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Li J, Lu L, Liu L, Ren X, Chen J, Yin X, Xiao Y, Li J, Wei G, Huang H, Wei W, Wong J. HDAC1/2/3 are major histone desuccinylases critical for promoter desuccinylation. Cell Discov 2023; 9:85. [PMID: 37580347 PMCID: PMC10425439 DOI: 10.1038/s41421-023-00573-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/02/2023] [Indexed: 08/16/2023] Open
Abstract
Lysine succinylation is one of the major post-translational modifications occurring on histones and is believed to have significant roles in regulating chromatin structure and function. Currently, histone desuccinylation is widely believed to be catalyzed by members of the SIRT family deacetylases. Here, we report that histone desuccinylation is in fact primarily catalyzed by the class I HDAC1/2/3. Inhibition or depletion of HDAC1/2/3 resulted in a marked increase of global histone succinylation, whereas ectopic expression of HDAC1/2/3 but not their deacetylase inactive mutants downregulated global histone succinylation. We demonstrated that the class I HDAC1/2/3 complexes have robust histone desuccinylase activity in vitro. Genomic landscape analysis revealed that histone succinylation is highly enriched at gene promoters and inhibition of HDAC activity results in marked elevation of promoter histone succinylation. Furthermore, our integrated analysis revealed that promoter histone succinylation positively correlates with gene transcriptional activity. Collectively, we demonstrate that the class I HDAC1/2/3 but not the SIRT family proteins are the major histone desuccinylases particularly important for promoter histone desuccinylation. Our study thus sheds new light on the role of histone succinylation in transcriptional regulation.
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Affiliation(s)
- Jialun Li
- Wuhu Hospital, East China Normal University, Wuhu, Anhui, China
| | - Lu Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Lingling Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xuelian Ren
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jiwei Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xingzhi Yin
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yanhui Xiao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Gang Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - He Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Wei Wei
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
| | - Jiemin Wong
- Wuhu Hospital, East China Normal University, Wuhu, Anhui, China.
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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2
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Liu Y, Liu X, Dong X, Yin Z, Xie Z, Luo Y. Systematic Analysis of Lysine Acetylation Reveals Diverse Functions in Azorhizobium caulinodans Strain ORS571. Microbiol Spectr 2023; 11:e0353922. [PMID: 36475778 PMCID: PMC9927263 DOI: 10.1128/spectrum.03539-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
Protein acetylation can quickly modify the physiology of bacteria to respond to changes in environmental or nutritional conditions, but little information on these modifications is available in rhizobia. In this study, we report the lysine acetylome of Azorhizobium caulinodans strain ORS571, a model rhizobium isolated from stem nodules of the tropical legume Sesbania rostrata that is capable of fixing nitrogen in the free-living state and during symbiosis. Antibody enrichment and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis were used to characterize the acetylome. There are 2,302 acetylation sites from 982 proteins, accounting for 20.8% of the total proteins. Analysis of the acetylated motifs showed the preferences for the amino acid residues around acetylated lysines. The response regulator CheY1, previously characterized to be involved in chemotaxis in strain ORS571, was identified as an acetylated protein, and a mutation of the acetylated site of CheY1 significantly impaired the strain's motility. In addition, a Zn+-dependent deacetylase (AZC_0414) was characterized, and the construction of a deletion mutant strain showed that it played a role in chemotaxis. Our study provides the first global analysis of lysine acetylation in ORS571, suggesting that acetylation plays a role in various physiological processes. In addition, we demonstrate its involvement in the chemotaxis process. The acetylome of ORS571 provides insights to investigate the regulation mechanism of rhizobial physiology. IMPORTANCE Acetylation is an important modification that regulates protein function and has been found to regulate physiological processes in various bacteria. The physiology of rhizobium A. caulinodans ORS571 is regulated by multiple mechanisms both when free living and in symbiosis with the host; however, the regulatory role of acetylation is not yet known. Here, we took an acetylome-wide approach to identify acetylated proteins in A. caulinodans ORS571 and performed clustering analyses. Acetylation of chemotaxis proteins was preliminarily investigated, and the upstream acetylation-regulating enzyme involved in chemotaxis was characterized. These findings provide new insights to explore the physiological mechanisms of rhizobia.
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Affiliation(s)
- Yanan Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Liu
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Xiaoyan Dong
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Taian, China
| | - Yongming Luo
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
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3
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Bolding JE, Martín‐Gago P, Rajabi N, Gamon LF, Hansen TN, Bartling CRO, Strømgaard K, Davies MJ, Olsen CA. Aryl Fluorosulfate Based Inhibitors That Covalently Target the SIRT5 Lysine Deacylase. Angew Chem Int Ed Engl 2022; 61:e202204565. [PMID: 36130196 PMCID: PMC9828517 DOI: 10.1002/anie.202204565] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 01/12/2023]
Abstract
The sirtuin enzymes are a family of lysine deacylases that regulate gene transcription and metabolism. Sirtuin 5 (SIRT5) hydrolyzes malonyl, succinyl, and glutaryl ϵ-N-carboxyacyllysine posttranslational modifications and has recently emerged as a vulnerability in certain cancers. However, chemical probes to illuminate its potential as a pharmacological target have been lacking. Here we report the harnessing of aryl fluorosulfate-based electrophiles as an avenue to furnish covalent inhibitors that target SIRT5. Alkyne-tagged affinity-labeling agents recognize and capture overexpressed SIRT5 in cultured HEK293T cells and can label SIRT5 in the hearts of mice upon intravenous injection of the compound. This work demonstrates the utility of aryl fluorosulfate electrophiles for targeting of SIRT5 and suggests this as a means for the development of potential covalent drug candidates. It is our hope that these results will serve as inspiration for future studies investigating SIRT5 and general sirtuin biology in the mitochondria.
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Affiliation(s)
- Julie E. Bolding
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Pablo Martín‐Gago
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Luke F. Gamon
- Department of Biomedical SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenBlegdamsvej 3DK-2200CopenhagenDenmark
| | - Tobias N. Hansen
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Christian R. O. Bartling
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
| | - Michael J. Davies
- Department of Biomedical SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenBlegdamsvej 3DK-2200CopenhagenDenmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals & Department of Drug Design and PharmacologyFaculty of Health and Medical SciencesUniversity of CopenhagenUniversitetsparken 2DK-2100CopenhagenDenmark
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4
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Vong P, Ouled-Haddou H, Garçon L. Histone Deacetylases Function in the Control of Early Hematopoiesis and Erythropoiesis. Int J Mol Sci 2022; 23:9790. [PMID: 36077192 PMCID: PMC9456231 DOI: 10.3390/ijms23179790] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Numerous studies have highlighted the role of post-translational modifications in the regulation of cell proliferation, differentiation and death. Among these modifications, acetylation modifies the physicochemical properties of proteins and modulates their activity, stability, localization and affinity for partner proteins. Through the deacetylation of a wide variety of functional and structural, nuclear and cytoplasmic proteins, histone deacetylases (HDACs) modulate important cellular processes, including hematopoiesis, during which different HDACs, by controlling gene expression or by regulating non-histone protein functions, act sequentially to provide a fine regulation of the differentiation process both in early hematopoietic stem cells and in more mature progenitors. Considering that HDAC inhibitors represent promising targets in cancer treatment, it is necessary to decipher the role of HDACs during hematopoiesis which could be impacted by these therapies. This review will highlight the main mechanisms by which HDACs control the hematopoietic stem cell fate, particularly in the erythroid lineage.
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Affiliation(s)
- Pascal Vong
- Université Picardie Jules Verne, HEMATIM UR4666, 80000 Amiens, France
| | | | - Loïc Garçon
- Université Picardie Jules Verne, HEMATIM UR4666, 80000 Amiens, France
- Service d’Hématologie Biologique, Centre Hospitalier Universitaire, CEDEX 1, 80054 Amiens, France
- Laboratoire de Génétique Constitutionnelle, Centre Hospitalier Universitaire, CEDEX 1, 80054 Amiens, France
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5
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Sinniah E, Wu Z, Shen S, Naval-Sanchez M, Chen X, Lim J, Helfer A, Iyer A, Tng J, Lucke AJ, Reid RC, Redd MA, Nefzger CM, Fairlie DP, Palpant NJ. Temporal perturbation of histone deacetylase activity reveals a requirement for HDAC1-3 in mesendoderm cell differentiation. Cell Rep 2022; 39:110818. [PMID: 35584683 DOI: 10.1016/j.celrep.2022.110818] [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: 05/11/2021] [Revised: 03/22/2022] [Accepted: 04/20/2022] [Indexed: 11/03/2022] Open
Abstract
Histone deacetylases (HDACs) are a class of enzymes that control chromatin state and influence cell fate. We evaluated the chromatin accessibility and transcriptome dynamics of zinc-containing HDACs during cell differentiation in vitro coupled with chemical perturbation to identify the role of HDACs in mesendoderm cell fate specification. Single-cell RNA sequencing analyses of HDAC expression during human pluripotent stem cell (hPSC) differentiation in vitro and mouse gastrulation in vivo reveal a unique association of HDAC1 and -3 with mesendoderm gene programs during exit from pluripotency. Functional perturbation with small molecules reveals that inhibition of HDAC1 and -3, but not HDAC2, induces mesoderm while impeding endoderm and early cardiac progenitor specification. These data identify unique biological functions of the structurally homologous enzymes HDAC1-3 in influencing hPSC differentiation from pluripotency toward mesendodermal and cardiac progenitor populations.
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Affiliation(s)
- Enakshi Sinniah
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Zhixuan Wu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Sophie Shen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Marina Naval-Sanchez
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Junxian Lim
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Abbigail Helfer
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Abishek Iyer
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Jiahui Tng
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew J Lucke
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert C Reid
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Meredith A Redd
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; ARC Centre of Excellence for Advanced Molecular Imaging, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia.
