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Asmamaw MD, He A, Zhang LR, Liu HM, Gao Y. Histone deacetylase complexes: Structure, regulation and function. Biochim Biophys Acta Rev Cancer 2024; 1879:189150. [PMID: 38971208 DOI: 10.1016/j.bbcan.2024.189150] [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: 12/15/2023] [Revised: 06/07/2024] [Accepted: 07/01/2024] [Indexed: 07/08/2024]
Abstract
Histone deacetylases (HDACs) are key epigenetic regulators, and transcriptional complexes with deacetylase function are among the epigenetic corepressor complexes in the nucleus that target the epigenome. HDAC-bearing corepressor complexes such as the Sin3 complex, NuRD complex, CoREST complex, and SMRT/NCoR complex are common in biological systems. These complexes activate the otherwise inactive HDACs in a solitary state. HDAC complexes play vital roles in the regulation of key biological processes such as transcription, replication, and DNA repair. Moreover, deregulated HDAC complex function is implicated in human diseases including cancer. Therapeutic strategies targeting HDAC complexes are being sought actively. Thus, illustration of the nature and composition of HDAC complexes is vital to understanding the molecular basis of their functions under physiologic and pathologic conditions, and for designing targeted therapies. This review presents key aspects of large multiprotein HDAC-bearing complexes including their structure, function, regulatory mechanisms, implication in disease development, and role in therapeutics.
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Affiliation(s)
- Moges Dessale Asmamaw
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Ang He
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China
| | - Li-Rong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory for Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
| | - Hong-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
| | - Ya Gao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan Province 450001, China.
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2
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Sowd GA, Stivison EA, Chapagain P, Hale AT, Poland JC, Rameh LE, Blind RD. IPMK regulates HDAC3 activity and histone H4 acetylation in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591660. [PMID: 38746349 PMCID: PMC11092501 DOI: 10.1101/2024.04.29.591660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Histone deacetylases (HDACs) repress transcription by catalyzing the removal of acetyl groups from histones. Class 1 HDACs are activated by inositol phosphate signaling molecules in vitro , but it is unclear if this regulation occurs in human cells. Inositol Polyphosphate Multikinase (IPMK) is required for production of inositol hexakisphosphate (IP6), pentakisphosphate (IP5) and certain tetrakisphosphate (IP4) species, all known activators of Class 1 HDACs in vitro . Here, we generated IPMK knockout (IKO) human U251 glioblastoma cells, which decreased cellular inositol phosphate levels and increased histone H4-acetylation by mass spectrometry. ChIP-seq showed IKO increased H4-acetylation at IKO-upregulated genes, but H4-acetylation was unchanged at IKO-downregulated genes, suggesting gene-specific responses to IPMK knockout. HDAC deacetylase enzyme activity was decreased in HDAC3 immunoprecipitates from IKO vs . wild-type cells, while deacetylase activity of other Class 1 HDACs had no detectable changes in activity. Wild-type IPMK expression in IKO cells fully rescued HDAC3 deacetylase activity, while kinase-dead IPMK expression had no effect. Further, the deficiency in HDAC3 activity in immunoprecipitates from IKO cells could be fully rescued by addition of synthesized IP4 (Ins(1,4,5,6)P4) to the enzyme assay, while control inositol had no effect. These data suggest that cellular IPMK-dependent inositol phosphates are required for full HDAC3 enzyme activity and proper histone H4-acetylation. Implications for targeting IPMK in HDAC3-dependent diseases are discussed.
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3
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Patel AB, He Y, Radhakrishnan I. Histone acetylation and deacetylation - Mechanistic insights from structural biology. Gene 2024; 890:147798. [PMID: 37726026 PMCID: PMC11253779 DOI: 10.1016/j.gene.2023.147798] [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: 07/10/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023]
Abstract
Histones are subject to a diverse array of post-translational modifications. Among them, lysine acetylation is not only the most pervasive and dynamic modification but also highly consequential for regulating gene transcription. Although enzymes responsible for the addition and removal of acetyl groups were discovered almost 30 years ago, high-resolution structures of the enzymes in the context of their native complexes are only now beginning to become available, thanks to revolutionary technologies in protein structure determination and prediction. Here, we will review our current understanding of the molecular mechanisms of acetylation and deacetylation engendered by chromatin-modifying complexes, compare and contrast shared features, and discuss some of the pressing questions for future studies.
