1
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Affiliation(s)
- Kangjing Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China
| | - Junjie Yuan
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China,Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, Beijing, China
| | - Youyang Sia
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China
| | - Zhucheng Chen
- MOE Key Laboratory of Protein Science, Tsinghua University, Beijing, P.R. China,School of Life Sciences, Tsinghua University, Beijing, P.R. China,Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing, Beijing, China,CONTACT Zhucheng Chen MOE Key Laboratory of Protein Science, Tsinghua University, Beijing100084, P.R. China
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2
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Torii T, Sugimoto W, Itoh K, Kinoshita N, Gessho M, Goto T, Uehara I, Nakajima W, Budirahardja Y, Miyoshi D, Nishikata T, Tanaka N, Hirata H, Kawauchi K. Loss of p53 function promotes DNA damage-induced formation of nuclear actin filaments. Cell Death Dis 2023; 14:766. [PMID: 38001089 PMCID: PMC10674001 DOI: 10.1038/s41419-023-06310-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 11/08/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023]
Abstract
Tumor suppressor p53 plays a central role in response to DNA damage. DNA-damaging agents modulate nuclear actin dynamics, influencing cell behaviors; however, whether p53 affects the formation of nuclear actin filaments remains unclear. In this study, we found that p53 depletion promoted the formation of nuclear actin filaments in response to DNA-damaging agents, such as doxorubicin (DOXO) and etoposide (VP16). Even though the genetic probes used for the detection of nuclear actin filaments exerted a promotive effect on actin polymerization, the detected formation of nuclear actin filaments was highly dependent on both p53 depletion and DNA damage. Whilst active p53 is known to promote caspase-1 expression, the overexpression of caspase-1 reduced DNA damage-induced formation of nuclear actin filaments in p53-depleted cells. In contrast, co-treatment with DOXO and the pan-caspase inhibitor Q-VD-OPh or the caspase-1 inhibitor Z-YVAD-FMK induced the formation of nuclear actin filament formation even in cells bearing wild-type p53. These results suggest that the p53-caspase-1 axis suppresses DNA damage-induced formation of nuclear actin filaments. In addition, we found that the expression of nLifeact-GFP, the filamentous-actin-binding peptide Lifeact fused with the nuclear localization signal (NLS) and GFP, modulated the structure of nuclear actin filaments to be phalloidin-stainable in p53-depleted cells treated with the DNA-damaging agent, altering the chromatin structure and reducing the transcriptional activity. The level of phosphorylated H2AX (γH2AX), a marker of DNA damage, in these cells also reduced upon nLifeact-GFP expression, whilst details of the functional relationship between the formation of nLifeact-GFP-decorated nuclear actin filaments and DNA repair remained to be elucidated. Considering that the loss of p53 is associated with cancer progression, the results of this study raise a possibility that the artificial reinforcement of nuclear actin filaments by nLifeact-GFP may enhance the cytotoxic effect of DNA-damaging agents in aggressive cancer cells through a reduction in gene transcription.
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Affiliation(s)
- Takeru Torii
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Wataru Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Katsuhiko Itoh
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Natsuki Kinoshita
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Masaya Gessho
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Toshiyuki Goto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Ikuno Uehara
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, 113-8602, Japan
| | - Wataru Nakajima
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, 113-8602, Japan
| | - Yemima Budirahardja
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Takahito Nishikata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan
| | - Nobuyuki Tanaka
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, 113-8602, Japan
| | - Hiroaki Hirata
- Department of Applied Bioscience, Kanazawa Institute of Technology, Hakusan, 924-0838, Japan.
| | - Keiko Kawauchi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, 650-0047, Japan.
- Department of Molecular Oncology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, 113-8602, Japan.
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3
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Stephan OOH. Effects of environmental stress factors on the actin cytoskeleton of fungi and plants: Ionizing radiation and ROS. Cytoskeleton (Hoboken) 2023; 80:330-355. [PMID: 37066976 DOI: 10.1002/cm.21758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 04/18/2023]
Abstract
Actin is an abundant and multifaceted protein in eukaryotic cells that has been detected in the cytoplasm as well as in the nucleus. In cooperation with numerous interacting accessory-proteins, monomeric actin (G-actin) polymerizes into microfilaments (F-actin) which constitute ubiquitous subcellular higher order structures. Considering the extensive spatial dimensions and multifunctionality of actin superarrays, the present study analyses the issue if and to what extent environmental stress factors, specifically ionizing radiation (IR) and reactive oxygen species (ROS), affect the cellular actin-entity. In that context, this review particularly surveys IR-response of fungi and plants. It examines in detail which actin-related cellular constituents and molecular pathways are influenced by IR and related ROS. This comprehensive survey concludes that the general integrity of the total cellular actin cytoskeleton is a requirement for IR-tolerance. Actin's functions in genome organization and nuclear events like chromatin remodeling, DNA-repair, and transcription play a key role. Beyond that, it is highly significant that the macromolecular cytoplasmic and cortical actin-frameworks are affected by IR as well. In response to IR, actin-filament bundling proteins (fimbrins) are required to stabilize cables or patches. In addition, the actin-associated factors mediating cellular polarity are essential for IR-survivability. Moreover, it is concluded that a cellular homeostasis system comprising ROS, ROS-scavengers, NADPH-oxidases, and the actin cytoskeleton plays an essential role here. Consequently, besides the actin-fraction which controls crucial genome-integrity, also the portion which facilitates orderly cellular transport and polarized growth has to be maintained in order to survive IR.
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Affiliation(s)
- Octavian O H Stephan
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Bavaria, 91058, Germany
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4
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Kurosawa K, Nakano M, Yokoseki I, Nagaoka M, Takemoto S, Sakai Y, Kobayashi K, Kazuki Y, Fukami T, Nakajima M. ncBAF enhances PXR-mediated transcriptional activation in the human and mouse liver. Biochem Pharmacol 2023; 215:115733. [PMID: 37543347 DOI: 10.1016/j.bcp.2023.115733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023]
Abstract
Pregnane X receptor (PXR) is one of the key regulators of drug metabolism, gluconeogenesis, and lipid synthesis in the human liver. Activation of PXR by drugs such as rifampicin, simvastatin, and efavirenz causes adverse reactions such as drug-drug interaction, hyperglycemia, and dyslipidemia. The inhibition of PXR activation has merit in preventing such adverse events. Here, we demonstrated that bromodomain containing protein 9 (BRD9), a component of non-canonical brahma-related gene 1-associated factor (ncBAF), one of the chromatin remodelers, interacts with PXR. Rifampicin-mediated induction of CYP3A4 expression was attenuated by iBRD9, an inhibitor of BRD9, in human primary hepatocytes and CYP3A/PXR-humanized mice, indicating that BRD9 enhances the transcriptional activation of PXR in vitro and in vivo. Chromatin immunoprecipitation assay reveled that iBRD9 treatment resulted in attenuation of the rifampicin-mediated binding of PXR to the CYP3A4 promoter region, suggesting that ncBAF functions to facilitate the binding of PXR to its response elements. Efavirenz-induced hepatic lipid accumulation was attenuated by iBRD9 in C57BL/6J mice, suggesting that the inhibition of BRD9 would be useful to reduce the risk of efavirenz-induced hepatic steatosis. Collectively, we found that inhibitors of BRD9, a component of ncBAF that plays a role in assisting transactivation by PXR, would be useful to reduce the risk of PXR-mediated adverse reactions.
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Affiliation(s)
- Kiamu Kurosawa
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Masataka Nakano
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPI Nano Life Science Institute (WPI-NanoLSI) Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Itsuki Yokoseki
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Mai Nagaoka
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Seiya Takemoto
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yoshiyuki Sakai
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kaoru Kobayashi
- Laboratory of Biopharmaceutics, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Yasuhiro Kazuki
- Department of Chromosome Biomedical Engineering, School of Life Science, Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan; Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishi-cho, Yonago, Tottori 683-8503, Japan
| | - Tatsuki Fukami
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPI Nano Life Science Institute (WPI-NanoLSI) Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Miki Nakajima
- Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPI Nano Life Science Institute (WPI-NanoLSI) Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
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5
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Wang L, Yu J, Yu Z, Wang Q, Li W, Ren Y, Chen Z, He S, Xu Y. Structure of nucleosome-bound human PBAF complex. Nat Commun 2022; 13:7644. [PMID: 36496390 PMCID: PMC9741621 DOI: 10.1038/s41467-022-34859-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
BAF and PBAF are mammalian SWI/SNF family chromatin remodeling complexes that possess multiple histone/DNA-binding subunits and create nucleosome-depleted/free regions for transcription activation. Despite previous structural studies and recent advance of SWI/SNF family complexes, it remains incompletely understood how PBAF-nucleosome complex is organized. Here we determined structure of 13-subunit human PBAF in complex with acetylated nucleosome in ADP-BeF3-bound state. Four PBAF-specific subunits work together with nine BAF/PBAF-shared subunits to generate PBAF-specific modular organization, distinct from that of BAF at various regions. PBAF-nucleosome structure reveals six histone-binding domains and four DNA-binding domains/modules, the majority of which directly bind histone/DNA. This multivalent nucleosome-binding pattern, not observed in previous studies, suggests that PBAF may integrate comprehensive chromatin information to target genomic loci for function. Our study reveals molecular organization of subunits and histone/DNA-binding domains/modules in PBAF-nucleosome complex and provides structural insights into PBAF-mediated nucleosome association complimentary to the recently reported PBAF-nucleosome structure.
