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Yang H, Su M, Liu M, Sheng Y, Zhu L, Yang L, Mu R, Zou J, Liu X, Liu L. Hepatic retinaldehyde deficiency is involved in diabetes deterioration by enhancing PCK1- and G6PC-mediated gluconeogenesis. Acta Pharm Sin B 2023; 13:3728-3743. [PMID: 37719384 PMCID: PMC10501888 DOI: 10.1016/j.apsb.2023.06.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/14/2023] [Accepted: 05/06/2023] [Indexed: 09/19/2023] Open
Abstract
Type 2 diabetes (T2D) is often accompanied with an induction of retinaldehyde dehydrogenase 1 (RALDH1 or ALDH1A1) expression and a consequent decrease in hepatic retinaldehyde (Rald) levels. However, the role of hepatic Rald deficiency in T2D progression remains unclear. In this study, we demonstrated that reversing T2D-mediated hepatic Rald deficiency by Rald or citral treatments, or liver-specific Raldh1 silencing substantially lowered fasting glycemia levels, inhibited hepatic glucogenesis, and downregulated phosphoenolpyruvate carboxykinase 1 (PCK1) and glucose-6-phosphatase (G6PC) expression in diabetic db/db mice. Fasting glycemia and Pck1/G6pc mRNA expression levels were strongly negatively correlated with hepatic Rald levels, indicating the involvement of hepatic Rald depletion in T2D deterioration. A similar result that liver-specific Raldh1 silencing improved glucose metabolism was also observed in high-fat diet-fed mice. In primary human hepatocytes and oleic acid-treated HepG2 cells, Rald or Rald + RALDH1 silencing resulted in decreased glucose production and downregulated PCK1/G6PC mRNA and protein expression. Mechanistically, Rald downregulated direct repeat 1-mediated PCK1 and G6PC expression by antagonizing retinoid X receptor α, as confirmed by luciferase reporter assays and molecular docking. These results highlight the link between hepatic Rald deficiency, glucose dyshomeostasis, and the progression of T2D, whilst also suggesting RALDH1 as a potential therapeutic target for T2D.
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Affiliation(s)
- Hanyu Yang
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Mengxiang Su
- Department of Pharmaceutical Analysis, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Ming Liu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yun Sheng
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Liang Zhu
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lu Yang
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Ruijing Mu
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jianjun Zou
- Department of Clinical Pharmacology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Xiaodong Liu
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Li Liu
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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2
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Rastinejad F. Retinoic acid receptor structures: the journey from single domains to full-length complex. J Mol Endocrinol 2022; 69:T25-T36. [PMID: 36069789 DOI: 10.1530/jme-22-0113] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 11/08/2022]
Abstract
The retinoic acid receptors (RARα, β, and γ) are multi-domain polypeptides that heterodimerize with retinoid X receptors (RXRα, β, and γ) to form functional transcription factors. Understanding the three-dimensional molecular organization of these nuclear receptors (NRs) began with RAR and RXR DNA-binding domains (DBDs), and were followed with studies on isolated ligand-binding domains (LBDs). The more complete picture emerged in 2017 with the multi-domain crystal structure of RXRα-RARβ on its response element with retinoic acid molecules and coactivator segments on both proteins. The analysis of that structure and its complementary studies have clarified the direct communication pathways within RXR-RAR polypeptides, through which DNA binding, protein-ligand, and protein-protein interactions are integrated for overall functional responses. Understanding the molecular connections in the RXR-RAR complex has benefited from direct observations of the multi-domain structures of RXRα-PPARγ, RXRα-LXRβ, HNF-4α homodimer, and androgen receptor homodimer, each bound to its response element. These comprehensive NR structures show unique quaternary architectures, yet all have DBD-DBD, LBD-LBD, and DBD-LBD domain-domain contacts within them. These convergence zones allow signals from discrete domains of their polypeptides to be propagated and integrated across their entire complex, shaping their overall responses in an allosteric fashion.
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Affiliation(s)
- Fraydoon Rastinejad
- Nuffield Department of Medicine, University of Oxford, Target Discovery Institute (NDM RB), Oxford, UK
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3
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Cassim Bawa FN, Gopoju R, Xu Y, Hu S, Zhu Y, Chen S, Jadhav K, Zhang Y. Retinoic Acid Receptor Alpha (RARα) in Macrophages Protects from Diet-Induced Atherosclerosis in Mice. Cells 2022; 11:3186. [PMID: 36291054 PMCID: PMC9600071 DOI: 10.3390/cells11203186] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 08/13/2023] Open
Abstract
Retinoic acid signaling plays an important role in regulating lipid metabolism and inflammation. However, the role of retinoic acid receptor alpha (RARα) in atherosclerosis remains to be determined. In the current study, we investigated the role of macrophage RARα in the development of atherosclerosis. Macrophages isolated from myeloid-specific Rarα-/- (RarαMac-/-) mice showed increased lipid accumulation and inflammation and reduced cholesterol efflux compared to Rarαfl/fl (control) mice. All-trans retinoic acid (AtRA) induced ATP-binding cassette subfamily A member 1 (Abca1) and Abcg1 expression and cholesterol efflux in both RarαMac-/- mice and Rarαfl/fl mice. In Ldlr-/- mice, myeloid ablation of RARα significantly reduced macrophage Abca1 and Abcg1 expression and cholesterol efflux, induced inflammatory genes, and aggravated Western diet-induced atherosclerosis. Our data demonstrate that macrophage RARα protects against atherosclerosis, likely via inducing cholesterol efflux and inhibiting inflammation.
