51
|
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: 105] [Impact Index Per Article: 11.7] [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.
Collapse
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
| |
Collapse
|
52
|
Jeong SA, Kim K, Lee JH, Cha JS, Khadka P, Cho HS, Chung IK. Akt-mediated phosphorylation increases the binding affinity of hTERT for importin α to promote nuclear translocation. J Cell Sci 2015; 128:2287-301. [DOI: 10.1242/jcs.166132] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 04/10/2015] [Indexed: 01/09/2023] Open
Abstract
ABSTRACT
Telomeres are essential for chromosome integrity and protection, and their maintenance requires the ribonucleoprotein enzyme telomerase. Previously, we have shown that human telomerase reverse transcriptase (hTERT) contains a bipartite nuclear localization signal (NLS; residues 222–240) that is responsible for nuclear import, and that Akt-mediated phosphorylation of residue S227 is important for efficient nuclear import of hTERT. Here, we show that hTERT binds to importin-α proteins through the bipartite NLS and that this heterodimer then forms a complex with importin-β proteins to interact with the nuclear pore complex. Depletion of individual importin-α proteins results in a failure of hTERT nuclear import, and the resulting cytoplasmic hTERT is degraded by ubiquitin-dependent proteolysis. Crystallographic analysis reveals that the bipartite NLS interacts with both the major and minor sites of importin-α proteins. We also show that Akt-mediated phosphorylation of S227 increases the binding affinity for importin-α proteins and promotes nuclear import of hTERT, thereby resulting in increased telomerase activity. These data provide details of a binding mechanism that enables hTERT to interact with the nuclear import receptors and of the control of the dynamic nuclear transport of hTERT through phosphorylation.
Collapse
Affiliation(s)
- Sun Ah Jeong
- Department of Integrated Omics for Biomedical Science, Yonsei University, Seoul 120-749, Korea
| | - Kuglae Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Ji Hoon Lee
- Department of Integrated Omics for Biomedical Science, Yonsei University, Seoul 120-749, Korea
| | - Jeong Seok Cha
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Prabhat Khadka
- Department of Integrated Omics for Biomedical Science, Yonsei University, Seoul 120-749, Korea
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - In Kwon Chung
- Department of Integrated Omics for Biomedical Science, Yonsei University, Seoul 120-749, Korea
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Korea
| |
Collapse
|
53
|
Hwang B, McCool K, Wan J, Wuerzberger-Davis SM, Young EWK, Choi EY, Cingolani G, Weaver BA, Miyamoto S. IPO3-mediated Nonclassical Nuclear Import of NF-κB Essential Modulator (NEMO) Drives DNA Damage-dependent NF-κB Activation. J Biol Chem 2015; 290:17967-17984. [PMID: 26060253 DOI: 10.1074/jbc.m115.645960] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Indexed: 11/06/2022] Open
Abstract
Activation of IκB kinase (IKK) and NF-κB by genotoxic stresses modulates apoptotic responses and production of inflammatory mediators, thereby contributing to therapy resistance and premature aging. We previously reported that genotoxic agents induce nuclear localization of NF-κB essential modulator (NEMO) via an undefined mechanism to arbitrate subsequent DNA damage-dependent IKK/NF-κB signaling. Here we show that a nonclassical nuclear import pathway via IPO3 (importin 3, transportin 2) mediates stress-induced NEMO nuclear translocation. We found putative nuclear localization signals in NEMO whose mutations disrupted stress-inducible nuclear translocation of NEMO and IKK/NF-κB activation in stably reconstituted NEMO-deficient cells. RNAi screening of both importin α and β family members, as well as co-immunoprecipitation analyses, revealed that a nonclassical importin β family member, IPO3, was the only importin that was able to associate with NEMO and whose reduced expression prevented genotoxic stress-induced NEMO nuclear translocation, IKK/NF-κB activation, and inflammatory cytokine transcription. Recombinant IPO3 interacted with recombinant NEMO but not the nuclear localization signal mutant version and induced nuclear import of NEMO in digitonin-permeabilized cells. We also provide evidence that NEMO is disengaged from IKK complex following genotoxic stress induction. Thus, the IPO3 nuclear import pathway is an early and crucial determinant of the IKK/NF-κB signaling arm of the mammalian DNA damage response.
Collapse
Affiliation(s)
- Byounghoon Hwang
- Department of Oncology, University of Wisconsin, Madison, Wisconsin
| | - Kevin McCool
- Department of Oncology, University of Wisconsin, Madison, Wisconsin; Molecular and Cellular Pharmacology Program, University of Wisconsin, Madison, Wisconsin
| | - Jun Wan
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin
| | - Shelly M Wuerzberger-Davis
- Department of Oncology, University of Wisconsin, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin
| | - Edmond W K Young
- Department of Mechanical and Industrial Engineering and Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G8, Canada
| | - Eun Young Choi
- Department of Oncology, University of Wisconsin, Madison, Wisconsin
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Beth A Weaver
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin
| | - Shigeki Miyamoto
- Department of Oncology, University of Wisconsin, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin.
| |
Collapse
|
54
|
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: 3.3] [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.
Collapse
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
| |
Collapse
|
55
|
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: 76] [Impact Index Per Article: 8.4] [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.
Collapse
|
56
|
Lieu KG, Shim EH, Wang J, Lokareddy RK, Tao T, Cingolani G, Zambetti GP, Jans DA. The p53-induced factor Ei24 inhibits nuclear import through an importin β-binding-like domain. ACTA ACUST UNITED AC 2014; 205:301-12. [PMID: 24821838 PMCID: PMC4018778 DOI: 10.1083/jcb.201304055] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The etoposide-induced protein Ei24 was initially identified as a p53-responsive, proapoptotic factor, but no clear function has been described. Here, we use a nonbiased proteomics approach to identify members of the importin (IMP) family of nuclear transporters as interactors of Ei24 and characterize an IMPβ-binding-like (IBBL) domain within Ei24. We show that Ei24 can bind specifically to IMPβ1 and IMPα2, but not other IMPs, and use a mutated IMPβ1 derivative to show that Ei24 binds to the same site on IMPβ1 as the IMPα IBB. Ectopic expression of Ei24 reduced the extent of IMPβ1- or IMPα/β1-dependent nuclear protein import specifically, whereas specific alanine substitutions within the IBBL abrogated this activity. Induction of endogenous Ei24 expression through etoposide treatment similarly inhibited nuclear import in a mouse embryonic fibroblast model. Thus, Ei24 can bind specifically to IMPβ1 and IMPα2 to impede their normal role in nuclear import, shedding new light on the cellular functions of Ei24 and its tumor suppressor role.
Collapse
Affiliation(s)
- Kim G Lieu
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | | | | | | | | | | | | | | |
Collapse
|
57
|
Danks JA, Freeman AN, Martin TJ. Historical Perspective and Evolutionary Origins of Parathyroid Hormone-Related Protein. Clin Rev Bone Miner Metab 2014. [DOI: 10.1007/s12018-014-9163-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
58
|
Tamura K, Hara-Nishimura I. Functional insights of nucleocytoplasmic transport in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:118. [PMID: 24765097 PMCID: PMC3980095 DOI: 10.3389/fpls.2014.00118] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/12/2014] [Indexed: 05/19/2023]
Abstract
Plant nucleocytoplasmic transport beyond the nuclear envelope is important not only for basic cellular functions but also for growth, development, hormonal signaling, and responses to environmental stimuli. Key components of this transport system include nuclear transport receptors and nucleoporins. The functional and physical interactions between receptors and the nuclear pore in the nuclear membrane are indispensable for nucleocytoplasmic transport. Recently, several groups have reported various plant mutants that are deficient in factors involved in nucleocytoplasmic transport. Here, we summarize the current state of knowledge about nucleocytoplasmic transport in plants, and we review the plant-specific regulation and roles of this process in plants.
