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Bonnici J, Oueini R, Salah E, Johansson C, Schofield CJ, Kawamura A. The catalytic domains of all human KDM5 JmjC demethylases catalyse N-methyl arginine demethylation. FEBS Lett 2023; 597:933-946. [PMID: 36700827 PMCID: PMC10952680 DOI: 10.1002/1873-3468.14586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/13/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023]
Abstract
The demethylation of Nε -methyllysine residues on histones by Jumonji-C lysine demethylases (JmjC-KDMs) has been established. A subset of JmjC-KDMs has also been reported to have Nω -methylarginine residue demethylase (RDM) activity. Here, we describe biochemical screening studies, showing that the catalytic domains of all human KDM5s (KDM5A-KDM5D), KDM4E and, to a lesser extent, KDM4A/D, have both KDM and RDM activities with histone peptides. Ras GTPase-activating protein-binding protein 1 peptides were shown to be RDM substrates for KDM5C/D. No RDM activity was observed with KDM1A and the other JmjC-KDMs tested. The results highlight the potential of JmjC-KDMs to catalyse reactions other than Nε -methyllysine demethylation. Although our study is limited to peptide fragments, the results should help guide biological studies investigating JmjC functions.
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Affiliation(s)
- Joanna Bonnici
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Chemistry – School of Natural and Environmental SciencesNewcastle UniversityUK
| | - Razanne Oueini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Catrine Johansson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Botnar Research Centre, NIHR Oxford Biomedical Research UnitUniversity of OxfordUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Chemistry – School of Natural and Environmental SciencesNewcastle UniversityUK
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Ahmad F, Dixit D, Joshi SD, Sen E. G9a inhibition induced PKM2 regulates autophagic responses. Int J Biochem Cell Biol 2016; 78:87-95. [PMID: 27417236 DOI: 10.1016/j.biocel.2016.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/04/2016] [Accepted: 07/11/2016] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation by histone methyltransferase G9a is known to control autophagic responses. As the link between autophagy and metabolic homeostasis is widely accepted, we investigated whether G9a affects metabolic circuitries to affect autophagic response in glioma cells. Both pharmacological inhibition and siRNA mediated knockdown of G9a increased autophagy marker LC3B in glioma cells. G9a inhibitor BIX-01294 (BIX) induced Akt-dependent increase in HIF-1α expression and activity. Inhibition of Akt-HIF-1α axis reversed BIX-mediated (i) increase in LC3B expression and (ii) decrease in Yes-associated protein 1 (YAP1) phosphorylation. YAP1 over-expression abrogated BIX induced increase in LC3B expression. Interestingly, BIX induced increase in metabolic modelers TIGAR (TP53-induced glycolysis and apoptosis regulator) and PKM2 (Pyruvate kinase M2) were crucial for BIX-mediated changes, as transfection with TIGAR mutant or PKM2 siRNA reversed BIX-mediated alterations in pYAP1 and LC3B expression. Coherent with the in vitro observation, BIX had no significant effect on the tumor burden in heterotypic xenograft glioma mouse model. Elevated LC3B and PKM2 in BIX-treated xenograft tissue was accompanied by decreased YAP1 levels. Taken together, our findings suggest that Akt-HIF-1α axis driven PKM2-YAP1 cross talk activates autophagic responses in glioma cells upon G9a inhibition.
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Affiliation(s)
- Fahim Ahmad
- National Brain Research Centre, Manesar, Haryana, India
| | - Deobrat Dixit
- National Brain Research Centre, Manesar, Haryana, India
| | | | - Ellora Sen
- National Brain Research Centre, Manesar, Haryana, India.
