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Kamagata K, Itoh Y, Tan C, Mano E, Wu Y, Mandali S, Takada S, Johnson RC. Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo. Nucleic Acids Res 2021; 49:8642-8664. [PMID: 34352099 PMCID: PMC8421229 DOI: 10.1093/nar/gkab658] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/10/2021] [Accepted: 07/22/2021] [Indexed: 01/06/2023] Open
Abstract
Architectural DNA-binding proteins (ADBPs) are abundant constituents of eukaryotic or bacterial chromosomes that bind DNA promiscuously and function in diverse DNA reactions. They generate large conformational changes in DNA upon binding yet can slide along DNA when searching for functional binding sites. Here we investigate the mechanism by which ADBPs diffuse on DNA by single-molecule analyses of mutant proteins rationally chosen to distinguish between rotation-coupled diffusion and DNA surface sliding after transient unbinding from the groove(s). The properties of yeast Nhp6A mutant proteins, combined with molecular dynamics simulations, suggest Nhp6A switches between two binding modes: a static state, in which the HMGB domain is bound within the minor groove with the DNA highly bent, and a mobile state, where the protein is traveling along the DNA surface by means of its flexible N-terminal basic arm. The behaviors of Fis mutants, a bacterial nucleoid-associated helix-turn-helix dimer, are best explained by mobile proteins unbinding from the major groove and diffusing along the DNA surface. Nhp6A, Fis, and bacterial HU are all near exclusively associated with the chromosome, as packaged within the bacterial nucleoid, and can be modeled by three diffusion modes where HU exhibits the fastest and Fis the slowest diffusion.
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Affiliation(s)
- Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Cheng Tan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Eriko Mano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Yining Wu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Sridhar Mandali
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Reid C Johnson
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737, USA.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Maly IV, Hofmann WA. Calcium-regulated import of myosin IC into the nucleus. Cytoskeleton (Hoboken) 2016; 73:341-50. [PMID: 27192697 DOI: 10.1002/cm.21310] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/09/2016] [Accepted: 05/16/2016] [Indexed: 01/07/2023]
Abstract
Myosin IC is a molecular motor involved in intracellular transport, cell motility, and transcription. Its mechanical properties are regulated by calcium via calmodulin binding, and its functions in the nucleus depend on import from the cytoplasm. The import has recently been shown to be mediated by the nuclear localization signal located within the calmodulin-binding domain. In the present paper, it is demonstrated that mutations in the calmodulin-binding sequence shift the intracellular distribution of myosin IC to the nucleus. The redistribution is displayed by isoform B, described originally as the "nuclear myosin," but is particularly pronounced with isoform C, the normally cytoplasmic isoform. Furthermore, experimental elevation of the intracellular calcium concentration induces a rapid import of myosin into the nucleus. The import is blocked by the importin β inhibitor importazole. These findings are consistent with a mechanism whereby calmodulin binding prevents recognition of the nuclear localization sequence by importin β, and the steric inhibition of import is released by cell signaling leading to the intracellular calcium elevation. The results establish a mechanistic connection between the calcium regulation of the motor function of myosin IC in the cytoplasm and the induction of its import into the nucleus. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ivan V Maly
- Department of Physiology and Biophysics, University at Buffalo-State University of New York, Buffalo, New York
| | - Wilma A Hofmann
- Department of Physiology and Biophysics, University at Buffalo-State University of New York, Buffalo, New York
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3
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Kelkar P, Walter A, Papadopoulos S, Mroß C, Munck M, Peche VS, Noegel AA. Nesprin-2 mediated nuclear trafficking and its clinical implications. Nucleus 2015; 6:479-89. [PMID: 26645154 PMCID: PMC4915507 DOI: 10.1080/19491034.2015.1128608] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Nuclear translocation of proteins has a crucial role in the pathogenesis of cancer, Alzheimer disease and viral infections. A complete understanding of nuclear trafficking mechanisms is therefore necessary in order to establish effective intervention strategies. Here we elucidate the role of Nesprin-2 in Ca2+/Calmodulin mediated nuclear transport. Nesprin-2 is an actin-binding nuclear envelope (NE) protein with roles in maintaining nuclear structure and location, regulation of transcription and mechanotransduction. Upon depletion of Nesprin-2 using shRNA, HaCaT cells show abnormal localization of the shuttling proteins BRCA1 and NF-κB. We show that their nuclear transport is unlikely due to the canonical RAN mediated nuclear import, but rather to a RAN independent Ca2+/Calmodulin driven mechanism involving Nesprin-2. We report novel interactions between the actin-binding domain of Nesprin-2 and Calmodulin and between the NLS containing region of BRCA1 and Calmodulin. Strikingly, displacing Nesprins from the NE resulted in increased steady state Ca2+ concentrations in the cytoplasm suggesting a previously unidentified role of Nesprins in Ca2+ regulation. On comparing Nesprin-2 and BRCA1 localization in the ovarian cancer cell lines SKOV-3 and Caov-3, Nesprin-2 and BRCA1 were localized to the NE envelope and the nucleus in SKOV-3, respectively, and to the cytoplasm in Caov-3 cells. Fibroblasts obtained from EDMD5 (Emery Dreifuss muscular dystrophy) patients showed loss of Nesprin-2 from the nuclear envelope, corresponding reduced nuclear localization of BRCA1 and enhanced cytoplasmic Ca2+. Taken together, the data suggests a novel role of Nesprin-2 in Ca2+/Calmodulin mediated nuclear trafficking and provides new insights which can guide future therapies.