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6
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Lassak J, Sieber A, Hellwig M. Exceptionally versatile take II: post-translational modifications of lysine and their impact on bacterial physiology. Biol Chem 2022; 403:819-858. [PMID: 35172419 DOI: 10.1515/hsz-2021-0382] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/05/2022] [Indexed: 01/16/2023]
Abstract
Among the 22 proteinogenic amino acids, lysine sticks out due to its unparalleled chemical diversity of post-translational modifications. This results in a wide range of possibilities to influence protein function and hence modulate cellular physiology. Concomitantly, lysine derivatives form a metabolic reservoir that can confer selective advantages to those organisms that can utilize it. In this review, we provide examples of selected lysine modifications and describe their role in bacterial physiology.
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Affiliation(s)
- Jürgen Lassak
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Alina Sieber
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Großhaderner Straße 2-4, D-82152 Planegg, Germany
| | - Michael Hellwig
- Technische Universität Braunschweig - Institute of Food Chemistry, Schleinitzstraße 20, D-38106 Braunschweig, Germany
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7
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Zhou L, Zheng S, Rosas Bringas FR, Bakker B, Simon JE, Bakker PL, Kazemier HG, Schubert M, Roorda M, van Vugt MATM, Chang M, Foijer F. A synthetic lethal screen identifies HDAC4 as a potential target in MELK overexpressing cancers. G3 (BETHESDA, MD.) 2021; 11:jkab335. [PMID: 34550356 PMCID: PMC8664443 DOI: 10.1093/g3journal/jkab335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022]
Abstract
Maternal embryonic leucine zipper kinase (MELK) is frequently overexpressed in cancer, but the role of MELK in cancer is still poorly understood. MELK was shown to have roles in many cancer-associated processes including tumor growth, chemotherapy resistance, and tumor recurrence. To determine whether the frequent overexpression of MELK can be exploited in therapy, we performed a high-throughput screen using a library of Saccharomyces cerevisiae mutants to identify genes whose functions become essential when MELK is overexpressed. We identified two such genes: LAG2 and HDA3. LAG2 encodes an inhibitor of the Skp, Cullin, F-box containing (SCF) ubiquitin-ligase complex, while HDA3 encodes a subunit of the HDA1 histone deacetylase complex. We find that one of these synthetic lethal interactions is conserved in mammalian cells, as inhibition of a human homolog of HDA3 (Histone Deacetylase 4, HDAC4) is synthetically toxic in MELK overexpression cells. Altogether, our work identified a novel potential drug target for tumors that overexpress MELK.
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Affiliation(s)
- Lin Zhou
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Siqi Zheng
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Fernando R Rosas Bringas
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Bjorn Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Judith E Simon
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Petra L Bakker
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Hinke G Kazemier
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Michael Schubert
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Maurits Roorda
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Michael Chang
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen 9713 AV, The Netherlands
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8
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Lammers M. Post-translational Lysine Ac(et)ylation in Bacteria: A Biochemical, Structural, and Synthetic Biological Perspective. Front Microbiol 2021; 12:757179. [PMID: 34721364 PMCID: PMC8556138 DOI: 10.3389/fmicb.2021.757179] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/10/2021] [Indexed: 12/21/2022] Open
Abstract
Ac(et)ylation is a post-translational modification present in all domains of life. First identified in mammals in histones to regulate RNA synthesis, today it is known that is regulates fundamental cellular processes also in bacteria: transcription, translation, metabolism, cell motility. Ac(et)ylation can occur at the ε-amino group of lysine side chains or at the α-amino group of a protein. Furthermore small molecules such as polyamines and antibiotics can be acetylated and deacetylated enzymatically at amino groups. While much research focused on N-(ε)-ac(et)ylation of lysine side chains, much less is known about the occurrence, the regulation and the physiological roles on N-(α)-ac(et)ylation of protein amino termini in bacteria. Lysine ac(et)ylation was shown to affect protein function by various mechanisms ranging from quenching of the positive charge, increasing the lysine side chains’ size affecting the protein surface complementarity, increasing the hydrophobicity and by interfering with other post-translational modifications. While N-(ε)-lysine ac(et)ylation was shown to be reversible, dynamically regulated by lysine acetyltransferases and lysine deacetylases, for N-(α)-ac(et)ylation only N-terminal acetyltransferases were identified and so far no deacetylases were discovered neither in bacteria nor in mammals. To this end, N-terminal ac(et)ylation is regarded as being irreversible. Besides enzymatic ac(et)ylation, recent data showed that ac(et)ylation of lysine side chains and of the proteins N-termini can also occur non-enzymatically by the high-energy molecules acetyl-coenzyme A and acetyl-phosphate. Acetyl-phosphate is supposed to be the key molecule that drives non-enzymatic ac(et)ylation in bacteria. Non-enzymatic ac(et)ylation can occur site-specifically with both, the protein primary sequence and the three dimensional structure affecting its efficiency. Ac(et)ylation is tightly controlled by the cellular metabolic state as acetyltransferases use ac(et)yl-CoA as donor molecule for the ac(et)ylation and sirtuin deacetylases use NAD+ as co-substrate for the deac(et)ylation. Moreover, the accumulation of ac(et)yl-CoA and acetyl-phosphate is dependent on the cellular metabolic state. This constitutes a feedback control mechanism as activities of many metabolic enzymes were shown to be regulated by lysine ac(et)ylation. Our knowledge on lysine ac(et)ylation significantly increased in the last decade predominantly due to the huge methodological advances that were made in fields such as mass-spectrometry, structural biology and synthetic biology. This also includes the identification of additional acylations occurring on lysine side chains with supposedly different regulatory potential. This review highlights recent advances in the research field. Our knowledge on enzymatic regulation of lysine ac(et)ylation will be summarized with a special focus on structural and mechanistic characterization of the enzymes, the mechanisms underlying non-enzymatic/chemical ac(et)ylation are explained, recent technological progress in the field are presented and selected examples highlighting the important physiological roles of lysine ac(et)ylation are summarized.
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Affiliation(s)
- Michael Lammers
- Synthetic and Structural Biochemistry, Institute for Biochemistry, University of Greifswald, Greifswald, Germany
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9
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Yruela I, Moreno-Yruela C, Olsen CA. Zn 2+-Dependent Histone Deacetylases in Plants: Structure and Evolution. TRENDS IN PLANT SCIENCE 2021; 26:741-757. [PMID: 33461867 DOI: 10.1016/j.tplants.2020.12.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/09/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Zn2+-dependent histone deacetylases are widely distributed in archaea, bacteria, and eukaryotes. Through deacetylation of histones and other biomolecules, these enzymes regulate mammalian gene expression, microtubule stability, and polyamine metabolism. In plants, they play essential roles in development and stress response, but little is known about their biochemistry. We provide here a holistic revision of plant histone deacetylase (HDA) phylogeny and translate recent lessons from other organisms. HDA evolution correlates with a gain of structural ductility/disorder, as observed for other proteins. We also highlight two recently identified Brassicaceae-specific HDAs, as well as unprecedented key mutations that would affect the catalytic activity of individual HDAs. This revised phylogeny will contextualize future studies and illuminate research on plant development and adaptation.
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Affiliation(s)
- Inmaculada Yruela
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Montañana 1005, 50059 Zaragoza, Spain; Group of Biochemistry, Biophysics, and Computational Biology (GBsC), Institute for Biocomputation and Physics of Complex Systems (BIFI) and Universidad de Zaragoza (UNIZAR) Joint Unit to CSIC, Zaragoza, Spain.
| | - Carlos Moreno-Yruela
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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10
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Shetty MG, Pai P, Deaver RE, Satyamoorthy K, Babitha KS. Histone deacetylase 2 selective inhibitors: A versatile therapeutic strategy as next generation drug target in cancer therapy. Pharmacol Res 2021; 170:105695. [PMID: 34082029 DOI: 10.1016/j.phrs.2021.105695] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/04/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Acetylation and deacetylation of histone and several non-histone proteins are the two important processes amongst the different modes of epigenetic modulation that are involved in regulating cancer initiation and development. Abnormal expression of histone deacetylases (HDACs) is often reported in various types of cancers. Few pan HDAC inhibitors have been approved for use as therapeutic interventions for cancer treatment including vorinostat, belinostat and panobinostat. However, not all the HDAC isoforms are abnormally expressed in certain cancers, such as in the case of, ovarian cancer where overexpression of HDAC1-3, lung cancer where overexpression of HDAC 1 and 3 and gastric cancer where overexpression of HDAC2 is seen. Therefore, pan-inhibition of HDAC is not an efficient way to combat cancer via HDAC inhibition. Hence, isoform-selective HDAC inhibition can be one of the best therapeutic strategies in the treatment of cancer. In this context since aberrant expression of HDAC2 largely contributes to cancer progression by silencing pro-apoptotic protein expressions such as NOXA and APAF1 (caspase 9-activating proteins) and inactivation of tumor suppressor p53, HDAC2 specific inhibitors may help to develop not only the direct targets but also indirect targets that are crucial for tumor development. However, to develop a HDAC2 specific and potent inhibitor, extensive knowledge of its structure and specific functions is essential. The present review updates details on the structural features, physiological functions, and roles of HDAC2 in different types of cancer, emphasizing the challenges and status of the development of HDAC2 selective inhibitors against various types of cancer.
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Affiliation(s)
| | - Padmini Pai
- Department of Biophysics, Manipal School of Life Sciences, MAHE, Manipal, India
| | - Renita Esther Deaver
- Department of Biotechnology, Manipal School of Life Sciences, MAHE, Manipal, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, MAHE, Manipal, India
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11
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Lee JH, Bollschweiler D, Schäfer T, Huber R. Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies. SCIENCE ADVANCES 2021; 7:7/2/eabd4413. [PMID: 33523989 PMCID: PMC7793584 DOI: 10.1126/sciadv.abd4413] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/11/2020] [Indexed: 05/12/2023]
Abstract
The chromatin-modifying histone deacetylases (HDACs) remove acetyl groups from acetyl-lysine residues in histone amino-terminal tails, thereby mediating transcriptional repression. Structural makeup and mechanisms by which multisubunit HDAC complexes recognize nucleosomes remain elusive. Our cryo-electron microscopy structures of the yeast class II HDAC ensembles show that the HDAC protomer comprises a triangle-shaped assembly of stoichiometry Hda12-Hda2-Hda3, in which the active sites of the Hda1 dimer are freely accessible. We also observe a tetramer of protomers, where the nucleosome binding modules are inaccessible. Structural analysis of the nucleosome-bound complexes indicates how positioning of Hda1 adjacent to histone H2B affords HDAC catalysis. Moreover, it reveals how an intricate network of multiple contacts between a dimer of protomers and the nucleosome creates a platform for expansion of the HDAC activities. Our study provides comprehensive insight into the structural plasticity of the HDAC complex and its functional mechanism of chromatin modification.
