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Yoshida SR, Maity BK, Chong S. Visualizing Protein Localizations in Fixed Cells: Caveats and the Underlying Mechanisms. J Phys Chem B 2023; 127:4165-4173. [PMID: 37161904 DOI: 10.1021/acs.jpcb.3c01658] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Fluorescence microscopy techniques have been widely adopted in biology for their ability to visualize the structure and dynamics of a wide range of cellular and subcellular processes. The specificity and sensitivity that these techniques afford have made them primary tools in the characterization of protein localizations within cells. Many of the fluorescence microscopy techniques require cells to be fixed via chemical or alternative methods before being imaged. However, some fixation methods have been found to induce the redistribution of particular proteins in the cell, resulting in artifacts in the characterization of protein localizations and functions under physiological conditions. Here, we review the ability of commonly used cell fixation methods to faithfully preserve the localizations of proteins that bind to chromatin, undergo liquid-liquid phase separation (LLPS), and are involved in the formation of various membrane-bound organelles. We also review the mechanisms underlying various fixation artifacts and discuss potential alternative fixation methods to minimize the artifacts while investigating different proteins and cellular structures. Overall, fixed-cell fluorescence microscopy is a very powerful tool in biomedical research; however, each experiment demands the careful selection of an appropriate fixation method to avoid potential artifacts and may benefit from live-cell imaging validation.
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Affiliation(s)
- Shawn R Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Barun K Maity
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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2
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Messina G, Atterrato MT, Prozzillo Y, Piacentini L, Losada A, Dimitri P. The human Cranio Facial Development Protein 1 (Cfdp1) gene encodes a protein required for the maintenance of higher-order chromatin organization. Sci Rep 2017; 7:45022. [PMID: 28367969 PMCID: PMC5377257 DOI: 10.1038/srep45022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
The human Cranio Facial Development Protein 1 (Cfdp1) gene maps to chromosome 16q22.2-q22.3 and encodes the CFDP1 protein, which belongs to the evolutionarily conserved Bucentaur (BCNT) family. Craniofacial malformations are developmental disorders of particular biomedical and clinical interest, because they represent the main cause of infant mortality and disability in humans, thus it is important to understand the cellular functions and mechanism of action of the CFDP1 protein. We have carried out a multi-disciplinary study, combining cell biology, reverse genetics and biochemistry, to provide the first in vivo characterization of CFDP1 protein functions in human cells. We show that CFDP1 binds to chromatin and interacts with subunits of the SRCAP chromatin remodeling complex. An RNAi-mediated depletion of CFDP1 in HeLa cells affects chromosome organization, SMC2 condensin recruitment and cell cycle progression. Our findings provide new insight into the chromatin functions and mechanisms of the CFDP1 protein and contribute to our understanding of the link between epigenetic regulation and the onset of human complex developmental disorders.
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Affiliation(s)
- Giovanni Messina
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Maria Teresa Atterrato
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Yuri Prozzillo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Lucia Piacentini
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | | | - Patrizio Dimitri
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
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3
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Abstract
Although convention dictates that G protein-coupled receptors localize to and signal at the plasma membrane, accumulating evidence suggests that G protein-coupled receptors localize to and signal at intracellular membranes, most notably the nucleus. In fact, there is now significant evidence indicating that endogenous alpha-1 adrenergic receptors (α1-ARs) localize to and signal at the nuclei in adult cardiac myocytes. Cumulatively, the data suggest that α1-ARs localize to the inner nuclear membrane, activate intranuclear signaling, and regulate physiologic function in adult cardiac myocytes. Although α1-ARs signal through Gαq, unlike other Gq-coupled receptors, α1-ARs mediate important cardioprotective functions including adaptive/physiologic hypertrophy, protection from cell death (survival signaling), positive inotropy, and preconditioning. Also unlike other Gq-coupled receptors, most, if not all, functional α1-ARs localize to the nuclei in adult cardiac myocytes, as opposed to the sarcolemma. Together, α1-AR nuclear localization and cardioprotection might suggest a novel model for compartmentalization of Gq-coupled receptor signaling in which nuclear Gq-coupled receptor signaling is cardioprotective.
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4
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González-Romero R, Eirín-López JM, Ausió J. Evolution of high mobility group nucleosome-binding proteins and its implications for vertebrate chromatin specialization. Mol Biol Evol 2014; 32:121-31. [PMID: 25281808 DOI: 10.1093/molbev/msu280] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
High mobility group (HMG)-N proteins are a family of small nonhistone proteins that bind to nucleosomes (N). Despite the amount of information available on their structure and function, there is an almost complete lack of information on the molecular evolutionary mechanisms leading to their exclusive differentiation. In the present work, we provide evidence suggesting that HMGN lineages constitute independent monophyletic groups derived from a common ancestor prior to the diversification of vertebrates. Based on observations of the functional diversification across vertebrate HMGN proteins and on the extensive silent nucleotide divergence, our results suggest that the long-term evolution of HMGNs occurs under strong purifying selection, resulting from the lineage-specific functional constraints of their different protein domains. Selection analyses on independent lineages suggest that their functional specialization was mediated by bursts of adaptive selection at specific evolutionary times, in a small subset of codons with functional relevance-most notably in HMGN1, and in the rapidly evolving HMGN5. This work provides useful information to our understanding of the specialization imparted on chromatin metabolism by HMGNs, especially on the evolutionary mechanisms underlying their functional differentiation in vertebrates.
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Affiliation(s)
| | - José M Eirín-López
- Chromatin Structure and Evolution (CHROMEVOL) Group, Department of Biological Sciences, Florida International University
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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5
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O'Connell TD, Jensen BC, Baker AJ, Simpson PC. Cardiac alpha1-adrenergic receptors: novel aspects of expression, signaling mechanisms, physiologic function, and clinical importance. Pharmacol Rev 2013; 66:308-33. [PMID: 24368739 DOI: 10.1124/pr.112.007203] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Adrenergic receptors (AR) are G-protein-coupled receptors (GPCRs) that have a crucial role in cardiac physiology in health and disease. Alpha1-ARs signal through Gαq, and signaling through Gq, for example, by endothelin and angiotensin receptors, is thought to be detrimental to the heart. In contrast, cardiac alpha1-ARs mediate important protective and adaptive functions in the heart, although alpha1-ARs are only a minor fraction of total cardiac ARs. Cardiac alpha1-ARs activate pleiotropic downstream signaling to prevent pathologic remodeling in heart failure. Mechanisms defined in animal and cell models include activation of adaptive hypertrophy, prevention of cardiac myocyte death, augmentation of contractility, and induction of ischemic preconditioning. Surprisingly, at the molecular level, alpha1-ARs localize to and signal at the nucleus in cardiac myocytes, and, unlike most GPCRs, activate "inside-out" signaling to cause cardioprotection. Contrary to past opinion, human cardiac alpha1-AR expression is similar to that in the mouse, where alpha1-AR effects are seen most convincingly in knockout models. Human clinical studies show that alpha1-blockade worsens heart failure in hypertension and does not improve outcomes in heart failure, implying a cardioprotective role for human alpha1-ARs. In summary, these findings identify novel functional and mechanistic aspects of cardiac alpha1-AR function and suggest that activation of cardiac alpha1-AR might be a viable therapeutic strategy in heart failure.
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Affiliation(s)
- Timothy D O'Connell
- VA Medical Center (111-C-8), 4150 Clement St., San Francisco, CA 94121. ; or Dr. Timothy D. O'Connell, E-mail:
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6
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Kugler JE, Horsch M, Huang D, Furusawa T, Rochman M, Garrett L, Becker L, Bohla A, Hölter SM, Prehn C, Rathkolb B, Racz I, Aguilar-Pimentel JA, Adler T, Adamski J, Beckers J, Busch DH, Eickelberg O, Klopstock T, Ollert M, Stöger T, Wolf E, Wurst W, Yildirim AÖ, Zimmer A, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Garfinkel B, Orly J, Ovcharenko I, Bustin M. High mobility group N proteins modulate the fidelity of the cellular transcriptional profile in a tissue- and variant-specific manner. J Biol Chem 2013; 288:16690-16703. [PMID: 23620591 DOI: 10.1074/jbc.m113.463315] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nuclei of most vertebrate cells contain members of the high mobility group N (HMGN) protein family, which bind specifically to nucleosome core particles and affect chromatin structure and function, including transcription. Here, we study the biological role of this protein family by systematic analysis of phenotypes and tissue transcription profiles in mice lacking functional HMGN variants. Phenotypic analysis of Hmgn1(tm1/tm1), Hmgn3(tm1/tm1), and Hmgn5(tm1/tm1) mice and their wild type littermates with a battery of standardized tests uncovered variant-specific abnormalities. Gene expression analysis of four different tissues in each of the Hmgn(tm1/tm1) lines reveals very little overlap between genes affected by specific variants in different tissues. Pathway analysis reveals that loss of an HMGN variant subtly affects expression of numerous genes in specific biological processes. We conclude that within the biological framework of an entire organism, HMGNs modulate the fidelity of the cellular transcriptional profile in a tissue- and HMGN variant-specific manner.