Collapse
Affiliation(s)
| | - Ikuko Hara-Nishimura
- *Correspondence: Ikuko Hara-Nishimura, Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan e-mail:
| |
Collapse
|
59
|
Roman N, Christie M, Swarbrick CMD, Kobe B, Forwood JK. Structural characterisation of the nuclear import receptor importin alpha in complex with the bipartite NLS of Prp20. PLoS One 2013; 8:e82038. [PMID: 24339986 PMCID: PMC3858281 DOI: 10.1371/journal.pone.0082038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/20/2013] [Indexed: 11/30/2022] Open
Abstract
The translocation of macromolecules into the nucleus is a fundamental eukaryotic process, regulating gene expression, cell division and differentiation, but which is impaired in a range of significant diseases including cancer and viral infection. The import of proteins into the nucleus is generally initiated by a specific, high affinity interaction between nuclear localisation signals (NLSs) and nuclear import receptors in the cytoplasm, and terminated through the disassembly of these complexes in the nucleus. For classical NLSs (cNLSs), this import is mediated by the importin-α (IMPα) adaptor protein, which in turn binds to IMPβ to mediate translocation of nuclear cargo across the nuclear envelope. The interaction and disassembly of import receptor:cargo complexes is reliant on the differential localisation of nucleotide bound Ran across the envelope, maintained in its low affinity, GDP-bound form in the cytoplasm, and its high affinity, GTP-bound form in the nucleus. This in turn is maintained by the differential localisation of Ran regulating proteins, with RanGAP in the cytoplasm maintaining Ran in its GDP-bound form, and RanGEF (Prp20 in yeast) in the nucleus maintaining Ran in its GTP-bound form. Here, we describe the 2.1 Å resolution x-ray crystal structure of IMPα in complex with the NLS of Prp20. We observe 1,091 Å2 of buried surface area mediated by an extensive array of contacts involving residues on armadillo repeats 2-7, utilising both the major and minor NLS binding sites of IMPα to contact bipartite NLS clusters 17RAKKMSK23 and 3KR4, respectively. One notable feature of the major site is the insertion of Prp20NLS Ala18 between the P0 and P1 NLS sites, noted in only a few classical bipartite NLSs. This study provides a detailed account of the binding mechanism enabling Prp20 interaction with the nuclear import receptor, and additional new information for the interaction between IMPα and cargo.
Collapse
Affiliation(s)
- Noelia Roman
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Mary Christie
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Crystall M. D. Swarbrick
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- * E-mail:
| |
Collapse
|
60
|
Zhang Y, Zhao Y, Li H, Li Y, Cai X, Shen Y, Shi H, Li L, Liu Q, Zhang X, Ye L. The nuclear import of oncoprotein hepatitis B X-interacting protein depends on interacting with c-Fos and phosphorylation of both proteins in breast cancer cells. J Biol Chem 2013; 288:18961-74. [PMID: 23667255 DOI: 10.1074/jbc.m113.458638] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aberrant nuclear localization of oncogenic transcription factors and coactivators always leads to the development of cancer. We have reported that the oncoprotein hepatitis B X-interacting protein (HBXIP) acts as a novel transcriptional coactivator to promote proliferation and migration of breast cancer cells. However, the mechanism of regulating the nuclear import of HBXIP remains unclear. In the present study, we found that HBXIP interacted with c-Fos through their leucine zipper domains in vitro and in vivo. Interestingly, the leucine zipper mutant of HBXIP (or c-Fos) was unavailable to bind to c-Fos (or HBXIP), resulting in the disappearance of nuclear localization of HBXIP. Moreover, we revealed that the nuclear import of HBXIP was required for phosphorylation of c-Fos at Thr(232), Thr(325), Thr(331), and Ser(374) by ERK1/2. In addition, the mutant of HBXIP at the Ser(108) phosphorylation site failed to import into the nucleus. Strikingly, we found that the kinase ataxia telangiectasia mutated (ATM) phosphorylated HBXIP at Ser(108). The knockdown of ATM by siRNA remarkably decreased the levels of serine phosphorylation and blocked the nuclear import of HBXIP. Then, we identified that ATM could bind to HBXIP. Moreover, we validated that the nuclear import of HBXIP contributed to its nuclear function. Therefore, we conclude that the nuclear import of the oncoprotein HBXIP requires interaction with c-Fos through their leucine zipper domains and phosphorylation of both proteins in breast cancer cells. Thus, our findings provide new insights into the mechanism of the nuclear import of HBXIP. Therapeutically, the block of the nuclear import of HBXIP is significant in breast cancer.
Collapse
Affiliation(s)
- Yingyi Zhang
- Department of Biochemistry, College of Life Sciences, Nankai University, Tianjin 300071, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
61
|
Gopal V. Bioinspired peptides as versatile nucleic acid delivery platforms. J Control Release 2013; 167:323-32. [DOI: 10.1016/j.jconrel.2013.02.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 02/11/2013] [Accepted: 02/21/2013] [Indexed: 01/28/2023]
|
62
|
Structural bioinformatics of the general transcription factor TFIID. Biochimie 2013; 95:680-91. [DOI: 10.1016/j.biochi.2012.10.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 10/29/2012] [Indexed: 11/19/2022]
|
63
|
Azar WJ, Zivkovic S, Werther GA, Russo VC. IGFBP-2 nuclear translocation is mediated by a functional NLS sequence and is essential for its pro-tumorigenic actions in cancer cells. Oncogene 2013; 33:578-88. [PMID: 23435424 DOI: 10.1038/onc.2012.630] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 11/11/2012] [Accepted: 12/05/2012] [Indexed: 12/29/2022]
Abstract
IGFBP-2 is highly expressed in both the serum and tumor tissues of most cancers, and is considered one of the most significant genes in the signature of major cancers. IGFBP-2 mainly modulates IGF actions in the pericellular space; however, there is considerable evidence to suggest that IGFBP-2 may also act independently of the IGFs. These IGF-independent actions of IGFBP-2 are exerted either via interactions at the cell surface or intracellularly, via interaction with cytoplasmic or nuclear-binding partners. The precise mechanism underlying the intracellular/intranuclear localization of IGFBP-2 remains unclear. In this study, we investigated IGFBP-2 nuclear localization in several common cancer cells with the aim of dissecting the mechanism of its nuclear trafficking. IGFBP-2 is detected in the nuclei of common cancer cells, including breast, prostate and several neuroblastoma cell lines, using cell fractionation and confocal microscopy. Via nuclear import assays, we show that nuclear entry of IGFBP-2 is mediated by the classical nuclear import mechanisms, primarily through importin-α, as demonstrated by the use of blocking, competition and co-immunoprecipitation assays. Bioinformatics analysis of the IGFBP-2 protein sequence with PSORT II identified a classical nuclear localization signal (cNLS) sequence at 179PKKLRPP185, within the IGFBP-2 linker domain, mutagenesis of which abolishes IGFBP-2 nuclear import. Accordingly, the NLSmutIGFBP-2 fails to activate the VEGF promoter, which would otherwise occur in the presence of wild-type IGFBP-2. As a consequence, no activation of angiogenic processes were observed in NLSmutIGFBP-2 expressing SHEP cells when implanted onto our in vivo quail chorio-allantoic membrane model. Taken together, these data show for the first time that IGFBP-2 possesses a functional NLS sequence and that IGFBP-2 actively translocates into the nucleus by a classical nuclear import mechanism, involving formation of IGFBP-2 complexes with importin-α. Nuclear IGFBP-2 is required for the activation of VEGF expression and consequent angiogenesis.
