1
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Hananya N, Koren S, Muir TW. Interrogating epigenetic mechanisms with chemically customized chromatin. Nat Rev Genet 2024; 25:255-271. [PMID: 37985791 PMCID: PMC11176933 DOI: 10.1038/s41576-023-00664-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2023] [Indexed: 11/22/2023]
Abstract
Genetic and genomic techniques have proven incredibly powerful for identifying and studying molecular players implicated in the epigenetic regulation of DNA-templated processes such as transcription. However, achieving a mechanistic understanding of how these molecules interact with chromatin to elicit a functional output is non-trivial, owing to the tremendous complexity of the biochemical networks involved. Advances in protein engineering have enabled the reconstitution of 'designer' chromatin containing customized post-translational modification patterns, which, when used in conjunction with sophisticated biochemical and biophysical methods, allow many mechanistic questions to be addressed. In this Review, we discuss how such tools complement established 'omics' techniques to answer fundamental questions on chromatin regulation, focusing on chromatin mark establishment and protein-chromatin interactions.
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Affiliation(s)
- Nir Hananya
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Shany Koren
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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2
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Pathak SJ, Baar K. Ketogenic Diets and Mitochondrial Function: Benefits for Aging But Not for Athletes. Exerc Sport Sci Rev 2023; 51:27-33. [PMID: 36123723 PMCID: PMC9762714 DOI: 10.1249/jes.0000000000000307] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2022] [Indexed: 12/24/2022]
Abstract
As humans age, we lose skeletal muscle mass, even in the absence of disease (sarcopenia), increasing the risk of death. Low mitochondrial mass and activity contributes to sarcopenia. It is our hypothesis that a ketogenic diet improves skeletal muscle mitochondrial mass and function when they have declined because of aging or disease, but not in athletes where mitochondrial quality is high.
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Affiliation(s)
- Suraj J. Pathak
- Department of Neurobiology, Physiology and Behavior
- Molecular, Cellular, and Integrative Physiology Graduate Group
| | - Keith Baar
- Department of Neurobiology, Physiology and Behavior
- Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, Davis, CA
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3
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Mladenov M, Bogdanov J, Bogdanov B, Hadzi-Petrushev N, Kamkin A, Stojchevski R, Avtanski D. Efficacy of the monocarbonyl curcumin analog C66 in the reduction of diabetes-associated cardiovascular and kidney complications. Mol Med 2022; 28:129. [PMID: 36316651 PMCID: PMC9620630 DOI: 10.1186/s10020-022-00559-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Curcumin is a polyphenolic compound derived from turmeric that has potential beneficial properties for cardiovascular and renal diseases and is relatively safe and inexpensive. However, the application of curcumin is rather problematic due to its chemical instability and low bioavailability. The experimental results showed improved chemical stability and potent pharmacokinetics of one of its analogs – (2E,6E)-2,6-bis[(2-trifluoromethyl)benzylidene]cyclohexanone (C66). There are several advantages of C66, like its synthetic accessibility, structural simplicity, improved chemical stability (in vitro and in vivo), presence of two reactive electrophilic centers, and good electron-accepting capacity. Considering these characteristics, we reviewed the literature on the application of C66 in resolving diabetes-associated cardiovascular and renal complications in animal models. We also summarized the mechanisms by which C66 is preventing the release of pro-oxidative and pro-inflammatory molecules in the priming and in activation stage of cardiomyopathy, renal fibrosis, and diabetic nephropathy. The cardiovascular protective effect of C66 against diabetes-induced oxidative damage is Nrf2 mediated but mainly dependent on JNK2. In general, C66 causes inhibition of JNK2, which reduces cardiac inflammation, fibrosis, oxidative stress, and apoptosis in the settings of diabetic cardiomyopathy. C66 exerts a powerful antifibrotic effect by reducing inflammation-related factors (MCP-1, NF-κB, TNF-α, IL-1β, COX-2, and CAV-1) and inducing the expression of anti-inflammatory factors (HO-1 and NEDD4), as well as targeting TGF-β/SMADs, MAPK/ERK, and PPAR-γ pathways in animal models of diabetic nephropathy. Based on the available evidence, C66 is becoming a promising drug candidate for improving cardiovascular and renal health.