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Affiliation(s)
- Avinash B Patel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Ishwar Radhakrishnan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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4
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Chen Y, Xu J, Liu X, Guo L, Yi P, Cheng C. Potential therapies targeting nuclear metabolic regulation in cancer. MedComm (Beijing) 2023; 4:e421. [PMID: 38034101 PMCID: PMC10685089 DOI: 10.1002/mco2.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/28/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023] Open
Abstract
The interplay between genetic alterations and metabolic dysregulation is increasingly recognized as a pivotal axis in cancer pathogenesis. Both elements are mutually reinforcing, thereby expediting the ontogeny and progression of malignant neoplasms. Intriguingly, recent findings have highlighted the translocation of metabolites and metabolic enzymes from the cytoplasm into the nuclear compartment, where they appear to be intimately associated with tumor cell proliferation. Despite these advancements, significant gaps persist in our understanding of their specific roles within the nuclear milieu, their modulatory effects on gene transcription and cellular proliferation, and the intricacies of their coordination with the genomic landscape. In this comprehensive review, we endeavor to elucidate the regulatory landscape of metabolic signaling within the nuclear domain, namely nuclear metabolic signaling involving metabolites and metabolic enzymes. We explore the roles and molecular mechanisms through which metabolic flux and enzymatic activity impact critical nuclear processes, including epigenetic modulation, DNA damage repair, and gene expression regulation. In conclusion, we underscore the paramount significance of nuclear metabolic signaling in cancer biology and enumerate potential therapeutic targets, associated pharmacological interventions, and implications for clinical applications. Importantly, these emergent findings not only augment our conceptual understanding of tumoral metabolism but also herald the potential for innovative therapeutic paradigms targeting the metabolism-genome transcriptional axis.
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Affiliation(s)
- Yanjie Chen
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Jie Xu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Xiaoyi Liu
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Linlin Guo
- Department of Microbiology and ImmunologyThe Indiana University School of MedicineIndianapolisIndianaUSA
| | - Ping Yi
- Department of Obstetrics and GynecologyThe Third Affiliated Hospital of Chongqing Medical UniversityChongqingChina
| | - Chunming Cheng
- Department of Radiation OncologyJames Comprehensive Cancer Center and College of Medicine at The Ohio State UniversityColumbusOhioUSA
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5
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Patel AB, Qing J, Tam KH, Zaman S, Luiso M, Radhakrishnan I, He Y. Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Nat Commun 2023; 14:3061. [PMID: 37244892 PMCID: PMC10224958 DOI: 10.1038/s41467-023-38687-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/11/2023] [Indexed: 05/29/2023] Open
Abstract
The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.
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Affiliation(s)
- Avinash B Patel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
| | - Jinkang Qing
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Kelly H Tam
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Sara Zaman
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Maria Luiso
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Ishwar Radhakrishnan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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Wan MSM, Muhammad R, Koliopoulos MG, Roumeliotis TI, Choudhary JS, Alfieri C. Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex. Nat Commun 2023; 14:2556. [PMID: 37137925 PMCID: PMC10156912 DOI: 10.1038/s41467-023-38276-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/22/2023] [Indexed: 05/05/2023] Open
Abstract
Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating the transcriptional output of each gene. Although these complexes are drug targets and crucial regulators of organismal physiology, their structure and mechanisms of action are largely unclear. Here, we present the structure of a complete human SIN3B histone deacetylase holo-complex with and without a substrate mimic. Remarkably, SIN3B encircles the deacetylase and contacts its allosteric basic patch thereby stimulating catalysis. A SIN3B loop inserts into the catalytic tunnel, rearranges to accommodate the acetyl-lysine moiety, and stabilises the substrate for specific deacetylation, which is guided by a substrate receptor subunit. Our findings provide a model of specificity for a main transcriptional regulator conserved from yeast to human and a resource of protein-protein interactions for future drug designs.