Collapse
Affiliation(s)
- W J Azar
- 1] Hormone Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia [2] Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - S Zivkovic
- Hormone Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - G A Werther
- 1] Hormone Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia [2] Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - V C Russo
- 1] Hormone Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia [2] Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| |
Collapse
|
64
|
Structural basis for the nuclear export activity of Importin13. EMBO J 2013; 32:899-913. [PMID: 23435562 DOI: 10.1038/emboj.2013.29] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/28/2013] [Indexed: 02/05/2023] Open
Abstract
Importin13 (Imp13) is a bidirectional karyopherin that can mediate both import and export of cargoes. Imp13 recognizes several import cargoes, which include the exon junction complex components Mago-Y14 and the E2 SUMO-conjugating enzyme Ubc9, and one known export cargo, the translation initiation factor 1A (eIF1A). To understand how Imp13 can perform double duty, we determined the 3.6-Å crystal structure of Imp13 in complex with RanGTP and with eIF1A. eIF1A binds at the inner surface of the Imp13 C-terminal arch adjacent and concomitantly to RanGTP illustrating how eIF1A can be exported by Imp13. Moreover, the 3.0-Å structure of Imp13 in its unbound state reveals the existence of an open conformation in the cytoplasm that explains export cargo release and completes the export branch of the Imp13 pathway. Finally, we demonstrate that Imp13 is able to bind and export eIF1A in vivo and that its function is essential.
Collapse
|
65
|
Gao R, Liu P, Wong SM. Identification of a plant viral RNA genome in the nucleus. PLoS One 2012; 7:e48736. [PMID: 23155403 PMCID: PMC3498252 DOI: 10.1371/journal.pone.0048736] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/28/2012] [Indexed: 01/04/2023] Open
Abstract
Viruses contain either DNA or RNA as genomes. DNA viruses replicate within nucleus, while most RNA viruses, especially (+)-sense single-stranded RNA, replicate and are present within cytoplasm. We proposed a new thought that is contrary to the common notion that (+)-sense single-stranded RNA viruses are present only in the cytoplasm. In this study, we question whether the genome of a plant RNA virus (non-retroviral) is present in the nucleus of infected cells? Hibiscus chlorotic ringspot virus (HCRSV) RNA was detected in the nucleus of infected cells, as shown by fluorescent in situ hybridization. Western blot using anti-histone 3 and anti-phosphoenolpyruvate carboxylase showed that nuclei were highly purified from mock and HCRSV-infected kenaf (Hibiscus cannabilis L.) leaves, respectively. The p23 and HCRSV coat protein (CP) coding regions were both amplified from total RNA extracted from isolated nuclei. Viral RNA in the nucleus may be used to generate viral microRNAs (vir-miRNAs), as five putative vir-miRNAs were predicted from HCRSV using the vir-miRNAs prediction database. The vir-miRNA (hcrsv-miR-H1-5p) was detected using TaqMan® stem-loop real-time PCR, and by northern blot using DIG-end labeled probe in HCRSV-infected kenaf leaves. Finally, a novel nuclear localization signal (NLS) was discovered in p23 of HCRSV. The NLS interacts with importin α and facilitates viral RNA genome to enter nucleus. We demonstrate the presence of a (+)-sense single-stranded viral RNA within nucleus.
Collapse
Affiliation(s)
- Ruimin Gao
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Peng Liu
- Temasek Life Sciences Laboratory, Singapore
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Singapore
- Temasek Life Sciences Laboratory, Singapore
- * E-mail:
| |
Collapse
|
66
|
Maass PG, Rump A, Schulz H, Stricker S, Schulze L, Platzer K, Aydin A, Tinschert S, Goldring MB, Luft FC, Bähring S. A misplaced lncRNA causes brachydactyly in humans. J Clin Invest 2012; 122:3990-4002. [PMID: 23093776 DOI: 10.1172/jci65508] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 08/28/2012] [Indexed: 12/24/2022] Open
Abstract
Translocations are chromosomal rearrangements that are frequently associated with a variety of disease states and developmental disorders. We identified 2 families with brachydactyly type E (BDE) resulting from different translocations affecting chromosome 12p. Both translocations caused downregulation of the parathyroid hormone-like hormone (PTHLH) gene by disrupting the cis-regulatory landscape. Using chromosome conformation capturing, we identified a regulator on chromosome 12q that interacts in cis with PTHLH over a 24.4-megabase distance and in trans with the sex-determining region Y-box 9 (SOX9) gene on chromosome 17q. The element also harbored a long noncoding RNA (lncRNA). Silencing of the lncRNA, PTHLH, or SOX9 revealed a feedback mechanism involving an expression-dependent network in humans. In the BDE patients, the human lncRNA was upregulated by the disrupted chromosomal association. Moreover, the lncRNA occupancy at the PTHLH locus was reduced. Our results document what we believe to be a novel in cis- and in trans-acting DNA and lncRNA regulatory feedback element that is reciprocally regulated by coding genes. Furthermore, our findings provide a systematic and combinatorial view of how enhancers encoding lncRNAs may affect gene expression in normal development.
Collapse
Affiliation(s)
- Philipp G Maass
- Experimental and Clinical Research Center, joint cooperation between Charité Medical Faculty and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
67
|
Larue R, Gupta K, Wuensch C, Shkriabai N, Kessl JJ, Danhart E, Feng L, Taltynov O, Christ F, Van Duyne GD, Debyser Z, Foster MP, Kvaratskhelia M. Interaction of the HIV-1 intasome with transportin 3 protein (TNPO3 or TRN-SR2). J Biol Chem 2012; 287:34044-58. [PMID: 22872640 PMCID: PMC3464514 DOI: 10.1074/jbc.m112.384669] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/01/2012] [Indexed: 01/14/2023] Open
Abstract
Transportin 3 (TNPO3 or TRN-SR2) has been shown to be an important cellular factor for early steps of lentiviral replication. However, separate studies have implicated distinct mechanisms for TNPO3 either through its interaction with HIV-1 integrase or capsid. Here we have carried out a detailed biophysical characterization of TNPO3 and investigated its interactions with viral proteins. Biophysical analyses including circular dichroism, analytical ultracentrifugation, small-angle x-ray scattering, and homology modeling provide insight into TNPO3 architecture and indicate that it is highly structured and exists in a monomer-dimer equilibrium in solution. In vitro biochemical binding assays argued against meaningful direct interaction between TNPO3 and the capsid cores. Instead, TNPO3 effectively bound to the functional intasome but not to naked viral DNA, suggesting that TNPO3 can directly engage the HIV-1 IN tetramer prebound to the cognate DNA. Mass spectrometry-based protein footprinting and site-directed mutagenesis studies have enabled us to map several interacting amino acids in the HIV-1 IN C-terminal domain and the cargo binding domain of TNPO3. Our findings provide important information for future genetic analysis to better understand the role of TNPO3 and its interacting partners for HIV-1 replication.
Collapse
Affiliation(s)
- Ross Larue
- From the Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy and
| | - Kushol Gupta
- the Department of Biochemistry and Biophysics and The Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, and
| | - Christiane Wuensch
- From the Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy and
| | - Nikolozi Shkriabai
- From the Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy and
| | - Jacques J. Kessl
- From the Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy and
| | - Eric Danhart
- the Department of Chemistry,The Ohio State University, Columbus, Ohio 43210
| | - Lei Feng
- From the Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy and
| | - Oliver Taltynov
- the Division of Molecular Medicine, Katholieke Universiteit Leuven, Leuven, Flanders 3000, Belgium
| | - Frauke Christ
- the Division of Molecular Medicine, Katholieke Universiteit Leuven, Leuven, Flanders 3000, Belgium
| | - Gregory D. Van Duyne
- the Department of Biochemistry and Biophysics and The Howard Hughes Medical Institute, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, and
| | - Zeger Debyser
- the Division of Molecular Medicine, Katholieke Universiteit Leuven, Leuven, Flanders 3000, Belgium
| | - Mark P. Foster
- the Department of Chemistry,The Ohio State University, Columbus, Ohio 43210
| | - Mamuka Kvaratskhelia
- From the Center for Retrovirus Research and Comprehensive Cancer Center, College of Pharmacy and
| |
Collapse
|
68
|
McCauley LK, Martin TJ. Twenty-five years of PTHrP progress: from cancer hormone to multifunctional cytokine. J Bone Miner Res 2012; 27:1231-9. [PMID: 22549910 PMCID: PMC4871126 DOI: 10.1002/jbmr.1617] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/04/2012] [Accepted: 03/20/2012] [Indexed: 01/30/2023]
Abstract
Twenty-five years ago a "new" protein was identified from cancers that caused hypercalcemia. It was credited for its ability to mimic parathyroid hormone (PTH), and hence was termed parathyroid hormone-related protein (PTHrP). Today it is recognized for its widespread distribution, its endocrine, paracrine, and intracrine modes of action driving numerous physiologic and pathologic conditions, and its central role in organogenesis. The multiple biological activities within a complex molecule with paracrine modulation of adjacent target cells present boundless possibilities. The protein structure of PTHrP has been traced, dissected, and deleted comprehensively and conditionally, yet numerous questions lurk in its past that will carry into the future. Issues of the variable segments of the protein, including the enigmatic nuclear localization sequence, are only recently being clarified. Aspects of PTHrP production and action in the menacing condition of cancer are emerging as dichotomies that may represent intended temporal actions of PTHrP. Relative to PTH, the hormone regulating calcium homeostasis, PTHrP "controls the show" locally at the PTH/PTHrP receptor throughout the body. Great strides have been made in our understanding of PTHrP actions, yet years of exciting investigation and discovery are imminent. © 2012 American Society for Bone and Mineral Research.
