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Pang N, Sun J, Che S, Yang N. Structural characterization of fungus-specific histone deacetylase Hos3 provides insights into developing selective inhibitors with antifungal activity. J Biol Chem 2022; 298:102068. [PMID: 35623387 PMCID: PMC9201020 DOI: 10.1016/j.jbc.2022.102068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/28/2022] Open
Abstract
Fungal infection has long been a chronic and even life-threatening problem for humans. The demand for new antifungal drugs has increased dramatically as fungal infections have continued to increase, yet no new classes of drugs have been approved for nearly 15 years due to either high toxicity or development of drug resistance. Thus, validating new drug targets, especially fungus-specific targets, may facilitate future drug design. Here, we report the crystal structure of yeast Hos3 (ScHos3), a fungus-specific histone deacetylase (HDAC) that plays an important role in the life span of fungi. As acetylation modifications are important to many aspects of fungal infection, the species specificity of Hos3 makes it an ideal target for the development of new antifungal drugs. In this study, we show that ScHos3 forms a functional homodimer in solution, and key residues for dimerization crucial for its deacetylation activity were identified. We used molecular dynamics simulation and structural comparison with mammalian hHDAC6 to determine unique features of the ScHos3 catalytic core. In addition, a small-molecule inhibitor with a preference for ScHos3 was identified through structure-based virtual screening and in vitro enzymatic assays. The structural information and regulatory interferences of ScHos3 reported here provide new insights for the design of selective inhibitors that target fungal HDAC with high efficiency and low toxicity or that have the potential to overcome the prevailing problem of drug resistance in combination therapy with other drugs.
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Affiliation(s)
- Ningning Pang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, China
| | - Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, China
| | - Shiyou Che
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, China; College of Chemistry, Tianjin Normal University, Tianjin, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, China.
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2
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Sauty SM, Shaban K, Yankulov K. Gene repression in S. cerevisiae-looking beyond Sir-dependent gene silencing. Curr Genet 2020; 67:3-17. [PMID: 33037902 DOI: 10.1007/s00294-020-01114-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 01/09/2023]
Abstract
Gene silencing by the SIR (Silent Information Region) family of proteins in S. cerevisiae has been extensively studied and has served as a founding paradigm for our general understanding of gene repression and its links to histone deacetylation and chromatin structure. In recent years, our understanding of other mechanisms of gene repression in S.cerevisiae was significantly advanced. In this review, we focus on such Sir-independent mechanisms of gene repression executed by various Histone Deacetylases (HDACs) and Histone Methyl Transferases (HMTs). We focus on the genes regulated by these enzymes and their known mechanisms of action. We describe the cooperation and redundancy between HDACs and HMTs, and their involvement in gene repression by non-coding RNAs or by their non-histone substrates. We also propose models of epigenetic transmission of the chromatin structures produced by these enzymes and discuss these in the context of gene repression phenomena in other organisms. These include the recycling of the epigenetic marks imposed by HMTs or the recycling of the complexes harboring HDACs.
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Affiliation(s)
- Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada.
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3
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Zimmermann A, Tadic J, Kainz K, Hofer SJ, Bauer MA, Carmona-Gutierrez D, Madeo F. Transcriptional and epigenetic control of regulated cell death in yeast. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 352:55-82. [PMID: 32334817 DOI: 10.1016/bs.ircmb.2019.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Unicellular organisms like yeast can undergo controlled demise in a manner that is partly reminiscent of mammalian cell death. This is true at the levels of both mechanistic and functional conservation. Yeast offers the combination of unparalleled genetic amenability and a comparatively simple biology to understand both the regulation and evolution of cell death. In this minireview, we address the capacity of the nucleus as a regulatory hub during yeast regulated cell death (RCD), which is becoming an increasingly central question in yeast RCD research. In particular, we explore and critically discuss the available data on stressors and signals that specifically impinge on the nucleus. Moreover, we also analyze the current knowledge on nuclear factors as well as on transcriptional control and epigenetic events that orchestrate yeast RCD. Altogether we conclude that the functional significance of the nucleus for yeast RCD in undisputable, but that further exploration beyond correlative work is necessary to disentangle the role of nuclear events in the regulatory network.
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Affiliation(s)
- Andreas Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Jelena Tadic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria; Division of Immunology and Pathophysiology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Sebastian J Hofer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - Maria A Bauer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | | | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria; BioTechMed Graz, Graz, Austria.