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Affiliation(s)
- Mandy S M Wan
- Division of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - Reyhan Muhammad
- Division of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - Marios G Koliopoulos
- Division of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics, Chester Beatty Laboratories, Cancer Biology Division, The Institute of Cancer Research, London, UK
| | - Jyoti S Choudhary
- Functional Proteomics, Chester Beatty Laboratories, Cancer Biology Division, The Institute of Cancer Research, London, UK
| | - Claudio Alfieri
- Division of Structural Biology, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK.
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7
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Zheng Y, Zong J, Liu J, Wang R, Chen J, Guo H, Kong W, Liu J, Chen Y. Mining for salt-tolerant genes from halophyte Zoysia matrella using FOX system and functional analysis of ZmGnTL. FRONTIERS IN PLANT SCIENCE 2022; 13:1063436. [PMID: 36466287 PMCID: PMC9714509 DOI: 10.3389/fpls.2022.1063436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Zoysia matrella is a salt-tolerant turfgrass grown in areas with high soil salinity irrigated with effluent water. Previous studies focused on explaining the regulatory mechanism of Z. matrella salt-tolerance at phenotypic and physiological levels. However, the molecular mechanism associated with salt tolerance of Z. matrella remained unclear. In this study, a high-efficient method named FOX (full-length cDNA overexpression) hunting system was used to search for salt-tolerant genes in Z. matrella. Eleven candidate genes, including several known or novel salt-tolerant genes involved in different metabolism pathways, were identified. These genes exhibited inducible expression under salt stress condition. Furthermore, a novel salt-inducible candidate gene ZmGnTL was transformed into Arabidopsis for functional analysis. ZmGnTL improved salt-tolerance through regulating ion homeostasis, reactive oxygen species scavenging, and osmotic adjustment. In summary, we demonstrated that FOX is a reliable system for discovering novel genes relevant to salt tolerance and several candidate genes were identified from Z. matrella that can assist molecular breeding for plant salt-tolerance improvement.
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Affiliation(s)
- Yuying Zheng
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Junqin Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jun Liu
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Ruying Wang
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Weiyi Kong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yu Chen
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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8
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Yazgili AS, Ebstein F, Meiners S. The Proteasome Activator PA200/PSME4: An Emerging New Player in Health and Disease. Biomolecules 2022; 12:1150. [PMID: 36009043 PMCID: PMC9406137 DOI: 10.3390/biom12081150] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022] Open
Abstract
Proteasomes comprise a family of proteasomal complexes essential for maintaining protein homeostasis. Accordingly, proteasomes represent promising therapeutic targets in multiple human diseases. Several proteasome inhibitors are approved for treating hematological cancers. However, their side effects impede their efficacy and broader therapeutic applications. Therefore, understanding the biology of the different proteasome complexes present in the cell is crucial for developing tailor-made inhibitors against specific proteasome complexes. Here, we will discuss the structure, biology, and function of the alternative Proteasome Activator 200 (PA200), also known as PSME4, and summarize the current evidence for its dysregulation in different human diseases. We hereby aim to stimulate research on this enigmatic proteasome regulator that has the potential to serve as a therapeutic target in cancer.