Collapse
Affiliation(s)
- Laurie K McCauley
- Department of Periodontics and Oral Medicine, University of Michigan, School of Dentistry, 1011 N. University Ave., Ann Arbor, MI 48105, USA.
| | | |
Collapse
|
69
|
Depping R, Schindler SG, Jacobi C, Kirschner KM, Scholz H. Nuclear transport of Wilms' tumour protein Wt1 involves importins α and β. Cell Physiol Biochem 2012; 29:223-32. [PMID: 22415091 DOI: 10.1159/000337603] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2011] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND/AIMS Wilms' tumour protein, Wt1, is a zinc finger molecule, which is required for normal embryonic development. Mutations of the WT1 gene can give rise to childhood cancer of the kidneys. Different Wt1 isoforms exist, which function either as transcription factors or have a presumed role in mRNA processing. Previous studies suggested that Wt1 undergoes nucleocytoplasmic shuttling, and cytoplasmic Wt1 was higher in malignant than in normal cells. The aim of this study was to analyse the molecular pathways along which Wt1 shuttles between the cytoplasm and nucleus. METHODS Interaction of Wt1 protein with various importin α subtypes and importin β was assessed in pull-down assays and co-immunoprecipitation experiments. Nuclear localisation signals (NLS) were identified by combining site-directed mutagenesis with subcellular immunodetection of the transfected Wt1 variants. RESULTS Wt1(+/-KTS) proteins were found to interact with importin α1 and importin β in vitro and in living cells in vivo. A NLS that was necessary and sufficient for nuclear import could be mapped to the third Wt1 zinc finger. Mutation of this NLS strongly weakened binding of Wt1 to importins. CONCLUSION Nuclear translocation of Wilms' tumour protein involves importins α and β, and a NLS in the third zinc finger.
Collapse
Affiliation(s)
- Reinhard Depping
- Institut für Physiologie, Zentrum für Medizinische Struktur- und Zellbiologie, Universität zu Lübeck, Lübeck, Germany
| | | | | | | | | |
Collapse
|
70
|
Cherezova L, Burnside KL, Rose TM. Conservation of complex nuclear localization signals utilizing classical and non-classical nuclear import pathways in LANA homologs of KSHV and RFHV. PLoS One 2011; 6:e18920. [PMID: 21559489 PMCID: PMC3084728 DOI: 10.1371/journal.pone.0018920] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 03/23/2011] [Indexed: 11/18/2022] Open
Abstract
ORF73 latency-associated nuclear antigen (LANA) of the Kaposi's sarcoma-associated herpesvirus (KSHV) is targeted to the nucleus of infected cells where it binds to chromatin and mediates viral episome persistence, interacts with cellular proteins and plays a role in latency and tumorigenesis. A structurally related LANA homolog has been identified in the retroperitoneal fibromatosis herpesvirus (RFHV), the macaque homolog of KSHV. Here, we report the evolutionary and functional conservation of a novel bi-functional nuclear localization signal (NLS) in KSHV and RFHV LANA. N-terminal peptides from both proteins were fused to EGFP or double EGFP fusions to examine their ability to induce nuclear transport of a heterologous protein. In addition, GST-pull down experiments were used to analyze the ability of LANA peptides to interact with members of the karyopherin family of nuclear transport receptors. Our studies revealed that both LANA proteins contain an N-terminal arginine/glycine (RG)-rich domain spanning a conserved chromatin-binding motif, which binds directly to importin β1 in a RanGTP-sensitive manner and serves as an NLS in the importin β1-mediated non-classical nuclear import pathway. Embedded within this domain is a conserved lysine/arginine-(KR)-rich bipartite motif that binds directly to multiple members of the importin α family of nuclear import adaptors in a RanGTP-insensitive manner and serves as an NLS in the classical importin α/β-mediated nuclear import pathway. The positioning of a classical bipartite kr-NLS embedded within a non-classical rg-NLS is a unique arrangement in these viral proteins, whose nuclear localization is critical to their functionality and to the virus life cycle. The ability to interact with multiple import receptors provides alternate pathways for nuclear localization of LANA. Since different import receptors can import cargo to distinct subnuclear compartments, a multifunctional NLS may provide LANA with an increased ability to interact with different nuclear components in its multifunctional role to maintain viral latency.
Collapse
Affiliation(s)
- Lidia Cherezova
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Center for Childhood Infections and Prematurity Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Kellie L. Burnside
- Center for Childhood Infections and Prematurity Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Timothy M. Rose
- Center for Childhood Infections and Prematurity Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
71
|
O'Reilly AJ, Dacks JB, Field MC. Evolution of the karyopherin-β family of nucleocytoplasmic transport factors; ancient origins and continued specialization. PLoS One 2011; 6:e19308. [PMID: 21556326 PMCID: PMC3083441 DOI: 10.1371/journal.pone.0019308] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 03/29/2011] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Macromolecular transport across the nuclear envelope (NE) is achieved through nuclear pore complexes (NPCs) and requires karyopherin-βs (KAP-βs), a family of soluble receptors, for recognition of embedded transport signals within cargo. We recently demonstrated, through proteomic analysis of trypanosomes, that NPC architecture is likely highly conserved across the Eukaryota, which in turn suggests conservation of the transport mechanisms. To determine if KAP-β diversity was similarly established early in eukaryotic evolution or if it was subsequently layered onto a conserved NPC, we chose to identify KAP-β sequences in a diverse range of eukaryotes and to investigate their evolutionary history. RESULTS Thirty six predicted proteomes were scanned for candidate KAP-β family members. These resulting sequences were resolved into fifteen KAP-β subfamilies which, due to broad supergroup representation, were most likely represented in the last eukaryotic common ancestor (LECA). Candidate members of each KAP-β subfamily were found in all eukaryotic supergroups, except XPO6, which is absent from Archaeplastida. Phylogenetic reconstruction revealed the likely evolutionary relationships between these different subfamilies. Many species contain more than one representative of each KAP-β subfamily; many duplications are apparently taxon-specific but others result from duplications occurring earlier in eukaryotic history. CONCLUSIONS At least fifteen KAP-β subfamilies were established early in eukaryote evolution and likely before the LECA. In addition we identified expansions at multiple stages within eukaryote evolution, including a multicellular plant-specific KAP-β, together with frequent secondary losses. Taken with evidence for early establishment of NPC architecture, these data demonstrate that multiple pathways for nucleocytoplasmic transport were established prior to the radiation of modern eukaryotes but that selective pressure continues to sculpt the KAP-β family.
