporin Mtor (the Drosophila orthologue of vertebrate Tpr). Surprisingly, Drosophila Nup107 shows no evidence of localization to kinetochores, despite the demonstrated importance of this association in mammalian cells.
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54
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Abstract
The small nuclear GTPase Ran controls the directionality of macromolecular transport between the nucleus and the cytoplasm. Ran also has important roles during mitosis, when the nucleus is dramatically reorganized to allow chromosome segregation. Ran directs the assembly of the mitotic spindle, nuclear-envelope dynamics and the timing of cell-cycle transitions. The mechanisms that underlie these functions provide insights into the spatial and temporal coordination of the changes that occur in intracellular organization during the cell-division cycle.
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Affiliation(s)
- Paul R Clarke
- Biomedical Research Centre, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, Scotland, UK.
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55
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Antonin W, Ellenberg J, Dultz E. Nuclear pore complex assembly through the cell cycle: regulation and membrane organization. FEBS Lett 2008; 582:2004-16. [PMID: 18328825 DOI: 10.1016/j.febslet.2008.02.067] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 02/28/2008] [Indexed: 12/22/2022]
Abstract
In eukaryotes, all macromolecules traffic between the nucleus and the cytoplasm through nuclear pore complexes (NPCs), which are among the largest supramolecular assemblies in cells. Although their composition in yeast and metazoa is well characterized, understanding how NPCs are assembled and form the pore through the double membrane of the nuclear envelope and how both processes are controlled still remains a challenge. Here, we summarize what is known about the biogenesis of NPCs throughout the cell cycle with special focus on the membrane reorganization and the regulation that go along with NPC assembly.
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Affiliation(s)
- Wolfram Antonin
- Friedrich Miescher Laboratory of the Max-Planck-Society, Spemannstrasse 39, 72076 Tübingen, Germany.
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56
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Cheeseman IM, Desai A. Molecular architecture of the kinetochore-microtubule interface. Nat Rev Mol Cell Biol 2008; 9:33-46. [PMID: 18097444 DOI: 10.1038/nrm2310] [Citation(s) in RCA: 688] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Segregation of the replicated genome during cell division in eukaryotes requires the kinetochore to link centromeric DNA to spindle microtubules. The kinetochore is composed of a number of conserved protein complexes that direct its specification and assembly, bind to spindle microtubules and regulate chromosome segregation. Recent studies have identified more than 80 kinetochore components, and are revealing how these proteins are organized into the higher order kinetochore structure, as well as how they function to achieve proper chromosome segregation.
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Affiliation(s)
- Iain M Cheeseman
- Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.
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57
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Lim RYH, Ullman KS, Fahrenkrog B. Biology and biophysics of the nuclear pore complex and its components. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 267:299-342. [PMID: 18544502 DOI: 10.1016/s1937-6448(08)00632-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleocytoplasmic exchange of proteins and ribonucleoprotein particles occurs via nuclear pore complexes (NPCs) that reside in the double membrane of the nuclear envelope (NE). Significant progress has been made during the past few years in obtaining better structural resolution of the three-dimensional architecture of NPC with the help of cryo-electron tomography and atomic structures of domains from nuclear pore proteins (nucleoporins). Biophysical and imaging approaches have helped elucidate how nucleoporins act as a selective barrier in nucleocytoplasmic transport. Nucleoporins act not only in trafficking of macromolecules but also in proper microtubule attachment to kinetochores, in the regulation of gene expression and signaling events associated with, for example, innate and adaptive immunity, development and neurodegenerative disorders. Recent research has also been focused on the dynamic processes of NPC assembly and disassembly that occur with each cell cycle. Here we review emerging results aimed at understanding the molecular arrangement of the NPC and how it is achieved, defining the roles of individual nucleoporins both at the NPC and at other sites within the cell, and finally deciphering how the NPC serves as both a barrier and a conduit of active transport.