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Affiliation(s)
- Jamie E Kugler
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Marion Horsch
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Di Huang
- Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Lillian Garrett
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alexander Bohla
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cornelia Prehn
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ildikó Racz
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Juan Antonio Aguilar-Pimentel
- Center of Allergy and Environment, Technische Universität München, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Dermatology and Allergy, Biederstein, Technische Universität München and Clinical Research Division of Molecular and Clinical Allergotoxicology, Technische Universität München, Munich, Germany
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Institute of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, München, Germany
| | - Jerzy Adamski
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Dirk H Busch
- Institute of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, München, Germany
| | - Oliver Eickelberg
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Vertigo and Balance Disorders, Technische Universität München, Munich, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen-German Center for Neurodegenerative Diseases, Site Munich, Munich, Germany
| | - Markus Ollert
- Department of Dermatology and Allergy, Biederstein, Technische Universität München and Clinical Research Division of Molecular and Clinical Allergotoxicology, Technische Universität München, Munich, Germany
| | - Tobias Stöger
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Eckhard Wolf
- Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen-German Center for Neurodegenerative Diseases, Site Munich, Munich, Germany; Max Planck Institute of Psychiatry, Munich, Germany; Developmental Genetics, Technische Universität München c/o Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ali Önder Yildirim
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Andreas Zimmer
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany; German Center for Vertigo and Balance Disorders, Technische Universität München, Munich, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Benny Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ivan Ovcharenko
- Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892.
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7
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Wright CD, Wu SC, Dahl EF, Sazama AJ, O'Connell TD. Nuclear localization drives α1-adrenergic receptor oligomerization and signaling in cardiac myocytes. Cell Signal 2012; 24:794-802. [PMID: 22120526 PMCID: PMC3393107 DOI: 10.1016/j.cellsig.2011.11.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 11/08/2011] [Indexed: 11/17/2022]
Abstract
Conventional models of G-protein coupled receptor (GPCR) signaling describe cell surface receptors binding to external ligands, such as hormones or circulating peptides, to induce intracellular signaling and a physiologic response. However, recent studies identify new paradigms indicating that GPCRs localize to and signal at the nucleus and that GPCR oligomers can influence receptor function. Previously, we reported that endogenous α1-adrenergic receptors (α1-ARs) localize to and signal at the nuclei in adult cardiac myocytes. In this study, we examined the mechanisms behind α1-AR nuclear localization and how nuclear localization impacted receptor function. We verified that endogenous α1-ARs localized to the nuclear membrane of intact nuclei isolated from wild-type adult cardiac myocytes. Next, we identified and disrupted putative nuclear localization sequences in both the α1A- and α1B-adrenergic receptors, which led to mis-localization of α1-ARs in cultured adult cardiac myocytes. Using these mutants, we demonstrated that nuclear localization was required for α1-signaling in adult cardiac myocytes. We also found that the nuclear export inhibitor leptomycin B inhibited α1-AR signaling, indicating α1-AR signaling must arise in the nucleus in adult cardiac myocytes. Finally, we found that co-localization of the α1-subtypes at the nuclei in adult cardiac myocytes facilitated the formation of receptor oligomers that could affect receptor signaling. In summary, our data indicate that α1-AR nuclear localization can drive the formation of receptor oligomers and regulate signaling in adult cardiac myocytes.
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MESH Headings
- Animals
- Cell Nucleus/metabolism
- Cells, Cultured
- Fluorescence Resonance Energy Transfer
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mutation
- Myocytes, Cardiac/cytology
- Myocytes, Cardiac/metabolism
- Protein Multimerization
- Receptors, Adrenergic, alpha-1/analysis
- Receptors, Adrenergic, alpha-1/genetics
- Receptors, Adrenergic, alpha-1/metabolism
- Signal Transduction
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Affiliation(s)
- Casey D Wright
- Cardiovascular Health Research Center, Sanford Research/USD, Sioux Falls, SD 57104, United States
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8
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The HMGN family of chromatin-binding proteins: dynamic modulators of epigenetic processes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:652-6. [PMID: 22326857 DOI: 10.1016/j.bbagrm.2012.01.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 01/19/2012] [Accepted: 01/21/2012] [Indexed: 12/21/2022]
Abstract
The HMGN family of proteins binds to nucleosomes without any specificity for the underlying DNA sequence. They affect the global and local structure of chromatin, as well as the levels of histone modifications and thus play a role in epigenetic regulation of gene expression. This review focuses on the recent studies that provide new insights on the interactions between HMGN proteins, nucleosomes, and chromatin, and the effects of these interactions on epigenetic and transcriptional regulation. This article is part of a Special Issue entitled: Chromatin in time and space.
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Stein GS, van Wijnen AJ, Imbalzano AN, Montecino M, Zaidi SK, Lian JB, Nickerson JA, Stein JL. Architectural genetic and epigenetic control of regulatory networks: compartmentalizing machinery for transcription and chromatin remodeling in nuclear microenvironments. Crit Rev Eukaryot Gene Expr 2011; 20:149-55. [PMID: 21133844 DOI: 10.1615/critreveukargeneexpr.v20.i2.50] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The regulatory machinery that governs genetic and epigenetic control of gene expression for biological processes and cancer is organized in nuclear microenvironments. Strategic placement of transcription factors at target gene promoters in punctate microenvironments of interphase nuclei supports scaffolding of co- regulatory proteins and the convergence as well as integration of regulatory networks. The organization and localization of regulatory complexes within the nucleus can provide signatures that are linked to regulatory activity. Retention of transcription factors at gene loci in mitotic chromosomes contributes to epigenetic control of cell fate and lineage commitment, as well as to persistence of transformed and tumor phenotypes. Mechanistic understanding of the architectural assembly of regulatory machinery can serve as a basis for treating cancer with high specificity and minimal off-target effects.
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Affiliation(s)
- Gary S Stein
- Department of Cell Biology, University of Massachusetts Medical School and Cancer Center, Worcester, MA 01655, USA.
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10
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Xue Y, O'Mara ML, Surawski PPT, Trau M, Mark AE. Effect of poly(ethylene glycol) (PEG) spacers on the conformational properties of small peptides: a molecular dynamics study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:296-303. [PMID: 21121595 DOI: 10.1021/la103800h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Poly(ethylene glycol) (PEG) is used as an inert spacer in a wide range of biotechnological applications such as to display peptides and proteins on surfaces for diagnostic purposes. In such applications it is critical that the peptide is accessible to solvent and that the PEG does not affect the conformational properties of the peptide to which it is attached. Using molecular dynamics (MD) simulation techniques, we have investigated the influence of a commonly used PEG spacer on the conformation properties of a series of five peptides with differing physical-chemical properties (YGSLPQ, VFVVFV, GSGGSG, EEGEEG, and KKGKKG). The conformational properties of the peptides were compared (a) free in solution, (b) attached to a PEG-11 spacer in solution, and (c) constrained to a two-dimensional lattice via a (PEG-11)(3) spacer, mimicking a peptide displayed on a surface as used in microarray techniques. The simulations suggest that the PEG spacer has little effect on the conformational properties of small neutral peptides but has a significant effect on the conformational properties of small highly charged peptides. When constrained to a two-dimensional surface at peptide densities similar to those used experimentally, it was found that the peptides, in particular the polar and nonpolar peptides, aggregated strongly. The peptides also partitioned into the PEG layer. Potentially, this means that at high packing densities only a small fraction of the peptide attached to the surface would in fact be accessible to a potential interaction partner.