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Affiliation(s)
- Jung-Hoon Lee
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
- Proteros biostructures GmbH, Bunsenstr 7a, 82152 Martinsried, Germany
| | - Daniel Bollschweiler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tillman Schäfer
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Robert Huber
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
- Proteros biostructures GmbH, Bunsenstr 7a, 82152 Martinsried, Germany
- Zentrum für Medizinische Biotechnologie, Universität Duisburg-Essen, 45117 Essen, Germany
- Fakultät für Chemie, Technische Universität München, 85747 Garching, Germany
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12
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Epigenetic Therapy as a Putative Molecular Target to Modulate B Cell Biology and Behavior in the Context of Immunological Disorders. J Immunol Res 2020; 2020:1589191. [PMID: 32090127 PMCID: PMC7031723 DOI: 10.1155/2020/1589191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 12/31/2022] Open
Abstract
Histone Deacetylase- (HDAC-) dependent epigenetic mechanisms have been widely explored in the last decade in different types of malignancies in preclinical studies. This effort led to the discovery and development of a range of new HDAC inhibitors (iHDAC) with different chemical properties and selective abilities. In fact, hematological malignancies were the first ones to have new iHDACs approved for clinical use, such as Vorinostat and Romidepsin for cutaneous T cell lymphoma and panobinostat for multiple myeloma. Besides these promising already approved iHDACs, we highlight a range of studies focusing on the HDAC-dependent epigenetic control of B cell development, behavior, and/or function. Here, we highlight 21 iHDACs which have been studied in the literature in the context of B cell development and/or dysfunction mostly focused on B cell lymphomagenesis. Regardless, we have identified 55 clinical trials using 6 out of 21 iHDACs to approach their putative roles on B cell malignancies; none of them focuses on peritoneal B cell populations. Since cells belonging to this peculiar body compartment, named B1 cells, may contribute to the development of autoimmune pathologies, such as lupus, a better understanding of the HDAC-dependent epigenetic mechanisms that control its biology and behavior might shed light on iHDAC use to manage these immunological dysfunctions. In this sense, iHDACs might emerge as a promising new approach for translational studies in this field. In this review, we discuss a putative role of iHDACs in the modulation of peritoneal B cell subpopulation's balance as well as their role as therapeutic agents in the context of chronic diseases mediated by peritoneal B cells.
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13
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Liu CF, Tang WW. Epigenetics in Cardiac Hypertrophy and Heart Failure. JACC Basic Transl Sci 2019; 4:976-993. [PMID: 31909304 PMCID: PMC6938823 DOI: 10.1016/j.jacbts.2019.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]
Abstract
Heart failure (HF) is a complex syndrome affecting millions of people around the world. Over the past decade, the therapeutic potential of targeting epigenetic regulators in HF has been discussed extensively. Recent advances in next-generation sequencing techniques have contributed substantial progress in our understanding of the role of DNA methylation, post-translational modifications of histones, adenosine triphosphate (ATP)-dependent chromatin conformation and remodeling, and non-coding RNAs in HF pathophysiology. In this review, we summarize epigenomic studies on human and animal models in HF.
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Key Words
- BET, bromodomain
- EZH2, Enhancer of zeste homolog 2
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- HDM, histone demethylase
- HF, heart failure
- HMT, histone methyltransferase
- PRC2, polycomb repressor complex 2
- PTMs, post-translational modifications
- TAD, topologically associating domains
- TMAO, trimethylamine N-oxide
- cardiac hypertrophy
- epigenetics
- heart failure
- lnc-RNAs, long ncRNAs
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Affiliation(s)
- Chia-Feng Liu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - W.H. Wilson Tang
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
- Department of Cardiovascular Medicine, Heart and Vascular Institute, Cleveland Clinic, Cleveland, Ohio
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14
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Vucicevic J, Nikolic K, Mitchell JB. Rational Drug Design of Antineoplastic Agents Using 3D-QSAR, Cheminformatic, and Virtual Screening Approaches. Curr Med Chem 2019; 26:3874-3889. [DOI: 10.2174/0929867324666170712115411] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/06/2017] [Accepted: 06/13/2017] [Indexed: 01/07/2023]
Abstract
Background:Computer-Aided Drug Design has strongly accelerated the development of novel antineoplastic agents by helping in the hit identification, optimization, and evaluation.Results:Computational approaches such as cheminformatic search, virtual screening, pharmacophore modeling, molecular docking and dynamics have been developed and applied to explain the activity of bioactive molecules, design novel agents, increase the success rate of drug research, and decrease the total costs of drug discovery. Similarity, searches and virtual screening are used to identify molecules with an increased probability to interact with drug targets of interest, while the other computational approaches are applied for the design and evaluation of molecules with enhanced activity and improved safety profile.Conclusion:In this review are described the main in silico techniques used in rational drug design of antineoplastic agents and presented optimal combinations of computational methods for design of more efficient antineoplastic drugs.
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Affiliation(s)
- Jelica Vucicevic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - John B.O. Mitchell
- EaStCHEM School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, St Andrews KY16 9ST, United Kingdom
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15
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Christensen DG, Xie X, Basisty N, Byrnes J, McSweeney S, Schilling B, Wolfe AJ. Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions. Front Microbiol 2019; 10:1604. [PMID: 31354686 PMCID: PMC6640162 DOI: 10.3389/fmicb.2019.01604] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Post-translational modifications (PTM) decorate proteins to provide functional heterogeneity to an existing proteome. The large number of known PTMs highlights the many ways that cells can modify their proteins to respond to diverse stimuli. Recently, PTMs have begun to receive increased interest because new sensitive proteomics workflows and structural methodologies now allow researchers to obtain large-scale, in-depth and unbiased information concerning PTM type and site localization. However, few PTMs have been extensively assessed for functional consequences, leaving a large knowledge gap concerning the inner workings of the cell. Here, we review understanding of N-𝜀-lysine acetylation in bacteria, a PTM that was largely ignored in bacteria until a decade ago. Acetylation is a modification that can dramatically change the function of a protein through alteration of its properties, including hydrophobicity, solubility, and surface properties, all of which may influence protein conformation and interactions with substrates, cofactors and other macromolecules. Most bacteria carry genes predicted to encode the lysine acetyltransferases and lysine deacetylases that add and remove acetylations, respectively. Many bacteria also exhibit acetylation activities that do not depend on an enzyme, but instead on direct transfer of acetyl groups from the central metabolites acetyl coenzyme A or acetyl phosphate. Regardless of mechanism, most central metabolic enzymes possess lysines that are acetylated in a regulated fashion and many of these regulated sites are conserved across the spectrum of bacterial phylogeny. The interconnectedness of acetylation and central metabolism suggests that acetylation may be a response to nutrient availability or the energy status of the cell. However, this and other hypotheses related to acetylation remain untested.
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Affiliation(s)
- David G. Christensen
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
| | - Xueshu Xie
- Buck Institute for Research on Aging, Novato, CA, United States
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, CA, United States
| | - James Byrnes
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | - Sean McSweeney
- Energy & Photon Sciences Directorate, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, United States
| | | | - Alan J. Wolfe
- Health Sciences Division, Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, United States
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16
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Histone acetyltransferase CBP-related H3K23 acetylation contributes to courtship learning in Drosophila. BMC DEVELOPMENTAL BIOLOGY 2018; 18:20. [PMID: 30458702 PMCID: PMC6247617 DOI: 10.1186/s12861-018-0179-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Background Histone modifications are critical in regulating neuronal processes. However, the impacts of individual histone modifications on learning and memory are elusive. Here, we investigated the contributions of histone H3 lysine modifications to learning and memory in Drosophila by using histone lysine-to-alanine mutants. Results Behavioural analysis indicated that compared to the H3WT group, mutants overexpressing H3K23A displayed impaired courtship learning. Chromatin immunoprecipitation analysis of H3K23A mutants showed that H3K23 acetylation (H3K23ac) levels were decreased on learning-related genes. Knockdown of CREB-binding protein (CBP) decreased H3K23ac levels, attenuated the expression of learning-related genes, led to a courtship learning defect and altered development of the mushroom bodies. A decline in courtship learning ability was observed in both larvae and adult treatments with ICG-001. Furthermore, treatment of Drosophila overexpressing mutated H3K23A with a CBP inhibitor did not aggravate the learning defect. Conclusions H3K23ac, catalysed by the acetyltransferases dCBP, contributes to Drosophila learning, likely by controlling the expression of specific genes. This is a novel epigenetic regulatory mechanism underlying neuronal behaviours. Electronic supplementary material The online version of this article (10.1186/s12861-018-0179-z) contains supplementary material, which is available to authorized users.
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17
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Tong B, Xia D, Lv S, Ma X. Cloning and expression analysis of PtHDT903, a HD2-type histone deacetylase gene in Populus trichocarpa. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1478749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Botong Tong
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Dean Xia
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Shibo Lv
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
| | - Xujun Ma
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin, PR China
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18
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Histone Deacetylase 11 Is an ε-N-Myristoyllysine Hydrolase. Cell Chem Biol 2018; 25:849-856.e8. [PMID: 29731425 DOI: 10.1016/j.chembiol.2018.04.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/26/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
Histone deacetylase (HDAC) enzymes regulate diverse biological function, including gene expression, rendering them potential targets for intervention in a number of diseases, with a handful of compounds approved for treatment of certain hematologic cancers. Among the human zinc-dependent HDACs, the most recently discovered member, HDAC11, is the only member assigned to subclass IV. It is the smallest protein and has the least well understood biological function. Here, we show that HDAC11 cleaves long-chain acyl modifications on lysine side chains with remarkable efficiency. We further show that several common types of HDAC inhibitors, including the approved drugs romidepsin and vorinostat, do not inhibit this enzymatic activity. Macrocyclic hydroxamic acid-containing peptides, on the other hand, potently inhibit HDAC11 demyristoylation activity. These findings should be taken carefully into consideration in future investigations of the biological function of HDAC11 and will serve as a foundation for the development of selective chemical probes targeting HDAC11.