Collapse
Affiliation(s)
- Amanda J. O'Reilly
- Department of Pathology, University of
Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Joel B. Dacks
- Department of Cell Biology, University of
Alberta, Edmonton, Canada
| | - Mark C. Field
- Department of Pathology, University of
Cambridge, Tennis Court Road, Cambridge, United Kingdom
- * E-mail:
| |
Collapse
|
72
|
Bier C, Knauer SK, Docter D, Schneider G, Krämer OH, Stauber RH. The Importin-Alpha/Nucleophosmin Switch Controls Taspase1 Protease Function. Traffic 2011; 12:703-14. [DOI: 10.1111/j.1600-0854.2011.01191.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
73
|
Kim DU, Cho SG, Kim KL, Cho HS. RETRACTED ARTICLE: Human MTERF3 crystal structure forms a left-handed superhelix. Mol Cells 2011. [PMID: 21448587 DOI: 10.1007/s10059-011-0264-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Revised: 03/03/2011] [Accepted: 03/08/2011] [Indexed: 11/28/2022] Open
Affiliation(s)
- Dong-Uk Kim
- Department of Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 120-749, Korea
| | | | | | | |
Collapse
|
74
|
Parathyroid hormone related protein (PTHrP) in tumor progression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 720:145-60. [PMID: 21901625 DOI: 10.1007/978-1-4614-0254-1_12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Parathyroid hormone-related protein (PTHrP) is widely expressed in fetal and adult tissues and is a key regulator for cellular calcium transport and smooth muscle cell contractility, as well as a crucial control factor in cell proliferation, development and differentiation. PTHrP stimulates or inhibits apoptosis in an autocrine/paracrine and intracrine fashion, and is particularly important for hair follicle and bone development, mammary epithelial development and tooth eruption. PTHrP's dysregulated expression has traditionally been associated with oncogenic pathologies as the major causative agent of malignancy-associated hypercalcemia, but recent evidence revealed a driving role in skeletal metastasis progression. Here, we demonstrate that PTHrP is also closely involved in breast cancer initiation, growth and metastasis through mechanisms separate from its bone turnover action, and we suggest that PTHrP as a facilitator of oncogenes would be a novel target for therapeutic purposes.
Collapse
|
75
|
Jamali T, Jamali Y, Mehrbod M, Mofrad MRK. Nuclear pore complex: biochemistry and biophysics of nucleocytoplasmic transport in health and disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 287:233-86. [PMID: 21414590 DOI: 10.1016/b978-0-12-386043-9.00006-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Nuclear pore complexes (NPCs) are the gateways connecting the nucleoplasm and cytoplasm. This structures are composed of over 30 different proteins and 60-125 MDa of mass depending on type of species. NPCs are bilateral pathways that selectively control the passage of macromolecules into and out of the nucleus. Molecules smaller than 40 kDa diffuse through the NPC passively while larger molecules require facilitated transport provided by their attachment to karyopherins. Kinetic studies have shown that approximately 1000 translocations occur per second per NPC. Maintaining its high selectivity while allowing for rapid translocation makes the NPC an efficient chemical nanomachine. In this review, we approach the NPC function via a structural viewpoint. Putting together different pieces of this puzzle, this chapter confers an overall insight into what molecular processes are engaged in import/export of active cargos across the NPC and how different transporters regulate nucleocytoplasmic transport. In the end, the correlation of several diseases and disorders with the NPC structural defects and dysfunctions is discussed.
Collapse
Affiliation(s)
- T Jamali
- Department of Bioengineering, University of California, Berkeley, California, USA
| | | | | | | |
Collapse
|
76
|
Nardozzi JD, Lott K, Cingolani G. Phosphorylation meets nuclear import: a review. Cell Commun Signal 2010; 8:32. [PMID: 21182795 PMCID: PMC3022542 DOI: 10.1186/1478-811x-8-32] [Citation(s) in RCA: 175] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 12/23/2010] [Indexed: 12/18/2022] Open
Abstract
Phosphorylation is the most common and pleiotropic modification in biology, which plays a vital role in regulating and finely tuning a multitude of biological pathways. Transport across the nuclear envelope is also an essential cellular function and is intimately linked to many degeneration processes that lead to disease. It is therefore not surprising that phosphorylation of cargos trafficking between the cytoplasm and nucleus is emerging as an important step to regulate nuclear availability, which directly affects gene expression, cell growth and proliferation. However, the literature on phosphorylation of nucleocytoplasmic trafficking cargos is often confusing. Phosphorylation, and its mirror process dephosphorylation, has been shown to have opposite and often contradictory effects on the ability of cargos to be transported across the nuclear envelope. Without a clear connection between attachment of a phosphate moiety and biological response, it is difficult to fully understand and predict how phosphorylation regulates nucleocytoplasmic trafficking. In this review, we will recapitulate clue findings in the field and provide some general rules on how reversible phosphorylation can affect the nuclear-cytoplasmic localization of substrates. This is only now beginning to emerge as a key regulatory step in biology.
Collapse
Affiliation(s)
- Jonathan D Nardozzi
- Dept, of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA.
| | | | | |
Collapse
|
77
|
Structure of Importin13-Ubc9 complex: nuclear import and release of a key regulator of sumoylation. EMBO J 2010; 30:427-38. [PMID: 21139563 DOI: 10.1038/emboj.2010.320] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 11/10/2010] [Indexed: 01/09/2023] Open
Abstract
Importin13 (Imp13) is an unusual β-karyopherin that is able to both import and export cargoes in and out of the nucleus. In the cytoplasm, Imp13 associates with different cargoes such as Mago-Y14 and Ubc9, and facilitates their import into the nucleus where RanGTP binding promotes the release of the cargo. In this study, we present the 2.8 Å resolution crystal structure of Imp13 in complex with the SUMO E2-conjugating enzyme, Ubc9. The structure shows an uncommon mode of cargo-karyopherin recognition with Ubc9 binding at the N-terminal portion of Imp13, occupying the entire RanGTP-binding site. Comparison of the Imp13-Ubc9 complex with Imp13-Mago-Y14 shows the remarkable plasticity of Imp13, whose conformation changes from a closed ring to an open superhelix when bound to the two different cargoes. The structure also shows that the binding mode is compatible with the sumoylated states of Ubc9. Indeed, we find that Imp13 is able to bind sumoylated Ubc9 in vitro and suppresses autosumoylation activity in the complex.
Collapse
|
78
|
Slootweg E, Roosien J, Spiridon LN, Petrescu AJ, Tameling W, Joosten M, Pomp R, van Schaik C, Dees R, Borst JW, Smant G, Schots A, Bakker J, Goverse A. Nucleocytoplasmic distribution is required for activation of resistance by the potato NB-LRR receptor Rx1 and is balanced by its functional domains. THE PLANT CELL 2010; 22:4195-215. [PMID: 21177483 PMCID: PMC3027179 DOI: 10.1105/tpc.110.077537] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2010] [Revised: 10/18/2010] [Accepted: 11/19/2010] [Indexed: 05/18/2023]
Abstract
The Rx1 protein, as many resistance proteins of the nucleotide binding-leucine-rich repeat (NB-LRR) class, is predicted to be cytoplasmic because it lacks discernable nuclear targeting signals. Here, we demonstrate that Rx1, which confers extreme resistance to Potato virus X, is located both in the nucleus and cytoplasm. Manipulating the nucleocytoplasmic distribution of Rx1 or its elicitor revealed that Rx1 is activated in the cytoplasm and cannot be activated in the nucleus. The coiled coil (CC) domain was found to be required for accumulation of Rx1 in the nucleus, whereas the LRR domain promoted the localization in the cytoplasm. Analyses of structural subdomains of the CC domain revealed no autonomous signals responsible for active nuclear import. Fluorescence recovery after photobleaching and nuclear fractionation indicated that the CC domain binds transiently to large complexes in the nucleus. Disruption of the Rx1 resistance function and protein conformation by mutating the ATP binding phosphate binding loop in the NB domain, or by silencing the cochaperone SGT1, impaired the accumulation of Rx1 protein in the nucleus, while Rx1 versions lacking the LRR domain were not affected in this respect. Our results support a model in which interdomain interactions and folding states determine the nucleocytoplasmic distribution of Rx1.