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Affiliation(s)
- Ying Xue
- School of Chemistry and Molecular Biosciences, and the Institute for Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia
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11
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Brocher J, Vogel B, Hock R. HMGA1 down-regulation is crucial for chromatin composition and a gene expression profile permitting myogenic differentiation. BMC Cell Biol 2010; 11:64. [PMID: 20701767 PMCID: PMC2928187 DOI: 10.1186/1471-2121-11-64] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 08/11/2010] [Indexed: 01/10/2023] Open
Abstract
Background High mobility group A (HMGA) proteins regulate gene transcription through architectural modulation of chromatin and the formation of multi-protein complexes on promoter/enhancer regions. Differential expression of HMGA variants has been found to be important for distinct differentiation processes and deregulated expression was linked to several disorders. Here we used mouse C2C12 myoblasts and C2C12 cells stably over-expressing HMGA1a-eGFP to study the impact of deregulated HMGA1 expression levels on cellular differentiation. Results We found that induction of the myogenic or osteogenic program of C2C12 cells caused an immediate down-regulation of HMGA1. In contrast to wild type C2C12 cells, an engineered cell line with stable over-expression of HMGA1a-eGFP failed to differentiate into myotubes. Immunolocalization studies demonstrated that sustained HMGA1a-eGFP expression prevented myotube formation and chromatin reorganization that normally accompanies differentiation. Western Blot analyses showed that elevated HMGA1a-eGFP levels affected chromatin composition through either down-regulation of histone H1 or premature expression of MeCP2. RT-PCR analyses further revealed that sustained HMGA1a expression also affected myogenic gene expression and caused either down-regulation of genes such as MyoD, myogenin, Igf1, Igf2, Igfbp1-3 or up-regulation of the transcriptional repressor Msx1. Interestingly, siRNA experiments demonstrated that knock-down of HMGA1a was required and sufficient to reactivate the myogenic program in induced HMGA1a over-expressing cells. Conclusions Our data demonstrate that HMGA1 down-regulation after induction is required to initiate the myogenic program in C2C12 cells. Sustained HMGA1a expression after induction prevents expression of key myogenic factors. This may be due to specific gene regulation and/or global effects on chromatin. Our data further corroborate that altered HMGA1 levels influence the expression of other chromatin proteins. Thus, HMGA1 is able to establish a specific chromatin composition. This work contributes to the understanding of how differential HMGA1 expression is involved in chromatin organization during cellular differentiation processes and it may help to comprehend effects of HMGA1 over-expression occurring in malign or benign tumours.
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Affiliation(s)
- Jan Brocher
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Block S1A, Level 6, 117543 Singapore
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12
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Zhang Q, Wang Y. HMG modifications and nuclear function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:28-36. [PMID: 20123066 DOI: 10.1016/j.bbagrm.2009.11.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 10/26/2009] [Accepted: 11/03/2009] [Indexed: 12/26/2022]
Abstract
High mobility group (HMG) proteins assume important roles in regulating chromatin dynamics, transcriptional activities of genes and other cellular processes. Post-translational modifications of HMG proteins can alter their interactions with DNA and proteins, and consequently, affect their biological activities. Although the mechanisms through which these modifications are involved in regulating biological processes in different cellular contexts are not fully understood, new insights into these modification "codes" have emerged from the increasing appreciation of the functions of these proteins. In this review, we focus on the chemical modifications of mammalian HMG proteins and highlight their roles in nuclear functions.
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Affiliation(s)
- Qingchun Zhang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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Zhu N, Hansen U. Transcriptional regulation by HMGN proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:74-9. [PMID: 20123070 DOI: 10.1016/j.bbagrm.2009.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 10/25/2009] [Accepted: 11/03/2009] [Indexed: 12/20/2022]
Abstract
High mobility group nucleosomal proteins (HMGNs) are small non-histone proteins associated with chromatin. HMGNs have the unique ability to bind to nucleosomes with higher affinity than to naked DNA [1]. They have been studied extensively for their ability to modulate transcription. Although initially viewed as general transcriptional activators on chromatin templates, it is now appreciated that they are instead highly specific modulators of gene expression. We review the mechanisms for targeting HMGNs to specific genes and for how they subsequently regulate transcription.
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Affiliation(s)
- Nan Zhu
- Department of Biology, Boston University, 5 Cummington Street, Boston, MA 02215, USA
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14
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Yamada M, Hamatani T, Akutsu H, Chikazawa N, Kuji N, Yoshimura Y, Umezawa A. Involvement of a novel preimplantation-specific gene encoding the high mobility group box protein Hmgpi in early embryonic development. Hum Mol Genet 2010; 19:480-93. [PMID: 19915186 PMCID: PMC2798723 DOI: 10.1093/hmg/ddp512] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 10/22/2009] [Accepted: 11/11/2009] [Indexed: 11/13/2022] Open
Abstract
Mining gene-expression-profiling data identified a novel gene that is specifically expressed in preimplantation embryos. Hmgpi, a putative chromosomal protein with two high-mobility-group boxes, is zygotically transcribed during zygotic genome activation, but is not transcribed postimplantation. The Hmgpi-encoded protein (HMGPI), first detected at the 4-cell stage, remains highly expressed in pre-implantation embryos. Interestingly, HMGPI is expressed in both the inner cell mass (ICM) and the trophectoderm, and translocated from cytoplasm to nuclei at the blastocyst stage, indicating differential spatial requirements before and after the blastocyst stage. siRNA (siHmgpi)-induced reduction of Hmgpi transcript levels caused developmental loss of preimplantation embryos and implantation failures. Furthermore, reduction of Hmgpi prevented blastocyst outgrowth leading to generation of embryonic stem cells. The siHmgpi-injected embryos also lost ICM and trophectoderm integrity, demarcated by reduced expressions of Oct4, Nanog and Cdx2. The findings implicated an important role for Hmgpi at the earliest stages of mammalian embryonic development.
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Affiliation(s)
- Mitsutoshi Yamada
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjyuku-ku, Tokyo 160-8582, Japan and
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Toshio Hamatani
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjyuku-ku, Tokyo 160-8582, Japan and
| | - Hidenori Akutsu
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Nana Chikazawa
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjyuku-ku, Tokyo 160-8582, Japan and
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
| | - Naoaki Kuji
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjyuku-ku, Tokyo 160-8582, Japan and
| | - Yasunori Yoshimura
- Department of Obstetrics and Gynecology, Keio University School of Medicine, 35 Shinanomachi Shinjyuku-ku, Tokyo 160-8582, Japan and
| | - Akihiro Umezawa
- Department of Reproductive Biology, National Research Institute for Child Health and Development, 2-10-1 Ohkura Setagaya-ku, Tokyo 157-8535, Japan
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15
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Zhang Q, Wang Y. High mobility group proteins and their post-translational modifications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1159-66. [PMID: 18513496 DOI: 10.1016/j.bbapap.2008.04.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 04/14/2008] [Accepted: 04/30/2008] [Indexed: 01/10/2023]
Abstract
The high mobility group (HMG) proteins, including HMGA, HMGB and HMGN, are abundant and ubiquitous nuclear proteins that bind to DNA, nucleosome and other multi-protein complexes in a dynamic and reversible fashion to regulate DNA processing in the context of chromatin. All HMG proteins, like histone proteins, are subjected to extensive post-translational modifications (PTMs), such as lysine acetylation, arginine/lysine methylation and serine/threonine phosphorylation, to modulate their interactions with DNA and other proteins. There is a growing appreciation for the complex relationship between the PTMs of HMG proteins and their diverse biological activities. Here, we reviewed the identified covalent modifications of HMG proteins, and highlighted how these PTMs affect the functions of HMG proteins in a variety of cellular processes.
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Affiliation(s)
- Qingchun Zhang
- Department of Chemistry, University of California, Riverside, CA 92521-0403, USA
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16
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Cherukuri S, Hock R, Ueda T, Catez F, Rochman M, Bustin M. Cell cycle-dependent binding of HMGN proteins to chromatin. Mol Biol Cell 2008; 19:1816-24. [PMID: 18287527 DOI: 10.1091/mbc.e07-10-1018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Throughout the cell cycle, the histones remain associated with DNA, but the repertoire of proteins associated with the chromatin fiber continuously changes. The chromatin interaction of HMGNs, a family of nucleosome binding proteins that modulates the structure and activity of chromatin, during the cell cycle is controversial. Immunofluorescence studies demonstrated that HMGNs are not associated with chromatin, whereas live cell imaging indicated that they are present in mitotic chromosomes. To resolve this controversy, we examined the organization of wild-type and mutated HMGN1 and HMGN2 proteins in the cell nucleus by using immunofluorescence studies, live cell imaging, gel mobility shift assays, and bimolecular fluorescence complementation (BiFC). We find that during interphase, HMGNs bind specifically to nucleosomes and form homodimeric complexes that yield distinct BiFC signals. In metaphase, the nucleosomal binding domain of the protein is inactivated, and the proteins associate with chromatin with low affinity as monomers, and they do not form specific complexes. Our studies demonstrate that the mode of binding of HMGNs to chromatin is cell cycle dependent.