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Affiliation(s)
- Li Wang
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.11841.3d0000 0004 0619 8943The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433 China
| | - Jiali Yu
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Zishuo Yu
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Qianmin Wang
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Wanjun Li
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Yulei Ren
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Zhenguo Chen
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443The Fifth People’s Hospital of Shanghai, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Key Laboratory of Medical Epigenetics, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032 China
| | - Shuang He
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China
| | - Yanhui Xu
- grid.11841.3d0000 0004 0619 8943Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.11841.3d0000 0004 0619 8943The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433 China
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6
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Ten Hoeve AL, Braun L, Rodriguez ME, Olivera GC, Bougdour A, Belmudes L, Couté Y, Saeij JPJ, Hakimi MA, Barragan A. The Toxoplasma effector GRA28 promotes parasite dissemination by inducing dendritic cell-like migratory properties in infected macrophages. Cell Host Microbe 2022; 30:1570-1588.e7. [PMID: 36309013 PMCID: PMC9710525 DOI: 10.1016/j.chom.2022.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/26/2022] [Accepted: 10/03/2022] [Indexed: 11/03/2022]
Abstract
Upon pathogen detection, macrophages normally stay sessile in tissues while dendritic cells (DCs) migrate to secondary lymphoid tissues. The obligate intracellular protozoan Toxoplasma gondii exploits the trafficking of mononuclear phagocytes for dissemination via unclear mechanisms. We report that, upon T. gondii infection, macrophages initiate the expression of transcription factors normally attributed to DCs, upregulate CCR7 expression with a chemotactic response, and perform systemic migration when adoptively transferred into mice. We show that parasite effector GRA28, released by the MYR1 secretory pathway, cooperates with host chromatin remodelers in the host cell nucleus to drive the chemotactic migration of parasitized macrophages. During in vivo challenge studies, bone marrow-derived macrophages infected with wild-type T. gondii outcompeted those challenged with MYR1- or GRA28-deficient strains in migrating and reaching secondary organs. This work reveals how an intracellular parasite hijacks chemotaxis in phagocytes and highlights a remarkable migratory plasticity in differentiated cells of the mononuclear phagocyte system.
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Affiliation(s)
- Arne L Ten Hoeve
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Laurence Braun
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Matias E Rodriguez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Gabriela C Olivera
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Alexandre Bougdour
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Lucid Belmudes
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Yohann Couté
- Univ. Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Jeroen P J Saeij
- Department of Pathology, Microbiology, and Immunology, University of California Davis, Davis, CA 95616, USA
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France.
| | - Antonio Barragan
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden.
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7
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Jacques CN, Favero DS, Kawamura A, Suzuki T, Sugimoto K, Neff MM. SUPPRESSOR OF PHYTOCHROME B-4 #3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days. BMC PLANT BIOLOGY 2022; 22:399. [PMID: 35965321 PMCID: PMC9377115 DOI: 10.1186/s12870-022-03737-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3) is a member of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors that are involved in light-mediated growth in Arabidopsis thaliana, affecting processes such as hypocotyl elongation. The majority of the research on the AHLs has been conducted in continuous light. However, there are unique molecular events that promote growth in short days (SD) compared to constant light conditions. Therefore, we investigated how AHLs affect hypocotyl elongation in SD. Firstly, we observed that AHLs inhibit hypocotyl growth in SD, similar to their effect in constant light. Next, we identified AHL-regulated genes in SD-grown seedlings by performing RNA-seq in two sob3 mutants at different time points. Our transcriptomic data indicate that PHYTOCHROME INTERACTING FACTORS (PIFs) 4, 5, 7, and 8 along with PIF-target genes are repressed by SOB3 and/or other AHLs. We also identified PIF target genes that are repressed and have not been previously described as AHL-regulated, including PRE1, PIL1, HFR1, CDF5, and XTR7. Interestingly, our RNA-seq data also suggest that AHLs activate the expression of growth repressors to control hypocotyl elongation, such as HY5 and IAA17. Notably, many growth-regulating and other genes identified from the RNA-seq experiment were differentially regulated between these two sob3 mutants at the time points tested. Surprisingly, our ChIP-seq data suggest that SOB3 mostly binds to similar genes throughout the day. Collectively, these data suggest that AHLs affect gene expression in a time point-specific manner irrespective of changes in binding to DNA throughout SD.
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Affiliation(s)
- Caitlin N Jacques
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Crops and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
| | - David S Favero
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan.
| | - Ayako Kawamura
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Biosciences and Biotechnology, Chubu University, Kasugai, Aichi, 487-8501, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
- Department of Biological Sciences, The University of Tokyo, Tokyo, 119-0033, Japan
| | - Michael M Neff
- Department of Crops and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA.
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8
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Xu G, Guo H, Yan M, Jia Z, Li Z, Chen M, Bao X. An actin‐like protein
Po
ARP9
involves in the regulation of development and cellulase and amylase expression in
Penicillium oxalicum. J Appl Microbiol 2022; 132:2894-2905. [DOI: 10.1111/jam.15466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/28/2021] [Accepted: 01/23/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Gen Xu
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Hao Guo
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Mengdi Yan
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Zhilei Jia
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Zhonghai Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Mei Chen
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
| | - Xiaoming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, School of bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering Qilu University of Technology Shandong Academy of Sciences Jinan P. R. China
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9
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Balachandra VK, Ghosh SK. Emerging roles of SWI/SNF remodelers in fungal pathogens. Curr Genet 2022; 68:195-206. [PMID: 35001152 DOI: 10.1007/s00294-021-01219-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/20/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022]
Abstract
Fungal pathogens constantly sense and respond to the environment they inhabit, and this interaction is vital for their survival inside hosts and exhibiting pathogenic traits. Since such responses often entail specific patterns of gene expression, regulators of chromatin structure contribute to the fitness and virulence of the pathogens by modulating DNA accessibility to the transcriptional machinery. Recent studies in several human and plant fungal pathogens have uncovered the SWI/SNF group of chromatin remodelers as an important determinant of pathogenic traits and provided insights into their mechanism of function. Here, we review these studies and highlight the differential functions of these remodeling complexes and their subunits in regulating fungal fitness and pathogenicity. As an extension of our previous study, we also show that loss of specific RSC subunits can predispose the human fungal pathogen Candida albicans cells to filamentous growth in a context-dependent manner. Finally, we consider the potential of targeting the fungal SWI/SNF remodeling complexes for antifungal interventions.
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Affiliation(s)
- Vinutha K Balachandra
- IITB-Monash Research Academy, Indian Institute of Technology Bombay, Mumbai, India
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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10
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Morgan A, LeGresley S, Fischer C. Remodeler Catalyzed Nucleosome Repositioning: Influence of Structure and Stability. Int J Mol Sci 2020; 22:ijms22010076. [PMID: 33374740 PMCID: PMC7793527 DOI: 10.3390/ijms22010076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
The packaging of the eukaryotic genome into chromatin regulates the storage of genetic information, including the access of the cell’s DNA metabolism machinery. Indeed, since the processes of DNA replication, translation, and repair require access to the underlying DNA, several mechanisms, both active and passive, have evolved by which chromatin structure can be regulated and modified. One mechanism relies upon the function of chromatin remodeling enzymes which couple the free energy obtained from the binding and hydrolysis of ATP to the mechanical work of repositioning and rearranging nucleosomes. Here, we review recent work on the nucleosome mobilization activity of this essential family of molecular machines.
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11
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Schroeder CM, Valenzuela JR, Mejia Natividad I, Hocky GM, Malik HS. A Burst of Genetic Innovation in Drosophila Actin-Related Proteins for Testis-Specific Function. Mol Biol Evol 2020; 37:757-772. [PMID: 31697328 PMCID: PMC7038667 DOI: 10.1093/molbev/msz262] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Many cytoskeletal proteins perform fundamental biological processes and are evolutionarily ancient. For example, the superfamily of actin-related proteins (Arps) specialized early in eukaryotic evolution for diverse cellular roles in the cytoplasm and the nucleus. Despite its strict conservation across eukaryotes, we find that the Arp superfamily has undergone dramatic lineage-specific diversification in Drosophila. Our phylogenomic analyses reveal four independent Arp gene duplications that occurred in the common ancestor of the obscura group of Drosophila and have been mostly preserved in this lineage. All four obscura-specific Arp paralogs are predominantly expressed in the male germline and have evolved under positive selection. We focus our analyses on the divergent Arp2D paralog, which arose via a retroduplication event from Arp2, a component of the Arp2/3 complex that polymerizes branched actin networks. Computational modeling analyses suggest that Arp2D can replace Arp2 in the Arp2/3 complex and bind actin monomers. Together with the signature of positive selection, our findings suggest that Arp2D may augment Arp2's functions in the male germline. Indeed, we find that Arp2D is expressed during and following male meiosis, where it localizes to distinct locations such as actin cones-specialized cytoskeletal structures that separate bundled spermatids into individual mature sperm. We hypothesize that this unprecedented burst of genetic innovation in cytoskeletal proteins may have been driven by the evolution of sperm heteromorphism in the obscura group of Drosophila.