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Affiliation(s)
- Fathima N. Cassim Bawa
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
- School of Biomedical Sciences, Kent State University, Kent, OH 44240, USA
| | - Raja Gopoju
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Yanyong Xu
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Shuwei Hu
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Yingdong Zhu
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
- School of Biomedical Sciences, Kent State University, Kent, OH 44240, USA
| | - Shaoru Chen
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Kavita Jadhav
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Yanqiao Zhang
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
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4
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Microsecond MD Simulations to Explore the Structural and Energetic Differences between the Human RXRα-PPARγ vs. RXRα-PPARγ-DNA. Molecules 2022; 27:molecules27185778. [PMID: 36144514 PMCID: PMC9503000 DOI: 10.3390/molecules27185778] [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: 08/08/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
The heterodimeric complex between retinoic X receptor alpha (RXRα) and peroxisome proliferator-activated receptor gamma (PPARγ) is one of the most important and predominant regulatory systems, controlling lipid metabolism by binding to specific DNA promoter regions. X-ray and molecular dynamics (MD) simulations have revealed the average conformation adopted by the RXRα-PPARγ heterodimer bound to DNA, providing information about how multiple domains communicate to regulate receptor properties. However, knowledge of the energetic basis of the protein-ligand and protein-protein interactions is still lacking. Here we explore the structural and energetic mechanism of RXRα-PPARγ heterodimer bound or unbound to DNA and forming complex with co-crystallized ligands (rosiglitazone and 9-cis-retinoic acid) through microsecond MD simulations, molecular mechanics generalized Born surface area binding free energy calculations, principal component analysis, the free energy landscape, and correlated motion analysis. Our results suggest that DNA binding alters correlated motions and conformational mobility within RXRα–PPARγ system that impact the dimerization and the binding affinity on both receptors. Intradomain correlated motions denotes a stronger correlation map for RXRα-PPARγ-DNA than RXRα-PPARγ, involving residues at the ligand binding site. In addition, our results also corroborated the greater role of PPARγ in regulation of the free and bound DNA state.
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5
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Prakash S, Saini S, Kumari S, Singh B, Kureel AK, Rai AK. Retinoic acid restores the levels of cellular cholesterol in Leishmania donovani infected macrophages by increasing npc1 and npc2 expressions. Biochimie 2022; 198:23-32. [PMID: 35272007 DOI: 10.1016/j.biochi.2022.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/20/2022]
Abstract
Visceral leishmaniasis (VL) is a fatal form among all forms of leishmaniasis and is caused by visceralization of the Leishmania donovani (Ld) parasite to the critical organs. Mild to severe malnutrition is common in VL patients and the deficiency of retinoic acid (RA), an important micronutrient, results in a compromised state of immune response in macrophages (mφ) leading to the increased parasite load. In the continuation of our earlier work, we observed loss of cellular cholesterol in infected mφ in the absence of RA i.e., upon inhibition of RALDH pathway. Moreover, the Leishmania utilizes host cholesterol for the establishment of infection and causes a decrease in the expressions of Niemann-Pick C2 (npc2) and Niemann-Pick C1 (npc1) genes involved in the uptake of extracellular cholesterol. This results in reduced levels of cellular cholesterol in infected mφ. Intrigued by this, as the first sign of our hypothesis, we investigated the presence of RA Response Element (RARE) sequences in the upstream of npc1 and npc2 genes. To functionally confirm this, we measured their expressions and the levels of cellular cholesterol in Ld infected mφ in the absence (i.e., using an inhibitor of RALDH pathway) and presence of RA. We found restoration of the levels of cellular cholesterol in infected mφ under the supplementation of RA resulting in the decreased parasite load. Hence, the supplementation of RA with the standard therapy and/or preventive use of RA could be potentially an advancement in the treatment and cure of VL patients.
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Affiliation(s)
- Satya Prakash
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, 211004, UP, India
| | - Sheetal Saini
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, 211004, UP, India
| | - Smita Kumari
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, 211004, UP, India
| | - Bharat Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, 211004, UP, India
| | - Amit Kumar Kureel
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, 211004, UP, India
| | - Ambak Kumar Rai
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, 211004, UP, India.
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6
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Osz J, McEwen AG, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mély Y, Cianférani S, Jeffries CM, Svergun DI, Rochel N. Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR-RXR. Nucleic Acids Res 2020; 48:9969-9985. [PMID: 32974652 PMCID: PMC7515732 DOI: 10.1093/nar/gkaa697] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/16/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
Abstract
Retinoic acid receptors (RARs) as a functional heterodimer with retinoid X receptors (RXRs), bind a diverse series of RA-response elements (RAREs) in regulated genes. Among them, the non-canonical DR0 elements are bound by RXR–RAR with comparable affinities to DR5 elements but DR0 elements do not act transcriptionally as independent RAREs. In this work, we present structural insights for the recognition of DR5 and DR0 elements by RXR–RAR heterodimer using x-ray crystallography, small angle x-ray scattering, and hydrogen/deuterium exchange coupled to mass spectrometry. We solved the crystal structures of RXR–RAR DNA-binding domain in complex with the Rarb2 DR5 and RXR–RXR DNA-binding domain in complex with Hoxb13 DR0. While cooperative binding was observed on DR5, the two molecules bound non-cooperatively on DR0 on opposite sides of the DNA. In addition, our data unveil the structural organization and dynamics of the multi-domain RXR–RAR DNA complexes providing evidence for DNA-dependent allosteric communication between domains. Differential binding modes between DR0 and DR5 were observed leading to differences in conformation and structural dynamics of the multi-domain RXR–RAR DNA complexes. These results reveal that the topological organization of the RAR binding element confer regulatory information by modulating the overall topology and structural dynamics of the RXR–RAR heterodimers.
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Affiliation(s)
- Judit Osz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Alastair G McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Maxime Bourguet
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Frédéric Przybilla
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pierre Poussin-Courmontagne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
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7
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Liu Y, Liu F, Liang W, Zhu L, Lantz RC, Zhu J, Chen Y. Arsenic represses airway epithelial mucin expression by affecting retinoic acid signaling pathway. Toxicol Appl Pharmacol 2020; 394:114959. [PMID: 32201329 PMCID: PMC10510759 DOI: 10.1016/j.taap.2020.114959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/14/2020] [Accepted: 03/18/2020] [Indexed: 12/31/2022]
Abstract
Arsenic is a ubiquitous environmental toxicant, found in high concentrations worldwide. Although abundant research has dealt with arsenic-induced cancers, studies on mechanisms of non-malignant lung diseases have not been complete. In addition, decades of research have mostly concentrated on high-dose arsenic exposure, which has very limited use in modeling the biological effects of today's low-dose exposures. Indeed, accumulated evidence has shown that low-dose arsenic exposure (i.e. ≤100 ppb) may also alter lung homeostasis by causing host susceptibility to viral infection. However, the underlying mechanism of this alteration is unknown. In this study, we found that low-dose sodium arsenite (As (III)) repressed major airway mucins-MUC5AC and MUC5B at both mRNA and protein levels. We further demonstrated that this repression was not caused by cellular toxicity or mediated by the reduction of a common mucin-inducing pathway-EGFR. Other established mucin activators- dsRNA, IL1β or IL17 were not able to override As (III)-induced mucin repression. Interestingly, the suppressing effect of As (III) appeared to be partially reversible, and supplementation of all trans retinoic acid (t-RA) doses dependently restored mucin gene expression. Further analyses indicated that As (III) treatment significantly reduced the protein level of retinoic acid receptors (RARα, γ and RXRα) as well as RARE promoter reporter activity. Therefore, our study fills in an important knowledge gap in the field of low-dose arsenic exposure. The interference of RA signaling, and mucin gene expression may be important pathogenic factors in low-dose arsenic induced lung toxicity.