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Jung ES, Sim YJ, Jeong HS, Kim SJ, Yun YJ, Song JH, Jeon SH, Choe C, Park KT, Kim CH, Kim KS. Jmjd2C increases MyoD transcriptional activity through inhibiting G9a-dependent MyoD degradation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1081-94. [PMID: 26149774 DOI: 10.1016/j.bbagrm.2015.07.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 06/17/2015] [Accepted: 07/02/2015] [Indexed: 01/05/2023]
Abstract
Skeletal muscle cell differentiation requires a family of proteins called myogenic regulatory factors (MRFs) to which MyoD belongs. The activity of MyoD is under epigenetic regulation, however, the molecular mechanism by which histone KMTs and KDMs regulate MyoD transcriptional activity through methylation remains to be determined. Here we provide evidence for a unique regulatory mechanism of MyoD transcriptional activity through demethylation by Jmjd2C demethylase whose level increases during muscle differentiation. G9a decreases MyoD stability via methylation-dependent MyoD ubiquitination. Jmjd2C directly associates with MyoD in vitro and in vivo to demethylate and stabilize MyoD. The hypo-methylated MyoD due to Jmjd2C is significantly more stable than hyper-methylated MyoD by G9a. Cul4/Ddb1/Dcaf1 pathway is essential for the G9a-mediated MyoD degradation in myoblasts. By the stabilization of MyoD, Jmjd2C increases myogenic conversion of mouse embryonic fibroblasts and MyoD transcriptional activity with erasing repressive H3K9me3 level at the promoter of MyoD target genes. Collectively, Jmjd2C increases MyoD transcriptional activity to facilitate skeletal muscle differentiation by increasing MyoD stability through inhibiting G9a-dependent MyoD degradation.
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Affiliation(s)
- Eun-Shil Jung
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Ye-Ji Sim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Hoe-Su Jeong
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Su-Jin Kim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Ye-Jin Yun
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Joo-Hoon Song
- Bio Focus Co., Ltd., Gyeonggi-do 437-753, Republic of Korea
| | - Su-Hee Jeon
- Department of Biological & Environmental Science, Dongguk University, Seoul 100-175, Republic of Korea
| | - Chungyoul Choe
- Samsung Biomedical Research Institute, School of Medicine, Sungkyunkwan University, Seoul 135-710, Republic of Korea
| | - Kyung-Tae Park
- Center for Cancer Research, Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Chang-Hoon Kim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea.
| | - Kye-Seong Kim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 133-791, Republic of Korea.
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Vavilala DT, Reddy S, Sachchidanand, Prakash S, Ponnaluri VKC, Kumar A, Mukherji M. Prohexadione, a plant growth regulator, inhibits histone lysine demethylases and modulates epigenetics. Toxicol Rep 2014; 1:1152-1161. [PMID: 28962325 PMCID: PMC5598483 DOI: 10.1016/j.toxrep.2014.10.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/11/2014] [Accepted: 10/25/2014] [Indexed: 12/25/2022] Open
Abstract
Background Epigenetic modifications, particularly DNA methylation and posttranslational histone modifications regulate heritable changes in transcription without changes in the DNA sequence. Despite a number of studies showing clear links between environmental factors and DNA methylation, little is known about the effect of environmental factors on the recently identified histone lysine methylation. Since their identification numerous studies have establish critical role played by these enzymes in mammalian development. Objectives Identification of the Jumonji (Jmj) domain containing histone lysine demethylase have added a new dimension to epigenetic control of gene expression by dynamic regulation of histone methylation marks. The objective of our study was to evaluate the effect of prohexadione and trinexapac, widely used plant growth regulators of the acylcyclohexanediones class, on the enzymatic activity of histone lysine demethylases and histone modifications during the neural stem/progenitor cell differentiation. Methods Here we show that prohexadione, but not trinexapac, directly inhibits non-heme iron (II), 2-oxoglutarate-dependent histone lysine demethylase such as Jmjd2a. We used molecular modeling to show binding of prohexadione to Jmjd2a. We also performed in vitro demethylation assays to show the inhibitory effect of prohexadione on Jmjd2a. Further we tested this molecule in cell culture model of mouse hippocampal neural stem/progenitor cells to demonstrate its effect toward neuronal proliferation and differentiation. Results Molecular modeling studies suggest that prohexadione binds to the 2-oxoglutarate binding site of Jmjd2a demethylase. Treatment of primary neural stem/progenitor cells with prohexadione showed a concentration dependent reduction in their proliferation. Further, the prohexadione treated neurospheres were induced toward neurogenic lineage upon differentiation. Conclusions Our results describe an important chemico-biological interaction of prohexadione, in light of critical roles played by histone lysine demethylases in human health and diseases.
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Affiliation(s)
- Divya Teja Vavilala
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Sujatha Reddy
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Andhra Pradesh, India
| | - Sachchidanand
- National Institute of Pharmaceutical Education & Research (NIPER), Hajipur 844101, Bihar, India
| | - Swami Prakash
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - V K Chaithanya Ponnaluri
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Arvind Kumar
- Centre for Cellular and Molecular Biology, Hyderabad 500007, Andhra Pradesh, India
| | - Mridul Mukherji
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA
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Zheng W, Huang Y. The chemistry and biology of the α-ketoglutarate-dependent histone Nε-methyl-lysine demethylases. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00325f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
This review describes the current knowledge of the chemistry and biology of the physiologically and therapeutically important histone/protein Nε-methyl-lysine demethylation reactions catalyzed by the JMJD2 and JARID1 families of the α-ketoglutarate-dependent demethylases.