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Affiliation(s)
- Pranav Kelkar
- a Institute for Biochemistry I; Medical Faculty; University of Cologne ; Köln , Germany.,b Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne ; Köln , Germany.,c Center for Molecular Medicine; University of Cologne ; Köln , Germany
| | - Anna Walter
- d Institute of Vegetative Physiology; Medical Faculty; University of Cologne ; Köln ; Germany
| | - Symeon Papadopoulos
- d Institute of Vegetative Physiology; Medical Faculty; University of Cologne ; Köln ; Germany
| | - Carmen Mroß
- a Institute for Biochemistry I; Medical Faculty; University of Cologne ; Köln , Germany.,b Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne ; Köln , Germany.,c Center for Molecular Medicine; University of Cologne ; Köln , Germany
| | - Martina Munck
- a Institute for Biochemistry I; Medical Faculty; University of Cologne ; Köln , Germany.,b Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne ; Köln , Germany.,c Center for Molecular Medicine; University of Cologne ; Köln , Germany
| | - Vivek S Peche
- a Institute for Biochemistry I; Medical Faculty; University of Cologne ; Köln , Germany.,b Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne ; Köln , Germany.,c Center for Molecular Medicine; University of Cologne ; Köln , Germany
| | - Angelika A Noegel
- a Institute for Biochemistry I; Medical Faculty; University of Cologne ; Köln , Germany.,b Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne ; Köln , Germany.,c Center for Molecular Medicine; University of Cologne ; Köln , Germany
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4
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Christie M, Chang CW, Róna G, Smith KM, Stewart AG, Takeda AAS, Fontes MRM, Stewart M, Vértessy BG, Forwood JK, Kobe B. Structural Biology and Regulation of Protein Import into the Nucleus. J Mol Biol 2015; 428:2060-90. [PMID: 26523678 DOI: 10.1016/j.jmb.2015.10.023] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/16/2015] [Accepted: 10/24/2015] [Indexed: 11/28/2022]
Abstract
Proteins are translated in the cytoplasm, but many need to access the nucleus to perform their functions. Understanding how these nuclear proteins are transported through the nuclear envelope and how the import processes are regulated is therefore an important aspect of understanding cell function. Structural biology has played a key role in understanding the molecular events during the transport processes and their regulation, including the recognition of nuclear targeting signals by the corresponding receptors. Here, we review the structural basis of the principal nuclear import pathways and the molecular basis of their regulation. The pathways involve transport factors that are members of the β-karyopherin family, which can bind cargo directly (e.g., importin-β, transportin-1, transportin-3, importin-13) or through adaptor proteins (e.g., importin-α, snurportin-1, symportin-1), as well as unrelated transport factors such as Hikeshi, involved in the transport of heat-shock proteins, and NTF2, involved in the transport of RanGDP. Solenoid proteins feature prominently in these pathways. Nuclear transport factors recognize nuclear targeting signals on the cargo proteins, including the classical nuclear localization signals, recognized by the adaptor importin-α, and the PY nuclear localization signals, recognized by transportin-1. Post-translational modifications, particularly phosphorylation, constitute key regulatory mechanisms operating in these pathways.
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Affiliation(s)
- Mary Christie
- The Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales Faculty of Medicine, Darlinghurst, NSW 2010, Australia
| | - Chiung-Wen Chang
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gergely Róna
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Kate M Smith
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Alastair G Stewart
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW 2006, Australia
| | - Agnes A S Takeda
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Marcos R M Fontes
- Department of Physics and Biophysics, Institute of Biosciences, Universidade Estadual Paulista, Botucatu, São Paulo 18618-000, Brazil
| | - Murray Stewart
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary; Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2650, Australia
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia.