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Affiliation(s)
- Ayse Seda Yazgili
- Comprehensive Pneumology Center (CPC), Helmholtz Center Munich, Max-Lebsche Platz 31, 81377 Munich, Germany
| | - Frédéric Ebstein
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Klinikum DZ/7, 17475 Greifswald, Germany
| | - Silke Meiners
- Research Center Borstel/Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
- Airway Research Center North (ARCN), German Center for Lung Research (DZL), 23845 Sülfeld, Germany
- Institute of Experimental Medicine, Christian-Albrechts University Kiel, 24118 Kiel, Germany
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9
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Dunaway LS, Pollock JS. HDAC1: an environmental sensor regulating endothelial function. Cardiovasc Res 2022; 118:1885-1903. [PMID: 34264338 PMCID: PMC9239577 DOI: 10.1093/cvr/cvab198] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/22/2021] [Indexed: 12/12/2022] Open
Abstract
The histone deacetylases (HDACs) are a family of enzymes that catalyse lysine deacetylation of both histone and non-histone proteins. Here, we review, summarize, and provide perspectives on the literature regarding one such HDAC, HDAC1, in endothelial biology. In the endothelium, HDAC1 mediates the effects of external and environmental stimuli by regulating major endothelial functions such as angiogenesis, inflammatory signalling, redox homeostasis, and nitric oxide signalling. Angiogenesis is most often, but not exclusively, repressed by endothelial HDAC1. The regulation of inflammatory signalling is more complex as HDAC1 promotes or suppresses inflammatory signalling depending upon the environmental stimuli. HDAC1 is protective in models of atherosclerosis where loss of HDAC1 results in increased cytokine and cell adhesion molecule (CAM) abundance. In other models, HDAC1 promotes inflammation by increasing CAMs and repressing claudin-5 expression. Consistently, from many investigations, HDAC1 decreases antioxidant enzyme expression and nitric oxide production in the endothelium. HDAC1 decreases antioxidant enzyme expression through the deacetylation of histones and transcription factors, and also regulates nitric oxide production through regulating both the expression and activity of nitric oxide synthase 3. The HDAC1-dependent regulation of endothelial function through the deacetylation of both histone and non-histone proteins ultimately impacts whole animal physiology and health.
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Affiliation(s)
- Luke S Dunaway
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Kaul Genetics Building Room 802A, 720 20th Street South, Birmingham, AL 35233, USA
| | - Jennifer S Pollock
- Section of Cardio-Renal Physiology and Medicine, Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Kaul Genetics Building Room 802A, 720 20th Street South, Birmingham, AL 35233, USA
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10
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Reyes AA, Fishbain S, He Y. Structural and functional analysis of the SET3 histone deacetylase complex. Acta Crystallogr F Struct Biol Commun 2022; 78:113-118. [PMID: 35234136 PMCID: PMC8900736 DOI: 10.1107/s2053230x22000553] [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: 11/18/2021] [Accepted: 01/16/2022] [Indexed: 11/10/2022] Open
Abstract
The SET3 complex (SET3C) is a seven-subunit histone deacetylase complex that is capable of transcriptional regulation. Methylated histone 3 marks recruit SET3C to the nucleosome, and the SET3C catalytic subunits deacetylate the histone 3 and 4 tails. There is very limited structural knowledge of the SET3C subunits, with most subunits having unknown structures or functions. Here, a catalytically active SET3 complex was endogenously purified from Saccharomyces cerevisiae and utilized for negative-stain electron microscopy (EM) to determine an apo model for the holo complex. The negative-stain EM 3D model revealed a three-lobe architecture, with each lobe extending from a central point.
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Affiliation(s)
- Alexis A. Reyes
- Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
| | - Susan Fishbain
- Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
| | - Yuan He
- Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, Illinois, USA
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11
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Unconventional metabolites in chromatin regulation. Biosci Rep 2022; 42:230604. [PMID: 34988581 PMCID: PMC8777195 DOI: 10.1042/bsr20211558] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromatin, the complex of DNA and histone proteins, serves as a main integrator of cellular signals. Increasing evidence links cellular functional to chromatin state. Indeed, different metabolites are emerging as modulators of chromatin function and structure. Alterations in chromatin state are decisive for regulating all aspects of genome function and ultimately have the potential to produce phenotypic changes. Several metabolites such as acetyl-CoA, S-adenosylmethionine (SAM) or adenosine triphosphate (ATP) have now been well characterized as main substrates or cofactors of chromatin-modifying enzymes. However, there are other metabolites that can directly interact with chromatin influencing its state or that modulate the properties of chromatin regulatory factors. Also, there is a growing list of atypical enzymatic and nonenzymatic chromatin modifications that originate from different cellular pathways that have not been in the limelight of chromatin research. Here, we summarize different properties and functions of uncommon regulatory molecules originating from intermediate metabolism of lipids, carbohydrates and amino acids. Based on the various modes of action on chromatin and the plethora of putative, so far not described chromatin-regulating metabolites, we propose that there are more links between cellular functional state and chromatin regulation to be discovered. We hypothesize that these connections could provide interesting starting points for interfering with cellular epigenetic states at a molecular level.