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Affiliation(s)
| | - John R Valenzuela
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Isabel Mejia Natividad
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA.,University of Puget Sound, Tacoma, WA
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, NY
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA
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12
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Willhoft O, Wigley DB. INO80 and SWR1 complexes: the non-identical twins of chromatin remodelling. Curr Opin Struct Biol 2020; 61:50-58. [PMID: 31838293 PMCID: PMC7171469 DOI: 10.1016/j.sbi.2019.09.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/07/2019] [Indexed: 02/06/2023]
Abstract
The INO80 family of chromatin remodellers are multisubunit complexes that perform a variety of tasks on nucleosomes. Family members are built around a heterohexamer of RuvB-like protein, an ATP-dependent DNA translocase,nuclear actin and actin-related proteins, and a few complex-specific subunits. They modify chromatin in a number of ways including nucleosome sliding and exchange of variant histones. Recent structural information on INO80 and SWR1 complexes has revealed similarities in the basic architecture of the complexes. However, structural and biochemical data on the complexes bound to nucleosomes reveal these similarities to be somewhat superficial and their biochemical activities and mechanisms are very different. Consequently, the INO80 family displays a surprising diversity of function that is based upon a similar structural framework.
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Affiliation(s)
- Oliver Willhoft
- Section of Structural and Synthetic Biology, Dept. Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Dale B Wigley
- Section of Structural and Synthetic Biology, Dept. Infectious Disease, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.
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13
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Nucleosome remodelling: structural insights into ATP-dependent remodelling enzymes. Essays Biochem 2019; 63:45-58. [PMID: 30967479 DOI: 10.1042/ebc20180059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/22/2022]
Abstract
ATP-dependent chromatin remodelling enzymes play a fundamental role in determining how nucleosomes are organised, and render DNA sequences accessible to interacting proteins, thereby enabling precise regulation of eukaryotic genes. Remodelers conserved from yeast to humans are classified into four families based on the domains and motifs present in their ATPase subunits. Insights into overall assembly and the mode of interaction to the nucleosome by these different families of remodelers remained limited due to the complexity of obtaining structural information on these challenging samples. Electron microscopy and single-particle methods have made advancement and uncovered vital structural information on the number of remodelling complexes. In this article, we highlight some of the recent structural work that advanced our understanding on the mechanisms and biological functions of these ATP-dependent remodelling machines.
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14
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Pillidge Z, Bray SJ. SWI/SNF chromatin remodeling controls Notch-responsive enhancer accessibility. EMBO Rep 2019; 20:embr.201846944. [PMID: 30914409 DOI: 10.15252/embr.201846944] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/18/2022] Open
Abstract
Notch signaling plays a key role in many cell fate decisions during development by directing different gene expression programs via the transcription factor CSL, known as Su(H) in Drosophila Which target genes are responsive to Notch signaling is influenced by the chromatin state of enhancers, yet how this is regulated is not fully known. Detecting a specific increase in the histone variant H3.3 in response to Notch signaling, we tested which chromatin remodelers or histone chaperones are required for the changes in enhancer accessibility to Su(H) binding. We show a crucial role for the Brahma SWI/SNF chromatin remodeling complex, including the actin-related BAP55 subunit, in conferring enhancer accessibility and enabling the transcriptional response to Notch activity. The Notch-responsive regions have high levels of nucleosome turnover which depend on the Brahma complex, increase in magnitude with Notch signaling, and primarily involve histone H3.3. Together these results highlight the importance of SWI/SNF-mediated nucleosome turnover in rendering enhancers responsive to Notch.
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Affiliation(s)
- Zoe Pillidge
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Sarah J Bray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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15
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Klages-Mundt NL, Kumar A, Zhang Y, Kapoor P, Shen X. The Nature of Actin-Family Proteins in Chromatin-Modifying Complexes. Front Genet 2018; 9:398. [PMID: 30319687 PMCID: PMC6167448 DOI: 10.3389/fgene.2018.00398] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/31/2018] [Indexed: 01/25/2023] Open
Abstract
Actin is not only one of the most abundant proteins in eukaryotic cells, but also one of the most versatile. In addition to its familiar involvement in enabling contraction and establishing cellular motility and scaffolding in the cytosol, actin has well-documented roles in a variety of processes within the confines of the nucleus, such as transcriptional regulation and DNA repair. Interestingly, monomeric actin as well as actin-related proteins (Arps) are found as stoichiometric subunits of a variety of chromatin remodeling complexes and histone acetyltransferases, raising the question of precisely what roles they serve in these contexts. Actin and Arps are present in unique combinations in chromatin modifiers, helping to establish structural integrity of the complex and enabling a wide range of functions, such as recruiting the complex to nucleosomes to facilitate chromatin remodeling and promoting ATPase activity of the catalytic subunit. Actin and Arps are also thought to help modulate chromatin dynamics and maintain higher-order chromatin structure. Moreover, the presence of actin and Arps in several chromatin modifiers is necessary for promoting genomic integrity and an effective DNA damage response. In this review, we discuss the involvement of actin and Arps in these nuclear complexes that control chromatin remodeling and histone modifications, while also considering avenues for future study to further shed light on their functional importance.
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Affiliation(s)
- Naeh L Klages-Mundt
- Science Park Research Division, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Ashok Kumar
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Yuexuan Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Prabodh Kapoor
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Xuetong Shen
- Science Park Research Division, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Program in Genetics & Epigenetics, The University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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16
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The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling. Nat Struct Mol Biol 2018; 25:823-832. [PMID: 30177756 DOI: 10.1038/s41594-018-0115-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2022]
Abstract
Nuclear actin (N-actin) and actin-related proteins (Arps) are critical components of several chromatin modulating complexes, including the chromatin remodeler INO80, but their function is largely elusive. Here, we report the crystal structure of the 180-kDa Arp8 module of Saccharomyces cerevisiae INO80 and establish its role in recognition of extranucleosomal linker DNA. Arp8 engages N-actin in a manner distinct from that of other actin-fold proteins and thereby specifies recruitment of the Arp4-N-actin heterodimer to a segmented scaffold of the helicase-SANT-associated (HSA) domain of Ino80. The helical HSA domain spans over 120 Å and provides an extended binding platform for extranucleosomal entry DNA that is required for nucleosome sliding and genome-wide nucleosome positioning. Together with the recent cryo-electron microscopy structure of INO80Core-nucleosome complex, our findings suggest an allosteric mechanism by which INO80 senses 40-bp linker DNA to conduct highly processive chromatin remodeling.
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17
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Sing TL, Hung MP, Ohnuki S, Suzuki G, San Luis BJ, McClain M, Unruh JR, Yu Z, Ou J, Marshall-Sheppard J, Huh WK, Costanzo M, Boone C, Ohya Y, Jaspersen SL, Brown GW. The budding yeast RSC complex maintains ploidy by promoting spindle pole body insertion. J Cell Biol 2018; 217:2445-2462. [PMID: 29875260 PMCID: PMC6028538 DOI: 10.1083/jcb.201709009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/13/2018] [Accepted: 05/09/2018] [Indexed: 01/31/2023] Open
Abstract
Ploidy is tightly regulated in eukaryotic cells and is critical for cell function and survival. Cells coordinate multiple pathways to ensure replicated DNA is segregated accurately to prevent abnormal changes in chromosome number. In this study, we characterize an unanticipated role for the Saccharomyces cerevisiae "remodels the structure of chromatin" (RSC) complex in ploidy maintenance. We show that deletion of any of six nonessential RSC genes causes a rapid transition from haploid to diploid DNA content because of nondisjunction events. Diploidization is accompanied by diagnostic changes in cell morphology and is stably maintained without further ploidy increases. We find that RSC promotes chromosome segregation by facilitating spindle pole body (SPB) duplication. More specifically, RSC plays a role in distributing two SPB insertion factors, Nbp1 and Ndc1, to the new SPB. Thus, we provide insight into a role for a SWI/SNF family complex in SPB duplication and ploidy maintenance.