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Affiliation(s)
- Srujana Cherukuri
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Ramírez T, Stopper H, Fischer T, Hock R, Herrera LA. S-adenosyl-L-methionine counteracts mitotic disturbances and cytostatic effects induced by sodium arsenite in HeLa cells. Mutat Res 2008; 637:152-60. [PMID: 17888458 DOI: 10.1016/j.mrfmmm.2007.08.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 05/17/2023]
Abstract
Aneuploidy represents a serious problem for human health. Toxicological data have shown that aneuploidy can be caused by exposure to chemical agents known as mitotic spindle poisons, since they arrest cell cycle in mitosis through their interaction with tubulin. Among these agents is arsenic. In previous reports, we demonstrated that the aneugenic events induced by sodium arsenite can be abolished by the exogenous addition of S-adenosyl-l-methionine (SAM). Nevertheless, the mechanisms involved are still unknown. The aim of the present work was to study the influence of SAM on the mitotic disturbances caused by sodium arsenite. To achieve this goal, we analyzed microtubule (MT) polymerization by immunolocalization and live cell microscopy of mitotic cells. Our findings indicate that sodium arsenite alters the dynamics of MT polymerization, induces centrosome amplification and delays mitosis. Furthermore, SAM reduces the alterations on MT dynamics, as well as centrosome amplification, and therefore diminishes the formation of multipolar spindles in treated HeLa cells. In addition, SAM decreases the progression time through mitosis. Taking these data together, we consider that the mechanism by which SAM reduces the frequency of aneuploid cells must be related to the modulation of the dynamics and organization of MT, suggesting a role of SAM on chromosome segregation, which should be further investigated in primary cells.
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Affiliation(s)
- Tzutzuy Ramírez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
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18
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Sodium arsenite modulates histone acetylation, histone deacetylase activity and HMGN protein dynamics in human cells. Chromosoma 2007; 117:147-57. [PMID: 17999076 DOI: 10.1007/s00412-007-0133-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 10/16/2007] [Indexed: 10/22/2022]
Abstract
Extensive epidemiological data indicate that inorganic arsenic is associated with several types of human cancer. Nevertheless, the underlying mechanisms are poorly understood. Among its mode of action are the alterations on DNA methylation, which provoke aberrant gene expression. However, beyond DNA methylation, little is known about arsenic's effects on chromatin. In this study, we investigated the effects of sodium arsenite (NaAsO(2)) on global histone modifications and nucleosome-associated proteins. Our findings revealed that NaAsO(2) exposure significantly increases global histone acetylation. This effect was related to the inhibition of histone deacetylase (HDAC) activity because NaAsO(2) was able to inhibit HDACs comparable to the well-known HDAC inhibitor trichostatin A (TSA). Furthermore, analyses of the dynamic properties of the nucleosome-associated high mobility group N proteins demonstrate that NaAsO(2) elevates their mobility. Thus, our data suggest that NaAsO(2) induces chromatin opening by histone hyperacetylation due to HDAC inhibition and increase of the mobility of nucleosome-associated proteins. As the chromatin compaction is crucial for the regulation of gene expression as well as for genome stability, we propose that chromatin opening by NaAsO(2) may play a significant role to impart its genotoxic effects.
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19
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Launholt D, Merkle T, Houben A, Schulz A, Grasser KD. Arabidopsis chromatin-associated HMGA and HMGB use different nuclear targeting signals and display highly dynamic localization within the nucleus. THE PLANT CELL 2006; 18:2904-18. [PMID: 17114349 PMCID: PMC1693932 DOI: 10.1105/tpc.106.047274] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 10/02/2006] [Accepted: 10/30/2006] [Indexed: 05/12/2023]
Abstract
In plants, the chromatin-associated high mobility group (HMG) proteins occur in two subfamilies termed HMGA and HMGB. The HMGA proteins are characterized by the presence of four AT-hook DNA binding motifs, and the HMGB proteins contain an HMG box DNA binding domain. As architectural factors, the HMG proteins appear to be involved in the regulation of transcription and other DNA-dependent processes. We have examined the subcellular localization of Arabidopsis thaliana HMGA, HMGB1, and HMGB5, revealing that they localize to the cell nucleus. They display a speckled distribution pattern throughout the chromatin of interphase nuclei, whereas none of the proteins associate with condensed mitotic chromosomes. HMGA is targeted to the nucleus by a monopartite nuclear localization signal, while efficient nuclear accumulation of HMGB1/5 requires large portions of the basic N-terminal part of the proteins. The acidic C-terminal domain interferes with nucleolar targeting of HMGB1. Fluorescence recovery after photobleaching experiments revealed that HMGA and HMGB proteins are extremely dynamic in the nucleus, indicating that they bind chromatin only transiently before moving on to the next site, thereby continuously scanning the genome for targets. By contrast, the majority of histone H2B is basically immobile within the nucleus, while linker histone H1.2 is relatively mobile.
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Affiliation(s)
- Dorte Launholt
- Department of Life Sciences, Aalborg University, DK-9000 Aalborg, Denmark
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20
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Jiang XG, Wang Y. Phosphorylation of human high mobility group N1 protein by protein kinase CK2. Biochem Biophys Res Commun 2006; 345:1497-503. [PMID: 16729963 DOI: 10.1016/j.bbrc.2006.05.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2006] [Accepted: 05/09/2006] [Indexed: 11/24/2022]
Abstract
High mobility group (HMG) N1 protein, formerly known as HMG 14, is a member of the chromosomal HMG protein family. Protein kinase CK2 was previously reported to be able to phosphorylate bovine HMGN1 in vitro; Ser89 and Ser99, corresponding to Ser88 and Ser98 in human HMGN1, were shown to be major and minor recognition sites, respectively. In this report, we employed mass spectrometry and examined both the extent and the sites of phosphorylation in HMGN1 protein catalyzed by recombinant human protein kinase CK2. We found that five serine residues, i.e., Ser6, Ser7, Ser85, Ser88, and Ser98, in HMGN1 can be phosphorylated by the kinase in vitro. All five sites were previously shown to be phosphorylated in MCF-7 human breast cancer cells in vivo. Among these five sites, Ser6, Ser7, and Ser85 were new sites of phosphorylation induced by protein kinase CK2 in vitro.
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Affiliation(s)
- Xinzhao Grace Jiang
- Department of Chemistry-027, University of California, Riverside, 92521-0403, USA
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21
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Feng Y, Huang N, Wu Q, Bao L, Wang BY. Alpha-helical domain is essential for antimicrobial activity of high mobility group nucleosomal binding domain 2 (HMGN2). Acta Pharmacol Sin 2005; 26:1087-92. [PMID: 16115376 DOI: 10.1111/j.1745-7254.2005.00132.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
AIM To examine the antimicrobial spectrum and functional structure of high mobility group nucleosomal binding domain 2 (HMGN2). METHODS OMIGA protein structure software was used to analyze the two-dimensional structure of HMGN2. Synthetic short peptides were generated for studying the relationship between function and structure. Prokaryotic expression vectors were constructed for the holo-HMGN2 and its helical domain. Their E coli-based products were also prepared for antimicrobial testing. The antimicrobial assay included minimal effective concentration, minimal inhibitory concentration, and minimal bactericidal concentration. RESULTS OMIGA protein structure software analysis revealed a transmembrane alpha-helical structure (the putative antimicrobial domain) located from position 18 to 48 of the HMGN2 protein sequence. The antimicrobial assay showed that the MIC of the recombinant holo-HMGN2 against E coli ML-35p (an ampicillin-resistance strain), Pseudomonas aeruginosa ATCC 27853 and Candida albicans ATCC 10231 were 12.5, 25, and 100 mg/L, respectively. Against the same microorganisms, the MIC of the synthetic HMGN2 alpha-helical domain were 12.5, 25, and 100 mg/L, respectively, that is, the same as with the recombinant form of HMGN2. In contrast, recombinant holo-HMGN2 was inactive against Staphylococcus aureus ATCC 25923. The synthetic N-terminal and C-terminal fragments of HMGN2 had no antimicrobial activity against E coli ML-35p, P aeruginosa ATCC 27853 or C albicans ATCC 10231. CONCLUSION HMGN2 showed potent antimicrobial activity against E coli ML-35p, P aeruginosa ATCC 27853 and, to some extent, against C albicans ATCC 10231, but was inactive against S aureus ATCC 25923 in these assay systems. Itos alpha-helical structure may be essential for the antimicrobial activity of HMGN2.
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Affiliation(s)
- Yun Feng
- Research Unit of Infection and Immunity, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu 610041, China.