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Affiliation(s)
- Mitko Mladenov
- grid.7858.20000 0001 0708 5391Faculty of Natural Sciences and Mathematics, Institute of Biology, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia ,grid.78028.350000 0000 9559 0613Department of Physiology, Pirogov Russian National Research Medical University, Ostrovityanova Street 1, Moscow, Russia
| | - Jane Bogdanov
- grid.7858.20000 0001 0708 5391Faculty of Natural Sciences and Mathematics, Institute of Chemistry, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
| | - Bogdan Bogdanov
- grid.7858.20000 0001 0708 5391Faculty of Natural Sciences and Mathematics, Institute of Chemistry, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
| | - Nikola Hadzi-Petrushev
- grid.7858.20000 0001 0708 5391Faculty of Natural Sciences and Mathematics, Institute of Biology, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia
| | - Andre Kamkin
- grid.78028.350000 0000 9559 0613Department of Physiology, Pirogov Russian National Research Medical University, Ostrovityanova Street 1, Moscow, Russia
| | - Radoslav Stojchevski
- grid.7858.20000 0001 0708 5391Faculty of Natural Sciences and Mathematics, Institute of Biology, Ss. Cyril and Methodius University in Skopje, Skopje, Macedonia ,grid.416477.70000 0001 2168 3646Friedman Diabetes Institute at Lenox Hill Hospital, Northwell Health, 110 E 59th Street, Suite 8B, Room 837, 10022 New York, NY USA
| | - Dimiter Avtanski
- grid.416477.70000 0001 2168 3646Friedman Diabetes Institute at Lenox Hill Hospital, Northwell Health, 110 E 59th Street, Suite 8B, Room 837, 10022 New York, NY USA ,grid.250903.d0000 0000 9566 0634Feinstein Institutes for Medical Research, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY USA
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4
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Pathak SJ, Zhou Z, Steffen D, Tran T, Ad Y, Ramsey JJ, Rutkowsky JM, Baar K. 2-month ketogenic diet preferentially alters skeletal muscle and augments cognitive function in middle aged female mice. Aging Cell 2022; 21:e13706. [PMID: 36148631 PMCID: PMC9577944 DOI: 10.1111/acel.13706] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/08/2022] [Accepted: 07/19/2022] [Indexed: 01/25/2023] Open
Abstract
The effect of a ketogenic diet (KD) on middle aged female mice is poorly understood as most of this work have been conducted in young female mice or diseased models. We have previously shown that an isocaloric KD started at middle age in male mice results in enhanced mitochondrial mass and function after 2 months on diet and improved cognitive behavior after being on diet for 14 months when compared with their control diet (CD) fed counterparts. Here, we aimed to investigate the effect of an isocaloric 2-month KD or CD on healthy 14-month-old female mice. At 16 months of age cognitive behavior tests were performed and then serum, skeletal muscle, cortex, and hippocampal tissues were collected for biochemical analysis. Two months on a KD resulted in enhanced cognitive behavior associated with anxiety, memory, and willingness to explore. The improved neurocognitive function was associated with increased PGC1α protein in the gastrocnemius (GTN) muscle and nuclear fraction. The KD resulted in a tissue specific increase in mitochondrial mass and kynurenine aminotransferase (KAT) levels in the GTN and soleus muscles, with a corresponding decrease in kynurenine and increase in kynurenic acid levels in serum. With KAT proteins being responsible for converting kynurenine into kynurenic acid, which is unable to cross the blood brain barrier and be turned into quinolinic acid-a potent neurotoxin, this study provides a potential mechanism of crosstalk between muscle and brain in mice on a KD that may contribute to improved cognitive function in middle-aged female mice.