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12
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Marcum RD, Hsieh J, Giljen M, Justice E, Daffern N, Zhang Y, Radhakrishnan I. A Capped Tudor Domain within a Core Subunit of the Sin3L/Rpd3L Histone Deacetylase Complex Binds to Nucleic Acid G-Quadruplexes. J Biol Chem 2021; 298:101558. [PMID: 34979096 PMCID: PMC8800102 DOI: 10.1016/j.jbc.2021.101558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 12/04/2022] Open
Abstract
Chromatin-modifying complexes containing histone deacetylase (HDAC) activities play critical roles in the regulation of gene transcription in eukaryotes. These complexes are thought to lack intrinsic DNA-binding activity, but according to a well-established paradigm, they are recruited via protein–protein interactions by gene-specific transcription factors and posttranslational histone modifications to their sites of action on the genome. The mammalian Sin3L/Rpd3L complex, comprising more than a dozen different polypeptides, is an ancient HDAC complex found in diverse eukaryotes. The subunits of this complex harbor conserved domains and motifs of unknown structure and function. Here, we show that Sds3, a constitutively-associated subunit critical for the proper functioning of the Sin3L/Rpd3L complex, harbors a type of Tudor domain that we designate the capped Tudor domain. Unlike canonical Tudor domains that bind modified histones, the Sds3 capped Tudor domain binds to nucleic acids that can form higher-order structures such as G-quadruplexes and shares similarities with the knotted Tudor domain of the Esa1 histone acetyltransferase that was previously shown to bind single-stranded RNA. Our findings expand the range of macromolecules capable of recruiting the Sin3L/Rpd3L complex and draw attention to potentially new biological roles for this HDAC complex.
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Affiliation(s)
- Ryan Dale Marcum
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500
| | - Joseph Hsieh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500
| | - Maksim Giljen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500
| | - Emily Justice
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500
| | - Nicolas Daffern
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500
| | - Yongbo Zhang
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500
| | - Ishwar Radhakrishnan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3500.
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13
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Banks CAS, Zhang Y, Miah S, Hao Y, Adams MK, Wen Z, Thornton JL, Florens L, Washburn MP. Integrative Modeling of a Sin3/HDAC Complex Sub-structure. Cell Rep 2021; 31:107516. [PMID: 32294434 PMCID: PMC7217224 DOI: 10.1016/j.celrep.2020.03.080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/12/2019] [Accepted: 03/23/2020] [Indexed: 12/26/2022] Open
Abstract
Sin3/HDAC complexes function by deacetylating histones, condensing chromatin, and modulating gene expression. Although components used to build these complexes have been well defined, we still have only a limited understanding of the structure of the Sin3/HDAC subunits assembled around the scaffolding protein SIN3A. To characterize the spatial arrangement of Sin3 subunits, we combined Halo affinity capture, chemical crosslinking, and high-resolution mass spectrometry (XL-MS) to determine intersubunit distance constraints, identifying 66 interprotein and 63 self-crosslinks for 13 Sin3 subunits. Having assessed crosslink authenticity by mapping self-crosslinks onto existing structures, we used distance restraints from interprotein crosslinks to guide assembly of a Sin3 complex substructure. We identified the relative positions of subunits SAP30L, HDAC1, SUDS3, HDAC2, and ING1 around the SIN3A scaffold. The architecture of this subassembly suggests that multiple factors have space to assemble to collectively influence the behavior of the catalytic subunit HDAC1. Banks et al. capture positional information for subunits within Sin3/HDAC complexes by combining crosslinking and high-resolution mass spectrometry. This information is then used to guide docking of Sin3 subunit structures to develop a model of a Sin3/HDAC complex sub-structure.
