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Nord MS, Bernis C, Carmona S, Garland DC, Travesa A, Forbes DJ. Exportins can inhibit major mitotic assembly events in vitro: membrane fusion, nuclear pore formation, and spindle assembly. Nucleus 2021; 11:178-193. [PMID: 32762441 PMCID: PMC7540616 DOI: 10.1080/19491034.2020.1798093] [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: 11/30/2022] Open
Abstract
Xenopus egg extracts are a powerful in vitro tool for studying complex biological processes, including nuclear reconstitution, nuclear membrane and pore assembly, and spindle assembly. Extracts have been further used to demonstrate a moonlighting regulatory role for nuclear import receptors or importins on these cell cycle assembly events. Here we show that exportins can also play a role in these events. Addition of Crm1, Exportin-t, or Exportin-5 decreased nuclear pore assembly in vitro. RanQ69L-GTP, a constitutively active form of RanGTP, ameliorated inhibition. Both Crm1 and Exportin-t inhibited fusion of nuclear membranes, again counteracted by RanQ69L-GTP. In mitotic extracts, Crm1 and Exportin-t negatively impacted spindle assembly. Pulldowns from the extracts using Crm1- or Exportin-t-beads revealed nucleoporins known to be essential for both nuclear pore and spindle assembly, with RanQ69L-GTP decreasing a subset of these target interactions. This study suggests a model where exportins, like importins, can regulate major mitotic assembly events.
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Affiliation(s)
- Matthew S Nord
- Section of Cell and Developmental Biology, Division of Biological Sciences 0347, University of California-San Diego , La Jolla, CA, USA
| | - Cyril Bernis
- Section of Cell and Developmental Biology, Division of Biological Sciences 0347, University of California-San Diego , La Jolla, CA, USA
| | - Sarah Carmona
- Section of Cell and Developmental Biology, Division of Biological Sciences 0347, University of California-San Diego , La Jolla, CA, USA
| | - Dennis C Garland
- Section of Cell and Developmental Biology, Division of Biological Sciences 0347, University of California-San Diego , La Jolla, CA, USA
| | - Anna Travesa
- Section of Cell and Developmental Biology, Division of Biological Sciences 0347, University of California-San Diego , La Jolla, CA, USA
| | - Douglass J Forbes
- Section of Cell and Developmental Biology, Division of Biological Sciences 0347, University of California-San Diego , La Jolla, CA, USA
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2
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Pantoja-Uceda D, Neira JL, Contreras LM, Manton CA, Welch DR, Rizzuti B. The isolated C-terminal nuclear localization sequence of the breast cancer metastasis suppressor 1 is disordered. Arch Biochem Biophys 2019; 664:95-101. [PMID: 30707944 DOI: 10.1016/j.abb.2019.01.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/26/2019] [Accepted: 01/28/2019] [Indexed: 02/02/2023]
Abstract
BRMS1 is a 246-residue-long protein belonging to the family of metastasis suppressors. It is a predominantly nuclear protein, although it can also function in the cytoplasm. At its C terminus, it has a region that is predicted to be a nuclear localization sequence (NLS); this region, NLS2, is necessary for metastasis suppression. We have studied in vitro and in silico the conformational preferences in aqueous solution of a peptide (NLS2-pep) that comprises the NLS2 of BRMS1, to test whether it has a preferred conformation that could be responsible for its function. Our spectroscopic (far-UV circular dichroism, DOSY-NMR and 2D-NMR) and computational (all-atom molecular dynamics) results indicate that NLS2-pep was disordered in aqueous solution. Furthermore, it did not acquire a structure even when experiments were performed in a more hydrophobic environment, such as the one provided by 2,2,2-trifluoroethanol (TFE). The hydrodynamic radius of the peptide in water was identical to that of a random-coil sequence, in agreement with both our molecular simulations and other theoretical predictions. Thus, we suggest that NLS2 is a disordered region, with non pre-formed structure, that participates in metastasis suppression.