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Affiliation(s)
- Yuchen Liu
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China; Department of Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, AZ 85724, United States of America
| | - Fangwei Liu
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, AZ 85724, United States of America
| | - Weifeng Liang
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China; Department of Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, AZ 85724, United States of America
| | - Lingxiang Zhu
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, AZ 85724, United States of America
| | - R Clark Lantz
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, United States of America
| | - Jiapeng Zhu
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China; Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu, China.
| | - Yin Chen
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Arizona, Tucson, AZ 85724, United States of America; Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ 85724, United States of America.
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8
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Abstract
Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) to regulate gene expression. The heterodimer recognizes the genome via a large and diverse repertoire of DNA response elements. Assessing the binding mode of RAR and RXR with various DNA response elements is important for understanding how they select their binding site and how DNA sequence and topology allosterically regulate RAR function. A number of complementary assays are often employed for analysis of the binding mode. To biochemically and structurally characterize RAR and RXR-DNA complexes, we describe how to express and purify RAR and RXR-DNA binding domains (DBDs) and multidomain constructs. We also describe the use of electrospray ionization mass spectrometry (ESI MS) and isothermal titration calorimetry (ITC) that give information about stoichiometry and binding affinity, as well as our approaches for co-crystallization of RAR and RXR DBDs with DNA.
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Affiliation(s)
- Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Judit Osz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France; Centre National de la Recherche Scientifique, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, Illkirch, France; Université de Strasbourg, Illkirch, France.
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9
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Penvose A, Keenan JL, Bray D, Ramlall V, Siggers T. Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity. Nat Commun 2019; 10:2514. [PMID: 31175293 PMCID: PMC6555819 DOI: 10.1038/s41467-019-10264-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 05/02/2019] [Indexed: 01/06/2023] Open
Abstract
The type II nuclear receptors (NRs) function as heterodimeric transcription factors with the retinoid X receptor (RXR) to regulate diverse biological processes in response to endogenous ligands and therapeutic drugs. DNA-binding specificity has been proposed as a primary mechanism for NR gene regulatory specificity. Here we use protein-binding microarrays (PBMs) to comprehensively analyze the DNA binding of 12 NR:RXRα dimers. We find more promiscuous NR-DNA binding than has been reported, challenging the view that NR binding specificity is defined by half-site spacing. We show that NRs bind DNA using two distinct modes, explaining widespread NR binding to half-sites in vivo. Finally, we show that the current models of NR specificity better reflect binding-site activity rather than binding-site affinity. Our rich dataset and revised NR binding models provide a framework for understanding NR regulatory specificity and will facilitate more accurate analyses of genomic datasets. The type II nuclear receptors (NRs) and the retinoid X receptor (RXR) form heterodimeric transcription factors to regulate development, metabolism, and inflammation. Here the authors employ protein-binding microarrays to comprehensively analyze the DNA binding of 12 NR:RXRα heterodimers, and report promiscuous NR-DNA binding.
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Affiliation(s)
- Ashley Penvose
- Department of Biology, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Jessica L Keenan
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - David Bray
- Biological Design Center, Boston University, Boston, MA, 02215, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - Vijendra Ramlall
- Department of Biology, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Trevor Siggers
- Department of Biology, Boston University, Boston, MA, 02215, USA. .,Biological Design Center, Boston University, Boston, MA, 02215, USA. .,Bioinformatics Program, Boston University, Boston, MA, 02215, USA.
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10
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Meijer FA, Leijten-van de Gevel IA, de Vries RMJM, Brunsveld L. Allosteric small molecule modulators of nuclear receptors. Mol Cell Endocrinol 2019; 485:20-34. [PMID: 30703487 DOI: 10.1016/j.mce.2019.01.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 02/08/2023]
Abstract
Nuclear Receptors (NRs) are multi-domain proteins, whose natural regulation occurs via ligands for a classical, orthosteric, binding pocket and via intra- and inter-domain allosteric mechanisms. Allosteric modulation of NRs via synthetic small molecules has recently emerged as an interesting entry to address the need for small molecules targeting NRs in pathology, via novel modes of action and with beneficial profiles. In this review the general concept of allosteric modulation in drug discovery is first discussed, serving as a background and inspiration for NRs. Subsequently, the review focuses on examples of small molecules that allosterically modulate NRs, with a strong focus on structural information and the ligand binding domain. Recently discovered nanomolar potent allosteric site NR modulators are catapulting allosteric targeting of NRs to the center of attention. The obtained insights serve as a basis for recommendations for the next steps to take in allosteric small molecular targeting of NRs.
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Affiliation(s)
- Femke A Meijer
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Iris A Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Rens M J M de Vries
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands.
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11
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Okafor CD, Colucci JK, Ortlund EA. Ligand-Induced Allosteric Effects Governing SR Signaling. NUCLEAR RECEPTOR RESEARCH 2019. [DOI: 10.32527/2019/101382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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12
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Abstract
The nuclear receptor family of transcription factor proteins mediates endocrine function and plays critical roles in the development, physiology and pharmacology. Malfunctioning nuclear receptors are associated with several disease states. The functional activity of nuclear receptors is regulated by small molecular hormonal and synthetic molecules. Multiple sources of evidence have identified and distinguished between the different allosteric pathways initiated by ligands, DNA and cofactors such as co-activators and co-repressors. Also, these biophysical studies are attempting to determine how these pathways that regulate co-activator and DNA recognition can control gene transcription. Thus, there is a growing interest in determining the genome-scale impact of allostery in nuclear receptors. Today, it is accepted that a detailed understanding of the allosteric regulatory pathways within the nuclear receptor molecular complex will enable the development of efficient drug therapies in the long term.