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Affiliation(s)
- Weiping Zheng
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Yajun Huang
- School of Pharmacy
- Jiangsu University
- Zhenjiang 212013
- P. R. China
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Epigenetic control and cancer: the potential of histone demethylases as therapeutic targets. Pharmaceuticals (Basel) 2012; 5:963-90. [PMID: 24280700 PMCID: PMC3816642 DOI: 10.3390/ph5090963] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/21/2012] [Accepted: 08/17/2012] [Indexed: 01/01/2023] Open
Abstract
The development of cancer involves an immense number of factors at the molecular level. These factors are associated principally with alterations in the epigenetic mechanisms that regulate gene expression profiles. Studying the effects of chromatin structure alterations, which are caused by the addition/removal of functional groups to specific histone residues, are of great interest as a promising way to identify markers for cancer diagnosis, classify the disease and determine its prognosis, and these markers could be potential targets for the treatment of this disease in its different forms. This manuscript presents the current point of view regarding members of the recently described family of proteins that exhibit histone demethylase activity; histone demethylases are genetic regulators that play a fundamental role in both the activation and repression of genes and whose expression has been observed to increase in many types of cancer. Some fundamental aspects of their association with the development of cancer and their relevance as potential targets for the development of new therapeutic strategies at the epigenetic level are discussed in the following manuscript.
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Abstract
Posttranslational modifications (PTMs) of histone proteins, such as acetylation, methylation, phosphorylation, and ubiquitylation, play essential roles in regulating chromatin dynamics. Combinations of different modifications on the histone proteins, termed 'histone code' in many cases, extend the information potential of the genetic code by regulating DNA at the epigenetic level. Many PTMs occur on non-histone proteins as well as histones, regulating protein-protein interactions, stability, localization, and/or enzymatic activities of proteins involved in diverse cellular processes. Although protein phosphorylation, ubiquitylation, and acetylation have been extensively studied, only a few proteins other than histones have been reported that can be modified by lysine methylation. This review summarizes the current progress on lysine methylation of non-histone proteins, and we propose that lysine methylation, like phosphorylation and acetylation, is a common PTM that regulates proteins in diverse cellular processes.
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Affiliation(s)
- Xi Zhang
- Department of Biochemistry & Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, 77030, USA
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Hillringhaus L, Yue WW, Rose NR, Ng SS, Gileadi C, Loenarz C, Bello SH, Bray JE, Schofield CJ, Oppermann U. Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family. J Biol Chem 2011; 286:41616-41625. [PMID: 21914792 PMCID: PMC3308871 DOI: 10.1074/jbc.m111.283689] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/09/2011] [Indexed: 12/13/2022] Open
Abstract
N(ε)-Methylations of histone lysine residues play critical roles in cell biology by "marking" chromatin for transcriptional activation or repression. Lysine demethylases reverse N(ε)-methylation in a sequence- and methylation-selective manner. The determinants of sequence selectivity for histone demethylases have been unclear. The human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone. Kinetic, crystallographic, and mutagenetic studies in vitro and in cells on KDM4A-E reveal that selectivity is determined by multiple interactions within the catalytic domain but outside the active site. Structurally informed phylogenetic analyses reveal that KDM4A-C orthologues exist in all genome-sequenced vertebrates with earlier animals containing only a single KDM4 enzyme. KDM4D orthologues only exist in eutherians (placental mammals) where they are conserved, including proposed substrate sequence-determining residues. The results will be useful for the identification of inhibitors for specific histone demethylases.
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Affiliation(s)
- Lars Hillringhaus
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Wyatt W Yue
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom
| | - Nathan R Rose
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Stanley S Ng
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom
| | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom
| | - Christoph Loenarz
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Simon H Bello
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - James E Bray
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Campus Roosevelt Drive, Headington, OX3 7DQ, United Kingdom; Botnar Research Centre, National Institute for Health Research Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology, and Musculoskeletal Sciences, Oxford, OX3 7LD, United Kingdom.
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