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Affiliation(s)
- Suraj J. Pathak
- Department of Neurobiology, Physiology and BehaviorUniversity of CaliforniaDavisCaliforniaUSA
| | - Zeyu Zhou
- Department of Molecular Biosciences, School of Veterinary MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Danielle Steffen
- Department of Neurobiology, Physiology and BehaviorUniversity of CaliforniaDavisCaliforniaUSA
| | - Tommy Tran
- Department of Neurobiology, Physiology and BehaviorUniversity of CaliforniaDavisCaliforniaUSA
| | - Yael Ad
- Department of Molecular Biosciences, School of Veterinary MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Jon J. Ramsey
- Department of Molecular Biosciences, School of Veterinary MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Jennifer M. Rutkowsky
- Department of Molecular Biosciences, School of Veterinary MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Keith Baar
- Department of Neurobiology, Physiology and BehaviorUniversity of CaliforniaDavisCaliforniaUSA,Department of Physiology and Membrane Biology, School of MedicineUniversity of CaliforniaDavisCaliforniaUSA
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5
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Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
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Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
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6
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Liu J, Jin L, Chen X, Yuan Y, Zuo Y, Miao Y, Feng Q, Zhang H, Huang F, Guo T, Zhang L, Zhu L, Qian F, Zhu C, Zheng H. USP12 translocation maintains interferon antiviral efficacy by inhibiting CBP acetyltransferase activity. PLoS Pathog 2020; 16:e1008215. [PMID: 31899788 PMCID: PMC6961928 DOI: 10.1371/journal.ppat.1008215] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/15/2020] [Accepted: 11/13/2019] [Indexed: 01/25/2023] Open
Abstract
CREB-binding protein (CBP) participates in numerous transcription events. However, cell-intrinsic inhibitors of CBP are poorly defined. Here, we found that cellular USP12 interacts with the HAT domain of CBP and inhibits CBP’s acetyltransferase activity. Interestingly, USP12 positively regulates interferon (IFN) antiviral signaling independently of its deubiquitinase activity. Furthermore, we found that in IFN signaling USP12 translocates from the cytoplasm to the nucleus. The decrease in cytoplasmic USP12 facilitates CBP-induced acetylation and activation of IFN signaling proteins in the cytoplasm. Moreover, USP12 accumulation in the nucleus blocks CBP-induced acetylation of phosphorylated STAT1 (p-STAT1) and therefore inhibits the dephosphorylation effects of TCPTP on p-STAT1, which finally maintains nuclear p-STAT1 levels and IFN antiviral efficacy. USP12 nuclear translocation extends our understanding of the regulation of the strength of IFN antiviral signaling. Our study uncovers a cell-intrinsic regulation of CBP acetyltransferase activity and may provide potential strategies for IFN-based antiviral therapy. Activated p-STAT1 is a determinant for the strength of IFN antiviral signaling. We and other groups have demonstrated that activated p-STAT1 is regulated by multiple protein post-translational modifications, including phosphorylation, acetylation and ubiquitination. In this study, we revealed that CBP-mediated acetylation regulation of p-STAT1 is modulated by the deubiquitinase USP12 in a deubiquitinase activity-independent manner. USP12 translocates into the nucleus in IFN signaling, which critically regulates nuclear p-STAT1 levels and IFN antiviral activity by inhibiting CBP’s acetyltransferase activity. Importantly, we demonstrated that USP12 is a cell-intrinsic inhibitor of the acetyltransferase CBP. These findings promote the understanding of delicate regulation of both CBP-mediated acetylation and IFN antiviral signaling.
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Affiliation(s)
- Jin Liu
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China.,The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Lincong Jin
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Xiangjie Chen
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Yukang Yuan
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Yibo Zuo
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Ying Miao
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Qian Feng
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Hongguang Zhang
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Fan Huang
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Tingting Guo
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Liting Zhang
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
| | - Li Zhu
- The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Feng Qian
- The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Chuanwu Zhu
- The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Hui Zheng
- International Institute of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Infection and Immunity, Soochow University, Suzhou, China
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7
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Bhat S, Hwang Y, Gibson MD, Morgan MT, Taverna SD, Zhao Y, Wolberger C, Poirier MG, Cole PA. Hydrazide Mimics for Protein Lysine Acylation To Assess Nucleosome Dynamics and Deubiquitinase Action. J Am Chem Soc 2018; 140:9478-9485. [PMID: 29991262 PMCID: PMC6070418 DOI: 10.1021/jacs.8b03572] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A range of acyl-lysine (acyl-Lys) modifications on histones and other proteins have been mapped over the past decade but for most, their functional and structural significance remains poorly characterized. One limitation in the study of acyl-Lys containing proteins is the challenge of producing them or their mimics in site-specifically modified forms. We describe a cysteine alkylation-based method to install hydrazide mimics of acyl-Lys post-translational modifications (PTMs) on proteins. We have applied this method to install mimics of acetyl-Lys, 2-hydroxyisobutyryl-Lys, and ubiquityl-Lys that could be recognized selectively by relevant acyl-Lys modification antibodies. The acyl-Lys modified histone H3 proteins were reconstituted into nucleosomes to study nucleosome dynamics and stability as a function of modification type and site. We also installed a ubiquityl-Lys mimic in histone H2B and generated a diubiquitin analog, both of which could be cleaved by deubiquitinating enzymes. Nucleosomes containing the H2B ubiquityl-Lys mimic were used to study the SAGA deubiquitinating module's molecular recognition. These results suggest that acyl-Lys mimics offer a relatively simple and promising strategy to study the role of acyl-Lys modifications in the function, structure, and regulation of proteins and protein complexes.