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Affiliation(s)
- Tina L Sing
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Minnie P Hung
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Godai Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Bryan-Joseph San Luis
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO
| | - Jiongwen Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jesse Marshall-Sheppard
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Won-Ki Huh
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Molecular and Integrative Physiology, University of Kansas Medical Centre, Kansas City, KS
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
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18
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Actin-related proteins regulate the RSC chromatin remodeler by weakening intramolecular interactions of the Sth1 ATPase. Commun Biol 2018; 1:1. [PMID: 29809203 PMCID: PMC5969521 DOI: 10.1038/s42003-017-0002-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The catalytic subunits of SWI/SNF-family and INO80-family chromatin remodelers bind actin and actin-related proteins (Arps) through an N-terminal helicase/SANT-associated (HSA) domain. Between the HSA and ATPase domains lies a conserved post-HSA (pHSA) domain. The HSA domain of Sth1, the catalytic subunit of the yeast SWI/SNF-family remodeler RSC, recruits the Rtt102-Arp7/9 heterotrimer. Rtt102-Arp7/9 regulates RSC function, but the mechanism is unclear. We show that the pHSA domain interacts directly with another conserved region of the catalytic subunit, protrusion-1. Rtt102-Arp7/9 binding to the HSA domain weakens this interaction and promotes the formation of stable, monodisperse complexes with DNA and nucleosomes. A crystal structure of Rtt102-Arp7/9 shows that ATP binds to Arp7 but not Arp9. However, Arp7 does not hydrolyze ATP. Together, the results suggest that Rtt102 and ATP stabilize a conformation of Arp7/9 that potentiates binding to the HSA domain, which releases intramolecular interactions within Sth1 and controls DNA and nucleosome binding. Bengi Turegun et al. report an interaction of the highly-conserved pHSA and P1 domains of Sth1, the catalytic subunit of the SWI/SNF-family chromatin remodeler RSC. This interaction is released when ATP-bound Rtt102-Arp7/9 binds to the HSA domain, modulating DNA and nucleosome binding by Sth.
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19
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Ojolo SP, Cao S, Priyadarshani SVGN, Li W, Yan M, Aslam M, Zhao H, Qin Y. Regulation of Plant Growth and Development: A Review From a Chromatin Remodeling Perspective. FRONTIERS IN PLANT SCIENCE 2018; 9:1232. [PMID: 30186301 PMCID: PMC6113404 DOI: 10.3389/fpls.2018.01232] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 08/03/2018] [Indexed: 05/04/2023]
Abstract
In eukaryotes, genetic material is packaged into a dynamic but stable nucleoprotein structure called chromatin. Post-translational modification of chromatin domains affects the expression of underlying genes and subsequently the identity of cells by conveying epigenetic information from mother to daughter cells. SWI/SNF chromatin remodelers are ATP-dependent complexes that modulate core histone protein polypeptides, incorporate variant histone species and modify nucleotides in DNA strands within the nucleosome. The present review discusses the SWI/SNF chromatin remodeler family, its classification and recent advancements. We also address the involvement of SWI/SNF remodelers in regulating vital plant growth and development processes such as meristem establishment and maintenance, cell differentiation, organ initiation, flower morphogenesis and flowering time regulation. Moreover, the role of chromatin remodelers in key phytohormone signaling pathways is also reviewed. The information provided in this review may prompt further debate and investigations aimed at understanding plant-specific epigenetic regulation mediated by chromatin remodeling under continuously varying plant growth conditions and global climate change.
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Affiliation(s)
- Simon P. Ojolo
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijiang Cao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - S. V. G. N. Priyadarshani
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weimin Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Yuan Qin, ;
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20
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The Genomic Landscape of the Fungus-Specific SWI/SNF Complex Subunit, Snf6, in Candida albicans. mSphere 2017; 2:mSphere00497-17. [PMID: 29152582 PMCID: PMC5687922 DOI: 10.1128/msphere.00497-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 12/14/2022] Open
Abstract
SWI/SNF is an ATP-dependent chromatin-remodeling complex that is required for the regulation of gene expression in eukaryotes. While most of the fungal SWI/SNF components are evolutionarily conserved with those of the metazoan SWI/SNF, subunits such as Snf6 are specific to certain fungi and thus represent potential antifungal targets. We have characterized the role of the Snf6 protein in Candida albicans. Our data showed that although there was low conservation of its protein sequence with other fungal orthologs, Snf6 was copurified with bona fide SWI/SNF complex subunits. The role of Snf6 in C. albicans was investigated by determining its genome-wide occupancy using chromatin immunoprecipitation coupled to tiling arrays in addition to transcriptional profiling of the snf6 conditional mutant. Snf6 directs targets that were enriched in functions related to carbohydrate and amino acid metabolic circuits, to cellular transport, and to heat stress responses. Under hypha-promoting conditions, Snf6 expanded its set of targets to include promoters of genes related to respiration, ribosome biogenesis, mating, and vesicle transport. In accordance with the genomic occupancy data, an snf6 doxycycline-repressible mutant exhibited growth defects in response to heat stress and also when grown in the presence of different fermentable and nonfermentable carbon sources. Snf6 was also required to differentiate invasive hyphae in response to different cues. This study represents the first comprehensive characterization, at the genomic level, of the role of SWI/SNF in the pathogenic yeast C. albicans and uncovers functions that are essential for fungal morphogenesis and metabolic flexibility. IMPORTANCECandida albicans is a natural component of the human microbiota but also an opportunistic pathogen that causes life-threatening infections in immunosuppressed patients. Current therapeutics include a limited number of molecules that suffer from limitations, including growing clinical resistance and toxicity. New molecules are being clinically investigated; however, the majority of these potential antifungals target the same processes as do the standard antifungals and might confront the same problems of toxicity and loss of efficiency due to the common resistance mechanisms. Here, we characterized the role of Snf6, a fungus-specific subunit of the chromatin-remodeling complex SWI/SNF. Our genomic and phenotypic data demonstrated a central role of Snf6 in biological processes that are critical for a fungal pathogen to colonize its host and cause disease, suggesting Snf6 as a possible antifungal target.
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21
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Helmlinger D, Tora L. Sharing the SAGA. Trends Biochem Sci 2017; 42:850-861. [PMID: 28964624 PMCID: PMC5660625 DOI: 10.1016/j.tibs.2017.09.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/30/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022]
Abstract
Transcription initiation is a major regulatory step in eukaryotic gene expression. Co-activators establish transcriptionally competent promoter architectures and chromatin signatures to allow the formation of the pre-initiation complex (PIC), comprising RNA polymerase II (Pol II) and general transcription factors (GTFs). Many GTFs and co-activators are multisubunit complexes, in which individual components are organized into functional modules carrying specific activities. Recent advances in affinity purification and mass spectrometry analyses have revealed that these complexes often share functional modules, rather than containing unique components. This observation appears remarkably prevalent for chromatin-modifying and remodeling complexes. Here, we use the modular organization of the evolutionary conserved Spt-Ada-Gcn5 acetyltransferase (SAGA) complex as a paradigm to illustrate how co-activators share and combine a relatively limited set of functional tools.
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Affiliation(s)
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France.
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22
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Clapier CR, Kasten MM, Parnell TJ, Viswanathan R, Szerlong H, Sirinakis G, Zhang Y, Cairns BR. Regulation of DNA Translocation Efficiency within the Chromatin Remodeler RSC/Sth1 Potentiates Nucleosome Sliding and Ejection. Mol Cell 2017; 62:453-461. [PMID: 27153540 DOI: 10.1016/j.molcel.2016.03.032] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 01/29/2016] [Accepted: 03/30/2016] [Indexed: 11/30/2022]
Abstract
The RSC chromatin remodeler slides and ejects nucleosomes, utilizing a catalytic subunit (Sth1) with DNA translocation activity, which can pump DNA around the nucleosome. A central question is whether and how DNA translocation is regulated to achieve sliding versus ejection. Here, we report the regulation of DNA translocation efficiency by two domains residing on Sth1 (Post-HSA and Protrusion 1) and by actin-related proteins (ARPs) that bind Sth1. ARPs facilitated sliding and ejection by improving "coupling"-the amount of DNA translocation by Sth1 relative to ATP hydrolysis. We also identified and characterized Protrusion 1 mutations that promote "coupling," and Post-HSA mutations that improve ATP hydrolysis; notably, the strongest mutations conferred efficient nucleosome ejection without ARPs. Taken together, sliding-to-ejection involves a continuum of DNA translocation efficiency, consistent with higher magnitudes of ATPase and coupling activities (involving ARPs and Sth1 domains), enabling the simultaneous rupture of multiple histone-DNA contacts facilitating ejection.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Margaret M Kasten
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Timothy J Parnell
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Ramya Viswanathan
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Heather Szerlong
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - George Sirinakis
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Bradley R Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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23
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Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2017; 7:2219-2226. [PMID: 28584079 PMCID: PMC5499129 DOI: 10.1534/g3.117.040022] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The yeast Saccharomyces cerevisiae has emerged as a superior model organism. Selection of distinct laboratory strains of S. cerevisiae with unique phenotypic properties, such as superior mating or sporulation efficiencies, has facilitated advancements in research. W303 is one such laboratory strain that is closely related to the first completely sequenced yeast strain, S288C. In this work, we provide a high-quality, annotated genome sequence for W303 for utilization in comparative analyses and genome-wide studies. Approximately 9500 variations exist between S288C and W303, affecting the protein sequences of ∼700 genes. A listing of the polymorphisms and divergent genes is provided for researchers interested in identifying the genetic basis for phenotypic differences between W303 and S288C. Several divergent functional gene families were identified, including flocculation and sporulation genes, likely representing selection for desirable laboratory phenotypes. Interestingly, remnants of ancestor wine strains were found on several chromosomes. Finally, as a test of the utility of the high-quality reference genome, variant mapping revealed more accurate identification of accumulated mutations in passaged mismatch repair-defective strains.