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19
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Tao NN, Zhou HZ, Tang H, Cai XF, Zhang WL, Ren JH, Zhou L, Chen X, Chen K, Li WY, Liu B, Yang QX, Cheng ST, Huang LX, Huang AL, Chen J. Sirtuin 3 enhanced drug sensitivity of human hepatoma cells through glutathione S-transferase pi 1/JNK signaling pathway. Oncotarget 2018; 7:50117-50130. [PMID: 27367026 PMCID: PMC5226572 DOI: 10.18632/oncotarget.10319] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 06/16/2016] [Indexed: 12/22/2022] Open
Abstract
SIRT3, a class III histone deacetylase, has been implicated in various cancers as a novel therapeutic target. In hepatocellular carcinoma (HCC), we previously reported that SIRT3 induced cell apoptosis by regulating GSK-3β/Bax signaling pathway. Downregulation of SIRT3 in HCC cells facilitates tumor cell survival. In this study, we found that chemotherapeutic agents (doxorubicin, cisplatin and epirubicin) and sorafenib treatment downregulated SIRT3 mRNA and protein levels in three HCC cell lines. MTS assay found that SIRT3 overexpression sensitized liver cancer cells to chemotherapeutic agents and sorafenib in SMMC-7721, Huh-7 and PLC/PRF/5 cell lines. Moreover, SIRT3 overexpression promoted chemotherapeutic agents-induced or sorafenib-induced apoptosis as evidenced by flow cytometry, enhanced PARP cleavage and enhanced Caspase-9 cleavage in three HCC cells. In contrast, SIRT3 silencing increased drug resistance of HCC cells to chemotherapeutic agents. Mechanistic study found that SIRT3 downregulated the mRNA and protein levels of glutathione S-transferase pi 1 (GSTP1), which is a member of phase II detoxification enzymes families involved in metabolizing for chemotherapeutic agents. Moreover, SIRT3 decreased the amount of GSTP1 that was associated with JNK, which finally contributed the activation of JNK activity and activation of downstream target c-Jun and Bim. Importantly, GSTP1 overexpression or JNK inhibitor abolished SIRT3-induced apoptosis in HCC cells exposed to chemotherapeutic agents. Finally, there was a negative correlation between SIRT3 expression and GSTP1 expression in human HCC tissues. Together, our findings revealed SIRT3 could enhance the drug sensitivity of HCC cells to an array of chemotherapeutic agents. SIRT3 may serve as a potential target for improving the chemosensitivity of HCC patients.
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Affiliation(s)
- Na-Na Tao
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hong-Zhong Zhou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Hua Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Zhejiang, China
| | - Xue-Fei Cai
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Wen-Lu Zhang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ji-Hua Ren
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Li Zhou
- Department of Epidemiology, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Xiang Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ke Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Wan-Yu Li
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Bo Liu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Qiu-Xia Yang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Sheng-Tao Cheng
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Li-Xia Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Ai-Long Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Zhejiang, China
| | - Juan Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
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20
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Rajabi N, Galleano I, Madsen AS, Olsen CA. Targeting Sirtuins: Substrate Specificity and Inhibitor Design. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 154:25-69. [PMID: 29413177 DOI: 10.1016/bs.pmbts.2017.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lysine residues across the proteome are modified by posttranslational modifications (PTMs) that significantly enhance the structural and functional diversity of proteins. For lysine, the most abundant PTM is ɛ-N-acetyllysine (Kac), which plays numerous roles in regulation of important cellular functions, such as gene expression (epigenetic effects) and metabolism. A family of enzymes, namely histone deacetylases (HDACs), removes these PTMs. A subset of these enzymes, the sirtuins (SIRTs), represent class III HDAC and, unlike the rest of the family, these hydrolases are NAD+-dependent. Although initially described as deacetylases, alternative deacylase functions for sirtuins have been reported, which expands the potential cellular roles of this class of enzymes. Currently, sirtuins are investigated as therapeutic targets for the treatment of diseases that span from cancers to neurodegenerative disorders. In the present book chapter, we review and discuss the current literature on novel ɛ-N-acyllysine PTMs, targeted by sirtuins, as well as mechanism-based sirtuin inhibitors inspired by their substrates.
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Affiliation(s)
- Nima Rajabi
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Iacopo Galleano
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Andreas S Madsen
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals, University of Copenhagen, Copenhagen, Denmark.
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21
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Rajabi N, Auth M, Troelsen KR, Pannek M, Bhatt DP, Fontenas M, Hirschey MD, Steegborn C, Madsen AS, Olsen CA. Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Marina Auth
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kathrin R. Troelsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Martin Pannek
- Universität Bayreuth; Lehrstuhl Biochemie und Forschungszentrum für Biomakromoleküle; Universitätsstrasse 30 95447 Bayreuth Germany
| | - Dhaval P. Bhatt
- Duke University Medical Center; Sarah W. Stedman Nutrition and Metabolism Center; 4321 Medical Park Drive Durham NC 27704 USA
| | - Martin Fontenas
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Matthew D. Hirschey
- Duke University Medical Center; Sarah W. Stedman Nutrition and Metabolism Center; 4321 Medical Park Drive Durham NC 27704 USA
| | - Clemens Steegborn
- Universität Bayreuth; Lehrstuhl Biochemie und Forschungszentrum für Biomakromoleküle; Universitätsstrasse 30 95447 Bayreuth Germany
| | - Andreas S. Madsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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22
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Rajabi N, Auth M, Troelsen KR, Pannek M, Bhatt DP, Fontenas M, Hirschey MD, Steegborn C, Madsen AS, Olsen CA. Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight. Angew Chem Int Ed Engl 2017; 56:14836-14841. [PMID: 29044784 PMCID: PMC5814306 DOI: 10.1002/anie.201709050] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Indexed: 12/18/2022]
Abstract
The sirtuin enzymes are important regulatory deacylases in a variety of biochemical contexts and may therefore be potential therapeutic targets through either activation or inhibition by small molecules. Here, we describe the discovery of the most potent inhibitor of sirtuin 5 (SIRT5) reported to date. We provide rationalization of the mode of binding by solving co-crystal structures of selected inhibitors in complex with both human and zebrafish SIRT5, which provide insight for future optimization of inhibitors with more "drug-like" properties. Importantly, enzyme kinetic evaluation revealed a slow, tight-binding mechanism of inhibition, which is unprecedented for SIRT5. This is important information when applying inhibitors to probe mechanisms in biology.
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Affiliation(s)
- Nima Rajabi
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Marina Auth
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Kathrin R Troelsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Martin Pannek
- Universität Bayreuth, Lehrstuhl Biochemie und Forschungszentrum für Biomakromoleküle, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Dhaval P Bhatt
- Duke University Medical Center, Sarah W. Stedman Nutrition and Metabolism Center, 4321 Medical Park Drive, Durham, NC, 27704, USA
| | - Martin Fontenas
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Matthew D Hirschey
- Duke University Medical Center, Sarah W. Stedman Nutrition and Metabolism Center, 4321 Medical Park Drive, Durham, NC, 27704, USA
| | - Clemens Steegborn
- Universität Bayreuth, Lehrstuhl Biochemie und Forschungszentrum für Biomakromoleküle, Universitätsstrasse 30, 95447, Bayreuth, Germany
| | - Andreas S Madsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
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23
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Niu S, Kim BC, Fierke CA, Ruotolo BT. Ion Mobility-Mass Spectrometry Reveals Evidence of Specific Complex Formation between Human Histone Deacetylase 8 and Poly-r(C)-binding Protein 1. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 420:9-15. [PMID: 28983190 PMCID: PMC5624731 DOI: 10.1016/j.ijms.2016.12.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Histone deacetylase 8, part of a broad class of proteins responsible for regulating transcription and many other cellular processes and directly linked to a host of human disease through its mis-function, has been canonically described as a zinc-based mettalo-enzyme for many years. Recent evidence, however, has linked this protein to iron incorporation, loaded through transient interactions with the poly r(C)-binding protein 1, a metallo-chaperone and storage protein. In this report, we construct and deploy an electrospray-mass spectrometry based assay aimed at quantifying the interaction strength between these two weakly-associated proteins, as well as the zinc and iron associated form of the histone deacetylase. Despite challenges derived from artifact protein complexes derived from the electrospray process, we use carefully-constructed positive and negative control experiments, along with detailed measurements of protein ionization efficiency to validate our dissociation constant measurements for protein dimers in this size range. Furthermore, our data strongly support that complexes between histone deacetylase 8 and poly r(C)-binding protein 1 are specific, and that they are equally strong when both zinc and iron-loaded proteins are involved, or perhaps mildly promoted in the latter case, suggesting an in vivo role for the non-canonical, iron-incorporated histone deacetylase.
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Mayo JC, Sainz RM, González Menéndez P, Cepas V, Tan DX, Reiter RJ. Melatonin and sirtuins: A "not-so unexpected" relationship. J Pineal Res 2017; 62. [PMID: 28109165 DOI: 10.1111/jpi.12391] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 01/17/2017] [Indexed: 12/11/2022]
Abstract
Epigenetic modifications, including methylation or acetylation as well as post-transcriptional modifications, are mechanisms used by eukaryotic cells to increase the genome diversity in terms of differential gene expression and protein diversity. Among these modifying enzymes, sirtuins, a class III histone deacetylase (HDAC) enzymes, are of particular importance. Sirtuins regulate the cell cycle, DNA repair, cell survival, and apoptosis, thus having important roles in normal and cancer cells. Sirtuins can also regulate metabolic pathways by changing preference for glycolysis under aerobic conditions as well as glutaminolysis. These actions make sirtuins a major target in numerous physiological processes as well as in other contexts such as calorie restriction-induced anti-aging, cancer, or neurodegenerative disease. Interestingly, melatonin, a nighttime-produced indole synthesized by pineal gland and many other organs, has important cytoprotective effects in many tissues including aging, neurodegenerative diseases, immunomodulation, and cancer. The pleiotropic actions of melatonin in different physiological and pathological conditions indicate that may be basic cellular targeted for the indole. Thus, much research has focused attention on the potential mechanisms of the indole in modulating expression and/or activity of sirtuins. Numerous findings report a rise in activity, especially on SIRT1, in a diversity of cells and animal models after melatonin treatment. This contrasts, however, with data reporting an inhibitory effect of melatonin on this sirtuin in some tumor cells. This review tabulates and discusses the recent findings relating melatonin with sirtuins, particularly SIRT1 and mitochondrial SIRT3, showing the apparent dichotomy with the differential actions documented in normal and in cancer cells.