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Affiliation(s)
- Shridhar Bhat
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Matthew D. Gibson
- Department of Physics, Ohio State University, Columbus, Ohio 43210, USA
| | - Michael T. Morgan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Yingming Zhao
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | | | - Philip A. Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Division of Genetics, Brigham and Women’s Hospital; Departments of Medicine and Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 77 Ave Louis Pasteur, HMS New Research Building, Boston, Massachusetts 02115, USA
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8
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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9
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Damiani E, Puebla-Osorio N, Lege BM, Liu J, Neelapu SS, Ullrich SE. Platelet activating factor-induced expression of p21 is correlated with histone acetylation. Sci Rep 2017; 7:41959. [PMID: 28157211 PMCID: PMC5291204 DOI: 10.1038/srep41959] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/30/2016] [Indexed: 02/07/2023] Open
Abstract
Ultraviolet (UV)-irradiated keratinocytes secrete the lipid mediator of inflammation, platelet-activating factor (PAF). PAF plays an essential role in UV-induced immune suppression and skin cancer induction. Dermal mast cell migration from the skin to the draining lymph nodes plays a prominent role in activating systemic immune suppression. UV-induced PAF activates mast cell migration by up-regulating mast cell CXCR4 surface expression. Recent findings indicate that PAF up-regulates CXCR4 expression via histone acetylation. UV-induced PAF also activates cell cycle arrest and disrupts DNA repair, in part by increasing p21 expression. Do epigenetic alterations play a role in p21 up-regulation? Here we show that PAF increases Acetyl-CREB-binding protein (CBP/p300) histone acetyltransferase expression in a time and dose-dependent fashion. Partial deletion of the HAT domain in the CBP gene, blocked these effects. Chromatin immunoprecipitation assays indicated that PAF-treatment activated the acetylation of the p21 promoter. PAF-treatment had no effect on other acetylating enzymes (GCN5L2, PCAF) indicating it is not a global activator of histone acetylation. This study provides further evidence that PAF activates epigenetic mechanisms to affect important cellular processes, and we suggest this bioactive lipid can serve as a link between the environment and the epigenome.
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Affiliation(s)
- Elisabetta Damiani
- Dipartimento di Scienze della Vita e dell'Ambiente, Universita' Politecnica delle Marche, Ancona, Italy
| | - Nahum Puebla-Osorio
- Department of Lymphoma and Myeloma, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Bree M Lege
- Department of Lymphoma and Myeloma, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Jingwei Liu
- Department of Lymphoma and Myeloma, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Sattva S Neelapu
- Department of Lymphoma and Myeloma, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
| | - Stephen E Ullrich
- Department of Immunology and The Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,The University of Texas Graduate School for Biomedical Sciences at Houston, The University of Texas, MD Anderson Cancer Center, Houston, Texas, USA
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10
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Abstract
Reversible protein phosphorylation is critically important in biology and medicine. Hundreds of thousands of sites of protein phosphorylation have been discovered but our understanding of the functions of the vast majority of these post-translational modifications is lacking. This review describes several chemical and biochemical methods that are under development and in current use to install phospho-amino acids and their mimics site-specifically into proteins. The relative merits of total chemical synthesis, semisynthesis, and nonsense suppression strategies for studying protein phosphorylation are discussed in terms of technical simplicity, scope, and versatility.
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Affiliation(s)
- Zan Chen
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, United States
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, United States.
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11
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Affiliation(s)
| | - Philip A. Cole
- Department
of Pharmacology
and Molecular Sciences, The Johns Hopkins
University School of Medicine, 725 North Wolfe Street, Hunterian 316, Baltimore, Maryland 21205, United States
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12
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Fan J, Krautkramer KA, Feldman JL, Denu JM. Metabolic regulation of histone post-translational modifications. ACS Chem Biol 2015; 10:95-108. [PMID: 25562692 DOI: 10.1021/cb500846u] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone post-translational modifications regulate transcription and other DNA-templated functions. This process is dynamically regulated by specific modifying enzymes whose activities require metabolites that either serve as cosubstrates or act as activators/inhibitors. Therefore, metabolism can influence histone modification by changing local concentrations of key metabolites. Physiologically, the epigenetic response to metabolism is important for nutrient sensing and environment adaption. In pathologic states, the connection between metabolism and histone modification mediates epigenetic abnormality in complex disease. In this review, we summarize recent studies of the molecular mechanisms involved in metabolic regulation of histone modifications and discuss their biological significance.