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Hodges C, Kirkland JG, Crabtree GR. The Many Roles of BAF (mSWI/SNF) and PBAF Complexes in Cancer. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026930. [PMID: 27413115 DOI: 10.1101/cshperspect.a026930] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During the last decade, a host of epigenetic mechanisms were found to contribute to cancer and other human diseases. Several genomic studies have revealed that ∼20% of malignancies have alterations of the subunits of polymorphic BRG-/BRM-associated factor (BAF) and Polybromo-associated BAF (PBAF) complexes, making them among the most frequently mutated complexes in cancer. Recurrent mutations arise in genes encoding several BAF/PBAF subunits, including ARID1A, ARID2, PBRM1, SMARCA4, and SMARCB1 These subunits share some degree of conservation with subunits from related adenosine triphosphate (ATP)-dependent chromatin remodeling complexes in model organisms, in which a large body of work provides insight into their roles in cancer. Here, we review the roles of BAF- and PBAF-like complexes in these organisms, and relate these findings to recent discoveries in cancer epigenomics. We review several roles of BAF and PBAF complexes in cancer, including transcriptional regulation, DNA repair, and regulation of chromatin architecture and topology. More recent results highlight the need for new techniques to study these complexes.
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Affiliation(s)
- Courtney Hodges
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Jacob G Kirkland
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Gerald R Crabtree
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
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25
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Actin, actin-binding proteins, and actin-related proteins in the nucleus. Histochem Cell Biol 2016; 145:373-88. [PMID: 26847179 DOI: 10.1007/s00418-015-1400-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2015] [Indexed: 10/25/2022]
Abstract
Extensive research in the past decade has significantly broadened our view about the role actin plays in the life of the cell and added novel aspects to actin research. One of these new aspects is the discovery of the existence of nuclear actin which became evident only recently. Nuclear activities including transcriptional activation in the case of all three RNA polymerases, editing and nuclear export of mRNAs, and chromatin remodeling all depend on actin. It also became clear that there is a fine-tuned equilibrium between cytoplasmic and nuclear actin pools and that this balance is ensured by an export-import system dedicated to actin. After over half a century of research on conventional actin and its organizing partners in the cytoplasm, it was also an unexpected finding that the nucleus contains more than 30 actin-binding proteins and new classes of actin-related proteins which are not able to form filaments but had evolved nuclear-specific functions. The actin-binding and actin-related proteins in the nucleus have been linked to RNA transcription and processing, nuclear transport, and chromatin remodeling. In this paper, we attempt to provide an overview of the wide range of information that is now available about actin, actin-binding, and actin-related proteins in the nucleus.
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26
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Nakazawa T, Ando Y, Hata T, Nakahori K. A mutation in the Cc.arp9 gene encoding a putative actin-related protein causes defects in fruiting initiation and asexual development in the agaricomycete Coprinopsis cinerea. Curr Genet 2016; 62:565-74. [DOI: 10.1007/s00294-015-0560-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 12/21/2015] [Accepted: 12/24/2015] [Indexed: 12/27/2022]
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27
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Kapoor P, Bao Y, Xiao J, Luo J, Shen J, Persinger J, Peng G, Ranish J, Bartholomew B, Shen X. Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex. Genes Dev 2015; 29:591-602. [PMID: 25792597 PMCID: PMC4378192 DOI: 10.1101/gad.257626.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Kapoor et al. found that the SWI/SNF chromatin remodeling complex is capable of regulating the activity of S. cerevisiae checkpoint kinase Mec1. SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dbp11. The subunit requirement of SWI/SNF-mediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. These findings suggest that ATP-dependent chromatin remodeling complexes can regulate non-chromatin substrates such as a checkpoint kinase. ATP-dependent chromatin remodeling complexes alter chromatin structure through interactions with chromatin substrates such as DNA, histones, and nucleosomes. However, whether chromatin remodeling complexes have the ability to regulate nonchromatin substrates remains unclear. Saccharomyces cerevisiae checkpoint kinase Mec1 (ATR in mammals) is an essential master regulator of genomic integrity. Here we found that the SWI/SNF chromatin remodeling complex is capable of regulating Mec1 kinase activity. In vivo, Mec1 activity is reduced by the deletion of Snf2, the core ATPase subunit of the SWI/SNF complex. SWI/SNF interacts with Mec1, and cross-linking studies revealed that the Snf2 ATPase is the main interaction partner for Mec1. In vitro, SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dpb11. The subunit requirement of SWI/SNF-mediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. Functionally, SWI/SNF-mediated Mec1 regulation specifically occurs in S phase of the cell cycle. Together, these findings identify a novel regulator of Mec1 kinase activity and suggest that ATP-dependent chromatin remodeling complexes can regulate nonchromatin substrates such as a checkpoint kinase.
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Affiliation(s)
- Prabodh Kapoor
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Yunhe Bao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Jing Xiao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, Washington 98109, USA
| | - Jianfeng Shen
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jim Persinger
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jeff Ranish
- Institute for Systems Biology, Seattle, Washington 98109, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Xuetong Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA;
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28
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D'Orso I. Mechanisms of eukaryotic transcription: A meeting report. Transcription 2014. [DOI: 10.4161/trns.27094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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29
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Gerhold CB, Gasser SM. INO80 and SWR complexes: relating structure to function in chromatin remodeling. Trends Cell Biol 2014; 24:619-31. [PMID: 25088669 DOI: 10.1016/j.tcb.2014.06.004] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 02/04/2023]
Abstract
Virtually all DNA-dependent processes require selective and controlled access to the DNA sequence. Governing this access are sophisticated molecular machines, nucleosome remodelers, which regulate the composition and structure of chromatin, allowing conversion from open to closed states. In most cases these multisubunit remodelers operate in concert to organize chromatin structure by depositing, moving, evicting, or selectively altering nucleosomes in an ATP-dependent manner. Despite sharing a conserved domain architecture, chromatin remodelers differ significantly in how they bind to their nucleosomal substrates. Recent structural studies link specific interactions between nucleosomes and remodelers to the diverse tasks they carry out. We review here insights into the modular organization of the INO80 family of nucleosome remodelers. Understanding their structural diversity will help to shed light on how these related ATPases modify their nucleosomal substrates.
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Affiliation(s)
- Christian B Gerhold
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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30
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Al-Ani G, Briggs K, Malik SS, Conner M, Azuma Y, Fischer CJ. Quantitative determination of binding of ISWI to nucleosomes and DNA shows allosteric regulation of DNA binding by nucleotides. Biochemistry 2014; 53:4334-45. [PMID: 24898734 PMCID: PMC4100786 DOI: 10.1021/bi500224t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The
regulation of chromatin structure is controlled by a family
of molecular motors called chromatin remodelers. The ability of these
enzymes to remodel chromatin structure is dependent on their ability
to couple ATP binding and hydrolysis into the mechanical work that
drives nucleosome repositioning. The necessary first step in determining
how these essential enzymes perform this function is to characterize
both how they bind nucleosomes and how this interaction is regulated
by ATP binding and hydrolysis. With this goal in mind, we monitored
the interaction of the chromatin remodeler ISWI with fluorophore-labeled
nucleosomes and DNA through associated changes in fluorescence anisotropy
of the fluorophore upon binding of ISWI to these substrates. We determined
that one ISWI molecule binds to a 20 bp double-stranded DNA substrate
with an affinity of 18 ± 2 nM. In contrast, two ISWI molecules
can bind to the core nucleosome with short linker DNA with stoichiometric
macroscopic equilibrium constants: 1/β1 = 1.3 ±
0.6 nM, and 1/β2 = 13 ± 7 nM2. Furthermore,
to improve our understanding of the mechanism of DNA translocation
by ISWI, and hence nucleosome repositioning, we determined the effect
of nucleotide analogues on substrate binding by ISWI. While the affinity
of ISWI for the nucleosome substrate with short lengths of flanking
DNA was not affected by the presence of nucleotides, the affinity
of ISWI for the DNA substrate is weakened in the presence of nonhydrolyzable
ATP analogues but not by ADP.