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Affiliation(s)
- Juan C Mayo
- Departamento de Morfología y Biología Celular, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario Oncológico del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
| | - Rosa M Sainz
- Departamento de Morfología y Biología Celular, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario Oncológico del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
| | - Pedro González Menéndez
- Departamento de Morfología y Biología Celular, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario Oncológico del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
| | - Vanesa Cepas
- Departamento de Morfología y Biología Celular, Facultad de Medicina, Universidad de Oviedo, Oviedo, Spain
- Instituto Universitario Oncológico del Principado de Asturias (IUOPA), University of Oviedo, Oviedo, Spain
| | - Dun-Xian Tan
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, TX, USA
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio (UTHSCSA), San Antonio, TX, USA
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Circulating Nucleosomes and Nucleosome Modifications as Biomarkers in Cancer. Cancers (Basel) 2017; 9:cancers9010005. [PMID: 28075351 PMCID: PMC5295776 DOI: 10.3390/cancers9010005] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/31/2016] [Accepted: 01/01/2017] [Indexed: 12/17/2022] Open
Abstract
Traditionally the stratification of many cancers involves combining tumour and clinicopathological features (e.g., patient age; tumour size, grade, receptor status and location) to inform treatment options and predict recurrence risk and survival. However, current biomarkers often require invasive excision of the tumour for profiling, do not allow monitoring of the response to treatment and stratify patients into broad heterogeneous groups leading to inconsistent treatment responses. Here we explore and describe the benefits of using circulating biomarkers (nucleosomes and/or modifications to nucleosomes) as a non-invasive method for detecting cancer and monitoring response to treatment. Nucleosomes (DNA wound around eight core histone proteins) are responsible for compacting our genome and their composition and post-translational modifications are responsible for regulating gene expression. Here, we focus on breast and colorectal cancer as examples where utilizing circulating nucleosomes as biomarkers hold real potential as liquid biopsies. Utilizing circulating nucleosomes as biomarkers is an exciting new area of research that promises to allow both the early detection of cancer and monitoring of treatment response. Nucleosome-based biomarkers combine with current biomarkers, increasing both specificity and sensitivity of current tests and have the potential to provide individualised precision-medicine based treatments for patients.
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YOSHIDA M, KUDO N, KOSONO S, ITO A. Chemical and structural biology of protein lysine deacetylases. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:297-321. [PMID: 28496053 PMCID: PMC5489435 DOI: 10.2183/pjab.93.019] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 03/21/2017] [Indexed: 05/27/2023]
Abstract
Histone acetylation is a reversible posttranslational modification that plays a fundamental role in regulating eukaryotic gene expression and chromatin structure/function. Key enzymes for removing acetyl groups from histones are metal (zinc)-dependent and NAD+-dependent histone deacetylases (HDACs). The molecular function of HDACs have been extensively characterized by various approaches including chemical, molecular, and structural biology, which demonstrated that HDACs regulate cell proliferation, differentiation, and metabolic homeostasis, and that their alterations are deeply involved in various human disorders including cancer. Notably, drug discovery efforts have achieved success in developing HDAC-targeting therapeutics for treatment of several cancers. However, recent advancements in proteomics technology have revealed much broader aspects of HDACs beyond gene expression control. Not only histones but also a large number of cellular proteins are subject to acetylation by histone acetyltransferases (HATs) and deacetylation by HDACs. Furthermore, some of their structures can flexibly accept and hydrolyze other acyl groups on protein lysine residues. This review mainly focuses on structural aspects of HDAC enzymatic activity regulated by interaction with substrates, co-factors, small molecule inhibitors, and activators.
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Affiliation(s)
- Minoru YOSHIDA
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Norio KUDO
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Saori KOSONO
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
- Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Akihiro ITO
- RIKEN Center for Sustainable Resource Science, Saitama, Japan
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The Interactome of the Glucocorticoid Receptor and Its Influence on the Actions of Glucocorticoids in Combatting Inflammatory and Infectious Diseases. Microbiol Mol Biol Rev 2016; 80:495-522. [PMID: 27169854 DOI: 10.1128/mmbr.00064-15] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Glucocorticoids (GCs) have been widely used for decades as a first-line treatment for inflammatory and autoimmune diseases. However, their use is often hampered by the onset of adverse effects or resistance. GCs mediate their effects via binding to glucocorticoid receptor (GR), a transcription factor belonging to the family of nuclear receptors. An important aspect of GR's actions, including its anti-inflammatory capacity, involves its interactions with various proteins, such as transcription factors, cofactors, and modifying enzymes, which codetermine receptor functionality. In this review, we provide a state-of-the-art overview of the protein-protein interactions (PPIs) of GR that positively or negatively affect its anti-inflammatory properties, along with mechanistic insights, if known. Emphasis is placed on the interactions that affect its anti-inflammatory effects in the presence of inflammatory and microbial diseases.
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Abstract
Sirtuins are NAD(+)-dependent enzymes universally present in all organisms, where they play central roles in regulating numerous biological processes. Although early studies showed that sirtuins deacetylated lysines in a reaction that consumes NAD(+), more recent studies have revealed that these enzymes can remove a variety of acyl-lysine modifications. The specificities for varied acyl modifications may thus underlie the distinct roles of the different sirtuins within a given organism. This review summarizes the structure, chemistry, and substrate specificity of sirtuins with a focus on how different sirtuins recognize distinct substrates and thus carry out specific functions.
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Affiliation(s)
- Poonam Bheda
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67404, France.,Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Hui Jing
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185;
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850.,Howard Hughes Medical Institute, Cornell University, Ithaca, New York 14850;
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Hsu CW, Shou D, Huang R, Khuc T, Dai S, Zheng W, Klumpp-Thomas C, Xia M. Identification of HDAC Inhibitors Using a Cell-Based HDAC I/II Assay. ACTA ACUST UNITED AC 2016; 21:643-52. [PMID: 26858181 DOI: 10.1177/1087057116629381] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 01/07/2016] [Indexed: 12/21/2022]
Abstract
Histone deacetylases (HDACs) are a class of epigenetic enzymes that regulate gene expression by histone deacetylation. Altered HDAC function has been linked to cancer and neurodegenerative diseases, making HDACs popular therapeutic targets. In this study, we describe a screening approach for identification of compounds that inhibit endogenous class I and II HDACs. A homogeneous, luminogenic HDAC I/II assay was optimized in a 1536-well plate format in several human cancer cell lines, including HCT116 and human neural stem cells. The assay confirmed 37 known HDAC inhibitors from two libraries of known epigenetics-active compounds. Using the assay, we identified a group of potential HDAC inhibitors by screening the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection of 2527 small-molecule drugs. The selected compounds showed similar HDAC I/II inhibitory potency and efficacy values in both HCT116 and neural stem cells. Several previously unidentified HDAC inhibitors were further evaluated and profiled for their selectivity against a panel of 10 HDAC I/II isoforms using fluorogenic HDAC biochemical assays. In summary, our results show that several novel HDAC inhibitors, including nafamostat and piceatannol, have been identified using the HDAC I/II cell-based assay, and multiple cell types have been validated for high-throughput screening of large chemical libraries.
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Affiliation(s)
- Chia-Wen Hsu
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - David Shou
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Thai Khuc
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Sheng Dai
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
| | | | - Menghang Xia
- National Center for Advancing Translational Sciences, Bethesda, MD, USA
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Hentchel KL, Escalante-Semerena JC. Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress. Microbiol Mol Biol Rev 2015; 79:321-46. [PMID: 26179745 PMCID: PMC4503791 DOI: 10.1128/mmbr.00020-15] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Acylation of biomolecules (e.g., proteins and small molecules) is a process that occurs in cells of all domains of life and has emerged as a critical mechanism for the control of many aspects of cellular physiology, including chromatin maintenance, transcriptional regulation, primary metabolism, cell structure, and likely other cellular processes. Although this review focuses on the use of acetyl moieties to modify a protein or small molecule, it is clear that cells can use many weak organic acids (e.g., short-, medium-, and long-chain mono- and dicarboxylic aliphatics and aromatics) to modify a large suite of targets. Acetylation of biomolecules has been studied for decades within the context of histone-dependent regulation of gene expression and antibiotic resistance. It was not until the early 2000s that the connection between metabolism, physiology, and protein acetylation was reported. This was the first instance of a metabolic enzyme (acetyl coenzyme A [acetyl-CoA] synthetase) whose activity was controlled by acetylation via a regulatory system responsive to physiological cues. The above-mentioned system was comprised of an acyltransferase and a partner deacylase. Given the reversibility of the acylation process, this system is also referred to as reversible lysine acylation (RLA). A wealth of information has been obtained since the discovery of RLA in prokaryotes, and we are just beginning to visualize the extent of the impact that this regulatory system has on cell function.