Collapse
Affiliation(s)
- Erik Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
79
|
Lott K, Cingolani G. The importin β binding domain as a master regulator of nucleocytoplasmic transport. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:1578-92. [PMID: 21029753 DOI: 10.1016/j.bbamcr.2010.10.012] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 10/11/2010] [Accepted: 10/19/2010] [Indexed: 12/16/2022]
Abstract
Specific and efficient recognition of import cargoes is essential to ensure nucleocytoplasmic transport. To this end, the prototypical karyopherin importin β associates with import cargoes directly or, more commonly, through import adaptors, such as importin α and snurportin. Adaptor proteins bind the nuclear localization sequence (NLS) of import cargoes while recruiting importin β via an N-terminal importin β binding (IBB) domain. The use of adaptors greatly expands and amplifies the repertoire of cellular cargoes that importin β can efficiently import into the cell nucleus and allows for fine regulation of nuclear import. Accordingly, the IBB domain is a dedicated NLS, unique to adaptor proteins that functions as a molecular liaison between importin β and import cargoes. This review provides an overview of the molecular role played by the IBB domain in orchestrating nucleocytoplasmic transport. Recent work has determined that the IBB domain has specialized functions at every step of the import and export pathway. Unexpectedly, this stretch of ~40 amino acids plays an essential role in regulating processes such as formation of the import complex, docking and translocation through the nuclear pore complex (NPC), release of import cargoes into the cell nucleus and finally recycling of import adaptors and importin β into the cytoplasm. Thus, the IBB domain is a master regulator of nucleocytoplasmic transport, whose complex molecular function is only recently beginning to emerge. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.
Collapse
Affiliation(s)
- Kaylen Lott
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, PA 19107, USA
| | | |
Collapse
|
80
|
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.
Collapse
Affiliation(s)
- Yuh Min Chook
- Department of Pharmacology, University of Texas Southerwestern Medical Center, Dallas, TX 75206, USA.
| | | |
Collapse
|
81
|
Marfori M, Mynott A, Ellis JJ, Mehdi AM, Saunders NFW, Curmi PM, Forwood JK, Bodén M, Kobe B. Molecular basis for specificity of nuclear import and prediction of nuclear localization. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1813:1562-77. [PMID: 20977914 DOI: 10.1016/j.bbamcr.2010.10.013] [Citation(s) in RCA: 303] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 10/15/2010] [Accepted: 10/19/2010] [Indexed: 01/03/2023]
Abstract
Although proteins are translated on cytoplasmic ribosomes, many of these proteins play essential roles in the nucleus, mediating key cellular processes including but not limited to DNA replication and repair as well as transcription and RNA processing. Thus, understanding how these critical nuclear proteins are accurately targeted to the nucleus is of paramount importance in biology. Interaction and structural studies in the recent years have jointly revealed some general rules on the specificity determinants of the recognition of nuclear targeting signals by their specific receptors, at least for two nuclear import pathways: (i) the classical pathway, which involves the classical nuclear localization sequences (cNLSs) and the receptors importin-α/karyopherin-α and importin-β/karyopherin-β1; and (ii) the karyopherin-β2 pathway, which employs the proline-tyrosine (PY)-NLSs and the receptor transportin-1/karyopherin-β2. The understanding of specificity rules allows the prediction of protein nuclear localization. We review the current understanding of the molecular determinants of the specificity of nuclear import, focusing on the importin-α•cargo recognition, as well as the currently available databases and predictive tools relevant to nuclear localization. This article is part of a Special Issue entitled: Regulation of Signaling and Cellular Fate through Modulation of Nuclear Protein Import.
Collapse
Affiliation(s)
- Mary Marfori
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|
82
|
Xu D, Farmer A, Chook YM. Recognition of nuclear targeting signals by Karyopherin-β proteins. Curr Opin Struct Biol 2010; 20:782-90. [PMID: 20951026 DOI: 10.1016/j.sbi.2010.09.008] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/10/2010] [Accepted: 09/15/2010] [Indexed: 12/22/2022]
Abstract
The Karyopherin-β family of nuclear transport factors mediates the majority of nucleocytoplasmic transport. Although each of the 19 Karyopherin-βs transports unique sets of cargos, only three classes of nuclear localization and export signals, or NLSs and NESs, have been characterized. The short basic classical-NLS was first discovered in the 1980s and their karyopherin-bound structures were first reported more than 10 years ago. More recently, structural and biophysical studies of Karyopherin-β2-cargo complexes led to definition of the complex and diverse PY-NLS. Structural knowledge of the leucine-rich NES is finally available more than 10 years after the discovery of its recognition by the exportin CRM1. We review recent findings relating to how these three classes of nuclear targeting signals are recognized by their Karyopherin-β nuclear transport factors.
Collapse
Affiliation(s)
- Darui Xu
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9041, USA
| | | | | |
Collapse
|
83
|
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]
|
84
|
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.
Collapse
Affiliation(s)
- Anshul Bhardwaj
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10th Street, Philadelphia, Pennsylvania 19107, USA
| | | |
Collapse
|
85
|
Song L, Rape M. Regulated degradation of spindle assembly factors by the anaphase-promoting complex. Mol Cell 2010; 38:369-82. [PMID: 20471943 DOI: 10.1016/j.molcel.2010.02.038] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 11/19/2009] [Accepted: 02/19/2010] [Indexed: 12/14/2022]
Abstract
The ubiquitin ligase anaphase-promoting complex (APC/C) is essential for cell division in all eukaryotes. Loss of APC/C activity arrests cells at metaphase and results in severe aberrations of the mitotic spindle, but how the APC/C regulates spindle formation is not understood. Here, we report that the APC/C promotes the ubiquitination and degradation of four proteins required for Ran-dependent spindle assembly: Bard1, Hmmr, HURP, and NuSAP. Among these substrates, HURP and NuSAP can be degraded during spindle formation when the spindle checkpoint is active. Their degradation requires additional layers of regulation, and both SAFs are only degraded after being released from their inhibitor importin beta by Ran(GTP). Our findings reveal a tightly regulated mechanism by which the APC/C and the GTPase Ran control the abundance of active spindle assembly factors to achieve the accurate formation of the mitotic spindle.
Collapse
Affiliation(s)
- Ling Song
- Department of Molecular Cell Biology, University of California, Berkeley, 16 Barker Hall, Berkeley, CA 94720, USA
| | | |
Collapse
|
86
|
Chumakov SP, Prassolov VS. Organization and regulation of nucleocytoplasmic transport. Mol Biol 2010; 44:186-201. [PMID: 32214470 PMCID: PMC7088953 DOI: 10.1134/s0026893310020020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 11/03/2009] [Indexed: 01/05/2023]
Abstract
Separation of DNA replication and transcription, which occur in the nucleus, from protein synthesis, which occurs in the cytoplasm, allows a more precise regulation of these processes. Selective exchange of macromolecules between the two compartments is mediated by proteins of the nuclear pore complex (NPC). Receptor proteins of the karyopherin family interact with NPC components and transfer their cargos between the nucleus and cytoplasm. Nucleocytoplasmic transport pathways are regulated at multiple levels by modulating the expression or function of individual cargoes, transport receptors, or the transport channel. The regulatory levels have increasingly broad effects on the transport pathways and affect a wide range of processes from gene expression to development and differentiation.
Collapse
Affiliation(s)
- S P Chumakov
- 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,2Department of Molecular Genetics, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195 USA
| | - V S Prassolov
- 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| |
Collapse
|
87
|
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.
Collapse
Affiliation(s)
- Kaylen Lott
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | | | | | | | | |
Collapse
|
88
|
Abstract
The central role of Raf protein kinase isoforms in human cancer demands specific anti-Raf therapeutic inhibitors. Parvoviruses are currently used in experimental cancer therapy due to their natural oncotropism and lytic life cycle. In searching for mechanisms underlying parvovirus oncolysis, we found that trimers of the major structural protein (VP) of the parvovirus minute virus of mice (MVM), which have to be imported into the nucleus for capsid assembly, undergo phosphorylation by the Raf-1 kinase. Purified Raf-1 phosphorylated the capsid subunits in vitro to the two-dimensional pattern found in natural MVM infections. VP trimers isolated from mammalian cells translocated into the nucleus of digitonin-permeabilized human cells. In contrast, VP trimers isolated from insect cells, which are devoid of Raf-1, were neither phosphorylated nor imported into the mammalian nucleus. However, the coexpression of a constitutively active Raf-1 kinase in insect cells restored VP trimer phosphorylation and nuclear transport competence. In MVM-infected normal and transformed cells, Raf-1 inhibition resulted in cytoplasmic retention of capsid proteins, preventing their nuclear assembly and progeny virus maturation. The level of Raf-1 activity in cancer cells was consistent with the extent of VP specific phosphorylation and with the permissiveness to MVM infection. Thus, Raf-1 control of nuclear translocation of MVM capsid assembly intermediates provides a novel target for viral oncolysis. MVM may reinforce specific therapies against frequent human cancers with deregulated Raf signaling.