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Affiliation(s)
- Gada Al-Ani
- Department of Molecular Biosciences, University of Kansas , 2034 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, Kansas 66045, United States
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31
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Prescott TAK, Rigby LP, Veitch NC, Simmonds MSJ. The haploinsufficiency profile of α-hederin suggests a caspofungin-like antifungal mode of action. PHYTOCHEMISTRY 2014; 101:116-120. [PMID: 24569176 DOI: 10.1016/j.phytochem.2014.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 06/03/2023]
Abstract
The leaves of common ivy (Hedera helix) contain the cytotoxic saponin α-hederin, which is inhibitory to Candida albicans at low concentrations. To investigate the mode of action of α-hederin, a haploinsufficiency screen was carried out using a library of 1152 Saccharomyces cerevisiae deletion strains. An ethanol ivy extract containing α-hederin was used in the initial screen to reduce the amount of compound required. Strains exhibiting disproportionately low growth were then examined in more detail by comparing growth curves in the presence and absence of α-hederin. This approach identified three hypersensitive strains carrying gene deletions for components of the transcription related proteins SWI/SNF, RNA polymerase II and the RSC complex. Saponin cytotoxicity is often attributed to membrane damage, however α-hederin did not induce hypersensitivity with an aminophospholipid translocase deletion strain that is frequently hypersensitive to membrane damaging agents. The haploinsufficiency profile of α-hederin is most similar to that reported for drugs such as caspofungin that inhibit synthesis of the fungal cell wall. Screening with plant extracts rather than isolated compounds, provides a valuable shortcut in haploinsufficiency screening provided hypersensitive strains are then confirmed as such using purified active principles.
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Affiliation(s)
| | - Luke P Rigby
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Nigel C Veitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
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32
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Abstract
A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).
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Affiliation(s)
- Blaine Bartholomew
- University of Texas MD Anderson Cancer Center, Department of Molecular Carcinogenesis, Smithville, Texas 78957;
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33
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Lobsiger J, Hunziker Y, Richmond TJ. Structure of the full-length yeast Arp7-Arp9 heterodimer. ACTA ACUST UNITED AC 2014; 70:310-6. [PMID: 24531465 DOI: 10.1107/s1399004713027417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 10/06/2013] [Indexed: 11/11/2022]
Abstract
The nuclear actin-related proteins Arp7 and Arp9 are components of the yeast SWI/SNF and RSC chromatin-remodelling complexes. The 3.1 Å resolution crystal structure reported here shows that the full-length Arp7 and Arp9 proteins exist as a dimer without a requirement for additional polypeptides. Of the 11 actin-related proteins, Arp7 and Arp9 are the only two directly demonstrated to form a dimer within this family. The Arp7-Arp9 heterodimer is unlikely to form an actin-like filament based on modelling using the structure. The Arp7-Arp9 structure reveals that its dimerization interface is not altered when bound in a complex with the SWI/SNF Snf2 HSA domain and the regulatory protein Rtt102.
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Affiliation(s)
- Joel Lobsiger
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Schafmattstrasse 20, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Yvonne Hunziker
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Schafmattstrasse 20, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Timothy J Richmond
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Schafmattstrasse 20, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
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34
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Turegun B, Kast DJ, Dominguez R. Subunit Rtt102 controls the conformation of the Arp7/9 heterodimer and its interactions with nucleotide and the catalytic subunit of SWI/SNF remodelers. J Biol Chem 2013; 288:35758-68. [PMID: 24189066 DOI: 10.1074/jbc.m113.514083] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromatin-remodeling complexes are assembled around a catalytic subunit that contains a central ATPase domain and flanking sequences that recruit auxiliary subunits. The catalytic subunits of SWI/SNF remodelers recruit Arp7/9 through a helicase/SANT-associated (HSA) domain N-terminal to the ATPase domain. Arp7/9-containing remodelers also carry the auxiliary subunit Rtt102, but the role of this subunit is poorly understood. Here, we show that Rtt102 binds with nanomolar affinity to the Arp7/9 heterodimer and modulates its conformation and interactions with the ATPase subunit and nucleotide. When bound to Rtt102, Arp7/9 interacts with a shorter segment of the HSA domain. Structural analysis by small-angle x-ray scattering further shows that when bound to Rtt102, the complex of Arp7/9 with the catalytic subunit assumes a more stable compact conformation. We also found that Arp7, Arp9, and Arp7/9 interact very weakly with ATP, but Rtt102 promotes high-affinity ATP binding to a single site in the heterodimer. Collectively, the results establish a function for subunit Rtt102 as a stabilizing factor for the Arp7/9 heterodimer, enhancing its interaction with nucleotide and controlling the conformation of SWI/SNF remodelers in an Arp7/9-dependent manner.
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35
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Abstract
In the cytoplasm, actin filaments form crosslinked networks that enable eukaryotic cells to transport cargo, change shape, and move. Actin is also present in the nucleus but, in this compartment, its functions are more cryptic and controversial. If we distill the substantial literature on nuclear actin down to its essentials, we find four, recurring, and more-or-less independent, claims: (1) crosslinked networks of conventional actin filaments span the nucleus and help maintain its structure and organize its contents; (2) assembly or contraction of filaments regulates specific nuclear events; (3) actin monomers moonlight as subunits of chromatin remodeling complexes, independent of their ability to form filaments; and (4) modified actin monomers or oligomers, structurally distinct from canonical, cytoskeletal filaments, mediate nuclear events by unknown mechanisms. We discuss the evidence underlying these claims and as well as their strengths and weaknesses. Next, we describe our recent work, in which we built probes specific for nuclear actin and used them to describe the form and distribution of actin in somatic cell nuclei. Finally, we discuss how different forms of nuclear actin may play different roles in different cell types and physiological contexts.
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Affiliation(s)
- Brittany J Belin
- Cellular and Molecular Pharmacology; University of California; San Francisco, CA USA
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36
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Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler. Proc Natl Acad Sci U S A 2013; 110:3345-50. [PMID: 23401505 DOI: 10.1073/pnas.1215379110] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The packaging of DNA into nucleosomal structures limits access for templated processes such as transcription and DNA repair. The repositioning or ejection of nucleosomes is therefore critically important for regulated events, including gene expression. This activity is provided by chromatin remodeling complexes, or remodelers, which are typically large, multisubunit complexes that use an ATPase subunit to translocate the DNA. Many remodelers contain pairs or multimers of actin-related proteins (ARPs) that contact the helicase-SANT-associated (HSA) domain within the catalytic ATPase subunit and are thought to regulate ATPase activity. Here, we determined the structure of a four-protein subcomplex within the SWI/SNF remodeler that comprises the Snf2 HSA domain, Arp7, Arp9, and repressor of Ty1 transposition, gene 102 (Rtt102). Surprisingly, unlike characterized actin-actin associations, the two ARPs pack like spoons and straddle the HSA domain, which forms a 92-Å-long helix. The ARP-HSA interactions are reminiscent of contacts between actin and many binding partners and are quite different from those in the Arp2/3 complex. Rtt102 wraps around one side of the complex in a highly extended conformation that contacts both ARPs and therefore stabilizes the complex, yet functions to reduce by ∼2.4-fold the remodeling and ATPase activity of complexes containing the Snf2 ATPase domain. Thus, our structure provides a foundation for developing models of remodeler function, including mechanisms of coupling between ARPs and the ATPase translocation activity.
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37
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Eastlund A, Malik SS, Fischer CJ. Kinetic mechanism of DNA translocation by the RSC molecular motor. Arch Biochem Biophys 2013; 532:73-83. [PMID: 23399434 DOI: 10.1016/j.abb.2013.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/21/2013] [Accepted: 01/30/2013] [Indexed: 01/29/2023]
Abstract
ATP-dependent nucleosome repositioning by chromatin remodeling enzymes requires the translocation of these enzymes along the nucleosomal DNA. Using a fluorescence stopped-flow assay we monitored DNA translocation by a minimal RSC motor and through global analysis of these time courses we have determined that this motor has a macroscopic translocation rate of 2.9 bp/s with a step size of 1.24 bp. From the complementary quantitative analysis of the associated time courses of ATP consumption during DNA translocation we have determined that this motor has an efficiency of 3.0 ATP/bp, which is slightly less that the efficiency observed for several genetically related DNA helicases and which likely results from random pausing by the motor during translocation. Nevertheless, this motor is able to exert enough force during translocation to displace streptavidin from biotinylated DNA. Taken together these results are the necessary first step for quantifying both the role of DNA translocation in nucleosome repositioning by RSC and the efficiency at which RSC couples ATP binding and hydrolysis to nucleosome repositioning.