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Affiliation(s)
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sayem Miah
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Yan Hao
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Mark K Adams
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Zhihui Wen
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Janet L Thornton
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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Lev S, Bowring B, Desmarini D, Djordjevic JT. Inositol polyphosphate-protein interactions: Implications for microbial pathogenicity. Cell Microbiol 2021; 23:e13325. [PMID: 33721399 PMCID: PMC9286782 DOI: 10.1111/cmi.13325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/03/2021] [Accepted: 03/07/2021] [Indexed: 11/29/2022]
Abstract
Inositol polyphosphates (IPs) and inositol pyrophosphates (PP-IPs) regulate diverse cellular processes in eukaryotic cells. IPs and PP-IPs are highly negatively charged and exert their biological effects by interacting with specific protein targets. Studies performed predominantly in mammalian cells and model yeasts have shown that IPs and PP-IPs modulate target function through allosteric regulation, by promoting intra- and intermolecular stabilization and, in the case of PP-IPs, by donating a phosphate from their pyrophosphate (PP) group to the target protein. Technological advances in genetics have extended studies of IP function to microbial pathogens and demonstrated that disrupting PP-IP biosynthesis and PP-IP-protein interaction has a profound impact on pathogenicity. This review summarises the complexity of IP-mediated regulation in eukaryotes, including microbial pathogens. It also highlights examples of poor conservation of IP-protein interaction outcome despite the presence of conserved IP-binding domains in eukaryotic proteomes.
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Affiliation(s)
- Sophie Lev
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,Sydney Medical School-Westmead, University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
| | - Bethany Bowring
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,Sydney Medical School-Westmead, University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
| | - Desmarini Desmarini
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,Sydney Medical School-Westmead, University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
| | - Julianne Teresa Djordjevic
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.,Sydney Medical School-Westmead, University of Sydney, Sydney, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, New South Wales, Australia
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15
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Role of Inositols and Inositol Phosphates in Energy Metabolism. Molecules 2020; 25:molecules25215079. [PMID: 33139672 PMCID: PMC7663797 DOI: 10.3390/molecules25215079] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Recently, inositols, especially myo-inositol and inositol hexakisphosphate, also known as phytic acid or IP6, with their biological activities received much attention for their role in multiple health beneficial effects. Although their roles in cancer treatment and prevention have been extensively reported, interestingly, they may also have distinctive properties in energy metabolism and metabolic disorders. We review inositols and inositol phosphate metabolism in mammalian cells to establish their biological activities and highlight their potential roles in energy metabolism. These molecules are known to decrease insulin resistance, increase insulin sensitivity, and have diverse properties with importance from cell signaling to metabolism. Evidence showed that inositol phosphates might enhance the browning of white adipocytes and directly improve insulin sensitivity through adipocytes. In addition, inositol pyrophosphates containing high-energy phosphate bonds are considered in increasing cellular energetics. Despite all recent advances, many aspects of the bioactivity of inositol phosphates are still not clear, especially their effects on insulin resistance and alteration of metabolism, so more research is needed.
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16
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Werbeck ND, Shukla VK, Kunze MBA, Yalinca H, Pritchard RB, Siemons L, Mondal S, Greenwood SOR, Kirkpatrick J, Marson CM, Hansen DF. A distal regulatory region of a class I human histone deacetylase. Nat Commun 2020; 11:3841. [PMID: 32737323 PMCID: PMC7395746 DOI: 10.1038/s41467-020-17610-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/09/2020] [Indexed: 01/05/2023] Open
Abstract
Histone deacetylases (HDACs) are key enzymes in epigenetics and important drug targets in cancer biology. Whilst it has been established that HDACs regulate many cellular processes, far less is known about the regulation of these enzymes themselves. Here, we show that HDAC8 is allosterically regulated by shifts in populations between exchanging states. An inactive state is identified, which is stabilised by a range of mutations and resembles a sparsely-populated state in equilibrium with active HDAC8. Computational models show that the inactive and active states differ by small changes in a regulatory region that extends up to 28 Å from the active site. The regulatory allosteric region identified here in HDAC8 corresponds to regions in other class I HDACs known to bind regulators, thus suggesting a general mechanism. The presented results pave the way for the development of allosteric HDAC inhibitors and regulators to improve the therapy for several disease states.