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4
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Gomar-Alba M, Mendoza M. Modulation of Cell Identity by Modification of Nuclear Pore Complexes. Front Genet 2020; 10:1301. [PMID: 31969901 PMCID: PMC6960265 DOI: 10.3389/fgene.2019.01301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/26/2019] [Indexed: 11/17/2022] Open
Abstract
Nuclear pore complexes (NPCs) are protein assemblies that form channels across the nuclear envelope to mediate communication between the nucleus and the cytoplasm. Additionally, NPCs interact with chromatin and influence the position and expression of multiple genes. Interestingly, the composition of NPCs can vary in different cell-types, tissues, and developmental states. Here, we review recent findings suggesting that modifications of NPC composition, including post-translational modifications, play an instructive role in cell fate establishment. In particular, we focus on the role of cell-specific NPC deacetylation in asymmetrically dividing budding yeast, which modulates transport-dependent and transport-independent NPC functions to determine the time of commitment to a new division cycle in daughter cells. By modulating protein localization and gene expression, NPCs are therefore emerging as central regulators of cell identity.
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Affiliation(s)
- Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Manuel Mendoza
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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5
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Mullis MN, Matsui T, Schell R, Foree R, Ehrenreich IM. The complex underpinnings of genetic background effects. Nat Commun 2018; 9:3548. [PMID: 30224702 PMCID: PMC6141565 DOI: 10.1038/s41467-018-06023-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 08/09/2018] [Indexed: 12/01/2022] Open
Abstract
Genetic interactions between mutations and standing polymorphisms can cause mutations to show distinct phenotypic effects in different individuals. To characterize the genetic architecture of these so-called background effects, we genotype 1411 wild-type and mutant yeast cross progeny and measure their growth in 10 environments. Using these data, we map 1086 interactions between segregating loci and 7 different gene knockouts. Each knockout exhibits between 73 and 543 interactions, with 89% of all interactions involving higher-order epistasis between a knockout and multiple loci. Identified loci interact with as few as one knockout and as many as all seven knockouts. In mutants, loci interacting with fewer and more knockouts tend to show enhanced and reduced phenotypic effects, respectively. Cross–environment analysis reveals that most interactions between the knockouts and segregating loci also involve the environment. These results illustrate the complicated interactions between mutations, standing polymorphisms, and the environment that cause background effects. Mutations often show distinct phenotypic effects across different genetic backgrounds. Here the authors describe the genetic basis of these so-called background effects using data on genotype and growth in 10 environments from 1411 segregants from a cross of two strains of budding yeast.
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Affiliation(s)
- Martin N Mullis
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
| | - Takeshi Matsui
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
| | - Rachel Schell
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Ryan Foree
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
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Kumar A, Sharma P, Gomar-Alba M, Shcheprova Z, Daulny A, Sanmartín T, Matucci I, Funaya C, Beato M, Mendoza M. Daughter-cell-specific modulation of nuclear pore complexes controls cell cycle entry during asymmetric division. Nat Cell Biol 2018. [PMID: 29531309 PMCID: PMC6029668 DOI: 10.1038/s41556-018-0056-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The acquisition of cellular identity is coupled to changes in the nuclear periphery and nuclear pore complexes (NPCs). Whether and how these changes determine cell fate remains unclear. We have uncovered a mechanism regulating NPC acetylation to direct cell fate after asymmetric division in budding yeast. The lysine deacetylase Hos3 associates specifically with daughter cell NPCs during mitosis to delay cell cycle entry (Start). Hos3-dependent deacetylation of nuclear basket and central channel nucleoporins establishes daughter cell-specific nuclear accumulation of the transcriptional repressor Whi5 during anaphase and perinuclear silencing of the CLN2 gene in the following G1 phase. Hos3-dependent coordination of both events restrains Start in daughter but not in mother cells. We propose that deacetylation modulates transport-dependent and -independent functions of NPCs, leading to differential cell cycle progression in mother and daughter cells. Similar mechanisms might regulate NPC functions in specific cell types and/or cell cycle stages in multicellular organisms.
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Affiliation(s)
- Arun Kumar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Priyanka Sharma
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mercè Gomar-Alba
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Zhanna Shcheprova
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anne Daulny
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Trinidad Sanmartín
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Irene Matucci
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Charlotta Funaya
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Manuel Mendoza
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France. .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France. .,Université de Strasbourg, Strasbourg, France.
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