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Affiliation(s)
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBSC-CSIC-BIFI, Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | - Lellys M Contreras
- Center for Environmental Biology and Chemistry Research, Facultad Experimental de Ciencias y Tecnología, Universidad de Carabobo, 2001, Valencia, Venezuela
| | - Christa A Manton
- Department of Cancer Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Danny R Welch
- Department of Cancer Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA; The University of Kansas Cancer Center, Kansas City, KS, 66160, USA
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036, Rende, Italy.
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3
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Swetha RG, Ramaiah S, Anbarasu A. R521C and R521H mutations in FUS result in weak binding with Karyopherinβ2 leading to Amyotrophic lateral sclerosis: a molecular docking and dynamics study. J Biomol Struct Dyn 2016; 35:2169-2185. [PMID: 27381509 DOI: 10.1080/07391102.2016.1209130] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fused in sarcoma (FUS) gene encodes the RNA binding protein FUS. This gene is mapped to chromosome 16p11.2. The FUS protein binds with karyopherineβ2 (Kapβ2) through its proline/tyrosine nuclear localization signal (PY-NLS) that helps in the localization of FUS protein within the nucleus. Arginine residue in 521 position (R521) of PY-NLS plays a vital role in the binding of FUS protein with Kapβ2. Mutations in this position (R521C and R521H) are the most predominant mutations associated with amyotrophic lateral sclerosis (ALS). However, the mechanism by which these mutations lead to ALS is poorly understood. We examined the binding behaviour of the mutants FUS (R521C) and FUS (R521H) with Kapβ2 through protein-protein docking and molecular dynamics simulation. The binding patterns of mutants were compared with the binding behaviour of wild FUS-Kapβ2. Our results suggest that these mutants have relatively weak binding affinity with Kapβ2 when compared with wild FUS-Kapβ2 as indicated by the lesser number of interactions found between the mutant FUS and Kapβ2. Hence, these mutations weakens the binding and this results in the cytoplasmic mislocalization of mutant FUS; and thereby it increases the severity of ALS.
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Affiliation(s)
- Rayapadi G Swetha
- a Medical & Biological Computing Laboratory, School of Biosciences and Technology , VIT University , Vellore 632 014 , Tamil Nadu , India
| | - Sudha Ramaiah
- a Medical & Biological Computing Laboratory, School of Biosciences and Technology , VIT University , Vellore 632 014 , Tamil Nadu , India
| | - Anand Anbarasu
- a Medical & Biological Computing Laboratory, School of Biosciences and Technology , VIT University , Vellore 632 014 , Tamil Nadu , India
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4
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Schwartz TU. The Structure Inventory of the Nuclear Pore Complex. J Mol Biol 2016; 428:1986-2000. [PMID: 27016207 DOI: 10.1016/j.jmb.2016.03.015] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/18/2022]
Abstract
The nuclear pore complex (NPC) is the principal gateway for molecular exchange between nucleus and cytoplasm across the nuclear envelope. Due to its sheer size of estimated 50-112MDa and its complex buildup from about 500-1000 individual proteins, it is a difficult object to study for structural biologists. Here, I review the extensive ensemble of high-resolution structures of the building blocks of the NPC. Concurrent with the increase in size and complexity, these latest, large structures and assemblies can now be used as the basis for hybrid approaches, primarily in combination with cryo-electron microscopic analysis, generating the first structure-based assembly models of the NPC. Going forward, the structures will be critically important for a detailed analysis of the NPC, including function, evolution, and assembly.
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Affiliation(s)
- Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA
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5
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Yamagishi R, Okuyama T, Oba S, Shimada J, Chaen S, Kaneko H. Comprehensive analysis of the dynamic structure of nuclear localization signals. Biochem Biophys Rep 2015; 4:392-396. [PMID: 29124229 PMCID: PMC5669441 DOI: 10.1016/j.bbrep.2015.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/02/2015] [Accepted: 11/02/2015] [Indexed: 01/04/2023] Open
Abstract
Most transcription and epigenetic factors in eukaryotic cells have nuclear localization signals (NLSs) and are transported to the nucleus by nuclear transport proteins. Understanding the features of NLSs and the mechanisms of nuclear transport might help understand gene expression regulation, somatic cell reprogramming, thus leading to the treatment of diseases associated with abnormal gene expression. Although many studies analyzed the amino acid sequence of NLSs, few studies investigated their three-dimensional structure. Therefore, we conducted a statistical investigation of the dynamic structure of NLSs by extracting the conformation of these sequences from proteins examined by X-ray crystallography and using a quantity defined as conformational determination rate (a ratio between the number of amino acids determining the conformation and the number of all amino acids included in a certain region). We found that determining the conformation of NLSs is more difficult than determining the conformation of other regions and that NLSs may tend to form more heteropolymers than monomers. Therefore, these findings strongly suggest that NLSs are intrinsically disordered regions.