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22
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Reeves R, Adair JE. Role of high mobility group (HMG) chromatin proteins in DNA repair. DNA Repair (Amst) 2005; 4:926-38. [PMID: 15916927 DOI: 10.1016/j.dnarep.2005.04.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2005] [Indexed: 12/29/2022]
Abstract
While the structure and composition of chromatin not only influences the type and extent of DNA damage incurred by eukaryotic cells, it also poses a major obstacle to the efficient repair of genomic lesions. Understanding how DNA repair processes occur in the context of nuclear chromatin is a current experimental challenge, especially in mammalian cells where the powerful tools of genetic analysis that have been so successful in elucidating repair mechanisms in yeast have seen only limited application. Even so, work over the last decade with both yeast and mammalian cells has provided a rather detailed description of how nucleosomes, the basic subunit of chromatin, influence both DNA damage and repair in all eukaryotic cells. The picture that has emerged is, nonetheless, incomplete since mammalian chromatin is far more complex than simply consisting of vast arrays of histone-containing nucleosome core particles. Members of the "High Mobility Group" (HMG) of non-histone proteins are essential, and highly dynamic, constituents of mammalian chromosomes that participate in all aspects of chromatin structure and function, including DNA repair processes. Yet comparatively little is known about how HMG proteins participate in the molecular events of DNA repair in vivo. What information is available, however, indicates that all three major families of mammalian HMG proteins (i.e., HMGA, HMGB and HMGN) participate in various DNA repair processes, albeit in different ways. For example, HMGN proteins have been shown to stimulate nucleotide excision repair (NER) of ultraviolet light (UV)-induced cyclobutane pyrimidine dimer (CPD) lesions of DNA in vivo. In contrast, HMGA proteins have been demonstrated to preferentially bind to, and inhibit NER of, UV-induced CPDs in stretches of AT-rich DNA both in vitro and in vivo. HMGB proteins, on the other hand, have been shown to both selectively bind to, and inhibit NER of, cisplatin-induced DNA intrastrand cross-links and to bind to misincorporated nucleoside analogs and, depending on the biological circumstances, either promote lesion repair or induce cellular apoptosis. Importantly, from a medical perspective, the ability of the HMGA and HMGB proteins to inhibit DNA repair in vivo suggests that they may be intimately involved with the accumulation of genetic mutations and chromosome instabilities frequently observed in cancers. Not surprisingly, therefore, the HMG proteins are being actively investigated as potential new therapeutic drug targets for the treatment of cancers and other diseases.
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Affiliation(s)
- Raymond Reeves
- School of Molecular Biosciences, Washington State University Pullman, WA 99164-4660, USA.
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23
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Abstract
HMGN proteins are architectural chromatin proteins that reduce the compaction of the chromatin fiber, facilitate access to nucleosomes and modulate replication and transcription processes. Here we demonstrate that in Xenopus laevis, the expression and cellular location of the HMGN proteins are developmentally regulated and that their misexpression leads to gross developmental defects in post-blastula embryos. HMGN transcripts and proteins are present throughout oogenesis; however, the proteins stored in the cytoplasm are not associated with lampbrush chromosomes, and are rapidly degraded when oocytes mature into eggs. During embryogenesis, HMGN expression is first detected in blastula stages and progresses to a tissue-specific expression reaching relative high levels in the mesodermal and neuroectodermal regions of tadpoles. Only after midblastula transition (MBT), alterations in the HMGN levels by either microinjection of recombinant proteins or by morpholino-antisense oligo treatments produced embryos with imperfectly closed blastopore, distorted body axis and showed abnormal head structures. Analyses of animal cap explants indicated that HMGN proteins are involved in the regulation of mesoderm specific genes. In addition, HMGN misexpression caused altered expression of specific genes at MBT rather than global changes of transcription rates. Our results demonstrate that proper embryonic development of Xenopus laevis requires precisely regulated levels of HMGN proteins and suggest that these nucleosomal binding proteins modulate the expression of specific genes.
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Affiliation(s)
- Ulrich Körner
- Department of Cell and Developmental Biology, Biocenter, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany
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24
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Lim JH, Catez F, Birger Y, Postnikov YV, Bustin M. Preparation and functional analysis of HMGN proteins. Methods Enzymol 2004; 375:323-42. [PMID: 14870676 DOI: 10.1016/s0076-6879(03)75021-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Affiliation(s)
- Jae-Hwan Lim
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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25
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The role of HMGN proteins in chromatin function. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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26
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Pallier C, Scaffidi P, Chopineau-Proust S, Agresti A, Nordmann P, Bianchi ME, Marechal V. Association of chromatin proteins high mobility group box (HMGB) 1 and HMGB2 with mitotic chromosomes. Mol Biol Cell 2003; 14:3414-26. [PMID: 12925773 PMCID: PMC181577 DOI: 10.1091/mbc.e02-09-0581] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2002] [Revised: 01/10/2003] [Accepted: 02/24/2003] [Indexed: 01/12/2023] Open
Abstract
High mobility group box (HMGB) 1 and 2 are two abundant nonhistone nuclear proteins that have been found in association with chromatin. Previous studies based on immunofluorescence analysis indicated that HMGB1 dissociates from chromosomes during mitosis. In the present work, HMGB1 and 2 subcellular localization was reinvestigated in living cells by using enhanced green fluorescent protein- and Discosome sp. red fluorescent protein-tagged proteins. Contrary to previous reports, HMGB1 and 2 were shown to be present under two forms in mitotic cells, i.e., free and associated with the condensed chromatin, which rapidly exchange. A detailed analysis of HMGB2 interaction with mitotic chromosomes indicated that two sites encompassing HMG-box A and B are responsible for binding. Importantly, this interaction was rapidly inactivated when cells were permeabilized or exposed to chemical fixatives that are widely used in immunodetection techniques. A comparable behavior was also observed for two proteins of the HMG-nucleosome binding (HMGN) group, namely, HMGN1 and HMGN2.
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Affiliation(s)
- Coralie Pallier
- Unité de Virologie, Service de Bactériologie-Virologie, Hôpital de Bicêtre, Assistance Publique/Hôpitaux de Paris, 94275 Le Kremlin Bicêtre, France
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27
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Catez F, Lim JH, Hock R, Postnikov YV, Bustin M. HMGN dynamics and chromatin function. Biochem Cell Biol 2003; 81:113-22. [PMID: 12897844 DOI: 10.1139/o03-040] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Recent studies indicate that most nuclear proteins, including histone H1 and HMG are highly mobile and their interaction with chromatin is transient. These findings suggest that the structure of chromatin is dynamic and the protein composition at any particular chromatin site is not fixed. Here we discuss how the dynamic behavior of the nucleosome binding HMGN proteins affects the structure and function of chromatin. The high intranuclear mobility of HMGN insures adequate supply of protein throughout the nucleus and serves to target these proteins to their binding sites. Transient interactions of the proteins with nucleosomes destabilize the higher order chromatin, enhance the access to nucleosomal DNA, and impart flexibility to the chromatin fiber. While roaming the nucleus, the HMGN proteins encounter binding partners and form metastable multiprotein complexes, which modulate their chromatin interactions. Studies with HMGN proteins underscore the important role of protein dynamics in chromatin function.
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Affiliation(s)
- Frédéric Catez
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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28
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Prymakowska-Bosak M, Hock R, Catez F, Lim JH, Birger Y, Shirakawa H, Lee K, Bustin M. Mitotic phosphorylation of chromosomal protein HMGN1 inhibits nuclear import and promotes interaction with 14.3.3 proteins. Mol Cell Biol 2002; 22:6809-19. [PMID: 12215538 PMCID: PMC134047 DOI: 10.1128/mcb.22.19.6809-6819.2002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Progression through mitosis is associated with reversible phosphorylation of many nuclear proteins including that of the high-mobility group N (HMGN) nucleosomal binding protein family. Here we use immunofluorescence and in vitro nuclear import studies to demonstrate that mitotic phosphorylation of the nucleosomal binding domain (NBD) of the HMGN1 protein prevents its reentry into the newly formed nucleus in late telophase. By microinjecting wild-type and mutant proteins into the cytoplasm of HeLa cells and expressing these proteins in HmgN1(-/-) cells, we demonstrate that the inability to enter the nucleus is a consequence of phosphorylation and is not due to the presence of negative charges. Using affinity chromatography with recombinant proteins and nuclear extracts prepared from logarithmically growing or mitotically arrested cells, we demonstrate that phosphorylation of the NBD of HMGN1 promotes interaction with specific 14.3.3 isotypes. We conclude that mitotic phosphorylation of HMGN1 protein promotes interaction with 14.3.3 proteins and suggest that this interaction impedes the reentry of the proteins into the nucleus during telophase. Taken together with the results of previous studies, our results suggest a dual role for mitotic phosphorylation of HMGN1: abolishment of chromatin binding and inhibition of nuclear import.
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Affiliation(s)
- Marta Prymakowska-Bosak
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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29
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Catez F, Brown DT, Misteli T, Bustin M. Competition between histone H1 and HMGN proteins for chromatin binding sites. EMBO Rep 2002; 3:760-6. [PMID: 12151335 PMCID: PMC1084210 DOI: 10.1093/embo-reports/kvf156] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2002] [Revised: 06/13/2002] [Accepted: 06/17/2002] [Indexed: 11/12/2022] Open
Abstract
The ability of regulatory factors to access their nucleosomal targets is modulated by nuclear proteins such as histone H1 and HMGN (previously named HMG-14/-17 family) that bind to nucleosomes and either stabilize or destabilize the higher-order chromatin structure. We tested whether HMGN proteins affect the interaction of histone H1 with chromatin. Using microinjection into living cells expressing H1-GFP and photobleaching techniques, we found that wild-type HMGN, but not HMGN point mutants that do not bind to nucleosomes, inhibits the binding of H1 to nucleosomes. HMGN proteins compete with H1 for nucleosome sites but do not displace statically bound H1 from chromatin. Our results provide evidence for in vivo competition among chromosomal proteins for binding sites on chromatin and suggest that the local structure of the chromatin fiber is modulated by a dynamic interplay between nucleosomal binding proteins.