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Affiliation(s)
- Kristy L Hentchel
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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Overexpression of cytoplasmic TcSIR2RP1 and mitochondrial TcSIR2RP3 impacts on Trypanosoma cruzi growth and cell invasion. PLoS Negl Trop Dis 2015; 9:e0003725. [PMID: 25875650 PMCID: PMC4398437 DOI: 10.1371/journal.pntd.0003725] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/30/2015] [Indexed: 11/19/2022] Open
Abstract
Background Trypanosoma cruzi is a protozoan pathogen responsible for Chagas disease. Current therapies are inadequate because of their severe host toxicity and numerous side effects. The identification of new biotargets is essential for the development of more efficient therapeutic alternatives. Inhibition of sirtuins from Trypanosoma brucei and Leishmania ssp. showed promising results, indicating that these enzymes may be considered as targets for drug discovery in parasite infection. Here, we report the first characterization of the two sirtuins present in T. cruzi. Methodology Dm28c epimastigotes that inducibly overexpress TcSIR2RP1 and TcSIR2RP3 were constructed and used to determine their localizations and functions. These transfected lines were tested regarding their acetylation levels, proliferation and metacyclogenesis rate, viability when treated with sirtuin inhibitors and in vitro infectivity. Conclusion TcSIR2RP1 and TcSIR2RP3 are cytosolic and mitochondrial proteins respectively. Our data suggest that sirtuin activity is important for the proliferation of T. cruzi replicative forms, for the host cell-parasite interplay, and for differentiation among life-cycle stages; but each one performs different roles in most of these processes. Our results increase the knowledge on the localization and function of these enzymes, and the overexpressing T. cruzi strains we obtained can be useful tools for experimental screening of trypanosomatid sirtuin inhibitors. Sirtuins are a family of deacetylases, evolutionary conserved from bacteria to mammals. They participate in the regulation of a wide range of nuclear, cytoplasmic and mitochondrial pathways, and are considered pro-life enzymes. In the last years the search for sirtuin inhibitors was a very active field of research, with potential applications in a large number of pathologies, including parasitic diseases. We are interested in the study of the two sirtuins present in the protozoan parasite Trypanosoma cruzi, being our objective to understand their function. First, we determined the localization of these enzymes in the parasite: TcSIR2RP1 is a cytoplasmic enzyme and TcSIR2RP3 localizes in the mitochondrion. When we overexpress cytoplasmic TcSIR2RP1, the transgenic parasites differentiate to metacyclic trypomastigotes and infect mammalian cells more efficiently. In contrast, the overexpression of mitochondrial TcSIR2RP3 does not affect metacyclogenesis but modifies epimastigotes growth and slightly increases the proliferation of the parasite in the intracellular stage. We also used these transgenic lines to test their sensibility to previously described sirtuin inhibitors.
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Tsuji M, Miyagawa K, Takeda H. Epigenetic regulation of resistance to emotional stress: possible involvement of 5-HT1A receptor-mediated histone acetylation. J Pharmacol Sci 2014; 125:347-54. [PMID: 25048113 DOI: 10.1254/jphs.14r07cp] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The ability to resist stress is an important defensive function of a living body. Thus, elucidation of the mechanisms by which the brain resists stress could help to pave the way for new therapeutic strategies for stress-related psychiatric disorders including depression. The present review focuses on the roles of brain 5-HT1A receptor-mediated epigenetic mechanisms in the development of resistance to emotional stress. Behavioral pharmacological studies have demonstrated that treatment with a 5-HT1A receptor agonist 24 h before testing suppressed the decrease in emotional behaviors induced by acute restraint stress. Studies with DNA microarray technology have revealed that histone deacetylase genes were decreased in the hippocampus of mice that had been pretreated with a 5-HT1A receptor agonist 24 h beforehand. This preliminary finding was supported by data that hippocampal acetylated histone H3 was increased in mice that had developed emotional resistance to acute restraint stress by 5-HT1A receptor agonist. Furthermore, the histone deacetylase inhibitor trichostatin A also protected against the emotional changes induced by acute restraint stress, accompanied by the induction of histone H3 acetylation. These findings suggest that epigenetic mechanisms that are functionally coupled with 5-HT1A receptors may play a key role in the development of resistance to emotional stress.
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Affiliation(s)
- Minoru Tsuji
- Department of Pharmacology, School of Pharmacy, International University of Health and Welfare, Japan
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Chen YC, Huang WJ, Hsu JL, Yu CC, Wang WT, Guh JH. A novel hydroxysuberamide derivative potentiates MG132-mediated anticancer activity against human hormone refractory prostate cancers--the role of histone deacetylase and endoplasmic reticulum stress. Prostate 2013; 73:1270-80. [PMID: 23813634 DOI: 10.1002/pros.22641] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/18/2012] [Indexed: 01/05/2023]
Abstract
BACKGROUND Histone deacetylase (HDAC) inhibitors are successful for treatment of advanced cutaneous T-cell lymphoma but only show modest effect in solid tumors. Approaches for HDAC inhibitors to improve activity against solid tumors are necessary. METHODS Sulforhodamine B assay and flow cytometric analysis detected cell proliferation and cell-cycle progression, respectively. Protein expression was determined by Western blotting. Comet assay and DNA end-binding activity of Ku proteins detected DNA damage and DNA repair activity, respectively. siRNA technique was used for knockdown of specific cellular target. RESULTS WJ25591 displayed inhibitory activity against HDAC1 and cell proliferation in human hormone-refractory prostate cancers PC-3 and DU-145. WJ25591 caused an arrest of cell-cycle at both G1- and G2-phase and increased protein expressions of p21 and cyclin E, followed by cell apoptosis. WJ25591-induced Bcl-2 down-regulation and activation of caspase-9, -8, and -3, suggesting apoptotic execution through both intrinsic and extrinsic apoptotic pathways. WJ25591 also significantly inhibited DNA repair activity but not directly induced DNA damage. Moreover, the proteasome inhibitor MG-132 dramatically sensitized WJ25591-induced cell apoptosis. The siRNA technique demonstrated that endoplasmic reticulum (ER) stress, in particular CHOP/GADD153 up-regulation, contributed to the synergistic effect. CONCLUSIONS The data suggest that WJ25591 inhibited HDAC activity, leading to cell-cycle arrest and inhibition of DNA repair. Caspase cascades are subsequently triggered to execute cell apoptosis. MG-132 dramatically sensitizes WJ25591-mediated apoptosis, at least partly, through ER stress response. The data also reveal that combination of HDAC inhibitors and proteasome inhibitors may be a potential strategy against hormone-refractory prostate cancers.
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Affiliation(s)
- Yi-Cheng Chen
- College of Medicine, School of Pharmacy, National Taiwan University, Taipei, Taiwan
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Zhou C, Liu WY, Feng F, Ye H, Wu CY. Determination and stress studies on YK-1101, a potential histone deacetylase, by HPLC–UV and HPLC–TOF/MS methods. J Pharm Anal 2013; 3:168-172. [PMID: 29403812 PMCID: PMC5760985 DOI: 10.1016/j.jpha.2013.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/08/2013] [Indexed: 11/29/2022] Open
Abstract
YK-1101, with its structure as S-((E)-4-((7S,10S,Z)-4-ethylidene-7-isopropyl-2,5,8,12-tetraoxo -9-oxa-16-thia-3,6,13,18-tetraazabicyclo[13.2.1]octadeca-1(17),15(18)-dien-10-yl)but-3-en-1-yl) ethanethioate, is synthesized as a potential histone deacetylase inhibitor. Its quality and stability under various stress conditions are not fully understood. In this study, a high performance liquid chromatographic (HPLC) method was established and validated for the analysis of YK-1101 bulk drug samples. The chromatographic separation was performed on a C18 column with acetonitrile and water as mobile phase in a gradient elution. Based on the established method, the stability studies of YK-1101 under various stress conditions were carried out. YK-1101 was shown to undergo degradation under basic and acidic stress conditions, while it was stable under oxidative, photolytic and thermal conditions. In addition, a time of flight mass spectrometer (TOF/MS) was coupled to HPLC for the characterization of major degradation products produced under basic and acidic stress conditions. Their degradation pathways were also discussed.
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Affiliation(s)
- Chen Zhou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Wen-Yuan Liu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
- Corresponding author. Tel.: +86 25 8327 1038; fax: +86 25 8327 1269.
| | - Feng Feng
- Department of Natural Medicine Chemistry, China Pharmaceutical University, Nanjing 211198, China
- Corresponding author.
| | - Hai Ye
- Yoko Pharma Co., Ltd., Nanjing 210000, China
| | - Chun-Yong Wu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
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A novel method for purification of polymerizable tubulin with a high content of the acetylated isotype. Biochem J 2013; 449:643-8. [DOI: 10.1042/bj20121439] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tubulin can be acetylated/deacetylated on Lys40 of the α-subunit. Studies of the post-translational acetylation/deacetylation of tubulin using biochemical techniques require tubulin preparations that are enriched in AcTubulin (acetylated tubulin) and (for comparison) preparations lacking AcTubulin. Assembly–disassembly cycling of microtubules gives tubulin preparations that contain little or no AcTubulin. In the present study we demonstrated that this result is owing to the presence of high deacetylating activity in the extracts. This deacetylating activity in rat brain homogenates was inhibited by TSA (Trichostatin A) and tubacin, but not by nicotinamide, indicating that HDAC6 (histone deacetylase 6) is involved. TSA showed no effect on microtubule polymerization or depolymerization. We utilized these properties of TSA to prevent deacetylation during the assembly–disassembly procedure. The effective inhibitory concentration of TSA was 3 μM in the homogenate and 1 μM in the subsequent cycling steps. By comparison with immunopurified AcTubulin, we estimated that ~64% of the tubulin molecules in the three cycled preparations were acetylated. The protein profiles of these tubulin preparations, as assessed by SDS/PAGE and Coomassie Blue staining, were identical to that of a preparation completely lacking AcTubulin obtained by assembly–disassembly cycles in the absence of TSA. The tyrosination state and in vitro assembly–disassembly kinetics were the same regardless of the degree of acetylation.