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Affiliation(s)
- Ryosuke Yamagishi
- Department of Integrated Sciences in Physics and Biology, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajousui, Setagaya, Tokyo 156-8550, Japan
| | - Takahide Okuyama
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajousui, Setagaya-ku, Tokyo 156-8550, Japan
| | - Shuntaro Oba
- Department of Integrated Sciences in Physics and Biology, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajousui, Setagaya, Tokyo 156-8550, Japan
| | - Jiro Shimada
- Department of Integrated Sciences in Physics and Biology, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajousui, Setagaya, Tokyo 156-8550, Japan
| | - Shigeru Chaen
- Department of Integrated Sciences in Physics and Biology, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajousui, Setagaya, Tokyo 156-8550, Japan
| | - Hiroki Kaneko
- Department of Integrated Sciences in Physics and Biology, College of Humanities and Sciences, Nihon University, 3-25-40 Sakurajousui, Setagaya, Tokyo 156-8550, Japan
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajousui, Setagaya-ku, Tokyo 156-8550, Japan
- National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka 675-0085, Japan
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6
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Abstract
The Karyopherin-β family of proteins mediates nuclear transport of macromolecules. Nuclear versus cytoplasmic localization of proteins is often suggested by the presence of NLSs (nuclear localization signals) or NESs (nuclear export signals). Import-Karyopherin-βs or Importins bind to NLSs in their protein cargos to transport them through nuclear pore complexes into the nucleus. Until recently, only two classes of NLS had been biochemically and structurally characterized: the classical NLS, which is recognized by the Importin-α/β heterodimer and the PY-NLS (proline-tyrosine NLS), which is recognized by Karyopherin-β2 or Transportin-1. Structures of two other Karyopherin-βs, Kap121 and Transportin-SR2, in complex with their respective cargos were reported for the first time recently, revealing two new distinct classes of NLSs. The present paper briefly describes the classical NLS, reviews recent literature on the PY-NLS and provides in-depth reviews of the two newly discovered classes of NLSs that bind Kap121p and Transportin-SR respectively.
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7
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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: 68] [Impact Index Per Article: 7.6] [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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8
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Kressler D, Bange G, Ogawa Y, Stjepanovic G, Bradatsch B, Pratte D, Amlacher S, Strauß D, Yoneda Y, Katahira J, Sinning I, Hurt E. Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Science 2012; 338:666-71. [PMID: 23118189 DOI: 10.1126/science.1226960] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Ribosomal proteins are synthesized in the cytoplasm, before nuclear import and assembly with ribosomal RNA (rRNA). Little is known about coordination of nucleocytoplasmic transport with ribosome assembly. Here, we identify a transport adaptor, symportin 1 (Syo1), that facilitates synchronized coimport of the two 5S-rRNA binding proteins Rpl5 and Rpl11. In vitro studies revealed that Syo1 concomitantly binds Rpl5-Rpl11 and furthermore recruits the import receptor Kap104. The Syo1-Rpl5-Rpl11 import complex is released from Kap104 by RanGTP and can be directly transferred onto the 5S rRNA. Syo1 can shuttle back to the cytoplasm by interaction with phenylalanine-glycine nucleoporins. X-ray crystallography uncovered how the α-solenoid symportin accommodates the Rpl5 amino terminus, normally bound to 5S rRNA, in an extended groove. Symportin-mediated coimport of Rpl5-Rpl11 could ensure coordinated and stoichiometric incorporation of these proteins into pre-60S ribosomes.