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Affiliation(s)
- Elias J Fernandez
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, USA.
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13
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Stebbins MJ, Lippmann ES, Faubion MG, Daneman R, Palecek SP, Shusta EV. Activation of RARα, RARγ, or RXRα Increases Barrier Tightness in Human Induced Pluripotent Stem Cell-Derived Brain Endothelial Cells. Biotechnol J 2018; 13:10.1002/biot.201700093. [PMID: 28960887 PMCID: PMC5796863 DOI: 10.1002/biot.201700093] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/18/2017] [Indexed: 12/14/2022]
Abstract
The blood-brain barrier (BBB) is critical to central nervous system (CNS) health. Brain microvascular endothelial cells (BMECs) are often used as in vitro BBB models for studying BBB dysfunction and therapeutic screening applications. Human pluripotent stem cells (hPSCs) can be differentiated to cells having key BMEC barrier and transporter properties, offering a renewable, scalable source of human BMECs. hPSC-derived BMECs have previously been shown to respond to all-trans retinoic acid (RA), and the goal of this study was to identify the stages at which differentiating human induced pluripotent stem cells (iPSCs) respond to activation of RA receptors (RARs) to impart BBB phenotypes. Here the authors identified that RA application to iPSC-derived BMECs at days 6-8 of differentiation led to a substantial elevation in transendothelial electrical resistance and induction of VE-cadherin expression. Specific RAR agonists identified RARα, RARγ, and RXRα as receptors capable of inducing barrier phenotypes. Moreover, RAR/RXRα costimulation elevated VE-cadherin expression and improved barrier fidelity to levels that recapitulated the effects of RA. This study elucidates the roles of RA signaling in iPSC-derived BMEC differentiation, and identifies directed agonist approaches that can improve BMEC fidelity for drug screening studies while also distinguishing potential nuclear receptor targets to explore in BBB dysfunction and therapy.
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Affiliation(s)
- Matthew J. Stebbins
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Ethan S. Lippmann
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, United States of America
| | - Madeline G. Faubion
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Richard Daneman
- Departments of Neuroscience and Pharmacology, University of California-San Diego, San Diego, CA, United States of America
| | - Sean P. Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Eric V. Shusta
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States of America
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14
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Chandra V, Wu D, Li S, Potluri N, Kim Y, Rastinejad F. The quaternary architecture of RARβ-RXRα heterodimer facilitates domain-domain signal transmission. Nat Commun 2017; 8:868. [PMID: 29021580 PMCID: PMC5636793 DOI: 10.1038/s41467-017-00981-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/09/2017] [Indexed: 12/11/2022] Open
Abstract
Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor β-retinoic X receptor α (RARβ-RXRα) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RARβ ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within their quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its heterodimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.Nuclear receptors (NR) are multidomain proteins, which makes their crystallization challenging. Here the authors present the crystal structure of the retinoic acid receptor β-retinoic X receptor α (RARβ-RXRα) heterodimer bound to DNA, ligands and coactivator peptides, which shows that NR quaternary architectures are variable.
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Affiliation(s)
- Vikas Chandra
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, 32827, USA
| | - Dalei Wu
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, 32827, USA
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Qingdao, Shandong, 266237, China
| | - Sheng Li
- Department of Medicine and UCSD DXMS Proteomics Resource, University of California, San Diego, La Jolla, CA, 92023, USA
| | - Nalini Potluri
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, 32827, USA
| | - Youngchang Kim
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Fraydoon Rastinejad
- Integrative Metabolism Program, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, 32827, USA.
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15
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GATA1 Binding Kinetics on Conformation-Specific Binding Sites Elicit Differential Transcriptional Regulation. Mol Cell Biol 2016; 36:2151-67. [PMID: 27215385 DOI: 10.1128/mcb.00017-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 05/17/2016] [Indexed: 01/19/2023] Open
Abstract
GATA1 organizes erythroid and megakaryocytic differentiation by orchestrating the expression of multiple genes that show diversified expression profiles. Here, we demonstrate that GATA1 monovalently binds to a single GATA motif (Single-GATA) while a monomeric GATA1 and a homodimeric GATA1 bivalently bind to two GATA motifs in palindromic (Pal-GATA) and direct-repeat (Tandem-GATA) arrangements, respectively, and form higher stoichiometric complexes on respective elements. The amino-terminal zinc (N) finger of GATA1 critically contributes to high occupancy of GATA1 on Pal-GATA. GATA1 lacking the N finger-DNA association fails to trigger a rate of target gene expression comparable to that seen with the wild-type GATA1, especially when expressed at low level. This study revealed that Pal-GATA and Tandem-GATA generate transcriptional responses from GATA1 target genes distinct from the response of Single-GATA. Our results support the notion that the distinct alignments in binding motifs are part of a critical regulatory strategy that diversifies and modulates transcriptional regulation by GATA1.
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16
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Bono MR, Tejon G, Flores-Santibañez F, Fernandez D, Rosemblatt M, Sauma D. Retinoic Acid as a Modulator of T Cell Immunity. Nutrients 2016; 8:E349. [PMID: 27304965 PMCID: PMC4924190 DOI: 10.3390/nu8060349] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 05/20/2016] [Accepted: 06/01/2016] [Indexed: 12/30/2022] Open
Abstract
Vitamin A, a generic designation for an array of organic molecules that includes retinal, retinol and retinoic acid, is an essential nutrient needed in a wide array of aspects including the proper functioning of the visual system, maintenance of cell function and differentiation, epithelial surface integrity, erythrocyte production, reproduction, and normal immune function. Vitamin A deficiency is one of the most common micronutrient deficiencies worldwide and is associated with defects in adaptive immunity. Reports from epidemiological studies, clinical trials and experimental studies have clearly demonstrated that vitamin A plays a central role in immunity and that its deficiency is the cause of broad immune alterations including decreased humoral and cellular responses, inadequate immune regulation, weak response to vaccines and poor lymphoid organ development. In this review, we will examine the role of vitamin A in immunity and focus on several aspects of T cell biology such as T helper cell differentiation, function and homing, as well as lymphoid organ development. Further, we will provide an overview of the effects of vitamin A deficiency in the adaptive immune responses and how retinoic acid, through its effect on T cells can fine-tune the balance between tolerance and immunity.