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5
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Wang W, Cai J, Lin Y, Liu Z, Ren Q, Hu L, Huang Z, Guo M, Li W. Zinc fingers function cooperatively with KRAB domain for nuclear localization of KRAB-containing zinc finger proteins. PLoS One 2014; 9:e92155. [PMID: 24647005 PMCID: PMC3960175 DOI: 10.1371/journal.pone.0092155] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 02/18/2014] [Indexed: 11/18/2022] Open
Abstract
Multiple nuclear localization domains have been identified in nuclear proteins, and they finely control nuclear import and functions of those proteins. ZNF268 is a typical KRAB-containing zinc finger protein (KRAB-ZFP), and previous studies have shown that the KRAB domain reinforces nuclear localization of KRAB-ZFPs by interacting with KAP1. In this study, we find that some of 24 zinc fingers of ZNF268 also possess nuclear localization activity. Results of mutagenesis studies suggest that KRAB and zinc fingers are both necessary, and they function both independently and cooperatively for the nuclear localization of ZNF268. However, the subnuclear targeting activities of KRAB and zinc fingers are different. KRAB targets proteins in nucleoplasm, but not in the nucleolus, which is mediated by interaction with KAP1, while zinc fingers target proteins in the whole nucleus uniformly. The cooperative activities of KAP1-KRAB-zinc fingers result in the precise nucleoplasmic, but not nucleolar localization of KRAB-ZFPs. Our studies reveal a novel mechanism for the subcellular localization of KRAB-ZFPs and may help us to further explore their biological functions.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jinyang Cai
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Lin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zikou Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qihao Ren
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li Hu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zan Huang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mingxiong Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (MG); (WL)
| | - Wenxin Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- * E-mail: (MG); (WL)
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6
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Huang Y, Zhang J, Halawa MA, Yao S. Nuclear localization signals of varicella zoster virus ORF4. Virus Genes 2014; 48:243-51. [PMID: 24398930 DOI: 10.1007/s11262-013-1006-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/29/2013] [Indexed: 02/01/2023]
Abstract
The varicella zoster virus (VZV) ORF4 protein, one of immediate-early genes protein, is associated with the tegument in purified virions. ORF4 protein functions at both transcriptional and post-transcriptional levels, present during different phase of whole VZV life cycle. ORF4 protein acts as a nucleocytoplasm shuttle protein, the precise nuclear location signals (NLS) and molecular mechanisms of nucleocytoplasm transport are not elucidated. At this study, we constructed a series of mutants, used fluorescence microscopy and Co-IP analysis to identify an unconventional bipartite NLS ((130)RKHRDRSLSNRRRRP(144)) in VZV ORF4. This study also demonstrates that nuclear import of VZV ORF4 occurs via a Ran-dependent pathway with importin-α5 and importin-β1. Additionally, NLS function of ORF4 is independent from VZV ORF62 protein. ORF62 protein cannot influence the intracellular distribution of ORF4 protein without NLS. So interaction between ORF4 and ORF62 protein is speculated to occur in nucleus. Thus, NLS is indispensable for the post-transcriptional function of ORF4.
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Affiliation(s)
- Yizhong Huang
- Department of Anesthesiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022, Hubei, People's Republic of China
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7
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Kaur G, Lieu KG, Jans DA. 70-kDa heat shock cognate protein hsc70 mediates calmodulin-dependent nuclear import of the sex-determining factor SRY. J Biol Chem 2012; 288:4148-57. [PMID: 23235156 DOI: 10.1074/jbc.m112.436741] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We recently showed that the developmentally important family of SOX (SRY (sex determining region on the Y chromosome)-related high mobility group (HMG) box) proteins require the calcium-binding protein calmodulin (CaM) for optimal nuclear accumulation, with clinical mutations in SRY that specifically impair nuclear accumulation via this pathway resulting in XY sex reversal. However, the mechanism by which CaM facilitates nuclear accumulation is unknown. Here, we show, for the first time, that the 70-kDa heat shock cognate protein hsc70 plays a key role in CaM-dependent nuclear import of SRY. Using a reconstituted nuclear import assay, we show that antibodies to hsc70 significantly reduce nuclear accumulation of wild type SRY and mutant derivatives thereof that retain CaM-dependent nuclear import, with an increased rate of nuclear accumulation upon addition of both CaM and hsc70, in contrast to an SRY mutant derivative with impaired CaM binding. siRNA knockdown of hsc70 in intact cells showed similar results, indicating clear dependence upon hsc70 for CaM-dependent nuclear import. Analysis using the technique of fluorescence recovery after photobleaching indicated that hsc70 is required for the maximal rate of SRY nuclear import in living cells but has no impact upon SRY nuclear retention/nuclear dynamics. Finally, we demonstrate direct binding of hsc70 to the SRY·CaM complex, with immunoprecipitation experiments from cell extracts showing association of hsc70 with wild type SRY, but not with a mutant derivative with impaired CaM binding, dependent on Ca(2+). Our novel findings strongly implicate hsc70 in CaM-dependent nuclear import of SRY.