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Affiliation(s)
- Dieter Kressler
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, Heidelberg D-69120, Germany.
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9
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Structural and energetic basis of ALS-causing mutations in the atypical proline-tyrosine nuclear localization signal of the Fused in Sarcoma protein (FUS). Proc Natl Acad Sci U S A 2012; 109:12017-21. [PMID: 22778397 DOI: 10.1073/pnas.1207247109] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mutations in the proline/tyrosine-nuclear localization signal (PY-NLS) of the Fused in Sarcoma protein (FUS) cause amyotrophic lateral sclerosis (ALS). Here we report the crystal structure of the FUS PY-NLS bound to its nuclear import receptor Karyopherinβ2 (Kapβ2; also known as Transportin). The FUS PY-NLS occupies the structurally invariant C-terminal arch of Kapβ2, tracing a path similar to that of other characterized PY-NLSs. Unlike other PY-NLSs, which generally bind Kapβ2 in fully extended conformations, the FUS peptide is atypical as its central portion forms a 2.5-turn α-helix. The Kapβ2-binding epitopes of the FUS PY-NLS consist of an N-terminal PGKM hydrophobic motif, a central arginine-rich α-helix, and a C-terminal PY motif. ALS mutations are found almost exclusively within these epitopes. Each ALS mutation site makes multiple contacts with Kapβ2 and mutations of these residues decrease binding affinities for Kapβ2 (K(D) for wild-type FUS PY-NLS is 9.5 nM) up to ninefold. Thermodynamic analyses of ALS mutations in the FUS PY-NLS show that the weakening of FUS-Kapβ2 binding affinity, the degree of cytoplasmic mislocalization, and ALS disease severity are correlated.
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10
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A jumbo problem: mapping the structure and functions of the nuclear pore complex. Curr Opin Cell Biol 2012; 24:92-9. [PMID: 22321828 DOI: 10.1016/j.ceb.2011.12.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 12/23/2011] [Accepted: 12/24/2011] [Indexed: 01/16/2023]
Abstract
Macromolecular assemblies can be intrinsically refractive to classical structural analysis, due to their size, complexity, plasticity and dynamic nature. One such assembly is the nuclear pore complex (NPC). The NPC is formed from ∼450 copies of 30 different proteins, called nucleoporins, and is the sole mediator of exchange between the nucleus and the cytoplasm in eukaryotic cells. Despite significant progress, it has become increasingly clear that new approaches, integrating different sources of structural and functional data, will be needed to understand the functional biology of the NPC. Here, we discuss the latest approaches trying to address this challenge.
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11
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Chook YM, Süel KE. Nuclear import by karyopherin-βs: recognition and inhibition. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:1593-606. [PMID: 21029754 DOI: 10.1016/j.bbamcr.2010.10.014] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/06/2010] [Accepted: 10/19/2010] [Indexed: 01/24/2023]
Abstract
Proteins in the karyopherin-β family mediate the majority of macromolecular transport between the nucleus and the cytoplasm. Eleven of the 19 known human karyopherin-βs and 10 of the 14S. cerevisiae karyopherin-βs mediate nuclear import through recognition of nuclear localization signals or NLSs in their cargos. This receptor-mediated process is essential to cellular viability as proteins are translated in the cytoplasm but many have functional roles in the nucleus. Many known karyopherin-β-cargo interactions were discovered through studies of the individual cargos rather than the karyopherins, and this information is thus widely scattered in the literature. We consolidate information about cargos that are directly recognized by import-karyopherin-βs and review common characteristics or lack thereof among cargos of different import pathways. Knowledge of karyopherin-β-cargo interactions is also critical for the development of nuclear import inhibitors and the understanding of their mechanisms of inhibition. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.
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Affiliation(s)
- Yuh Min Chook
- Department of Pharmacology, University of Texas Southerwestern Medical Center, Dallas, TX 75206, USA.