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Affiliation(s)
- Maria Rosa Bono
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile.
| | - Gabriela Tejon
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile.
| | - Felipe Flores-Santibañez
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile.
| | - Dominique Fernandez
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile.
| | - Mario Rosemblatt
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile.
- Fundacion Ciencia & Vida, Santiago 7780272, Chile.
- Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago 8370146, Chile.
| | - Daniela Sauma
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile.
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17
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Olivares AM, Moreno-Ramos OA, Haider NB. Role of Nuclear Receptors in Central Nervous System Development and Associated Diseases. J Exp Neurosci 2016; 9:93-121. [PMID: 27168725 PMCID: PMC4859451 DOI: 10.4137/jen.s25480] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/13/2022] Open
Abstract
The nuclear hormone receptor (NHR) superfamily is composed of a wide range of receptors involved in a myriad of important biological processes, including development, growth, metabolism, and maintenance. Regulation of such wide variety of functions requires a complex system of gene regulation that includes interaction with transcription factors, chromatin-modifying complex, and the proper recognition of ligands. NHRs are able to coordinate the expression of genes in numerous pathways simultaneously. This review focuses on the role of nuclear receptors in the central nervous system and, in particular, their role in regulating the proper development and function of the brain and the eye. In addition, the review highlights the impact of mutations in NHRs on a spectrum of human diseases from autism to retinal degeneration.
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Affiliation(s)
- Ana Maria Olivares
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Oscar Andrés Moreno-Ramos
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Neena B Haider
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
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18
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Chen J, Li Q. Implication of retinoic acid receptor selective signaling in myogenic differentiation. Sci Rep 2016; 6:18856. [PMID: 26830006 PMCID: PMC4735650 DOI: 10.1038/srep18856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/25/2015] [Indexed: 11/18/2022] Open
Abstract
Signaling molecules are important for committing individual cells into tissue-specific lineages during early vertebrate development. Retinoic acid (RA) is an important vertebrate morphogen, in that its concentration gradient is essential for correct patterning of the vertebrate embryo. RA signaling is mediated through the activation of retinoic acid receptors (RARs), which function as ligand-dependent transcription factors. In this study, we examined the molecular mechanisms of RAR-selective signaling in myogenic differentiation. We found that just like natural ligand RA, a RAR-selective ligand is an effective enhancer in the commitment of skeletal muscle lineage at the early stage of myogenic differentiation. Interestingly, the kinetics and molecular basis of the RAR-selective ligand in myogenic differentiation are similar to that of natural ligand RA. Also similar to natural ligand RA, the RAR-selective ligand enhances myogenic differentiation through β-catenin signaling pathway while inhibiting cardiac differentiation. Furthermore, while low concentrations of natural ligand RA or RAR-selective ligand regulate myogenic differentiation through RAR function and coactivator recruitment, high concentrations are critical to the expression of a model RA-responsive gene. Thus our data suggests that RAR-mediated gene regulation may be highly context-dependent, affected by locus-specific interaction or local chromatin environment.
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Affiliation(s)
- Jihong Chen
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Qiao Li
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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19
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Ricci CG, Silveira RL, Rivalta I, Batista VS, Skaf MS. Allosteric Pathways in the PPARγ-RXRα nuclear receptor complex. Sci Rep 2016; 6:19940. [PMID: 26823026 PMCID: PMC4731802 DOI: 10.1038/srep19940] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/07/2015] [Indexed: 02/08/2023] Open
Abstract
Understanding the nature of allostery in DNA-nuclear receptor (NR) complexes is of fundamental importance for drug development since NRs regulate the transcription of a myriad of genes in humans and other metazoans. Here, we investigate allostery in the peroxisome proliferator-activated/retinoid X receptor heterodimer. This important NR complex is a target for antidiabetic drugs since it binds to DNA and functions as a transcription factor essential for insulin sensitization and lipid metabolism. We find evidence of interdependent motions of Ω-loops and PPARγ-DNA binding domain with contacts susceptible to conformational changes and mutations, critical for regulating transcriptional functions in response to sequence-dependent DNA dynamics. Statistical network analysis of the correlated motions, observed in molecular dynamics simulations, shows preferential allosteric pathways with convergence centers comprised of polar amino acid residues. These findings are particularly relevant for the design of allosteric modulators of ligand-dependent transcription factors.
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Affiliation(s)
- Clarisse G Ricci
- Institute of Chemistry, University of Campinas-UNICAMP, Cx. P. 6154, Campinas SP 13084-862, Brazil
| | - Rodrigo L Silveira
- Institute of Chemistry, University of Campinas-UNICAMP, Cx. P. 6154, Campinas SP 13084-862, Brazil
| | - Ivan Rivalta
- Université de Lyon, CNRS, Laboratoire de Chimie, École Normale Supérieure de Lyon, UMR 5182, 46 Allée d'Italie, 69364 Lyon, Cedex 07, France.,Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8167, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520-8167, United States
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas-UNICAMP, Cx. P. 6154, Campinas SP 13084-862, Brazil
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20
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Chen Y, Sakamuru S, Huang R, Reese DH, Xia M. Identification of compounds that modulate retinol signaling using a cell-based qHTS assay. Toxicol In Vitro 2016; 32:287-96. [PMID: 26820057 DOI: 10.1016/j.tiv.2016.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/15/2016] [Accepted: 01/20/2016] [Indexed: 01/12/2023]
Abstract
In vertebrates, the retinol (vitamin A) signaling pathway (RSP) controls the biosynthesis and catabolism of all-trans retinoic acid (atRA), which regulates transcription of genes essential for embryonic development. Chemicals that interfere with the RSP to cause abnormal intracellular levels of atRA are potential developmental toxicants. To assess chemicals for the ability to interfere with retinol signaling, we have developed a cell-based RARE (Retinoic Acid Response Element) reporter gene assay to identify RSP disruptors. To validate this assay in a quantitative high-throughput screening (qHTS) platform, we screened the Library of Pharmacologically Active Compounds (LOPAC) in both agonist and antagonist modes. The screens detected known RSP agonists, demonstrating assay reliability, and also identified novel RSP agonists including kenpaullone, niclosamide, PD98059 and SU4312, and RSP antagonists including Bay 11-7085, LY294002, 3,4-Methylenedioxy-β-nitrostyrene, and topoisomerase inhibitors (camptothecin, topotecan, amsacrine hydrochloride, and idarubicin). When evaluated in the P19 pluripotent cell, these compounds were found to affect the expression of the Hoxa1 gene that is essential for embryo body patterning. These results show that the RARE assay is an effective qHTS approach for screening large compound libraries to identify chemicals that have the potential to adversely affect embryonic development through interference with retinol signaling.