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Affiliation(s)
- Frédéric Catez
- National Cancer Institute, National Institutes of Health, Bethesda, Md 20892, USA
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30
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Lim JH, Bustin M, Ogryzko VV, Postnikov YV. Metastable macromolecular complexes containing high mobility group nucleosome-binding chromosomal proteins in HeLa nuclei. J Biol Chem 2002; 277:20774-82. [PMID: 11909857 DOI: 10.1074/jbc.m200404200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
High mobility group nucleosome-binding (HMGN) proteins belong to a family of nuclear proteins that bind to nucleosomes and enhance transcription from chromatin templates by altering the structure of the chromatin fiber. The intranuclear organization of these proteins is dynamic and related to the metabolic state of the cell. Here we report that approximately 50% of the HMGN proteins are organized into macromolecular complexes in a fashion that is similar to that of other nuclear activities that modify the structure of the chromatin fiber. We identify several distinct HMGN-containing complexes that are relatively unstable and find that the inclusion of HMGN in the complexes varies according to the metabolic state of the cell. The nucleosome binding ability of HMGN in the complex is stronger than that of the free HMGN. We suggest that the inclusion of HMGN proteins into metastable multiprotein complexes serves to target the HMGN proteins to specific sites in chromatin and enhances their interaction with nucleosomes.
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Affiliation(s)
- Jae-Hwan Lim
- Protein Section, CCR, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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31
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Leong PWF, Liew K, Lim W, Chow VTK. Differential display RT-PCR analysis of enterovirus-71-infected rhabdomyosarcoma cells reveals mRNA expression responses of multiple human genes with known and novel functions. Virology 2002; 295:147-59. [PMID: 12033773 DOI: 10.1006/viro.2002.1353] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In order to better understand cellular responses to viral infection at the transcriptional level, we employed differential display RT-PCR to analyze mRNAs from RD rhabdomyosarcoma cells following infection with a neurovirulent enterovirus 71 (EV71) strain, compared with mRNAs from uninfected cells. Of 250 expressed sequence tags (ESTs) isolated, sequenced, and identified, all were of cellular origin except 1 that was of viral origin. Of these, 156 were individual distinctive clones, comprising 45 mRNAs showing unaltered expression and 111 mRNAs exhibiting upregulation or downregulation. Of the 45 uniformly expressed mRNAs, 14 represented unknown genes. Of the 111 differentially expressed mRNAs, 63 did not match any known genes. Forty-eight of the 111 mRNAs modified by EV71 infection matched known genes, including those encoding components of cell cycle, cytoskeleton, and cell death mediators; protein degradation mediators; mitochondrial-related proteins; components of protein translation and modification; and cellular transport proteins. The altered expression profiles of representative genes were authenticated by semiquantitative RT-PCR and real-time RT-PCR. We also identified a novel alternatively spliced transcript of TRIP7 thyroid receptor interactor protein; the putative human homolog of murine mc7 mRNA predominantly expressed in the brain; and a novel mRNA similar to that encoding vacuolar protein 8 involved in protein targeting. These results underscore the applicability of the mRNA differential display technique for elucidating the expression profiles of known and even novel genes in response to cellular infection with pathogenic viruses.
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Affiliation(s)
- Peter W F Leong
- Human Genome Laboratory, National University of Singapore, Kent Ridge, 117597, Singapore
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32
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Lührs H, Hock R, Schauber J, Weihrauch M, Harrer M, Melcher R, Scheppach W, Bustin M, Menzel T. Modulation of HMG-N2 binding to chromatin by butyrate-induced acetylation in human colon adenocarcinoma cells. Int J Cancer 2002; 97:567-73. [PMID: 11807779 DOI: 10.1002/ijc.10098] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Butyrate, a short chain fatty acid (SCFA), is generated by anaerobic fermentation of undigested carbohydrates within the colon. Butyrate enhances acetylation of core histones, a process directly linked to the formation of active chromatin and gene expression. However, additional chromatin components also contribute to the formation of transcriptionally active chromatin. The high mobility group protein N2 (HMG-N2), a nonhistone protein, is involved in chromatin structure modulation. We examined the effects of butyrate on HMG-N2 expression, hyperacetylation and chromatin binding. HT29 human adenocarcinoma cells were incubated with butyrate. Levels of HMG-N2 mRNA and of total or acetylated HMG-N2 protein were analyzed. Protein dynamics were investigated with transfected cells expressing HMG-N2-EGFP fusion proteins. Treatment of HT29 cells with butyrate led to significant hyperacetylation of HMG-N2. Levels of HMG-N2 protein remained unchanged. Northern blot analysis revealed a significant reduction in HMG-N2 mRNA levels after treatment with butyrate. Analysis of HMG-N2-EGFP transfected HT29 cells demonstrated that butyrate treatment changes the binding properties of HMG-N2-EGFP to chromatin. In addition, butyrate treatment resulted in solubilization of endogenous acetylated HMG-N2 into the supernatant of permeabilized cells. We demonstrate that butyrate treatment is associated with hyperacetylation of HMG-N2 protein in HT29 cells. The modulation of this nonhistone chromatin protein resulted in altered binding properties to chromatin. This may represent an additional step in changing chromatin structure and composition with subsequent consequences for transcription and gene expression. Modulation of nonhistone chromatin proteins, like the ubiquitous HMG-N2 proteins, may be partly responsible for the wide range of butyrate-associated effects.
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Affiliation(s)
- Hardi Lührs
- Department of Medicine, University of Würzburg, Würzburg, Germany.
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33
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Czura CJ, Wang H, Tracey KJ. Dual roles for HMGB1: DNA binding and cytokine. JOURNAL OF ENDOTOXIN RESEARCH 2002; 7:315-21. [PMID: 11717586 DOI: 10.1177/09680519010070041401] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Effective therapies against overwhelming Gram-negative bacteremia, or sepsis, have eluded successful development. The discovery that tumor necrosis factor (TNF), a host-derived inflammatory mediator, was both necessary and sufficient to recapitulate Gram-negative sepsis raised cautious optimism for developing a targeted therapeutic. However, the rapid kinetics of the TNF response to infection defined an extremely narrow window of opportunity during which anti-TNF therapeutics could be successfully administered. HMGB1 was previously studied as a DNA-binding protein involved in DNA replication, repair, and transcription; and as a membrane-associated protein that mediates neurite outgrowth. A decade-long search has culminated in our identification of HMGB1 as a late mediator of endotoxemia. HMGB1 is released by macrophages upon exposure to endotoxin, activates many other pro-inflammatory mediators, and is lethal to otherwise healthy animals. Elevated levels of HMGB1 are observed in the serum of patients with sepsis, and the highest levels were found in those patients that died. The delayed kinetics of HMGB1 release indicate that it may be useful to target this toxic cytokine in the development of future therapies.
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Affiliation(s)
- C J Czura
- Laboratory of Biomedical Science, North Shore/Long Island Jewish Research Institute, Manhasset, New York 11030, USA
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34
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Prymakowska-Bosak M, Misteli T, Herrera JE, Shirakawa H, Birger Y, Garfield S, Bustin M. Mitotic phosphorylation prevents the binding of HMGN proteins to chromatin. Mol Cell Biol 2001; 21:5169-78. [PMID: 11438671 PMCID: PMC87241 DOI: 10.1128/mcb.21.15.5169-5178.2001] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Condensation of the chromatin fiber and transcriptional inhibition during mitosis is associated with the redistribution of many DNA- and chromatin-binding proteins, including members of the high-mobility-group N (HMGN) family. Here we study the mechanism governing the organization of HMGN proteins in mitosis. Using site-specific antibodies and quantitative gel analysis with proteins extracted from synchronized HeLa cells, we demonstrate that, during mitosis, the conserved serine residues in the nucleosomal binding domain (NBD) of this protein family are highly and specifically phosphorylated. Nucleosome mobility shift assays with both in vitro-phosphorylated proteins and with point mutants bearing negative charges in the NBD demonstrate that the negative charge abolishes the ability of the proteins to bind to nucleosomes. Fluorescence loss of photobleaching demonstrates that, in living cells, the negative charge in the NBD increases the intranuclear mobility of the protein and significantly decreases the relative time that it is bound to chromatin. Expression of wild-type and mutant proteins in HmgN1(-/-) cells indicates that the negatively charged protein is not bound to chromosomes. We conclude that during mitosis the NBD of HMGN proteins is highly phosphorylated and that this modification regulates the interaction of the proteins with chromatin.