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12
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Forwood JK, Lange A, Zachariae U, Marfori M, Preast C, Grubmüller H, Stewart M, Corbett AH, Kobe B. Quantitative Structural Analysis of Importin-β Flexibility: Paradigm for Solenoid Protein Structures. Structure 2010; 18:1171-83. [DOI: 10.1016/j.str.2010.06.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 05/04/2010] [Accepted: 06/01/2010] [Indexed: 12/24/2022]
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13
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Bhardwaj A, Cingolani G. Conformational selection in the recognition of the snurportin importin beta binding domain by importin beta. Biochemistry 2010; 49:5042-7. [PMID: 20476751 DOI: 10.1021/bi100292y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural flexibility of beta-karyopherins is critical to mediate the interaction with transport substrates, nucleoporins, and the GTPase Ran. In this paper, we provide structural evidence that the molecular recognition of the transport adaptor snurportin by importin beta follows the population selection mechanism. We have captured two drastically different conformations of importin beta bound to the snurportin importin beta binding domain trapped in the same crystallographic asymmetric unit. We propose the population selection may be a general mechanism used by beta-karyopherins to recognize transport substrates.
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Affiliation(s)
- Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania 19107, USA
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14
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Lott K, Bhardwaj A, Mitrousis G, Pante N, Cingolani G. The importin beta binding domain modulates the avidity of importin beta for the nuclear pore complex. J Biol Chem 2010; 285:13769-80. [PMID: 20197273 DOI: 10.1074/jbc.m109.095760] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Importin beta mediates active passage of cellular substrates through the nuclear pore complex (NPC). Adaptors such as importin alpha and snurportin associate with importin beta via an importin beta binding (IBB) domain. The intrinsic structural flexibility of importin beta allows its concerted interactions with IBB domains, phenylalanine-glycine nucleoporins, and the GTPase Ran during transport. In this paper, we provide evidence that the nature of the IBB domain modulates the affinity of the import complex for the NPC. In permeabilized cells, importin beta imports a cargo fused to the snurportin IBB (sIBB) with approximately 70% reduced energy requirement as compared with the classical importin alpha IBB. At the molecular level, this is explained by approximately 200-fold reduced affinity of importin beta for Nup62, when bound to the sIBB. Consistently, in vivo, the importin beta.sIBB complex has greatly reduced persistence inside the central channel of the NPC. We propose that by controlling the degree of strain in the tertiary structure of importin beta, the IBB domain modulates the affinity of the import complex for nucleoporins, thus dictating its persistence inside the NPC.
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Affiliation(s)
- Kaylen Lott
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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15
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Tartakoff AM, Tao T. Comparative and evolutionary aspects of macromolecular translocation across membranes. Int J Biochem Cell Biol 2009; 42:214-29. [PMID: 19643202 DOI: 10.1016/j.biocel.2009.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 07/21/2009] [Accepted: 07/21/2009] [Indexed: 01/10/2023]
Abstract
Membrane barriers preserve the integrity of organelles of eukaryotic cells, yet the genesis and ongoing functions of the same organelles requires that their limiting membranes allow import and export of selected macromolecules. Multiple distinct mechanisms are used for this purpose, only some of which have been traced to prokaryotes. Some can accommodate both monomeric and also large heterooligomeric cargoes. The best characterized of these is nucleocytoplasmic transport. This synthesis compares the unidirectional and bidirectional mechanisms of macromolecular transport of the endoplasmic reticulum, mitochondria, peroxisomes and the nucleus, calls attention to the powerful experimental approaches which have been used for their elucidation, discusses their regulation and evolutionary origins, and highlights relatively unexplored areas.
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Affiliation(s)
- Alan M Tartakoff
- Department of Pathology & Cell Biology Program, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
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16
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Roman N, Kirkby B, Marfori M, Kobe B, Forwood JK. Crystallization of the flexible nuclear import receptor importin-beta in the unliganded state. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:625-8. [PMID: 19478448 DOI: 10.1107/s1744309109016820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 05/05/2009] [Indexed: 11/10/2022]
Abstract
The transport of macromolecules across the nuclear envelope is an essential eukaryotic process that enables proteins such as transcription factors, polymerases and histones to gain access to the genetic material contained within the nucleus. Importin-beta plays a central role in the nucleocytoplasmic transport process, mediating nuclear import through a range of interactions with cytoplasmic, nuclear and nuclear pore proteins such as importin-alpha, Ran, nucleoporins and various cargo molecules. The unliganded form of the full-length yeast importin-beta has been expressed and crystallized. The crystals were obtained by vapour diffusion at pH 6.5 and 290 K. The crystals belonged to space group P2(1) (unit-cell parameters a = 58.17, b = 127.25, c = 68.52 A, beta = 102.23). One molecule is expected in the asymmetric unit. The crystals diffracted to 2.4 A resolution using a laboratory X-ray source and were suitable for crystal structure determination.