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Affiliation(s)
- Roderick Y H Lim
- M.E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056 Basel, Switzerland
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58
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Green RA, Audhya A, Pozniakovsky A, Dammermann A, Pemble H, Monen J, Portier N, Hyman A, Desai A, Oegema K. Expression and imaging of fluorescent proteins in the C. elegans gonad and early embryo. Methods Cell Biol 2008; 85:179-218. [PMID: 18155464 DOI: 10.1016/s0091-679x(08)85009-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Caenorhabditis elegans gonad and early embryo have recently emerged as an attractive metazoan model system for studying cell and developmental biology. The success of this system is attributable to the stereotypical architecture and reproducible cell divisions of the gonad/early embryo, coupled with penetrant RNAi-mediated protein depletion. These features have facilitated the development of visual assays with high spatiotemporal resolution to monitor specific subcellular processes. Assay development has relied heavily on the emergence of methods to circumvent germline silencing to allow the expression of transgenes encoding fluorescent fusion proteins. In this chapter, we discuss methods for the expression and imaging of fluorescent proteins in the C. elegans germline, including the design of transgenes for optimal expression, the generation of transgenic worm lines by ballistic bombardment, the construction of multimarker lines by mating, and methods for live imaging of the gonad and early embryo.
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Affiliation(s)
- Rebecca A Green
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
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Gillespie PJ, Khoudoli GA, Stewart G, Swedlow JR, Blow J. ELYS/MEL-28 chromatin association coordinates nuclear pore complex assembly and replication licensing. Curr Biol 2007; 17:1657-62. [PMID: 17825564 PMCID: PMC2267255 DOI: 10.1016/j.cub.2007.08.041] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 07/27/2007] [Accepted: 08/10/2007] [Indexed: 10/30/2022]
Abstract
Xenopus egg extract supports all the major cell-cycle transitions in vitro. We have used a proteomics approach to identify proteins whose abundance on chromatin changes during the course of an in vitro cell cycle. One of the proteins we identified was ELYS/MEL-28, which has recently been described as the earliest-acting factor known to be required for nuclear pore complex (NPC) assembly [1-4]. ELYS interacts with the Nup107-160 complex and is required for its association with chromatin. ELYS contains an AT-hook domain, which we show binds to chromatin with a high affinity. This domain can compete with full-length ELYS for chromatin association, thereby blocking NPC assembly. This provides evidence that ELYS interacts directly with chromatin and that this interaction is essential for NPC assembly and compartmentalization of chromosomal DNA within the cell. Furthermore, we detected a physical association on chromatin between ELYS and the Mcm2-7 replication-licensing proteins. ELYS chromatin loading, NPC assembly, and nuclear growth were delayed when Mcm2-7 was prevented from loading onto chromatin. Because nuclear assembly is required to shut down licensing prior to entry into S phase, our results suggest a mechanism by which these two early cell-cycle events are coordinated with one another.
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Affiliation(s)
- Peter J. Gillespie
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Guennadi A. Khoudoli
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Graeme Stewart
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Jason R. Swedlow
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - J. Julian Blow
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
- Corresponding author
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60
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Gorjánácz M, Jaedicke A, Mattaj IW. What can Caenorhabditis elegans tell us about the nuclear envelope? FEBS Lett 2007; 581:2794-801. [PMID: 17418822 DOI: 10.1016/j.febslet.2007.03.052] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 03/18/2007] [Indexed: 02/01/2023]
Abstract
The nuclear envelope (NE) of the eukaryotic cell provides an essential barrier that separates the nuclear compartment from the cytoplasm. In addition, the NE is involved in essential functions such as nuclear stability, regulation of gene expression, centrosome separation and nuclear migration and positioning. In metazoa the NE breaks down and re-assembles around the segregated chromatids during each cell division. In this review we discuss the molecular constituents of the Caenorhabditis elegans NE and describe their role in post-mitotic NE re-formation, as well as the usefulness of C. elegans as an in vivo system for analyzing NE dynamics.