Collapse
|
89
|
Flexible gates: dynamic topologies and functions for FG nucleoporins in nucleocytoplasmic transport. EUKARYOTIC CELL 2009; 8:1814-27. [PMID: 19801417 DOI: 10.1128/ec.00225-09] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The nuclear envelope is a physical barrier between the nucleus and cytoplasm and, as such, separates the mechanisms of transcription from translation. This compartmentalization of eukaryotic cells allows spatial regulation of gene expression; however, it also necessitates a mechanism for transport between the nucleus and cytoplasm. Macromolecular trafficking of protein and RNA occurs exclusively through nuclear pore complexes (NPCs), specialized channels spanning the nuclear envelope. A novel family of NPC proteins, the FG-nucleoporins (FG-Nups), coordinates and potentially regulates NPC translocation. The extensive repeats of phenylalanine-glycine (FG) in each FG-Nup directly bind to shuttling transport receptors moving through the NPC. In addition, FG-Nups are essential components of the nuclear permeability barrier. In this review, we discuss the structural features, cellular functions, and evolutionary conservation of the FG-Nups.
Collapse
|
90
|
Miyauchi Y, Sakaguchi N, Okada T, Makishima M, Ozono K, Michigami T. Oncogenic nucleoporin CAN/Nup214 interacts with vitamin D receptor and modulates its function. J Cell Biochem 2009; 106:1090-101. [DOI: 10.1002/jcb.22101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
91
|
Kopito RB, Elbaum M. Nucleocytoplasmic transport: a thermodynamic mechanism. HFSP JOURNAL 2009; 3:130-41. [PMID: 19794817 DOI: 10.2976/1.3080807] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Accepted: 01/23/2009] [Indexed: 01/09/2023]
Abstract
The nuclear pore supports molecular communication between cytoplasm and nucleus in eukaryotic cells. Selective transport of proteins is mediated by soluble receptors, whose regulation by the small GTPase Ran leads to cargo accumulation in, or depletion from, the nucleus, i.e., nuclear import or nuclear export. We consider the operation of this transport system by a combined analytical and experimental approach. Provocative predictions of a simple model were tested using cell-free nuclei reconstituted in Xenopus egg extract, a system well suited to quantitative studies. We found that accumulation capacity is limited, so that introduction of one import cargo leads to egress of another. Clearly, the pore per se does not determine transport directionality. Moreover, different cargo reach a similar ratio of nuclear to cytoplasmic concentration in steady-state. The model shows that this ratio should in fact be independent of the receptor-cargo affinity, though kinetics may be strongly influenced. Numerical conservation of the system components highlights a conflict between the observations and the popular concept of transport cycles. We suggest that chemical partitioning provides a framework to understand the capacity to generate concentration gradients by equilibration of the receptor-cargo intermediary.
Collapse
Affiliation(s)
- Ronen Benjamine Kopito
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel
| | | |
Collapse
|
92
|
Andrake MD, Sauter MM, Boland K, Goldstein AD, Hussein M, Skalka AM. Nuclear import of Avian Sarcoma Virus integrase is facilitated by host cell factors. Retrovirology 2008; 5:73. [PMID: 18687138 PMCID: PMC2527327 DOI: 10.1186/1742-4690-5-73] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Accepted: 08/07/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Integration of retroviral DNA into the host cell genome is an obligatory step in the virus life cycle. In previous reports we identified a sequence (amino acids 201-236) in the linker region between the catalytic core and C-terminal domains of the avian sarcoma virus (ASV) integrase protein that functions as a transferable nuclear localization signal (NLS) in mammalian cells. The sequence is distinct from all known NLSs but, like many, contains basic residues that are essential for activity. RESULTS Our present studies with digitonin-permeabilized HeLa cells show that nuclear import mediated by the NLS of ASV integrase is an active, saturable, and ATP-dependent process. As expected for transport through nuclear pore complexes, import is blocked by treatment of cells with wheat germ agglutinin. We also show that import of ASV integrase requires soluble cellular factors but does not depend on binding the classical adapter Importin-alpha. Results from competition studies indicate that ASV integrase relies on one or more of the soluble components that mediate transport of the linker histone H1. CONCLUSION These results are consistent with a role for ASV integrase and cytoplasmic cellular factors in the nuclear import of its viral DNA substrate, and lay the foundation for identification of host cell components that mediate this reaction.
Collapse
Affiliation(s)
- Mark D Andrake
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
| | | | | | | | | | | |
Collapse
|
93
|
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.
Collapse
|
94
|
Expression of parathyroid hormone-related protein during immortalization of human peripheral blood mononuclear cells by HTLV-1: implications for transformation. Retrovirology 2008; 5:46. [PMID: 18541021 PMCID: PMC2435116 DOI: 10.1186/1742-4690-5-46] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Accepted: 06/09/2008] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Adult T-cell leukemia/lymphoma (ATLL) is initiated by infection with human T-lymphotropic virus type-1 (HTLV-1); however, additional host factors are also required for T-cell transformation and development of ATLL. The HTLV-1 Tax protein plays an important role in the transformation of T-cells although the exact mechanisms remain unclear. Parathyroid hormone-related protein (PTHrP) plays an important role in the pathogenesis of humoral hypercalcemia of malignancy (HHM) that occurs in the majority of ATLL patients. However, PTHrP is also up-regulated in HTLV-1-carriers and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) patients without hypercalcemia, indicating that PTHrP is expressed before transformation of T-cells. The expression of PTHrP and the PTH/PTHrP receptor during immortalization or transformation of lymphocytes by HTLV-1 has not been investigated. RESULTS We report that PTHrP was up-regulated during immortalization of lymphocytes from peripheral blood mononuclear cells by HTLV-1 infection in long-term co-culture assays. There was preferential utilization of the PTHrP-P2 promoter in the immortalized cells compared to the HTLV-1-transformed MT-2 cells. PTHrP expression did not correlate temporally with expression of HTLV-1 tax. HTLV-1 infection up-regulated the PTHrP receptor (PTH1R) in lymphocytes indicating a potential autocrine role for PTHrP. Furthermore, co-transfection of HTLV-1 expression plasmids and PTHrP P2/P3-promoter luciferase reporter plasmids demonstrated that HTLV-1 up-regulated PTHrP expression only mildly, indicating that other cellular factors and/or events are required for the very high PTHrP expression observed in ATLL cells. We also report that macrophage inflammatory protein-1alpha (MIP-1alpha), a cellular gene known to play an important role in the pathogenesis of HHM in ATLL patients, was highly expressed during early HTLV-1 infection indicating that, unlike PTHrP, its expression was enhanced due to activation of lymphocytes by HTLV-1 infection. CONCLUSION These data demonstrate that PTHrP and its receptor are up-regulated specifically during immortalization of T-lymphocytes by HTLV-1 infection and may facilitate the transformation process.