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Affiliation(s)
- Gurpreet Kaur
- Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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8
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Structural characterization of the interaction of human lactoferrin with calmodulin. PLoS One 2012; 7:e51026. [PMID: 23236421 PMCID: PMC3516504 DOI: 10.1371/journal.pone.0051026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 10/29/2012] [Indexed: 12/21/2022] Open
Abstract
Lactoferrin (Lf) is an 80 kDa, iron (Fe3+)-binding immunoregulatory glycoprotein secreted into most exocrine fluids, found in high concentrations in colostrum and milk, and released from neutrophil secondary granules at sites of infection and inflammation. In a number of cell types, Lf is internalized through receptor-mediated endocytosis and targeted to the nucleus where it has been demonstrated to act as a transcriptional trans-activator. Here we characterize human Lf’s interaction with calmodulin (CaM), a ubiquitous, 17 kDa regulatory calcium (Ca2+)-binding protein localized in the cytoplasm and nucleus of activated cells. Due to the size of this intermolecular complex (∼100 kDa), TROSY-based NMR techniques were employed to structurally characterize Ca2+-CaM when bound to intact apo-Lf. Both CaM’s backbone amides and the ε-methyl group of key methionine residues were used as probes in chemical shift perturbation and cross-saturation experiments to define the binding interface of apo-Lf on Ca2+-CaM. Unlike the collapsed conformation through which Ca2+-CaM binds the CaM-binding domains of its classical targets, Ca2+-CaM assumes an extended structure when bound to apo-Lf. Apo-Lf appears to interact predominantly with the C-terminal lobe of Ca2+-CaM, enabling the N-terminal lobe to potentially bind another target. Our use of intact apo-Lf has made possible the identification of a secondary interaction interface, removed from CaM’s primary binding domain. Secondary interfaces play a key role in the target’s response to CaM binding, highlighting the importance of studying intact complexes. This solution-based approach can be applied to study other regulatory calcium-binding EF-hand proteins in intact intermolecular complexes.
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9
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On the segregation of protein ionic residues by charge type. Amino Acids 2012; 43:2231-47. [PMID: 23081700 DOI: 10.1007/s00726-012-1418-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 10/06/2012] [Indexed: 10/27/2022]
Abstract
Based on ubiquitous presence of large ionic motifs and clusters in proteins involved in gene transcription and protein synthesis, we analyzed the distribution of ionizable sidechains in a broad selection of proteins with regulatory, metabolic, structural and adhesive functions, in agonist, antagonist, toxin and antimicrobial peptides, and in self-excising inteins and intron-derived proteins and sequence constructs. All tested groups, regardless of taxa or sequence size, show considerable segregation of ionizable sidechains into same type charge (homoionic) tracts. These segments in most cases exceed half of the sequence length and comprise more than two-thirds of all ionizable sidechains. This distribution of ionic residues apparently reflects a fundamental advantage of sorted electrostatic contacts in association of sequence elements within and between polypeptides, as well as in interaction with polynucleotides. While large ionic densities are encountered in highly interactive proteins, the average ionic density in most sets does not change appreciably with size of the homoionic segments, which supports the segregation as a modular feature favoring association.