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Affiliation(s)
- M Prymakowska-Bosak
- Protein Section, Laboratory of Metabolism, DBS, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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35
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Abstract
The high mobility group N (HMGN) proteins are a family of nuclear proteins that binds to nucleosomes, changes the architecture of chromatin, and enhances transcription and replication from chromatin templates. The intracellular organization of the HMGN (previously known as HMG-14/17) proteins is dynamic and is related to both cell-cycle and transcriptional events. These proteins roam the nucleus, perhaps as part of multiprotein complexes, and their target interactions are modulated by posttranslational modifications. Functional studies on HMGN proteins provide insights into the molecular mechanisms by which structural proteins affect DNA-dependent activities in the context of chromatin.
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Affiliation(s)
- M Bustin
- Protein Section, Laboratory of Metabolism, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, 20892, Bethesda, MD, USA.
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36
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Lehtonen S, Lehtonen E. HMG-17 is an early marker of inductive interactions in the developing mouse kidney. Differentiation 2001; 67:154-63. [PMID: 11683498 DOI: 10.1046/j.1432-0436.2001.670407.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We studied the relationship between proliferation, differentiation, and the expression of high-mobility-group protein 17 (HMG-17) during metanephric kidney development. Proliferating cells were found homogenously throughout the early kidney rudiment. The expression pattern of HMG-17 mRNA, on the other hand, was distinctly uneven: In the undifferentiated mesenchyme, the cells in the cranial "tail" part of the mesenchyme showed only a weak signal, whereas a group of cells lying close to the tip of the ureteric bud showed strong HMG-17 expression. The region distinctly positive for HMG-17 is known to contain the first cells to undergo mesenchyme-to-epithelium transition. Using the transfilter model system, strong expression of HMG-17 mRNA, followed by mesenchyme-to-epithelium transition, could be induced also in the "tail" part of the mesenchyme. The upregulation of HMG-17 in the metanephrogenic mesenchyme thus results from interaction with an inductor tissue. Throughout the renal development, the HMG-17 mRNA was also abundant in those epithelial and mesenchymal cells that were undergoing active cell differentiation, and the transcript was downregulated in mature cells. HMG-17 expression thus correlated with the processes of induction and differentiation rather than with proliferation. The present results suggest that HMG-17 could have a role in the activation of the genes regulating kidney organogenesis.
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Affiliation(s)
- S Lehtonen
- Department of Pathology, Haartman Institute University of Helsinki, Finland
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37
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West KL, Ito Y, Birger Y, Postnikov Y, Shirakawa H, Bustin M. HMGN3a and HMGN3b, two protein isoforms with a tissue-specific expression pattern, expand the cellular repertoire of nucleosome-binding proteins. J Biol Chem 2001; 276:25959-69. [PMID: 11356838 DOI: 10.1074/jbc.m101692200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
HMGN1 (HMG-14) and HMGN2 (HMG-17) are nuclear proteins that bind specifically to nucleosomes, reduce the compactness of the chromatin fiber, and enhance transcription from chromatin templates. Here we report that many vertebrates contain an additional type of HMGN protein named HMGN3 (Trip 7). The human HMGN3 gene is located on chromosome 6 and spans 32 kilobase pairs, which is nearly 10-fold longer than the closely related HMGN2 gene. However, the intron/exon boundaries of the HMGN3 gene are identical to those of HMGN1 and HMGN2. Unique within the HMGN family, the HMGN3 transcript undergoes alternative splicing and generates two different variants, HMGN3a and HMGN3b. The shorter variant, HMGN3b, arises from an additional splice site that truncates exon V and causes a frameshift. The resulting HMGN3b protein lacks the majority of the C-terminal chromatin-unfolding domain. Both splice variants are found in many vertebrates from frogs to man and are expressed in many tissues. The pattern of tissue-specific expression differs considerably from those of HMGN1 and HMGN2 at both the mRNA and the protein level. Our results expand the multiplicity of the HMGN protein family and raise the possibility that these nucleosome-binding proteins function as co-activators in tissue-specific gene expression.
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Affiliation(s)
- K L West
- Protein Section, Laboratory of Metabolism, Division of Basic Science, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA.
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38
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Birger Y, Ito Y, West KL, Landsman D, Bustin M. HMGN4, a newly discovered nucleosome-binding protein encoded by an intronless gene. DNA Cell Biol 2001; 20:257-64. [PMID: 11410162 DOI: 10.1089/104454901750232454] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe a newly discovered nuclear protein, HMGN4, that is closely related to the canonical HMGN2 nucleosome-binding protein. The protein is encoded by an intronless gene, which, in humans, is located in the hereditary hemochromatosis [correction of hemachromatosis] region at position 6p21.3. A single approximately 2-kb HMGN4 mRNA was found to be expressed, in variable amounts, in all human tissues tested; however, the HMGN4 transcript was significantly less abundant than that of HMGN2. The HMGN4 protein could be detected in HeLa cells by Western analysis with an antibody elicited against a unique region of the protein. Transfection of HeLa cells with a plasmid expressing HMGN4-GFP indicated that the protein localizes to the nucleus. Our results expand the multiplicity of the HMGN protein family and increase the known cellular repertoire of nucleosome-binding proteins.
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Affiliation(s)
- Y Birger
- Protein Section, Laboratory of Metabolism, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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39
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Mohamed OA, Bustin M, Clarke HJ. High-mobility group proteins 14 and 17 maintain the timing of early embryonic development in the mouse. Dev Biol 2001; 229:237-49. [PMID: 11133167 DOI: 10.1006/dbio.2000.9942] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The high-mobility group (HMG) proteins 14 and 17 are abundant chromosomal proteins that bind to nucleosomes and enhance transcription. We report that both mRNA species and both proteins are present throughout oogenesis and preimplantation development of the mouse. When antisense oligonucleotides targeting each mRNA species are injected into one-cell embryos, the proteins become depleted at the two- and four-cell stages and reaccumulate at the eight-cell stage. One-cell embryos injected with antisense oligonucleotides targeting both HMG-14 and HMG-17 cleave to the two-cell stage. Subsequent cleavages, however, are delayed compared with control-injected embryos. Nevertheless, these embryos ultimately reach the blastocyst stage. Similarly, injection into the nuclei of two-cell embryos of a peptide corresponding to the common nucleosome-binding domain of HMG-14 and HMG-17 delays progression to the four-cell stage. Furthermore, both RNA and protein synthesis is transiently reduced in antisense-injected embryos compared with injected controls. These results identify HMG-14 and HMG-17 as constitutive components of mouse oocyte and embryonic chromatin and establish a link between the structure of embryonic chromatin and the normal progression of embryonic development.
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Affiliation(s)
- O A Mohamed
- Department of Obstetrics & Gynecology, McGill University, Montreal, Quebec, H3A 1A1, Canada
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40
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Shirakawa H, Herrera JE, Bustin M, Postnikov Y. Targeting of high mobility group-14/-17 proteins in chromatin is independent of DNA sequence. J Biol Chem 2000; 275:37937-44. [PMID: 10973947 DOI: 10.1074/jbc.m000989200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromosomal proteins high mobility group (HMG)-14 and HMG-17 are nucleosomal-binding proteins that unfold the chromatin fiber and enhance transcription from chromatin templates. Their intracellular organization is dynamic and related to both cell cycle and transcription. Here we examine possible mechanisms for targeting HMG-14/-17 to specific regions in chromatin. Chromatin immunoprecipitation assays indicate that HMG-17 protein is not preferentially associated with chromatin regions containing transcriptionally active genes, or any type of specific DNA. We used a modification of the random amplified polymorphic DNA method to analyze DNA in various HMG-14/-17.nucleosome complexes. We found that although HMG-14 or HMG-17 proteins preferentially associate with core particles in which the DNA has a low frequency of CG dinucleotides, the genome does not contain consensus sequences that serve as specific targeting sites for the binding of either HMG-14 or HMG-17 proteins to nucleosomes. We used size exclusion and ion exchange chromatography to demonstrate that nuclei contain a large portion of HMG-17 associated with other proteins in a multiprotein complex. We suggest that these complexes regulate the dynamic organization of HMG-14/-17 in the nucleus and serve to target the proteins to specific sites in chromatin.