Collapse
|
95
|
Keskin O, Gursoy A, Ma B, Nussinov R. Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact? Chem Rev 2008; 108:1225-44. [DOI: 10.1021/cr040409x] [Citation(s) in RCA: 476] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
96
|
Sorokin AV, Kim ER, Ovchinnikov LP. Nucleocytoplasmic transport of proteins. BIOCHEMISTRY (MOSCOW) 2008; 72:1439-57. [PMID: 18282135 DOI: 10.1134/s0006297907130032] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In eukaryotic cells, the movement of macromolecules between the nucleus and cytoplasm occurs through the nuclear pore complex (NPC)--a large protein complex spanning the nuclear envelope. The nuclear transport of proteins is usually mediated by a family of transport receptors known as karyopherins. Karyopherins bind to their cargoes via recognition of nuclear localization signal (NLS) for nuclear import or nuclear export signal (NES) for export to form a transport complex. Its transport through NPC is facilitated by transient interactions between the karyopherins and NPC components. The interactions of karyopherins with their cargoes are regulated by GTPase Ran. In the current review, we describe the NPC structure, NLS, and NES, as well as the model of classic Ran-dependent transport, with special emphasis on existing alternative mechanisms; we also propose a classification of the basic mechanisms of protein transport regulation.
Collapse
Affiliation(s)
- A V Sorokin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | | | | |
Collapse
|
97
|
Delmar VA, Chan RC, Forbes DJ. Xenopus importin beta validates human importin beta as a cell cycle negative regulator. BMC Cell Biol 2008; 9:14. [PMID: 18366719 PMCID: PMC2324082 DOI: 10.1186/1471-2121-9-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 03/22/2008] [Indexed: 11/12/2022] Open
Abstract
Background Human importin beta has been used in all Xenopus laevis in vitro nuclear assembly and spindle assembly studies. This disconnect between species raised the question for us as to whether importin beta was an authentic negative regulator of cell cycle events, or a dominant negative regulator due to a difference between the human and Xenopus importin beta sequences. No Xenopus importin beta gene was yet identified at the time of those studies. Thus, we first cloned, identified, and tested the Xenopus importin beta gene to address this important mechanistic difference. If human importin beta is an authentic negative regulator then we would expect human and Xenopus importin beta to have identical negative regulatory effects on nuclear membrane fusion and pore assembly. If human importin beta acts instead as a dominant negative mutant inhibitor, we should then see no inhibitory effect when we added the Xenopus homologue. Results We found that Xenopus importin beta acts identically to its human counterpart. It negatively regulates both nuclear membrane fusion and pore assembly. Human importin beta inhibition was previously found to be reversible by Ran for mitotic spindle assembly and nuclear membrane fusion, but not nuclear pore assembly. During the present study, we observed that this differing reversibility varied depending on the presence or absence of a tag on importin beta. Indeed, when untagged importin beta, either human or Xenopus, was used, inhibition of nuclear pore assembly proved to be Ran-reversible. Conclusion We conclude that importin beta, human or Xenopus, is an authentic negative regulator of nuclear assembly and, presumably, spindle assembly. A difference in the Ran sensitivity between tagged and untagged importin beta in pore assembly gives us mechanistic insight into nuclear pore formation.
Collapse
Affiliation(s)
- Valerie A Delmar
- Section of Cell and Developmental Biology, Division of Biological Sciences 0347, University of California - San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0347, USA.
| | | | | |
Collapse
|
98
|
Lange A, Mills RE, Devine SE, Corbett AH. A PY-NLS nuclear targeting signal is required for nuclear localization and function of the Saccharomyces cerevisiae mRNA-binding protein Hrp1. J Biol Chem 2008; 283:12926-34. [PMID: 18343812 DOI: 10.1074/jbc.m800898200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins destined for import into the nucleus contain nuclear localization signals (NLSs) that are recognized by import receptors termed karyopherins or importins. Until recently, the only nuclear import sequence that had been well defined and characterized was the classical NLS (cNLS), which is recognized by importin alpha. However, Chook and coworkers (Lee, B. J., Cansizoglu, A. E., Süel, K. E., Louis, T. H., Zhang, Z., and Chook, Y. M. (2006) Cell 126, 543-558) have provided new insight into nuclear targeting with their identification of a novel NLS, termed the PY-NLS, that is recognized by the human karyopherin beta2/transportin (Kapbeta2) receptor. Here, we demonstrate that the PY-NLS is conserved in Saccharomyces cerevisiae and show for the first time that the PY-NLS is a functional nuclear targeting sequence in vivo. The apparent ortholog of Kapbeta2 in yeast, Kap104, has two known cargos, the mRNA-binding proteins Hrp1 and Nab2, which both contain putative PY-NLS-like sequences. We find that the PY-NLS-like sequence within Hrp1, which closely matches the PY-NLS consensus, is both necessary and sufficient for nuclear import and is also required for receptor binding and protein function. In contrast, the PY-NLS-like sequences in Nab2, which vary from the PY-NLS consensus, are not required for proper import or protein function, suggesting that Kap104 may interact with different cargos using multiple mechanisms. Dissection of the PY-NLS consensus reveals that the minimal PY-NLS in yeast consists of the C-terminal portion of the human consensus, R/H/KX(2-5)PY, with upstream basic or hydrophobic residues enhancing the targeting function. Finally, we apply this analysis to a bioinformatic search of the yeast proteome as a preliminary search for new potential Kap104 cargos.
Collapse
Affiliation(s)
- Allison Lange
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | | | | | | |
Collapse
|
99
|
Cansizoglu AE, Chook YM. Conformational heterogeneity of karyopherin beta2 is segmental. Structure 2008; 15:1431-41. [PMID: 17997969 DOI: 10.1016/j.str.2007.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 09/02/2007] [Accepted: 09/10/2007] [Indexed: 10/22/2022]
Abstract
Karyopherinbeta2 (Kap beta2) or transportin imports numerous RNA binding proteins into the nucleus. Kap beta2 binds substrates in the cytoplasm and targets them through the nuclear pore complex, where RanGTP dissociates them in the nucleus. Here we report the 3.0 A crystal structure of unliganded Kap beta2, which consists of a superhelix of 20 HEAT repeats. Together with previously reported structures of NLS and Ran complexes, this structure provides understanding of conformational heterogeneity that accompanies ligand binding. The Kap beta2 superhelix is divided into three major segments. Two of them (HEAT repeats 9-13 and 14-18), which constitute the substrate binding site, are rigid elements that rotate relative to each other about a flexible hinge. The third (HEAT repeats 1-8), which constitutes the Ran binding site, exhibits conformational changes throughout its length. An analogous segmental architecture is also observed in Importin beta, suggesting that it is functionally significant and may be conserved in other import karyopherins.
Collapse
Affiliation(s)
- Ahmet E Cansizoglu
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park, Dallas, TX 75390-9041, USA
| | | |
Collapse
|
100
|
Iosef C, Gkourasas T, Jia CYH, Li SSC, Han VKM. A functional nuclear localization signal in insulin-like growth factor binding protein-6 mediates its nuclear import. Endocrinology 2008; 149:1214-26. [PMID: 18039785 DOI: 10.1210/en.2007-0959] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
IGF binding protein (IGFBP)-6 is a member of the IGFBP family that regulates the actions of IGFs. Although IGFBPs exert their functions extracellularly in an autocrine/paracrine manner, several members of the family, such as IGFBP-3 and -5, possess nuclear localization signals (NLS). To date, no NLS has been described for IGFBP-6, an IGFBP that binds preferentially to IGF-II. We report here that both exogenous and endogenous IGFBP-6 could be imported into the nuclei of rhabdomyosarcoma and HEK-293 cells. Nuclear import of IGFBP-6 was mediated by a NLS sequence that bears limited homology to those found in IGFBP-3 and -5. IGFBP-6 nuclear translocation was an active process that required importins. A peptide corresponding to the IGFBP-6 NLS bound preferentially to importin-alpha. A comprehensive peptide array study revealed that, in addition to positively charged residues such as Arg and Lys, amino acids, notably Gly and Pro, within the NLS, played an important part in binding to importins. Overexpression of wild-type IGFBP-6 increased apoptosis, and the addition of IGF-II did not negate this effect. Only the deletion of the NLS segment abolished the apoptosis effect. Taken together, these results suggest that IGFBP-6 is translocated to the nucleus with functional consequences and that different members of the IGFBP family have specific nuclear import mechanisms.
Collapse
Affiliation(s)
- Cristiana Iosef
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1
| | | | | | | | | |
Collapse
|