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Affiliation(s)
- Noelia Roman
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
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17
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Dong X, Biswas A, Süel KE, Jackson LK, Martinez R, Gu H, Chook YM. Structural basis for leucine-rich nuclear export signal recognition by CRM1. Nature 2009; 458:1136-41. [PMID: 19339969 PMCID: PMC3437623 DOI: 10.1038/nature07975] [Citation(s) in RCA: 254] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 03/06/2009] [Indexed: 01/17/2023]
Abstract
CRM1 (also known as XPO1 and exportin 1) mediates nuclear export of hundreds of proteins through the recognition of the leucine-rich nuclear export signal (LR-NES). Here we present the 2.9 A structure of CRM1 bound to snurportin 1 (SNUPN). Snurportin 1 binds CRM1 in a bipartite manner by means of an amino-terminal LR-NES and its nucleotide-binding domain. The LR-NES is a combined alpha-helical-extended structure that occupies a hydrophobic groove between two CRM1 outer helices. The LR-NES interface explains the consensus hydrophobic pattern, preference for intervening electronegative residues and inhibition by leptomycin B. The second nuclear export signal epitope is a basic surface on the snurportin 1 nucleotide-binding domain, which binds an acidic patch on CRM1 adjacent to the LR-NES site. Multipartite recognition of individually weak nuclear export signal epitopes may be common to CRM1 substrates, enhancing CRM1 binding beyond the generally low affinity LR-NES. Similar energetic construction is also used in multipartite nuclear localization signals to provide broad substrate specificity and rapid evolution in nuclear transport.
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Affiliation(s)
- Xiuhua Dong
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park, Dallas, Texas 75390-9041, USA
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18
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Kap95p binding induces the switch loops of RanGDP to adopt the GTP-bound conformation: implications for nuclear import complex assembly dynamics. J Mol Biol 2008; 383:772-82. [PMID: 18708071 DOI: 10.1016/j.jmb.2008.07.090] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 07/31/2008] [Accepted: 07/31/2008] [Indexed: 11/20/2022]
Abstract
The asymmetric distribution of the nucleotide-bound state of Ran across the nuclear envelope is crucial for determining the directionality of nuclear transport. In the nucleus, Ran is primarily in the guanosine 5'-triphosphate (GTP)-bound state, whereas in the cytoplasm, Ran is primarily guanosine 5'-diphosphate (GDP)-bound. Conformational changes within the Ran switch I and switch II loops are thought to modulate its affinity for importin-beta. Here, we show that RanGDP and importin-beta form a stable complex with a micromolar dissociation constant. This complex can be dissociated by importin-beta binding partners such as importin-alpha. Surprisingly, the crystal structure of the Kap95p-RanGDP complex shows that Kap95p induces the switch I and II regions of RanGDP to adopt a conformation that resembles that of the GTP-bound form. The structure of the complex provides insights into the structural basis for the gradation of affinities regulating nuclear protein transport.