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Affiliation(s)
- H Shirakawa
- Protein Section, Division of Basic Sciences, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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41
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Christophe D, Christophe-Hobertus C, Pichon B. Nuclear targeting of proteins: how many different signals? Cell Signal 2000; 12:337-41. [PMID: 10822175 DOI: 10.1016/s0898-6568(00)00077-2] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The nuclear import of proteins into the cell nucleus involves the recognition of a nuclear localization signal sequence, borne by the protein to be transported, by complex molecules called importins, that will subsequently mediate the crossing over of the nuclear envelope. The most frequently encountered signal sequence is made up of short stretches of basic amino acid residues and is recognized by importins alpha and/or beta. Other signal sequences have been described, and some have been shown to mediate the association with importins other than importin alpha or beta. Recently, approaches have been developed that allow the cloning, on a functional basis, of sequences able to specify the nuclear localization of proteins. A variety of peptidic motifs of limited size which do not contain previously described signal sequences were isolated in such assays. It reveals that the spectrum of sequences that are able to target a protein to the cell nucleus may be wider than currently expected. It will probably also lead to the identification of novel target sequences for importins and will demonstrate the implication of additional members of this family of proteins in nuclear transport.
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Affiliation(s)
- D Christophe
- Institut de Biologie et de Médecine Moléculaires (IBMM), IRIBHN-Faculté de Médecine, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, 6041, Gosselies, Belgique.
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42
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Abstract
The bovine papillomavirus E2 transactivator protein is a multifunctional protein that activates viral transcription, cooperates in initiation of viral DNA replication, and is required for long-term episomal maintenance of viral genomes. We have shown previously that the E2 transactivator protein and bovine papillomavirus type 1 genomes are associated with mitotic chromosomes and have proposed that E2 links the genomes to cellular chromosomes to ensure segregation to daughter nuclei. In this study, we show that E2 is associated with cellular chromosomes at all stages of mitosis. We also further map the regions of E2 that are required for this association. The transactivation domain of E2 is necessary and sufficient to mediate the interaction with mitotic chromosomes; the DNA binding domain, and the flexible hinge region that separates the two domains, is not required. Furthermore, mutation of previously identified phosphorylation sites (serine residues 235, 298, and 301) has no effect on the ability of the E2 protein to bind mitotic chromosomes.
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Affiliation(s)
- N Bastien
- Laboratory of Viral Diseases, National Institutes of Health, Bethesda, Maryland 20892-0455, USA
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43
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Bergel M, Herrera JE, Thatcher BJ, Prymakowska-Bosak M, Vassilev A, Nakatani Y, Martin B, Bustin M. Acetylation of novel sites in the nucleosomal binding domain of chromosomal protein HMG-14 by p300 alters its interaction with nucleosomes. J Biol Chem 2000; 275:11514-20. [PMID: 10753971 DOI: 10.1074/jbc.275.15.11514] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The reversible acetylation of histones is associated with structural alterations in the chromatin fiber that affect various DNA-related activities. Here we show that the histone acetyltransferase p300 specifically acetylates HMG-14, a nonhistone structural protein that binds to nucleosomes and reduces the compactness of the chromatin fiber. We identify 7 major acetylation sites, 6 of which are novel and have not been known to be acetylated in either HMG-14 or the closely related HMG-17 protein. All the acetylation sites involve evolutionarily conserved residues: 3 within the HMG-14/-17 nucleosomal binding domain and 4 in or near the bipartite nuclear localization domains of the proteins. In tissue culture cells the acetylation pattern is indicative of a selective process in which a subfraction of HMG-14 is preferentially acetylated. We find that the nucleosomal binding domain is a major target for acetylation in vivo and that the specific acetylation of HMG-14 by p300 weakens its interaction with nucleosome cores. Our results suggest that p300 modulates the interaction of HMG-14 with nucleosomes. Thus, p300 may affect chromatin-related activities not only by modifying histones or transcription factors but also by targeting structural nonhistone proteins.
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Affiliation(s)
- M Bergel
- Protein Section, Division of Basic Science, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA.
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44
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Shirakawa H, Landsman D, Postnikov YV, Bustin M. NBP-45, a novel nucleosomal binding protein with a tissue-specific and developmentally regulated expression. J Biol Chem 2000; 275:6368-74. [PMID: 10692437 DOI: 10.1074/jbc.275.9.6368] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here we characterize a novel murine nuclear protein, which we named NBP-45, that is related to the ubiquitous nuclear proteins HMG-14/-17, binds specifically to nucleosome core particles, and can function as a transcriptional activator. NBP-45 mRNA is expressed at low levels and in variable amounts in all mouse tissues tested but is especially abundant in RNA extracted from 7-day-old mouse embryos, suggesting that it functions in early embryonic development. NBP-45 is composed of 406 amino acids and is encoded by a single size transcript. The region spanning the N-terminal 85 amino acids contains three segments that are highly homologous to functionally important domains in the HMG-14/-17 protein family: the nuclear localization signal, the nucleosome binding domain, and the chromatin unfolding domain. The protein region spanning the C-terminal 321 amino acids has a 42% content of negatively charged residues. The first 23 amino acids contain a region necessary for nuclear entry of the protein, the region spanning residues 12-40 is the main nucleosomal binding domain of the protein, and the negatively charged, C-terminal domain is necessary for transcription activation. The functional domains of NBP-45 are indicative of a nuclear protein that binds to nucleosomes, thereby creating a chromatin region of high local negative charge. Our studies establish the nucleosomal binding domain as a protein motif that is present in other than just the ubiquitous HMG-14/-17 proteins. We suggest that the nucleosomal binding domain motif is a protein module that facilitates binding to nucleosomes in chromatin.
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Affiliation(s)
- H Shirakawa
- Institute of Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892, USA
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45
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Johnson-Saliba M, Siddon NA, Clarkson MJ, Tremethick DJ, Jans DA. Distinct importin recognition properties of histones and chromatin assembly factors. FEBS Lett 2000; 467:169-74. [PMID: 10675532 DOI: 10.1016/s0014-5793(00)01142-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Synthesis of the protein components of nuclear chromatin occurs in the cytoplasm, necessitating specific import into the nucleus. Here, we report the binding affinities of the nuclear localisation sequence (NLS)-binding importin subunits for a range of histones and chromatin assembly factors. The results suggest that import of histones to the nucleus may be mediated predominantly by importin beta1, whereas the import of the other components probably relies on the conventional alpha/beta1 import pathway. Differences in recognition by importin beta1 were observed between histone H2A and the variant H2AZ, as well as between histone H3/4 with or without acetylation. The results imply that different histone variants may possess distinct nuclear import properties, with acetylation possibly playing an inhibitory role through NLS masking.
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Affiliation(s)
- M Johnson-Saliba
- Nuclear Signalling Laboratory, Division of Biochemistry, John Curtin School of Medical Research, Australian National University, 0200, Canberra, N.S.W. Australia
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46
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Louie DF, Gloor KK, Galasinski SC, Resing KA, Ahn NG. Phosphorylation and subcellular redistribution of high mobility group proteins 14 and 17, analyzed by mass spectrometry. Protein Sci 2000; 9:170-9. [PMID: 10739259 PMCID: PMC2144438 DOI: 10.1110/ps.9.1.170] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
High mobility group (HMG) proteins 14 and 17 are nonhistone nuclear proteins that have been implicated in control of transcription and chromatin structure. To examine the posttranslational modifications of HMG-14 and -17 in vivo, HMG proteins were prepared from nuclear vs. cytosolic fractions of human K562 cells treated with 12-O-tetradecanoylphorbol 13-acetate (TPA) or okadaic acid (OA) and examined by electrospray mass spectrometry. Analysis of full-length masses demonstrated mono-, di-, and triphosphorylation of HMG-14 and mono- and diphosphorylation of HMG-17 from OA treated cells, whereas HMG-14 and -17 from TPA treated cells were monophosphorylated. Peptide mass and sequence analysis showed major and minor phosphorylation sites, respectively, at Ser24 and Ser28 in HMG-17, and Ser20 and Ser24 in HMG-14. These sites were found in the consensus sequence RRSARLSAK, within the nucleosomal binding domain of each protein. A third phosphorylation site in HMG-14 was located at either Ser6 or Ser7. Interestingly, the proportion of HMG-14 and -17 found in cytosolic pools increased significantly after 1 h of treatment compared to control cells and showed preferential phosphorylation compared with proteins from nuclear fractions. These results suggest that phosphorylation of HMG-14 and -7 interferes with nuclear localization mechanisms in a manner favoring release from nuclei.
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Affiliation(s)
- D F Louie
- Howard Hughes Medical Institute, University of Colorado, Boulder 80309, USA
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47
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Bustin M. Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins. Mol Cell Biol 1999; 19:5237-46. [PMID: 10409715 PMCID: PMC84367 DOI: 10.1128/mcb.19.8.5237] [Citation(s) in RCA: 653] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- M Bustin
- Protein Section, Laboratory of Molecular Carcinogenesis, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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