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Affiliation(s)
- Jing Fan
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - Kimberly A. Krautkramer
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - Jessica L. Feldman
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
| | - John M. Denu
- Department of Biomolecular Chemistry and the Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
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13
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Wang Y, Wang Y, Luo M, Wu H, Kong L, Xin Y, Cui W, Zhao Y, Wang J, Liang G, Miao L, Cai L. Novel curcumin analog C66 prevents diabetic nephropathy via JNK pathway with the involvement of p300/CBP-mediated histone acetylation. Biochim Biophys Acta Mol Basis Dis 2014; 1852:34-46. [PMID: 25446993 DOI: 10.1016/j.bbadis.2014.11.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 11/01/2014] [Accepted: 11/04/2014] [Indexed: 01/08/2023]
Abstract
Glomerulosclerosis and interstitial fibrosis represent the key events in development of diabetic nephropathy (DN), with connective tissue growth factor (CTGF), plasminogen activator inhibitor-1 (PAI-1) and fibronectin 1 (FN-1) playing important roles in these pathogenic processes. To investigate whether the plant metabolite curcumin, which exerts epigenetic modulatory properties when applied as a pharmacological agent, may prevent DN via inhibition of the JNK pathway and epigenetic histone acetylation, diabetic and age-matched non-diabetic control mice were administered a 3-month course of curcumin analogue (C66), c-Jun N-terminal kinase inhibitor (JNKi, sp600125), or vehicle alone. At treatment end, half of the mice were sacrificed for analysis and the other half were maintained without treatment for an additional 3 months. Renal JNK phosphorylation was found to be significantly increased in the vehicle-treated diabetic mice, but not the C66- and JNKi-treated diabetic mice, at both the 3-month and 6-month time points. C66 and JNKi treatment also significantly prevented diabetes-induced renal fibrosis and dysfunction. Diabetes-related increases in histone acetylation, histone acetyl transferases' (HATs) activity, and the p300/CBP HAT expression were also significantly attenuated by C66 or JNKi treatment. Chromatin immunoprecipitation assays showed that C66 and JNKi treatments decreased H3-lysine9/14-acetylation (H3K9/14Ac) level and p300/CBP occupancy at the CTGF, PAI-1 and FN-1 gene promoters. Thus, C66 may significantly and persistently prevent renal injury and dysfunction in diabetic mice via down-regulation of diabetes-related JNK activation and consequent suppression of the diabetes-related increases in HAT activity, p300/CBP expression, and histone acetylation.
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Affiliation(s)
- Yangwei Wang
- Department of Nephrology, Second Hospital of Jilin University, Changchun, China; Kosair Children's Hospital Research Institute and Department of Pediatrics of University of Louisville, Louisville, KY, USA
| | - Yonggang Wang
- Kosair Children's Hospital Research Institute and Department of Pediatrics of University of Louisville, Louisville, KY, USA; Cardiovascular Center, First Hospital of Jilin University, Changchun, China
| | - Manyu Luo
- Department of Nephrology, Second Hospital of Jilin University, Changchun, China; Kosair Children's Hospital Research Institute and Department of Pediatrics of University of Louisville, Louisville, KY, USA
| | - Hao Wu
- Department of Nephrology, Second Hospital of Jilin University, Changchun, China; Kosair Children's Hospital Research Institute and Department of Pediatrics of University of Louisville, Louisville, KY, USA
| | - Lili Kong
- Department of Nephrology, Second Hospital of Jilin University, Changchun, China; Kosair Children's Hospital Research Institute and Department of Pediatrics of University of Louisville, Louisville, KY, USA
| | - Ying Xin
- Kosair Children's Hospital Research Institute and Department of Pediatrics of University of Louisville, Louisville, KY, USA; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Wenpeng Cui
- Department of Nephrology, Second Hospital of Jilin University, Changchun, China; Kosair Children's Hospital Research Institute and Department of Pediatrics of University of Louisville, Louisville, KY, USA
| | - Yunjie Zhao
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jingying Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Lining Miao
- Department of Nephrology, Second Hospital of Jilin University, Changchun, China.
| | - Lu Cai
- Kosair Children's Hospital Research Institute and Department of Pediatrics of University of Louisville, Louisville, KY, USA; Department of Radiation Oncology, University of Louisville, Louisville, KY, USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY, USA.