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10
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Staresincic L, Walker J, Dirac-Svejstrup AB, Mitter R, Svejstrup JQ. GTP-dependent binding and nuclear transport of RNA polymerase II by Npa3 protein. J Biol Chem 2011; 286:35553-35561. [PMID: 21844196 PMCID: PMC3195585 DOI: 10.1074/jbc.m111.286161] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Indexed: 11/06/2022] Open
Abstract
We identified XAB1 in a proteomic screen for factors that interact with human RNA polymerase II (RNAPII). Because XAB1 has a conserved Saccharomyces cerevisiae homologue called Npa3, yeast genetics and biochemical analysis were used to dissect the significance of the interaction. Degron-dependent Npa3 depletion resulted in genome-wide transcription decreases, correlating with a loss of RNAPII from genes as measured by chromatin immunoprecipitation. Surprisingly, however, transcription in vitro was unaffected by Npa3, suggesting that it affects a process that is not required for transcription in yeast extracts. Indeed, Npa3 depletion in vivo affects nuclear localization of RNAPII; the polymerase accumulates in the cytoplasm. Npa3 is a member of the GPN-LOOP family of GTPases. Npa3 mutants that either cannot bind GTP or that bind but cannot hydrolyze it are inviable and unable to support nuclear transport of RNAPII. Surprisingly, we were unable to detect interactions between Npa3 and proteins in the classical importin α/β pathway for nuclear import. Interestingly, Npa3-RNAPII binding is significantly increased by the addition of GTP or its slowly hydrolyzable analogue guanosine 5'-3-O-(thio)triphosphate (GTPγS). Moreover, the Npa3 mutant that binds GTP, but cannot hydrolyze it, binds RNAPII even in the absence of added GTP, whereas the mutant that cannot bind GTP is unable to bind the polymerase. Together, our data suggest that Npa3 defines an unconventional pathway for nuclear import of RNAPII, which involves GTP-dependent binding of Npa3 to the polymerase.
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Affiliation(s)
- Lidija Staresincic
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms EN6 3LD
| | - Jane Walker
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms EN6 3LD
| | - A Barbara Dirac-Svejstrup
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms EN6 3LD
| | - Richard Mitter
- Bioinformatics and Biostatistics Group, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, United Kingdom
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms EN6 3LD.
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11
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Sim H, Argentaro A, Czech DP, Bagheri-Fam S, Sinclair AH, Koopman P, Boizet-Bonhoure B, Poulat F, Harley VR. Inhibition of SRY-calmodulin complex formation induces ectopic expression of ovarian cell markers in developing XY gonads. Endocrinology 2011; 152:2883-93. [PMID: 21558314 DOI: 10.1210/en.2010-1475] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The transcription factor sex-determining region of the Y chromosome (SRY) plays a key role in human sex determination, because mutations in SRY cause disorders of sex development in XY individuals. During gonadal development, Sry in pre-Sertoli cells activates Sox9 gene transcription, committing the fate of the bipotential gonad to become a testis rather than an ovary. The high-mobility group domain of human SRY contains two independent nuclear localization signals, one bound by calmodulin (CaM) and the other by importin-β. Although XY females carry SRY mutations in these nuclear localization signals that affect SRY nuclear import in transfected cells, it is not known whether these transport mechanisms are essential for gonadal development and sex determination. Here, we show that mouse Sry protein binds CaM and that a CaM antagonist reduces CaM binding, nuclear accumulation, and transcriptional activity of Sry in transfected cells. CaM antagonist treatment of cultured, sexually indifferent XY mouse fetal gonads led to reduced expression of the Sry target gene Sox9, defects in testicular cord formation, and ectopic expression of the ovarian markers Rspondin1 and forkhead box L2. These results indicate the importance of CaM for SRY nuclear import, transcriptional activity, testis differentiation, and sex determination.
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Affiliation(s)
- Helena Sim
- Molecular Genetics and Development Division, Prince Henry's Institute of Medical Research, Level 4 Block E, Monash Medical Centre, 246 Clayton Road, Clayton, Melbourne, Victoria 3168, Australia
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12
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Kaur G, Jans DA. Dual nuclear import mechanisms of sex determining factor SRY: intracellular Ca2+ as a switch. FASEB J 2010; 25:665-75. [PMID: 21051653 DOI: 10.1096/fj.10-173351] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The sex-determining region on the Y chromosome (SRY) has 2 nuclear localization signals (NLSs) that flank the DNA binding high mobility group (HMG) domain; the β-NLS and the CaM-NLS, which mediate nuclear transport through importin β1 (Impβ1) and the calcium-binding protein calmodulin (CaM), respectively. Here we reconstitute the nuclear import mediated by the 2 NLSs for the first time in vitro, establishing Ran independence of CaM-NLS-dependent transport. The β- and CaM-NLSs were found to be independently functional out of the context of the SRY HMG domain, dependent on Impβ1 and CaM binding, respectively. Intriguingly, direct protein binding assays also indicated competitive binding of Impβ1 and CaM to the SRY HMG domain. To assess the potential role of intracellular calcium in modulating SRY nuclear accumulation, Cos-7 cells expressing SRY and control constructs were treated with agents elevating or reducing intracellular Ca(2+) levels. The in vivo results, supported by experiments in vitro where transport was assessed with or without 2 μM Ca(2+), indicate a Ca(2+)-dependent mode of nuclear transport via the CaM-NLS/CaM, with inhibition of β-NLS/Impβ1-mediated nuclear import by intracellular Ca(2+). The results imply mutual exclusivity of nuclear transport via the 2 NLSs with intracellular Ca(2+) as the switch between the 2.