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Tsai YC, Greco TM, Boonmee A, Miteva Y, Cristea IM. Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Mol Cell Proteomics 2012; 11:60-76. [PMID: 22586326 DOI: 10.1074/mcp.a111.015156] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Among mammalian sirtuins, SIRT7 is the only enzyme residing in nucleoli where ribosomal DNA is transcribed. Recent reports established that SIRT7 associates with RNA Pol I machinery and is required for rDNA transcription. Although defined by its homology to the yeast histone deacetylase Sir2, current knowledge suggests that SIRT7 itself has little to no deacetylase activity. Because only two SIRT7 interactions have been thus far described: RNA Pol I and upstream binding factor, identification of proteins and complexes associating with SIRT7 is critical to understanding its functions. Here, we present the first characterization of SIRT7 interaction networks. We have systematically investigated protein interactions of three EGFP-tagged SIRT7 constructs: wild type, a point mutation affecting rDNA transcription, and a deletion mutant lacking the predicted coiled-coil domain. A combinatorial proteomics and bioinformatics approach was used to integrate gene ontology classifications, functional protein networks, and normalized abundances of proteins co-isolated with SIRT7. The resulting refined proteomic data set confirmed SIRT7 interactions with RNA Pol I and upstream binding factor and highlighted association with factors involved in RNA Pol I- and II-dependent transcriptional processes and several nucleolus-localized chromatin remodeling complexes. Particularly enriched were members of the B-WICH complex, such as Mybbp1a, WSTF, and SNF2h. Prominent interactions were validated by a selected reaction monitoring-like approach using metabolic labeling with stable isotopes, confocal microscopy, reciprocal immunoaffinity precipitation, and co-isolation with endogenous SIRT7. To extend the current knowledge of mechanisms involved in SIRT7-dependent regulation of rDNA transcription, we showed that small interfering RNA-mediated SIRT7 knockdown leads to reduced levels of RNA Pol I protein, but not messenger RNA, which was confirmed in diverse cell types. The down-regulation of RNA Pol I protein levels placed in the context of SIRT7 interaction networks led us to propose that SIRT7 plays a crucial role in connecting the function of chromatin remodeling complexes to RNA Pol I machinery during transcription.
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Affiliation(s)
- Yuan-Chin Tsai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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Bodai L, Zsindely N, Gáspár R, Kristó I, Komonyi O, Boros IM. Ecdysone induced gene expression is associated with acetylation of histone H3 lysine 23 in Drosophila melanogaster. PLoS One 2012; 7:e40565. [PMID: 22808194 PMCID: PMC3393682 DOI: 10.1371/journal.pone.0040565] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 06/09/2012] [Indexed: 11/24/2022] Open
Abstract
Posttranslational modification of histones regulates transcription but the exact role that acetylation of specific lysine residues plays in biological processes in vivo is still not clearly understood. To assess the contribution of different histone modifications to transcriptional activation in vivo, we determined the acetylation patterns on the ecdysone induced Eip74EF and Eip75B genes in Drosophila melanogaster larvae by chromatin immunoprecipitation. We found that acetylation of histone H3 lysine 23 is localized to promoters and correlates with endogenous ecdysone induced gene activation. In contrast, acetylation of lysines 8, 12 and 16 of histone H4 and lysine 9 of histone H3 showed minor differences in their distribution on the regulatory and transcribed regions tested, and had limited or no correlation with ecdysone induced transcriptional activity. We found that dCBP, which is encoded by the nejire gene, acetylates H3 lysine 23 in vivo, and silencing of nejire leads to reduced expression of the Eip74EF and Eip75B genes. Our results suggest that acetylation of specific lysine residues of histones contribute specifically to the dynamic regulation of transcription. Furthermore, along with previous studies identify CBP dependent H3 lysine 23 acetylation as an evolutionarily conserved chromatin modification involved in steroid induced gene activation.
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Affiliation(s)
- László Bodai
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary.
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Smoum R, Rubinstein A, Dembitsky VM, Srebnik M. Boron containing compounds as protease inhibitors. Chem Rev 2012; 112:4156-220. [PMID: 22519511 DOI: 10.1021/cr608202m] [Citation(s) in RCA: 300] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Reem Smoum
- The School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel.
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Drzewiecka H, Jagodzinski PP. Trichostatin A reduced phospholipase C gamma-1 transcript and protein contents in MCF-7 breast cancer cells. Biomed Pharmacother 2011; 66:1-5. [PMID: 22257695 DOI: 10.1016/j.biopha.2011.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 09/06/2011] [Indexed: 01/07/2023] Open
Abstract
It has recently been demonstrated that phospholipase C gamma-1 (PLCγ1) activation may contribute to breast carcinoma cell motility and their metastasis. Employing MCF-7 breast cancer cells, we showed the effect of trichostatin A (TSA) on the cellular contents of the PLCγ1 molecule. Using reverse transcription, real-time quantitative PCR and western blot analysis, we demonstrated that TSA reduced the PLCγ1 transcript and protein levels in MCF-7 cells. We also found that TSA decreased the half-life of the PLCγ1 transcript from approximately 7hours to 5hours. Moreover, we observed that protein synthesis appears to be essential in the TSA reduction of PLCγ1 mRNA stability. Since PLCγ1 activation is considered a key factor in the initiation of events that increase malignant cell motility, our observations may support the validity of TSA in anticancer studies.
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Affiliation(s)
- H Drzewiecka
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781 Poznań, Poland
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40
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Tsai YC, Greco TM, Boonmee A, Miteva Y, Cristea IM. Functional proteomics establishes the interaction of SIRT7 with chromatin remodeling complexes and expands its role in regulation of RNA polymerase I transcription. Mol Cell Proteomics 2011; 11:M111.015156. [PMID: 22147730 DOI: 10.1074/mcp.m111.015156] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Among mammalian sirtuins, SIRT7 is the only enzyme residing in nucleoli where ribosomal DNA is transcribed. Recent reports established that SIRT7 associates with RNA Pol I machinery and is required for rDNA transcription. Although defined by its homology to the yeast histone deacetylase Sir2, current knowledge suggests that SIRT7 itself has little to no deacetylase activity. Because only two SIRT7 interactions have been thus far described: RNA Pol I and upstream binding factor, identification of proteins and complexes associating with SIRT7 is critical to understanding its functions. Here, we present the first characterization of SIRT7 interaction networks. We have systematically investigated protein interactions of three EGFP-tagged SIRT7 constructs: wild type, a point mutation affecting rDNA transcription, and a deletion mutant lacking the predicted coiled-coil domain. A combinatorial proteomics and bioinformatics approach was used to integrate gene ontology classifications, functional protein networks, and normalized abundances of proteins co-isolated with SIRT7. The resulting refined proteomic data set confirmed SIRT7 interactions with RNA Pol I and upstream binding factor and highlighted association with factors involved in RNA Pol I- and II-dependent transcriptional processes and several nucleolus-localized chromatin remodeling complexes. Particularly enriched were members of the B-WICH complex, such as Mybbp1a, WSTF, and SNF2h. Prominent interactions were validated by a selected reaction monitoring-like approach using metabolic labeling with stable isotopes, confocal microscopy, reciprocal immunoaffinity precipitation, and co-isolation with endogenous SIRT7. To extend the current knowledge of mechanisms involved in SIRT7-dependent regulation of rDNA transcription, we showed that small interfering RNA-mediated SIRT7 knockdown leads to reduced levels of RNA Pol I protein, but not messenger RNA, which was confirmed in diverse cell types. The down-regulation of RNA Pol I protein levels placed in the context of SIRT7 interaction networks led us to propose that SIRT7 plays a crucial role in connecting the function of chromatin remodeling complexes to RNA Pol I machinery during transcription.
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Affiliation(s)
- Yuan-Chin Tsai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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41
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The sirtuin pathway in ageing and Alzheimer disease: mechanistic and therapeutic considerations. Lancet Neurol 2011; 10:275-9. [PMID: 21349442 DOI: 10.1016/s1474-4422(11)70013-8] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Advances in gerontology have yielded crucial insights into the molecular and biochemical aspects of the ageing process. The sirtuin pathway, which is most notable for its association with the anti-ageing effects of calorie restriction, has received particular attention, and pharmacological or transgenic upregulation of the sirtuin pathway has shown promising results in laboratory models of ageing. Alzheimer's disease is a neurodegenerative disease that is imposing an increasing burden on society, and is the leading cause of senile dementia worldwide. The lack of therapies for Alzheimer's disease provides a strong incentive for the development of an effective treatment strategy and, interestingly, research has uncovered a mechanism of action of the sirtuin pathway that might have therapeutic potential for Alzheimer's disease. RECENT DEVELOPMENTS SIRT1, one of the seven mammalian proteins of the sirtuin family of NAD(+)-dependent deacetylases, has recently been shown to attenuate amyloidogenic processing of amyloid-β protein precursor (APP) in cell culture studies in vitro and in transgenic mouse models of Alzheimer's disease. Mechanistically, SIRT1 increases α-secretase production and activity through activation of the α-secretase gene ADAM10. Because α-secretase is the enzyme responsible for the non-amyloidogenic cleavage of APP, upregulation of α-secretase shifts APP processing to reduce the pathological accumulation of the presumptive toxic Aβ species that results from β-secretase and γ-secretase activity. Interestingly, the spatial patterns of Aβ deposition in the brain might correlate with increased aerobic glycolysis in those regions. Because aerobic glycolysis depletes cellular levels of NAD(+) (through a decreased NAD(+)/NADH ratio), it is possible that a corresponding downregulation of the NAD(+)-dependent sirtuin pathway contributes to the amyloidogenic processing of APP. WHERE NEXT?: The specific inhibition of Aβ generation by SIRT1 coupled with the potential link between aerobic glycolysis, NAD(+) depletion, and amyloidogenesis through the sirtuin pathway has translational implications. On the one hand, the possible underlying role of the sirtuin pathway in Alzheimer's disease onset and development might increase our understanding of this devastating condition. On the other hand, therapeutic upregulation of SIRT1 might provide opportunities for the amelioration of Alzheimer's-disease-type neuropathology through inhibition of amyloidogenesis. Ultimately, further analysis into both aspects is necessary if any progress is to be made.
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Mitochondrial sirtuins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1645-51. [DOI: 10.1016/j.bbapap.2009.12.021] [Citation(s) in RCA: 182] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 12/18/2009] [Accepted: 12/24/2009] [Indexed: 12/11/2022]
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Xu Q, Lu R, Zhu ZF, Lv JQ, Wang LJ, Zhang W, Hu JW, Meng J, Lin G, Yao Z. Effects of tyroservatide on histone acetylation in lung carcinoma cells. Int J Cancer 2010; 128:460-72. [PMID: 20309941 DOI: 10.1002/ijc.25346] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 02/25/2010] [Indexed: 12/19/2022]
Abstract
Tyroservatide (YSV) is an active, low-molecular weight polypeptide shown to have antitumor effects on experimental hepatocarcinoma and lung carcinoma. The focus of our study was to observe the effects of YSV on several human lung carcinoma cell lines and explore its antitumor mechanism via its effect on histone acetylation. Our results showed that YSV significantly inhibited the proliferation of human lung carcinoma A549, NCIH460, NCIH292 and NCIH1299 cells, induced G(0) /G(1) cell cycle arrest and increased protein and mRNA levels of p21 and p27. Moreover, YSV treatment significantly inhibited histone deacetylase (HDAC) activity and resulted in the accumulation of acetylated histones H3 and H4 in total cellular chromatin and p21 gene-associated chromatin regions. Together these data suggest that the antitumor effects of YSV might be mediated by its inhibition of HDAC activity, selectively upregulating the expression of p21 by increasing the acetylation of histones associated with p21 gene regions, resulting in an induction of G₀/G₁ cell cycle arrest and inhibition of the proliferation of tumor cells. Our findings demonstrate that YSV may exhibit potent therapeutical effects on lung carcinoma.