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Structural and functional studies of Nup107/Nup133 interaction and its implications for the architecture of the nuclear pore complex. Mol Cell 2008; 30:721-31. [PMID: 18570875 DOI: 10.1016/j.molcel.2008.04.022] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 02/20/2008] [Accepted: 04/15/2008] [Indexed: 01/16/2023]
Abstract
Nuclear pore complexes (NPCs) are 40-60 MDa protein assemblies embedded in the nuclear envelope of eukaryotic cells. NPCs exclusively mediate all transport between cytoplasm and nucleus. The nucleoporins that build the NPC are arranged in a stable core of module-like subcomplexes with eight-fold rotational symmetry. To gain insight into the intricate assembly of the NPC, we have solved the crystal structure of a protein complex between two nucleoporins, human Nup107 and Nup133. Both proteins form elongated structures that interact tightly via a compact interface in tail-to-tail fashion. Additional experiments using structure-guided mutants show that Nup107 is the critical anchor for Nup133 to the NPC, positioning Nup133 at the periphery of the NPC. The significant topological differences between Nup107 and Nup133 suggest that *-helical nucleoporin domains of the NPC scaffold fall in different classes and fulfill largely nonredundant functions.
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Structural basis for RanGTP independent entry of spliceosomal U snRNPs into the nucleus. J Mol Biol 2007; 374:1129-38. [PMID: 18028944 DOI: 10.1016/j.jmb.2007.09.065] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 09/14/2007] [Accepted: 09/18/2007] [Indexed: 12/22/2022]
Abstract
The nuclear import of assembled spliceosomal subunits, the uridine-rich small nuclear ribonucleoprotein particles (U snRNPs), is mediated by a nuclear import receptor adaptor couple of importin beta (Imp beta) and snurportin1 (SPN1). In contrast to any other characterized active nuclear import, the Imp beta/SPN1/U snRNP complex does not require RanGTP for the terminal release from the nuclear basket of the nuclear pore complex (NPC). The crystal structure of Imp beta (127-876) in complex with the Imp beta-binding (IBB) domain of SPN1 (1-65) at 2.8-A resolution reveals that Imp beta adopts an open conformation, which is unique for a functional Imp beta/cargo complex, and rather surprisingly, it resembles the conformation of the Imp beta/RanGTP complex. As binding of RanGTP to Imp beta usually triggers the release of import complexes from the NPC, we propose that by already mimicking a conformation similar to Imp beta/RanGTP the independent dissociation of Imp beta/SPN1 from the nuclear basket is energetically aided.
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Jeudy S, Schwartz TU. Crystal structure of nucleoporin Nic96 reveals a novel, intricate helical domain architecture. J Biol Chem 2007; 282:34904-12. [PMID: 17897938 DOI: 10.1074/jbc.m705479200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The nuclear pore complex (NPC) is an elaborate protein machine that mediates macromolecular transport across the nuclear envelope in all eukaryotes. The NPC is formed by nucleoporins that assemble in multiple copies around an 8-fold symmetry axis. Homology modeling suggests that most architectural nucleoporins are composed of simple beta-propeller and alpha-helical repeat domains. Here we present the crystal structure of Nic96, the Nup93 homolog in Saccharomyces cerevisiae, one of the major components of the NPC. This is the first structure of an alpha-helical nucleoporin domain. The protein folds into an elongated, mostly alpha-helical structure. Characteristically, non-canonical architectural features define the Nic96 structure. Sequence conservation among Nup93 homologs across all eukaryotes strongly suggests that the distinct topology is evolutionarily well maintained. We propose that the unique Nic96/Nup93 fold has a conserved function in all eukaryotes.
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Affiliation(s)
- Sandra Jeudy
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Abstract
In eukaryotic cells, segregation of DNA replication and RNA biogenesis in the nucleus and protein synthesis in the cytoplasm poses the requirement of transporting thousands of macromolecules between the two cellular compartments. Transport between nucleus and cytoplasm is mediated by soluble receptors that recognize specific cargoes and carry them through the nuclear pore complex (NPC), the sole gateway between the two compartments at interphase. Nucleocytoplasmic transport is specific not only in terms of cargo recognition, but also in terms of directionality, with nuclear proteins imported into the nucleus and RNAs exported from it. How is directionality achieved? How can the receptors be both specific and versatile in recognizing a multitude of cargoes? And how can their interaction with NPCs allow fast translocation? We describe the molecular mechanisms underlying nucleocytoplasmic transport as they have been revealed by structural studies of the receptors and regulators in different steps of transport cycles.
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Affiliation(s)
- Atlanta Cook
- European Molecular Biology Laboratory, D-69117 Heidelberg, Germany.
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