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Affiliation(s)
- Gurpreet Kaur
- Nuclear Signalling Laboratory, Department of Biochemistry and Molecular Biology, Monash University Bldg. 77, Monash Vic. 3800, Australia
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Ely D, Underwood A, Dunphy G, Boehme S, Turner M, Milsted A. Review of the Y chromosome, Sry and hypertension. Steroids 2010; 75:747-53. [PMID: 19914267 PMCID: PMC2891862 DOI: 10.1016/j.steroids.2009.10.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 10/26/2009] [Accepted: 10/27/2009] [Indexed: 01/03/2023]
Abstract
The following review examines the role of the SHR Y chromosome and specifically the Sry gene complex in hypertension and potential mechanisms that involve the sympathetic nervous system and renin-angiotensin system. There are consistent gender differences in hypertension, with a greater proportion of males affected than females in most mammalian populations. Our earlier studies demonstrated that a portion of the gender differences in blood pressure (BP) in the SHR rat mapped to the SHR Y chromosome. In rats, males with the SHR Y chromosome have higher BP than females, or males with a different Y chromosome. Consistent with these results, several human population studies have confirmed a Y chromosome effect on BP. Our more recent studies focus on a transcription factor, Sry, as the locus involved in not only BP modulation but effects on other phenotypes. The Sry locus is an evolutionarily conserved locus on the mammalian Y chromosome responsible for testis determination and is a transcription factor. The Sry locus contains a highly conserved High Mobility Group (HMG) box region responsible for DNA binding. Mutations in the HMG box result in sex reversal. We have found multiple functional copies of Sry in SHR and WKY male rats. There is abundant evidence that testes determination may not be Sry's only function as it is expressed in the brain, kidney and adrenal gland of adult males. These findings have potential implications for gender physiology research which involves, the sympathetic nervous system, renin-angiotensin system, androgen receptor regulation and prostate physiology.
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Affiliation(s)
- Daniel Ely
- Department of Biology, University of Akron, 185 S Mill St., Akron, OH 44325-3908, United States.
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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: 307] [Impact Index Per Article: 21.9] [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.
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Affiliation(s)
- Mary Marfori
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland 4072, Australia
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15
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Calmodulin-dependent nuclear import of HMG-box family nuclear factors: importance of the role of SRY in sex reversal. Biochem J 2010; 430:39-48. [PMID: 20528776 PMCID: PMC2911679 DOI: 10.1042/bj20091758] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The HMG (high-mobility group)-box-containing chromatin-remodelling factor SRY (sex-determining region on the Y chromosome) plays a key role in sex determination. Its role in the nucleus is critically dependent on two NLSs (nuclear localization signals) that flank its HMG domain: the C-terminally located 'beta-NLS' that mediates nuclear transport through Impbeta1 (importin beta1) and the N-terminally located 'CaM-NLS' which is known to recognize the calcium-binding protein CaM (calmodulin). In the present study, we examined a number of missense mutations in the SRY CaM-NLS from human XY sex-reversed females for the first time, showing that they result in significantly reduced nuclear localization of GFP (green fluorescent protein)-SRY fusion proteins in transfected cells compared with wild-type. The CaM antagonist CDZ (calmidazolium chloride) was found to significantly reduce wild-type SRY nuclear accumulation, indicating dependence of SRY nuclear import on CaM. Intriguingly, the CaM-NLS mutants were all resistant to CDZ's effects, implying a loss of interaction with CaM, which was confirmed by direct binding experiments. CaM-binding/resultant nuclear accumulation was the only property of SRY found to be impaired by two of the CaM-NLS mutations, implying that inhibition of CaM-dependent nuclear import is the basis of sex reversal in these cases. Importantly, the CaM-NLS is conserved in other HMG-box-domain-containing proteins such as SOX-2, -9, -10 and HMGN1, all of which were found for the first time to rely on CaM for optimal nuclear localization. CaM-dependent nuclear translocation is thus a common mechanism for this family of important transcription factors.