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Affiliation(s)
- Qiong Xu
- Department of Immunology, Tianjin Medical University, Tianjin, China
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44
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Bertrand P. Inside HDAC with HDAC inhibitors. Eur J Med Chem 2010; 45:2095-116. [PMID: 20223566 DOI: 10.1016/j.ejmech.2010.02.030] [Citation(s) in RCA: 254] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 02/09/2010] [Accepted: 02/10/2010] [Indexed: 11/17/2022]
Abstract
Histone deacetylase inhibitors are a large group of diverse molecules intrinsically able to inhibit cell proliferation in various cancer cell lines. Their apoptotic effects have been linked to the modulation in the expression of several regulatory tumor suppressor genes caused by the modified status of histone acetylation, a key event in chromatin remodelling. As the initial histone deacetylase activity of HDAC has been extended to other proteins, the possible other biological mechanisms modified by HDAC inhibitor treatments are still to be clarified. The need for HDAC isoform selective inhibitors is an important issue to serve this goal. This review discusses the approaches proposed by several research groups working on the synthesis of HDAC inhibitors, based on modelling studies and the way these findings were used to obtain new HDAC inhibitors with possible isoform selectivity.
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Affiliation(s)
- Philippe Bertrand
- Laboratoire Synthèse et Réactivité des Substances Naturelles, Université de Poitiers, CNRS-UMR 6514, 40 Avenue du Recteur Pineau, Poitiers, F-86022, France.
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Dowling DP, Gantt SL, Gattis SG, Fierke CA, Christianson DW. Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry 2009; 47:13554-63. [PMID: 19053282 DOI: 10.1021/bi801610c] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metal-dependent histone deacetylases (HDACs) require Zn(2+) or Fe(2+) to regulate the acetylation of lysine residues in histones and other proteins in eukaryotic cells. Isozyme HDAC8 is perhaps the archetypical member of the class I HDAC family and serves as a paradigm for studying structure-function relationships. Here, we report the structures of HDAC8 complexes with trichostatin A and 3-(1-methyl-4-phenylacetyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamide (APHA) in a new crystal form. The structure of the APHA complex reveals that the hydroxamate CO group accepts a hydrogen bond from Y306 but does not coordinate to Zn(2+) with favorable geometry, perhaps due to the constraints of its extended pi system. Additionally, since APHA binds to only two of the three protein molecules in the asymmetric unit of this complex, the structure of the third monomer represents the first structure of HDAC8 in the unliganded state. Comparison of unliganded and liganded structures illustrates ligand-induced conformational changes in the L2 loop that likely accompany substrate binding and catalysis. Furthermore, these structures, along with those of the D101N, D101E, D101A, and D101L variants, support the proposal that D101 is critical for the function of the L2 loop. However, amino acid substitutions for D101 can also trigger conformational changes of Y111 and W141 that perturb the substrate binding site. Finally, the structure of H143A HDAC8 complexed with an intact acetylated tetrapeptide substrate molecule confirms the importance of D101 for substrate binding and reveals how Y306 and the active site zinc ion together bind and activate the scissile amide linkage of acetyllysine.
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Affiliation(s)
- Daniel P Dowling
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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Gallo P, Latronico MVG, Gallo P, Grimaldi S, Borgia F, Todaro M, Jones P, Gallinari P, De Francesco R, Ciliberto G, Steinkühler C, Esposito G, Condorelli G. Inhibition of class I histone deacetylase with an apicidin derivative prevents cardiac hypertrophy and failure. Cardiovasc Res 2008; 80:416-24. [PMID: 18697792 DOI: 10.1093/cvr/cvn215] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
AIMS Recent studies have demonstrated the importance of chromatin remodelling via histone acetylation/deacetylation for the control of cardiac gene expression. Specific histone deacetylases (HDACs) can, in fact, play a positive or negative role in determining cardiac myocyte (CM) size. Here, we report on the effect on hypertrophy development of three inhibitors (HDACi) of class I HDACs. METHODS AND RESULTS The compounds were first analysed in vitro by scoring hypertrophy, expression of foetal genes, and apoptosis of neonatal rat CMs stimulated with phenylephrine, an alpha1-adrenergic agonist. This initial screening indicated that a truncated derivative of apicidin with class I HDAC specificity, denoted API-D, had the highest efficacy to toxicity ratio, and was thus selected for further analysis in vivo. Administration of this drug significantly decreased myocardial hypertrophy and foetal gene expression after 1 week of pressure overload induced by thoracic aortic constriction (TAC) in mice. After 9 weeks of TAC, when manifest heart failure is encountered, mice treated with API-D presented with significantly improved echocardiographic and haemodynamic parameters of cardiac function when compared with untreated TAC-operated mice. CONCLUSION The apicidin derivative, API-D, is capable of reducing hypertrophy and, consequently, the transition to heart failure in mice subjected to TAC. Treatment with this substance, therefore, holds promise as an important therapeutic option for heart failure.
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Affiliation(s)
- Pasquale Gallo
- Laboratory of Molecular Cardiology, San Raffaele Science Park Foundation, Rome, Italy
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Dowling DP, Di Costanzo L, Gennadios HA, Christianson DW. Evolution of the arginase fold and functional diversity. Cell Mol Life Sci 2008; 65:2039-55. [PMID: 18360740 PMCID: PMC2653620 DOI: 10.1007/s00018-008-7554-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Novel structural superfamilies can be identified among the large number of protein structures deposited in the Protein Data Bank based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein Evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. Here, we review the unique alpha/beta fold first observed in the manganese metalloenzyme rat liver arginase, consisting of a parallel eight-stranded beta-sheet surrounded by several helices, and its evolutionary relationship with the zinc-requiring and/or iron-requiring histone deacetylases and acetylpolyamine amidohydrolases. Structural comparisons reveal key features of the core alpha/beta fold that contribute to the divergent metal ion specificity and stoichiometry required for the chemical and biological functions of these enzymes.
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Affiliation(s)
- D. P. Dowling
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323 USA
| | - L. Di Costanzo
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323 USA
| | - H. A. Gennadios
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323 USA
| | - D. W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323 USA
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Sirtuins: novel targets for metabolic disease in drug development. Biochem Biophys Res Commun 2008; 373:341-4. [PMID: 18577374 DOI: 10.1016/j.bbrc.2008.06.048] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 06/16/2008] [Indexed: 01/22/2023]
Abstract
Calorie restriction extends lifespan and produces a metabolic profile desirable for treating diseases such as type 2 diabetes. SIRT1, an NAD(+)-dependent deacetylase, is a principal modulator of pathways downstream of calorie restriction that produces beneficial effects on glucose homeostasis and insulin sensitivity. Activation of SIRT1 leads to enhanced activity of multiple proteins, including peroxisome proliferator-activated receptor coactivator-1alpha (PGC-1alpha) and FOXO which helps to mediate some of the in vitro and in vivo effects of sirtuins. Resveratrol, a polyphenolic SIRT1 activator, mimics the effects of calorie restriction in lower organisms and in mice fed a high-fat diet ameliorates insulin resistance. In this review, we summarize recent research advances in unveiling the molecular mechanisms that underpin sirtuin as therapeutic candidates and discuss the possibility of using resveratrol as potential drug for treatment of diabetes.
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Biochemical and mutational analyses of AcuA, the acetyltransferase enzyme that controls the activity of the acetyl coenzyme a synthetase (AcsA) in Bacillus subtilis. J Bacteriol 2008; 190:5132-6. [PMID: 18487328 DOI: 10.1128/jb.00340-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The acuABC genes of Bacillus subtilis comprise a putative posttranslational modification system. The AcuA protein is a member of the Gcn5-related N-acetyltransferase (GNAT) superfamily, the AcuC protein is a class I histone deacetylase, and the role of the AcuB protein is not known. AcuA controls the activity of acetyl coenzyme A synthetase (AcsA; EC 6.2.1.1) in this bacterium by acetylating residue Lys549. Here we report the kinetic analysis of wild-type and variant AcuA proteins. We contrived a genetic scheme for the identification of AcuA residues critical for activity. Changes at residues H177 and G187 completely inactivated AcuA and led to its rapid turnover. Changes at residues R42 and T169 were less severe. In vitro assay conditions were optimized, and an effective means of inactivating the enzyme was found. The basic kinetic parameters of wild-type and variant AcuA proteins were obtained and compared to those of eukaryotic GNATs. Insights into how the isolated mutations may exert their deleterious effect were investigated by using the crystal structure of an AcuA homolog.
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Abstract
It has recently been suggested that perhaps as many as 20% of all mitochondrial proteins are regulated through lysine acetylation while SIRT3 has been implicated as an important mitochondrial protein deacetylase. It is therefore of crucial importance that the mitochondrial localization of potential protein deacetylases is unambiguously established. Although mouse SIRT3 was recently shown to be mitochondrial, HsSIRT3 (human SIRT3) was reported to be both nuclear and mitochondrial and to relocate from the nucleus to the mitochondrion upon cellular stress. In the present study we show, using various HsSIRT3 expression constructs and a combination of immunofluorescence and careful subcellular fractionation, that in contrast with earlier reports HsSIRT3 is exclusively mitochondrial. We discuss possible experimental explanations for these discrepancies. In addition we suggest, on the basis of the analysis of public genome databases, that the full-length mouse SIRT3 protein is a 37 kDa mitochondrial precursor protein contrary to the previously suggested 29 kDa protein.
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