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Affiliation(s)
- Mátyás Gorjánácz
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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61
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Franz C, Walczak R, Yavuz S, Santarella R, Gentzel M, Askjaer P, Galy V, Hetzer M, Mattaj IW, Antonin W. MEL-28/ELYS is required for the recruitment of nucleoporins to chromatin and postmitotic nuclear pore complex assembly. EMBO Rep 2007; 8:165-72. [PMID: 17235358 PMCID: PMC1796766 DOI: 10.1038/sj.embor.7400889] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 11/17/2006] [Accepted: 11/22/2006] [Indexed: 11/09/2022] Open
Abstract
The metazoan nuclear envelope (NE) breaks down and re-forms during each cell cycle. Nuclear pore complexes (NPCs), which allow nucleocytoplasmic transport during interphase, assemble into the re-forming NE at the end of mitosis. Using in vitro NE assembly, we show that the vertebrate homologue of MEL-28 (maternal effect lethal), a recently discovered NE component in Caenorhabditis elegans, functions in postmitotic NPC assembly. MEL-28 interacts with the Nup107-160 complex (Nup for nucleoporin), an important building block of the NPC, and is essential for the recruitment of the Nup107-160 complex to chromatin. We suggest that MEL-28 acts as a seeding point for NPC assembly.
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Affiliation(s)
- Cerstin Franz
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Rudolf Walczak
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Sevil Yavuz
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Rachel Santarella
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Marc Gentzel
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Peter Askjaer
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Vincent Galy
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Martin Hetzer
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | - Iain W Mattaj
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
- Tel: +49 6221 387200; Fax: +49 6221 387211; E-mail:
| | - Wolfram Antonin
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
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63
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Rasala BA, Orjalo AV, Shen Z, Briggs S, Forbes DJ. ELYS is a dual nucleoporin/kinetochore protein required for nuclear pore assembly and proper cell division. Proc Natl Acad Sci U S A 2006; 103:17801-6. [PMID: 17098863 PMCID: PMC1635652 DOI: 10.1073/pnas.0608484103] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Nuclear pores span the nuclear envelope and act as gated aqueous channels to regulate the transport of macromolecules between the nucleus and cytoplasm, from individual proteins and RNAs to entire viral genomes. By far the largest subunit of the nuclear pore is the Nup107-160 complex, which consists of nine proteins and is critical for nuclear pore assembly. At mitosis, the Nup107-160 complex localizes to kinetochores, suggesting that it may also function in chromosome segregation. To investigate the dual roles of the Nup107-160 complex at the pore and during mitosis, we set out to identify binding partners by immunoprecipitation from both interphase and mitotic Xenopus egg extracts and mass spectrometry. ELYS, a putative transcription factor, was discovered to copurify with the Nup107-160 complex in Xenopus interphase extracts, Xenopus mitotic extracts, and human cell extracts. Indeed, a large fraction of ELYS localizes to the nuclear pore complexes of HeLa cells. Importantly, depletion of ELYS by RNAi leads to severe disruption of nuclear pores in the nuclear envelope, whereas lamin, Ran, and tubulin staining appear normal. At mitosis, ELYS targets to kinetochores, and RNAi depletion from HeLa cells leads to an increase in cytokinesis defects. Thus, we have identified an unexpected member of the nuclear pore and kinetochore that functions in both pore assembly at the nucleus and faithful cell division.
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Affiliation(s)
- Beth A. Rasala
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347
| | - Arturo V. Orjalo
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347
| | - Zhouxin Shen
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347
| | - Steven Briggs
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347
- To whom correspondence may be addressed. E-mail:
| | - Douglass J. Forbes
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347
- To whom correspondence may be addressed at:
Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347. E-mail:
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64
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Abstract
Reassembly of the nuclear envelope following mitosis is a fundamental process that remains only partially understood. Two recent reports by and in the September 5 issue of Current Biology identify a novel protein, MEL-28, that shuttles between the nuclear pore complex and kinetochore and is essential for envelope assembly in C. elegans early embryos.
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Affiliation(s)
- Kyle J Roux
- Department of Anatomy and Cell Biology, The University of Florida College of Medicine, 1600 SW Archer Road, Gainesville, 32606, USA
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