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Stillman DJ. Nhp6: a small but powerful effector of chromatin structure in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:175-80. [PMID: 20123079 DOI: 10.1016/j.bbagrm.2009.11.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 10/28/2009] [Accepted: 11/03/2009] [Indexed: 10/19/2022]
Abstract
The small Nhp6 protein from budding yeast is an abundant protein that binds DNA non-specifically and bends DNA sharply. It contains only a single HMGB domain that binds DNA in the minor groove and a basic N-terminal extension that wraps around DNA to contact the major groove. This review describes the genetic and biochemical experiments that indicate Nhp6 functions in promoting RNA pol III transcription, in formation of preinitiation complexes at promoters transcribed by RNA pol II, and in facilitating the activity of chromatin modifying complexes. The FACT complex may provide a paradigm for how Nhp6 functions with chromatin factors, as Nhp6 allows Spt16-Pob3 to bind to and reorganize nucleosomes in vitro.
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Affiliation(s)
- David J Stillman
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT 84112, USA.
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Lahaye F, Lespinasse F, Staccini P, Palin L, Paquis-Flucklinger V, Santucci-Darmanin S. hMSH5 is a nucleocytoplasmic shuttling protein whose stability depends on its subcellular localization. Nucleic Acids Res 2010; 38:3655-71. [PMID: 20185565 PMCID: PMC2887964 DOI: 10.1093/nar/gkq098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MSH5 is a MutS-homologous protein required for meiotic DNA recombination. In addition, recent studies suggest that the human MSH5 protein (hMSH5) participates to mitotic recombination and to the cellular response to DNA damage and thus raise the possibility that a tight control of hMSH5 function(s) may be important for genomic stability. With the aim to characterize mechanisms potentially involved in the regulation of hMSH5 activity, we investigated its intracellular trafficking properties. We demonstrate that hMSH5 possesses a CRM1-dependent nuclear export signal (NES) and a nuclear localization signal that participates to its nuclear targeting. Localization analysis of various mutated forms of hMSH5 by confocal microscopy indicates that hMSH5 shuttles between the nucleus and the cytoplasm. We also provide evidence suggesting that hMSH5 stability depends on its subcellular compartmentalization, hMSH5 being much less stable in the nucleus than in the cytoplasm. Together, these data suggest that hMSH5 activity may be regulated by nucleocytoplasmic shuttling and nuclear proteasomal degradation, both of these mechanisms contributing to the control of nuclear hMSH5 content. Moreover, data herein also support that in tissues where both hMSH5 and hMSH4 proteins are expressed, hMSH5 might be retained in the nucleus through masking of its NES by binding of hMSH4.
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Affiliation(s)
- François Lahaye
- FRE 3086 Instabilité génétique: Maladies rares et cancers, Université de Nice Sophia-Antipolis, CNRS, Nice Cedex 2, France
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Ishida H, Rainaldi M, Vogel HJ. Structural studies of soybean calmodulin isoform 4 bound to the calmodulin-binding domain of tobacco mitogen-activated protein kinase phosphatase-1 provide insights into a sequential target binding mode. J Biol Chem 2009; 284:28292-28305. [PMID: 19667066 PMCID: PMC2788880 DOI: 10.1074/jbc.m109.025080] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/10/2009] [Indexed: 01/22/2023] Open
Abstract
The calcium regulatory protein calmodulin (CaM) binds in a calcium-dependent manner to numerous target proteins. The calmodulin-binding domain (CaMBD) region of Nicotiana tabacum MAPK phosphatase has an amino acid sequence that does not resemble the CaMBD of any other known Ca(2+)-CaM-binding proteins. Using a unique fusion protein strategy, we have been able to obtain a high resolution solution structure of the complex of soybean Ca(2+)-CaM4 (SCaM4) and this CaMBD. Complete isotope labeling of both parts of the complex in the fusion protein greatly facilitated the structure determination by NMR. The 12-residue CaMBD region was found to bind exclusively to the C-lobe of SCaM4. A specific Trp and Leu side chain are utilized to facilitate strong binding through a novel "double anchor" motif. Moreover, the orientation of the helical peptide on the surface of Ca(2+)-SCaM4 is distinct from other known complexes. The N-lobe of Ca(2+)-SCaM4 in the complex remains free for additional interactions and could possibly act as a calcium-dependent adapter protein. Signaling through the MAPK pathway and increases in intracellular Ca(2+) are both hallmarks of the plant stress response, and our data support the notion that coordination of these responses may occur through the formation of a unique CaM-MAPK phosphatase multiprotein complex.