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Affiliation(s)
- Allen Eastlund
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, KS 66045, USA
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38
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Nair SS, Kumar R. Chromatin remodeling in cancer: a gateway to regulate gene transcription. Mol Oncol 2012; 6:611-9. [PMID: 23127546 PMCID: PMC3538127 DOI: 10.1016/j.molonc.2012.09.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 09/30/2012] [Indexed: 01/01/2023] Open
Abstract
Cancer cells are remarkably adaptive to diverse survival strategies, probably due to its ability to interpret signaling cues differently than the normal cells. It appears as if cancer cells are constantly sampling, selecting and adapting signaling pathways to favor its proliferation. This process of successful adaptive evolution eventually renders a retractile nature to therapeutic regimens, fueling to the process of cancer progression. Based on plethora of available information, it is now evident that multiple signaling pathways eventually converge, perhaps, in a tempo-spatial manner, onto DNA template-dependent dynamic processes. Considering the complexity and packaging of eukaryotic genome, this process involves energy-dependent sub-events mediated by chromatin remodelers. Chromatin remodeler proteins function as gatekeepers and constitute a major determinant of accessibility of accessory factors to nucleosome DNA, allowing a wide repertoire of biological functions. And thus, aberrant expression or epigenetic modulation of remodeler proteins confers a unique ability to cancer cells to reprogram its genome for the maintenance of oncogenic phenotypes. Cancer cells can uniquely select a multi-subunit remodeler proteome for oncogenic advantage. This review summarizes our current understanding and importance of remodeler and chromatin proteins in cancer biology and also highlights the paradoxical role of proteins with or without dual-regulator functions. It is our hope that an in-depth understanding of these events is likely to provide a next set of opportunities for novel strategies for targeted cancer therapeutics.
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Affiliation(s)
- Sujit S Nair
- Department of Biochemistry and Molecular Biology, The McCormick Genomic and Proteomic Center, The School of Medicine & Health Sciences, The George Washington University, Washington, DC 20037, USA
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39
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Abstract
The SWI/SNF chromatin remodeling complex changes the positions where nucleosomes are bound to DNA, exchanges out histone dimers, and disassembles nucleosomes. All of these activities depend on ATP hydrolysis by the catalytic subunit Snf2, containing a DNA-dependent ATPase domain. Here we examine the role of another domain in Snf2 called SnAC (Snf2 ATP coupling) that was shown previously to regulate the ATPase activity of SWI/SNF. We have found that SnAC has another function besides regulation of ATPase activity that is even more critical for nucleosome remodeling by SWI/SNF. We have found that deletion of the SnAC domain strongly uncouples ATP hydrolysis from nucleosome movement. Deletion of SnAC does not adversely affect the rate, processivity, or pulling force of SWI/SNF to translocate along free DNA in an ATP-dependent manner. The uncoupling of ATP hydrolysis from nucleosome movement is shown to be due to loss of SnAC binding to the histone surface of nucleosomes. While the SnAC domain targets both the ATPase domain and histones, the SnAC domain as a histone anchor plays a more critical role in remodeling because it is required to convert DNA translocation into nucleosome movement.
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40
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Gerhold CB, Winkler DD, Lakomek K, Seifert FU, Fenn S, Kessler B, Witte G, Luger K, Hopfner KP. Structure of Actin-related protein 8 and its contribution to nucleosome binding. Nucleic Acids Res 2012; 40:11036-46. [PMID: 22977180 PMCID: PMC3510490 DOI: 10.1093/nar/gks842] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/18/2012] [Accepted: 08/13/2012] [Indexed: 12/18/2022] Open
Abstract
Nuclear actin-related proteins (Arps) are subunits of several chromatin remodelers, but their molecular functions within these complexes are unclear. We report the crystal structure of the INO80 complex subunit Arp8 in its ATP-bound form. Human Arp8 has several insertions in the conserved actin fold that explain its inability to polymerize. Most remarkably, one insertion wraps over the active site cleft and appears to rigidify the domain architecture, while active site features shared with actin suggest an allosterically controlled ATPase activity. Quantitative binding studies with nucleosomes and histone complexes reveal that Arp8 and the Arp8-Arp4-actin-HSA sub-complex of INO80 strongly prefer nucleosomes and H3-H4 tetramers over H2A-H2B dimers, suggesting that Arp8 functions as a nucleosome recognition module. In contrast, Arp4 prefers free (H3-H4)(2) over nucleosomes and may serve remodelers through binding to (dis)assembly intermediates in the remodeling reaction.
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Affiliation(s)
- Christian B. Gerhold
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany, Department of Biochemistry and Molecular Biology Howard Hughes Medical Institute and Colorado State University, Fort Collins, CO 80523, USA and Center for Integrated Protein Sciences (CIPSM), Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Duane D. Winkler
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany, Department of Biochemistry and Molecular Biology Howard Hughes Medical Institute and Colorado State University, Fort Collins, CO 80523, USA and Center for Integrated Protein Sciences (CIPSM), Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Kristina Lakomek
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany, Department of Biochemistry and Molecular Biology Howard Hughes Medical Institute and Colorado State University, Fort Collins, CO 80523, USA and Center for Integrated Protein Sciences (CIPSM), Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Florian U. Seifert
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany, Department of Biochemistry and Molecular Biology Howard Hughes Medical Institute and Colorado State University, Fort Collins, CO 80523, USA and Center for Integrated Protein Sciences (CIPSM), Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Sebastian Fenn
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany, Department of Biochemistry and Molecular Biology Howard Hughes Medical Institute and Colorado State University, Fort Collins, CO 80523, USA and Center for Integrated Protein Sciences (CIPSM), Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Brigitte Kessler
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany, Department of Biochemistry and Molecular Biology Howard Hughes Medical Institute and Colorado State University, Fort Collins, CO 80523, USA and Center for Integrated Protein Sciences (CIPSM), Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Gregor Witte
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany, Department of Biochemistry and Molecular Biology Howard Hughes Medical Institute and Colorado State University, Fort Collins, CO 80523, USA and Center for Integrated Protein Sciences (CIPSM), Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Karolin Luger
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany, Department of Biochemistry and Molecular Biology Howard Hughes Medical Institute and Colorado State University, Fort Collins, CO 80523, USA and Center for Integrated Protein Sciences (CIPSM), Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry, Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany, Department of Biochemistry and Molecular Biology Howard Hughes Medical Institute and Colorado State University, Fort Collins, CO 80523, USA and Center for Integrated Protein Sciences (CIPSM), Gene Center of the Ludwig-Maximilians-University Munich, Feodor-Lynen-Str. 25, D-81377 Munich, Germany
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App C, Knop J, Mannherz HG, Hannappel E. Identification of interaction partners of β-thymosins: application of thymosin β4 labeled by transglutaminase. Ann N Y Acad Sci 2012; 1270:98-104. [PMID: 23050824 DOI: 10.1111/j.1749-6632.2012.06658.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this review, we identify potential interaction partners of the β-thymosin family. The proteins of this family are highly conserved peptides in mammals and yet only one intracellular (G-actin) and one cell-surface protein (β subunit of F(1) -F(0) ATP synthase) were identified as interaction partners of thymosin β4. Cross-linking experiments may be a possible approach to discover additional proteins that interact with the β-thymosin family. It has previously been shown that thymosin β4 can be labeled at its glutaminyl residues with various cadaverines using tissue transglutaminase. Here, we illuminate recent results and give an outlook on upcoming work in the field.
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Affiliation(s)
- Christine App
- Institute of Biochemistry, Friedrich Alexander University, Erlangen, Germany.
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Abstract
Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field.
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Nishimoto N, Watanabe M, Watanabe S, Sugimoto N, Yugawa T, Ikura T, Koiwai O, Kiyono T, Fujita M. Heterocomplex Formation by Arp4 and β-Actin Involved in Integrity of the Brg1 Chromatin Remodeling Complex. J Cell Sci 2012; 125:3870-82. [DOI: 10.1242/jcs.104349] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although nuclear actin and Arps (actin-related proteins) are often identified as components of multi-protein, chromatin-modifying enzyme complexes such as chromatin remodeling and histone acetyltransferase (HAT) complexes, their molecular functions still remain largely elusive. We have investigated the role of BAF53/human Arp4 in Brg1 chromatin remodeling complexes. Depletion of Arp4 by RNA interference impaired their integrity and accelerated degradation of Brg1, indicating a crucial role in maintenance, at least in certain human cell lines. We further found that Arp4 can form a heterocomplex with β-actin. Based on structural similarities between conventional actin and Arp4 and the assumption that actin-Arp4 binding might mimic actin-actin binding, we introduced a series of mutations in Arp4 by which interactions with β-actin might be impaired. Some of them indeed caused reduced binding to β-actin. Interestingly, such mutant Arp4 proteins also showed reduced incorporation into Brg1 complexes and interactions with c-myc-associated complexes as well as Tip60 HAT complexes were also impaired. Based on these findings, we propose that β-actin-Arp4 complex formation may be a crucial feature in some chromatin-modifying enzyme complexes like the Brg1 complex.
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Nucleocytoplasmic shuttling of cytoskeletal proteins: molecular mechanism and biological significance. Int J Cell Biol 2011; 2012:494902. [PMID: 22229032 PMCID: PMC3249633 DOI: 10.1155/2012/494902] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/03/2011] [Accepted: 10/06/2011] [Indexed: 01/04/2023] Open
Abstract
Various nuclear functional complexes contain cytoskeletal proteins as regulatory subunits; for example, nuclear actin participates in transcriptional complexes, and actin-related proteins are integral to chromatin remodeling complexes. Nuclear complexes such as these are involved in both basal and adaptive nuclear functions. In addition to nuclear import via classical nuclear transport pathways or passive diffusion, some large cytoskeletal proteins spontaneously migrate into the nucleus in a karyopherin-independent manner. The balance of nucleocytoplasmic distribution of such proteins can be altered by several factors, such as import versus export, or capture and release by complexes. The resulting accumulation or depletion of the nuclear populations thereby enhances or attenuates their nuclear functions. We propose that such molecular dynamics constitute a form of cytoskeleton-modulated regulation of nuclear functions which is mediated by the translocation of cytoskeletal components in and out of the nucleus.