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Affiliation(s)
- Nicolas D Werbeck
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
- Nuvisan ICB GmbH, Innovation Campus Berlin, Müllerstraße 178, 13353, Berlin, Germany
| | - Vaibhav Kumar Shukla
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Micha B A Kunze
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Havva Yalinca
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Ruth B Pritchard
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Lucas Siemons
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Somnath Mondal
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Simon O R Greenwood
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
- Department of Chemistry, University College London, London, WC1E 6BT, UK
| | - John Kirkpatrick
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Charles M Marson
- Department of Chemistry, University College London, London, WC1E 6BT, UK
| | - D Flemming Hansen
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, UK.
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17
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Samec M, Liskova A, Koklesova L, Mestanova V, Franekova M, Kassayova M, Bojkova B, Uramova S, Zubor P, Janikova K, Danko J, Samuel SM, Büsselberg D, Kubatka P. Fluctuations of Histone Chemical Modifications in Breast, Prostate, and Colorectal Cancer: An Implication of Phytochemicals as Defenders of Chromatin Equilibrium. Biomolecules 2019; 9:E829. [PMID: 31817446 PMCID: PMC6995638 DOI: 10.3390/biom9120829] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
Natural substances of plant origin exert health beneficiary efficacy due to the content of various phytochemicals. Significant anticancer abilities of natural compounds are mediated via various processes such as regulation of a cell's epigenome. The potential antineoplastic activity of plant natural substances mediated by their action on posttranslational histone modifications (PHMs) is currently a highly evaluated area of cancer research. PHMs play an important role in maintaining chromatin structure and regulating gene expression. Aberrations in PHMs are directly linked to the process of carcinogenesis in cancer such as breast (BC), prostate (PC), and colorectal (CRC) cancer, common malignant diseases in terms of incidence and mortality among both men and women. This review summarizes the effects of plant phytochemicals (isolated or mixtures) on cancer-associated PHMs (mainly modulation of acetylation and methylation) resulting in alterations of chromatin structure that are related to the regulation of transcription activity of specific oncogenes, which are crucial in the development of BC, PC, and CRC. Significant effectiveness of natural compounds in the modulation of aberrant PHMs were confirmed by a number of in vitro or in vivo studies in preclinical cancer research. However, evidence concerning PHMs-modulating abilities of plant-based natural substances in clinical trials is insufficient.
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Affiliation(s)
- Marek Samec
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Alena Liskova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Lenka Koklesova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Veronika Mestanova
- Department of Histology and Embryology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Maria Franekova
- Department of Medical Biology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Monika Kassayova
- Department of Animal Physiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University, 04001 Kosice, Slovakia; (M.K.); (B.B.)
| | - Bianka Bojkova
- Department of Animal Physiology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University, 04001 Kosice, Slovakia; (M.K.); (B.B.)
| | - Sona Uramova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
| | - Pavol Zubor
- OBGY Health & Care, Ltd., 01026 Zilina, Slovakia;
| | - Katarina Janikova
- Department of Pathological Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Jan Danko
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia; (M.S.); (A.L.); (L.K.); (J.D.)
| | - Samson Mathews Samuel
- Department of Physiology and Biophysics, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha 24144, Qatar;
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine in Qatar, Education City, Qatar Foundation, Doha 24144, Qatar;
| | - Peter Kubatka
- Department of Medical Biology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia;
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