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Affiliation(s)
- Yanling Chen
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, United States.
| | - Srilatha Sakamuru
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, United States
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, United States
| | - David H Reese
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, United States
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, United States
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21
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Niu H, Hadwiger G, Fujiwara H, Welch JS. Pathways of retinoid synthesis in mouse macrophages and bone marrow cells. J Leukoc Biol 2016; 99:797-810. [PMID: 26768478 DOI: 10.1189/jlb.2hi0415-146rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 12/18/2015] [Indexed: 12/31/2022] Open
Abstract
In vivo pathways of natural retinoid metabolism and elimination have not been well characterized in primary myeloid cells, even though retinoids and retinoid receptors have been strongly implicated in regulating myeloid maturation. With the use of a upstream activation sequence-GFP reporter transgene and retrovirally expressed Gal4-retinoic acid receptor α in primary mouse bone marrow cells, we identified 2 distinct enzymatic pathways used by mouse myeloid cells ex vivo to synthesize retinoic acid receptor α ligands from free vitamin A metabolites (retinyl acetate, retinol, and retinal). Bulk Kit(+) bone marrow progenitor cells use diethylaminobenzaldehyde-sensitive enzymes, whereas bone marrow-derived macrophages use diethylaminobenzaldehyde-insensitive enzymes to synthesize natural retinoic acid receptor α-activating retinoids (all-trans retinoic acid). Bone marrow-derived macrophages do not express the diethylaminobenzaldehyde-sensitive enzymes Aldh1a1, Aldh1a2, or Aldh1a3 but instead, express Aldh3b1, which we found is capable of diethylaminobenzaldehyde-insensitive synthesis of all trans-retinoic acid. However, under steady-state and stimulated conditions in vivo, diverse bone marrow cells and peritoneal macrophages showed no evidence of intracellular retinoic acid receptor α-activating retinoids, despite expression of these enzymes and a vitamin A-sufficient diet, suggesting that the enzymatic conversion of retinal is not the rate-limiting step in the synthesis of intracellular retinoic acid receptor α-activating retinoids in myeloid bone marrow cells and that retinoic acid receptor α remains in an unliganded configuration during adult hematopoiesis.
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Affiliation(s)
- Haixia Niu
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA and
| | - Gayla Hadwiger
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA and
| | - Hideji Fujiwara
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John S Welch
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA and
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22
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Zhang R, Wang Y, Li R, Chen G. Transcriptional Factors Mediating Retinoic Acid Signals in the Control of Energy Metabolism. Int J Mol Sci 2015; 16:14210-44. [PMID: 26110391 PMCID: PMC4490549 DOI: 10.3390/ijms160614210] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 02/07/2023] Open
Abstract
Retinoic acid (RA), an active metabolite of vitamin A (VA), is important for many physiological processes including energy metabolism. This is mainly achieved through RA-regulated gene expression in metabolically active cells. RA regulates gene expression mainly through the activation of two subfamilies in the nuclear receptor superfamily, retinoic acid receptors (RARs) and retinoid X receptors (RXRs). RAR/RXR heterodimers or RXR/RXR homodimers bind to RA response element in the promoters of RA target genes and regulate their expressions upon ligand binding. The development of metabolic diseases such as obesity and type 2 diabetes is often associated with profound changes in the expressions of genes involved in glucose and lipid metabolism in metabolically active cells. RA regulates some of these gene expressions. Recently, in vivo and in vitro studies have demonstrated that status and metabolism of VA regulate macronutrient metabolism. Some studies have shown that, in addition to RARs and RXRs, hepatocyte nuclear factor 4α, chicken ovalbumin upstream promoter-transcription factor II, and peroxisome proliferator activated receptor β/δ may function as transcriptional factors mediating RA response. Herein, we summarize current progresses regarding the VA metabolism and the role of nuclear receptors in mediating RA signals, with an emphasis on their implication in energy metabolism.
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Affiliation(s)
- Rui Zhang
- State Food and Drug Administration Hubei Center for Medical Equipment Quality Supervision and Testing, 666 High-Tech Avenue, Wuhan 430000, China.
| | - Yueqiao Wang
- Department of Nutrition and Food Hygiene, Wuhan University, 185 East Lake Road, Wuhan 430071, China.
| | - Rui Li
- Department of Nutrition and Food Hygiene, Wuhan University, 185 East Lake Road, Wuhan 430071, China.
| | - Guoxun Chen
- Department of Nutrition, University of Tennessee at Knoxville, 1215 West Cumberland Avenue, Knoxville, TN 37996, USA.
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23
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Guo Y, Brown C, Ortiz C, Noelle RJ. Leukocyte homing, fate, and function are controlled by retinoic acid. Physiol Rev 2015; 95:125-48. [PMID: 25540140 DOI: 10.1152/physrev.00032.2013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Although vitamin A was recognized as an "anti-infective vitamin" over 90 years ago, the mechanism of how vitamin A regulates immunity is only beginning to be understood. Early studies which focused on the immune responses in vitamin A-deficient (VAD) animals clearly demonstrated compromised immunity and consequently increased susceptibility to infectious disease. The active form of vitamin A, retinoic acid (RA), has been shown to have a profound impact on the homing and differentiation of leukocytes. Both pharmacological and genetic approaches have been applied to the understanding of how RA regulates the development and differentiation of various immune cell subsets, and how RA influences the development of immunity versus tolerance. These studies clearly show that RA profoundly impacts on cell- and humoral-mediated immunity. In this review, the early findings on the complex relationship between VAD and immunity are discussed as well as vitamin A metabolism and signaling within hematopoietic cells. Particular attention is focused on how RA impacts on T-cell lineage commitment and plasticity in various diseases.