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14
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Wang Y, Kavran JM, Chen Z, Karukurichi KR, Leahy DJ, Cole PA. Regulation of S-adenosylhomocysteine hydrolase by lysine acetylation. J Biol Chem 2014; 289:31361-72. [PMID: 25248746 DOI: 10.1074/jbc.m114.597153] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
S-Adenosylhomocysteine hydrolase (SAHH) is an NAD(+)-dependent tetrameric enzyme that catalyzes the breakdown of S-adenosylhomocysteine to adenosine and homocysteine and is important in cell growth and the regulation of gene expression. Loss of SAHH function can result in global inhibition of cellular methyltransferase enzymes because of high levels of S-adenosylhomocysteine. Prior proteomics studies have identified two SAHH acetylation sites at Lys(401) and Lys(408) but the impact of these post-translational modifications has not yet been determined. Here we use expressed protein ligation to produce semisynthetic SAHH acetylated at Lys(401) and Lys(408) and show that modification of either position negatively impacts the catalytic activity of SAHH. X-ray crystal structures of 408-acetylated SAHH and dually acetylated SAHH have been determined and reveal perturbations in the C-terminal hydrogen bonding patterns, a region of the protein important for NAD(+) binding. These crystal structures along with mutagenesis data suggest that such hydrogen bond perturbations are responsible for SAHH catalytic inhibition by acetylation. These results suggest how increased acetylation of SAHH may globally influence cellular methylation patterns.
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Affiliation(s)
- Yun Wang
- From the Deptartments of Pharmacology and Molecular Sciences and
| | - Jennifer M Kavran
- Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Zan Chen
- From the Deptartments of Pharmacology and Molecular Sciences and
| | | | - Daniel J Leahy
- From the Deptartments of Pharmacology and Molecular Sciences and Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Philip A Cole
- From the Deptartments of Pharmacology and Molecular Sciences and
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15
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Zhang X, Ouyang S, Kong X, Liang Z, Lu J, Zhu K, Zhao D, Zheng M, Jiang H, Liu X, Marmorstein R, Luo C. Catalytic mechanism of histone acetyltransferase p300: from the proton transfer to acetylation reaction. J Phys Chem B 2014; 118:2009-19. [PMID: 24521098 DOI: 10.1021/jp409778e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The transcriptional coactivator and histone acetyltransferase (HAT) p300 acetylates the four core histones and other transcription factors to regulate a plethora of fundamental biological processes including cell growth, development, oncogenesis and apoptosis. Recent structural and biochemical studies on the p300 HAT domain revealed a Theorell-Chance, or "hit-and-run", catalytic mechanism. Nonetheless, the chemical mechanism of the entire reaction process including the proton transfer (PT) scheme and consequent acetylation reaction route remains unclear. In this study, a combined computational strategy consisting of molecular modeling, molecular dynamic (MD) simulation, and quantum mechanics/molecular mechanics (QM/MM) simulation was applied to elucidate these important issues. An initial p300/H3/Ac-CoA complex structure was modeled and optimized using a 100 ns MD simulation. Residues that play important roles in substrate binding and the acetylation reaction were comprehensively investigated. For the first time, these studies reveal a plausible PT scheme consisting of Y1394, D1507, and a conserved crystallographic water molecule, with all components of the scheme being stable during the MD simulation and the energy barrier low for PT to occur. The two-dimensional potential energy surface for the nucleophilic attack process was also calculated. The comparison of potential energies for two possible elimination half-reaction mechanisms revealed that Y1467 reprotonates the coenzyme-A leaving group to form product. This study provides new insights into the detailed catalytic mechanism of p300 and has important implications for the discovery of novel small molecule regulators for p300.
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Affiliation(s)
- Xinlei Zhang
- Department of Medicinal Chemistry and Pharmaceutical Analysis, School of Pharmacy, Fourth Military Medical University , Xi'an 710032, China
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16
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Yu Y, Lutz S. Circular permutation: a different way to engineer enzyme structure and function. Trends Biotechnol 2011; 29:18-25. [DOI: 10.1016/j.tibtech.2010.10.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 10/11/2010] [Accepted: 10/18/2010] [Indexed: 12/15/2022]
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17
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Plass T, Schultz C. Covalent Labeling of Biomolecules in Living Cells. ADVANCED FLUORESCENCE REPORTERS IN CHEMISTRY AND BIOLOGY III 2011. [DOI: 10.1007/978-3-642-18035-4_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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