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Malik SS, Rich E, Viswanathan R, Cairns BR, Fischer CJ. Allosteric interactions of DNA and nucleotides with S. cerevisiae RSC. Biochemistry 2011; 50:7881-90. [PMID: 21834590 DOI: 10.1021/bi200837b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RSC (remodel the structure of chromatin) is an essential chromatin remodeler of Saccharomyces cerevisiae that has been shown to have DNA translocase properties. We studied the DNA binding properties of a "trimeric minimal RSC" (RSCt) of the RSC chromatin remodeling complex and the effect of nucleotides on this interaction using fluorescence anisotropy. RSCt binds to 20 bp fluorescein-labeled double-stranded DNA with a K(d) of ∼100 nM. The affinity of RSCt for DNA is reduced in the presence of AMP-PNP and ADP in a concentration-dependent manner with the addition of AMP-PNP having more pronounced effect. These differences in the magnitude at which the binding of ADP and AMP-PNP affects the affinity of DNA binding by RSCt suggest that the physical movement of the enzyme along DNA begins between the binding of ATP and its subsequent hydrolysis. Furthermore, the fact that the highest affinity for DNA binding by RSCt occurs in the absence of bound nucleotide offers a mechanistic explanation for the apparent low processivity of DNA translocation by the enzyme.
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Affiliation(s)
- Shuja Shafi Malik
- Department of Physics and Astronomy, University of Kansas, 1251 Wescoe Hall Dr., 1082 Malott Hall, Lawrence, Kansas 66045, USA
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Spinoculation triggers dynamic actin and cofilin activity that facilitates HIV-1 infection of transformed and resting CD4 T cells. J Virol 2011; 85:9824-33. [PMID: 21795326 DOI: 10.1128/jvi.05170-11] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Centrifugal inoculation, or spinoculation, is widely used in virology research to enhance viral infection. However, the mechanism remained obscure. Using HIV-1 infection of human T cells as a model, we demonstrate that spinoculation triggers dynamic actin and cofilin activity, probably resulting from cellular responses to centrifugal stress. This actin activity also leads to the upregulation of the HIV-1 receptor and coreceptor, CD4 and CXCR4, enhancing viral binding and entry. We also demonstrate that an actin inhibitor, jasplakinolide, diminishes spin-mediated enhancement. In addition, small interfering RNA (siRNA) knockdown of LIMK1, a cofilin kinase, decreases the enhancement. These results suggest that spin-mediated enhancement cannot be explained simply by a virus-concentrating effect; rather, it is coupled with spin-induced cytoskeletal dynamics that promote receptor mobilization, viral entry, and postentry processes. Our results highlight the importance of cofilin and a dynamic cytoskeleton for the initiation of viral infection. Our results also indicate that caution needs to be taken in data interpretation when cells are spinoculated; some of the spin-induced cellular permissiveness may be beyond the natural capacity of an infecting virus.
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Niederacher G, Klopf E, Schüller C. Interplay of dynamic transcription and chromatin remodeling: lessons from yeast. Int J Mol Sci 2011; 12:4758-69. [PMID: 21954323 PMCID: PMC3179130 DOI: 10.3390/ijms12084758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/15/2011] [Accepted: 07/20/2011] [Indexed: 12/25/2022] Open
Abstract
Regulation of transcription involves dynamic rearrangements of chromatin structure. The budding yeast Saccharomyces cerevisiae has a variety of highly conserved factors necessary for these reconstructions. Chromatin remodelers, histone modifiers and histone chaperones directly associate to promoters and open reading frames of exposed genes and facilitate activation and repression of transcription. We compare two distinct patterns of induced transcription: Sustained transcribed genes switch to an activated state where they remain as long as the induction signal is present. In contrast, single pulsed transcribed genes show a quick and strong induction pulse resulting in high transcript levels followed by adaptation and repression to basal levels. We discuss intensively studied promoters and coding regions from both groups for their co-factor requirements during transcription. Interplay between chromatin restructuring factors and dynamic transcription is highly variable and locus dependent.
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Affiliation(s)
- Gerhard Niederacher
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, University of Vienna, 1030 Vienna, Austria; E-Mails: (G.N.); (E.K.)
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, UFT Campus Tulln, 3430 Tulln, Austria
| | - Eva Klopf
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, University of Vienna, 1030 Vienna, Austria; E-Mails: (G.N.); (E.K.)
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, UFT Campus Tulln, 3430 Tulln, Austria
| | - Christoph Schüller
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, University of Vienna, 1030 Vienna, Austria; E-Mails: (G.N.); (E.K.)
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, UFT Campus Tulln, 3430 Tulln, Austria
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +43-1-4277-52815; Fax: +43-1-4277-9528
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Chatterjee N, Sinha D, Lemma-Dechassa M, Tan S, Shogren-Knaak MA, Bartholomew B. Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms. Nucleic Acids Res 2011; 39:8378-91. [PMID: 21749977 PMCID: PMC3201869 DOI: 10.1093/nar/gkr535] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is a close relationship between histone acetylation and ATP-dependent chromatin remodeling that is not fully understood. We show that acetylation of histone H3 tails affects SWI/SNF (mating type switching/ sucrose non fermenting) and RSC (remodels structure of chromatin) remodeling in several distinct ways. Acetylation of the histone H3 N-terminal tail facilitated recruitment and nucleosome mobilization by the ATP-dependent chromatin remodelers SWI/SNF and RSC. Tetra-acetylated H3, but not tetra-acetylated H4 tails, increased the affinity of RSC and SWI/SNF for nucleosomes while also changing the subunits of SWI/SNF that interact with the H3 tail. The enhanced recruitment of SWI/SNF due to H3 acetylation is bromodomain dependent, but is not further enhanced by additional bromodomains found in RSC. The combined effect of H3 acetylation and transcription activators is greater than either separately which suggests they act in parallel to recruit SWI/SNF. Besides enhancing recruitment, H3 acetylation increased nucleosome mobilization and H2A/H2B displacement by RSC and SWI/SNF in a bromodomain dependent manner and to a lesser extent enhanced ATP hydrolysis independent of bromodomains. H3 and H4 acetylation did not stimulate disassembly of adjacent nucleosomes in short arrays by SWI/SNF or RSC. These data illustrate how histone acetylation modulates RSC and SWI/SNF function, and provide a mechanistic insight into their collaborative efforts to remodel chromatin.
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Affiliation(s)
- Nilanjana Chatterjee
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901-4413, USA
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Fenn S, Gerhold CB, Hopfner KP. Nuclear actin-related proteins take shape. BIOARCHITECTURE 2011; 1:192-195. [PMID: 22069513 DOI: 10.4161/bioa.1.4.17643] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 08/04/2011] [Indexed: 12/30/2022]
Abstract
The function of nuclear actin is poorly understood. It is known to be a discrete component of several chromatin-modifying complexes. Nevertheless, filamentous forms of actin are important for various nuclear processes as well. Nuclear actin is often associated with nuclear actin-related protein Arp4 and other actin-related proteins like Arp8 in the INO80 chromatin remodeler. We recently determined the crystal structure of S. cerevisiae Arp4 that explains why Arp4 is unable to form actin like filaments and shows that it is constitutively bound to an ATP nucleotide. More interestingly, in vitro activities of Arp4 and Arp8 seem to be directed towards stabilizing monomeric actin and to integrate it stoichiometrically into the INO80 complex. Based on this activity, we discuss possible roles of nuclear Arps in chromatin modifying complexes and in regulating more general aspects of nuclear actin dynamics.
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The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes. EMBO J 2011; 30:1277-88. [PMID: 21343911 DOI: 10.1038/emboj.2011.43] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 01/26/2011] [Indexed: 11/08/2022] Open
Abstract
Nucleosomes impede access to DNA. Therefore, nucleosome positioning is fundamental to genome regulation. Nevertheless, the molecular nucleosome positioning mechanisms are poorly understood. This is partly because in vitro reconstitution of in vivo-like nucleosome positions from purified components is mostly lacking, barring biochemical studies. Using a yeast extract in vitro reconstitution system that generates in vivo-like nucleosome patterns at S. cerevisiae loci, we find that the RSC chromatin remodelling enzyme is necessary for nucleosome positioning. This was previously suggested by genome-wide in vivo studies and is confirmed here in vivo for individual loci. Beyond the limitations of conditional mutants, we show biochemically that RSC functions directly, can be sufficient, but mostly relies on other factors to properly position nucleosomes. Strikingly, RSC could not be replaced by either the closely related SWI/SNF or the Isw2 remodelling enzyme. Thus, we pinpoint that nucleosome positioning specifically depends on the unique properties of the RSC complex.
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