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Affiliation(s)
- Yanxia Guo
- Department of Microbiology and Immunology, Dartmouth Medical School, Norris Cotton Cancer Center, Lebanon, New Hampshire; and Medical Research Council Centre of Transplantation, Guy's Hospital, King's College London, King's Health Partners, London, United Kingdom
| | - Chrysothemis Brown
- Department of Microbiology and Immunology, Dartmouth Medical School, Norris Cotton Cancer Center, Lebanon, New Hampshire; and Medical Research Council Centre of Transplantation, Guy's Hospital, King's College London, King's Health Partners, London, United Kingdom
| | - Carla Ortiz
- Department of Microbiology and Immunology, Dartmouth Medical School, Norris Cotton Cancer Center, Lebanon, New Hampshire; and Medical Research Council Centre of Transplantation, Guy's Hospital, King's College London, King's Health Partners, London, United Kingdom
| | - Randolph J Noelle
- Department of Microbiology and Immunology, Dartmouth Medical School, Norris Cotton Cancer Center, Lebanon, New Hampshire; and Medical Research Council Centre of Transplantation, Guy's Hospital, King's College London, King's Health Partners, London, United Kingdom
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24
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Structural basis of natural promoter recognition by the retinoid X nuclear receptor. Sci Rep 2015; 5:8216. [PMID: 25645674 PMCID: PMC4314640 DOI: 10.1038/srep08216] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/29/2014] [Indexed: 01/07/2023] Open
Abstract
Retinoid X receptors (RXRs) act as homodimers or heterodimerisation partners of class II nuclear receptors. RXR homo- and heterodimers bind direct repeats of the half-site (A/G)G(G/T)TCA separated by 1 nucleotide (DR1). We present a structural characterization of RXR-DNA binding domain (DBD) homodimers on several natural DR1s and an idealized symmetric DR1. Homodimers displayed asymmetric binding, with critical high-affinity interactions accounting for the 3' positioning of RXR in heterodimers on DR1s. Differing half-site and spacer DNA sequence induce changes in RXR-DBD homodimer conformation notably in the dimerization interface such that natural DR1s are bound with higher affinity than an idealized symmetric DR1. Subtle changes in the consensus DR1 DNA sequence therefore specify binding affinity through altered RXR-DBD-DNA contacts and changes in DBD conformation suggesting a general model whereby preferential half-site recognition determines polarity of heterodimer binding to response elements.
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25
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Understanding the roadmaps to induced pluripotency. Cell Death Dis 2014; 5:e1232. [PMID: 24832604 PMCID: PMC4047905 DOI: 10.1038/cddis.2014.205] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/24/2014] [Accepted: 04/04/2014] [Indexed: 11/23/2022]
Abstract
Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) by ectopic expression of transcription factors Oct4, Sox2, Klf4 and cMyc. Recent advancements have shown that small-molecule compounds can induce pluripotency, indicating that cell fate can be regulated by direct manipulation of intrinsic cell signaling pathways, thereby innovating our current understanding of reprogramming. The fact that lineage specifiers can induce pluripotency suggests that the pluripotent state is a fine balance between competing differentiation forces. Dissection of pluripotent roadmaps indicates that reprogramming is a process of reverse development, involving a series of complicated and distinct reprogramming stages. Evidence from mouse iPSC transplantation studies demonstrated that some certain but not all cells derived from iPSCs are immunogenic. These studies provide new ways to minimize reprogramming-induced abnormalities and maximize reprogramming efficiency to facilitate clinical development and use of iPSCs.
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26
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Abstract
Retinoid X Receptors (RXR) were initially identified as nuclear receptors binding with stereo-selectivity the vitamin A derivative 9-cis retinoic acid, although the relevance of this molecule as endogenous activator of RXRs is still elusive. Importantly, within the nuclear receptor superfamily, RXRs occupy a peculiar place, as they are obligatory partners for a number of other nuclear receptors, thus integrating the corresponding signaling pathways. In this chapter, we describe the structural features allowing RXR to form homo- and heterodimers, and the functional consequences of this unique ability. Furthermore, we discuss the importance of studying RXR activity at a genome-wide level in order to comprehensively address the biological implications of their action that is fundamental to understand to what extent RXRs could be exploited as new therapeutic targets.
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Affiliation(s)
- Federica Gilardi
- Center for Integrative Genomics, University of Lausanne, Genopode Building, 1015, Lausanne, Switzerland,
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Rastinejad F, Huang P, Chandra V, Khorasanizadeh S. Understanding nuclear receptor form and function using structural biology. J Mol Endocrinol 2013; 51:T1-T21. [PMID: 24103914 PMCID: PMC3871882 DOI: 10.1530/jme-13-0173] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear receptors (NRs) are a major transcription factor family whose members selectively bind small-molecule lipophilic ligands and transduce those signals into specific changes in gene programs. For over two decades, structural biology efforts were focused exclusively on the individual ligand-binding domains (LBDs) or DNA-binding domains of NRs. These analyses revealed the basis for both ligand and DNA binding and also revealed receptor conformations representing both the activated and repressed states. Additionally, crystallographic studies explained how NR LBD surfaces recognize discrete portions of transcriptional coregulators. The many structural snapshots of LBDs have also guided the development of synthetic ligands with therapeutic potential. Yet, the exclusive structural focus on isolated NR domains has made it difficult to conceptualize how all the NR polypeptide segments are coordinated physically and functionally in the context of receptor quaternary architectures. Newly emerged crystal structures of the peroxisome proliferator-activated receptor-γ-retinoid X receptor α (PPARγ-RXRα) heterodimer and hepatocyte nuclear factor (HNF)-4α homodimer have recently revealed the higher order organizations of these receptor complexes on DNA, as well as the complexity and uniqueness of their domain-domain interfaces. These emerging structural advances promise to better explain how signals in one domain can be allosterically transmitted to distal receptor domains, also providing much better frameworks for guiding future drug discovery efforts.