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Affiliation(s)
- Hiroaki Ishida
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Mario Rainaldi
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Hans J Vogel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
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Hanover JA, Love DC, Prinz WA. Calmodulin-driven nuclear entry: trigger for sex determination and terminal differentiation. J Biol Chem 2009; 284:12593-7. [PMID: 19126540 DOI: 10.1074/jbc.r800076200] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We originally proposed that Ca(2+)-calmodulin mediates a novel nuclear entry pathway distinct from the canonic Ran-dependent pathway (Sweitzer, T. D., and Hanover, J. A. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 14574-14579). Although seemingly redundant, Ca(2+)-calmodulin-driven nuclear entry is now known to facilitate nuclear delivery of architectural transcription factors to chromatin. Intriguingly, defects in calmodulin-driven nuclear import of the transcription factors SRY and SOX9 in Sertoli cells lead to human sex reversal diseases with altered male gonad development. Calmodulin-triggered nuclear entry is an evolutionarily ancient feature of eukaryotes observed from yeast to man. Ca(2+)-calmodulin-triggered nuclear entry of key architectural transcription factors is a potentially key epigenetic regulator of terminal differentiation in response to cell signaling.
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Affiliation(s)
- John A Hanover
- Laboratory of Cell Biochemistry and Biology, NIDDK, NIH, Bethesda, MD 20892, USA.
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Sim H, Argentaro A, Harley VR. Boys, girls and shuttling of SRY and SOX9. Trends Endocrinol Metab 2008; 19:213-22. [PMID: 18585925 DOI: 10.1016/j.tem.2008.04.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 03/21/2008] [Accepted: 04/04/2008] [Indexed: 01/24/2023]
Abstract
In the mammalian embryo, SRY and SOX9 are key Sertoli cell proteins that drive the development of the bipotential gonad into a testes rather than an ovary, leading ultimately to the male phenotype. Clinical SRY and SOX9 mutations causing disorders of sex development (DSD) highlight defective protein-protein interactions between SRY or SOX9, and carrier proteins required for nuclear import (importin-b and calmodulin) and nuclear export (CRM-1). The fine balance between import and export determines the levels of transcriptionally active SRY and SOX9 in the nucleus. Recently, post-translational modifications of SRY and SOX9 have been identified which affect nuclear transport. It is therefore timely that the consequences of sex-reversal mutation upon nuclear transport be reviewed. SRY and SOX9 mutations in DSD have uncovered regulatory sites for sumoylation, ubiquitination, acetylation and phosphorylation, many of which are essential for their transport and sex determining functions.
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Affiliation(s)
- Helena Sim
- Human Molecular Genetics Laboratory, Prince Henry's Institute of Medical Research, Level 4 Block E, Monash Medical Centre, 246 Clayton Rd, Clayton, Melbourne, VIC 3168, Australia
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Theodore M, Kawai Y, Yang J, Kleshchenko Y, Reddy SP, Villalta F, Arinze IJ. Multiple nuclear localization signals function in the nuclear import of the transcription factor Nrf2. J Biol Chem 2008; 283:8984-94. [PMID: 18238777 DOI: 10.1074/jbc.m709040200] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Nuclear factor erythroid 2-related factor 2 (Nrf2) mediates the transcriptional response of cells to oxidative stress and is translocated into the nucleus following, or concomitant with, its activation by electrophiles or reactive oxygen species. The mechanism of its translocation into the nucleus is not entirely elucidated. Here we have identified two novel nuclear localization signal (NLS) motifs in murine Nrf2, one located near the N-terminal region (amino acid residues 42-53) and the other (residues 587-593) located near the C-terminal region. Imaging of green fluorescent protein (GFP)-tagged Nrf2 revealed that mutation(s) in any of these sequences resulted in decreased nuclear fluorescence intensity compared with the wild-type Nrf2 when Nrf2 activation was induced with the electrophile tert-butylhydroquinone. The mutations also impaired Nrf2-induced transactivation of antioxidant response element-driven reporter gene expression to the same extent as the Nrf2 construct bearing mutation in a previously identified bipartite NLS that maps at residues 494-511. When linked to GFP or to GFP-PEPCK-C each of the novel NLS motifs was sufficient to drive nuclear translocation of the fusion proteins. Co-immunoprecipitation assays demonstrated that importins alpha5 and beta1 associate with Nrf2, an interaction that was blocked by the nuclear import inhibitor SN50. SN50 also blocked tert-butylhydroquinone-induced nuclear fluorescence of GFP-Nrf2 in cells transfected with wild-type GFP-Nrf2. Overall these results reveal that multiple NLS motifs in Nrf2 function in its nuclear translocation in response to pro-oxidant stimuli and that the importin alpha-beta heterodimer nuclear import receptor system plays a critical role in the import process.
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Affiliation(s)
- Melanie Theodore
- School of Medicine, Meharry Medical College, Nashville, TN 37208-3599, USA
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