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Affiliation(s)
- Fraydoon Rastinejad
- Metabolic Signaling and Disease Program, Sanford-Burnham Medical Research Institute, Orlando, Florida 32827, USA
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28
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Siggers T, Gordân R. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res 2013; 42:2099-111. [PMID: 24243859 PMCID: PMC3936734 DOI: 10.1093/nar/gkt1112] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Binding of proteins to particular DNA sites across the genome is a primary determinant of specificity in genome maintenance and gene regulation. DNA-binding specificity is encoded at multiple levels, from the detailed biophysical interactions between proteins and DNA, to the assembly of multi-protein complexes. At each level, variation in the mechanisms used to achieve specificity has led to difficulties in constructing and applying simple models of DNA binding. We review the complexities in protein–DNA binding found at multiple levels and discuss how they confound the idea of simple recognition codes. We discuss the impact of new high-throughput technologies for the characterization of protein–DNA binding, and how these technologies are uncovering new complexities in protein–DNA recognition. Finally, we review the concept of multi-protein recognition codes in which new DNA-binding specificities are achieved by the assembly of multi-protein complexes.
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Affiliation(s)
- Trevor Siggers
- Department of Biology, Boston University, Boston, MA 02215, USA, Departments of Biostatistics and Bioinformatics, Computer Science, and Molecular Genetics and Microbiology, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
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29
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Chen J, Li Q. Enhancing myogenic differentiation of pluripotent stem cells with small molecule inducers. Cell Biosci 2013; 3:40. [PMID: 24172312 PMCID: PMC3953345 DOI: 10.1186/2045-3701-3-40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/16/2013] [Indexed: 03/01/2023] Open
Abstract
Pluripotent stem cells are able to differentiate into many types of cell lineages in response to differentiation cues. However, a pure population of lineage-specific cells is desirable for any potential clinical application. Therefore, induction of the pluripotent stem cells with lineage-specific regulatory signals, or small molecule inducers, is a prerequisite for effectively directing lineage specification for cell-based therapeutics. In this article, we provide in-depth analysis of recent research findings on small molecule inducers of the skeletal muscle lineage. We also provide perspectives on how different signaling pathways and chromatin dynamics converge to direct the differentiation of skeletal myocytes.
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Affiliation(s)
| | - Qiao Li
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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30
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Chen G. Roles of Vitamin A Metabolism in the Development of Hepatic Insulin Resistance. ISRN HEPATOLOGY 2013; 2013:534972. [PMID: 27335827 PMCID: PMC4890907 DOI: 10.1155/2013/534972] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/18/2013] [Indexed: 02/07/2023]
Abstract
The increase in the number of people with obesity- and noninsulin-dependent diabetes mellitus has become a major public health concern. Insulin resistance is a common feature closely associated with human obesity and diabetes. Insulin regulates metabolism, at least in part, via the control of the expression of the hepatic genes involved in glucose and fatty acid metabolism. Insulin resistance is always associated with profound changes of the expression of hepatic genes for glucose and lipid metabolism. As an essential micronutrient, vitamin A (VA) is needed in a variety of physiological functions. The active metablite of VA, retinoic acid (RA), regulates the expression of genes through the activation of transcription factors bound to the RA-responsive elements in the promoters of RA-targeted genes. Recently, retinoids have been proposed to play roles in glucose and lipid metabolism and energy homeostasis. This paper summarizes the recent progresses in our understanding of VA metabolism in the liver and of the potential transcription factors mediating RA responses. These transcription factors are the retinoic acid receptor, the retinoid X receptor, the hepatocyte nuclear factor 4α, the chicken ovalbumin upstream promoter-transcription factor II, and the peroxisome proliferator-activated receptor β/δ. This paper also summarizes the effects of VA status and RA treatments on the glucose and lipid metabolism in vivo and the effects of retinoid treatments on the expression of insulin-regulated genes involved in the glucose and fatty acid metabolism in the primary hepatocytes. I discuss the roles of RA production in the development of insulin resistance in hepatocytes and proposes a mechanism by which RA production may contribute to hepatic insulin resistance. Given the large amount of information and progresses regarding the physiological functions of VA, this paper mainly focuses on the findings in the liver and hepatocytes and only mentions the relative findings in other tissues and cells.
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Affiliation(s)
- Guoxun Chen
- Department of Nutrition, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
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31
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Mechanisms of action and resistance to all-trans retinoic acid (ATRA) and arsenic trioxide (As2O3) in acute promyelocytic leukemia. Int J Hematol 2013; 97:717-25. [DOI: 10.1007/s12185-013-1354-4] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 04/26/2013] [Accepted: 05/01/2013] [Indexed: 01/10/2023]
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32
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Liu S, Han SJ, Smith CL. Cooperative activation of gene expression by agonists and antagonists mediated by estrogen receptor heteroligand dimer complexes. Mol Pharmacol 2013; 83:1066-77. [PMID: 23462505 DOI: 10.1124/mol.112.084228] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Estrogen receptor (ER) antagonists are generally thought to inhibit estrogen action through competitive inhibition, resulting in receptor binding to antagonist rather than agonist. However, microarray analyses reveal a group of genes for which ER agonist and antagonist cooperatively regulate expression, suggesting additional models of combined agonist/antagonist action must exist. In conjunction with a chimeric reporter gene and two modified ERs, one [ERα(GSCKV)] with a mutation in the DNA-binding domain and the other (ERα-G521R) with a ligand-binding specificity mutation, we herein demonstrate that ER agonist and antagonist cooperatively activate gene expression through an ER heteroligand dimer complex (ER-HLD) consisting of one subunit of the receptor dimer bound to agonist and another occupied by antagonist. Coimmunoprecipitation experiments confirmed interaction between the agonist-bound and antagonist-bound receptors. This cooperative activation of gene expression was enhanced by steroid receptor coactivator 3 coactivator, and required each ligand-bound subunit of the dimer to bind to DNA, as well as both activation function 1 domains for maximal transcriptional activity. Ligand combinations able to induce ER-HLD transcriptional activity include the agonists 17β-estradiol or conjugated estrogens with the antagonists tamoxifen, raloxifene, bazedoxifene, or fulvestrant. Moreover, ER-HLD can activate transcription in the context of a natural promoter. Taken together, these findings broaden our understanding of the complex relationship between ER agonist and antagonist, and suggest a novel model by which cell and tissue selective effects of antiestrogens may be achieved.
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Affiliation(s)
- Shuang Liu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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33
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Al Tanoury Z, Piskunov A, Rochette-Egly C. Vitamin A and retinoid signaling: genomic and nongenomic effects. J Lipid Res 2013; 54:1761-75. [PMID: 23440512 DOI: 10.1194/jlr.r030833] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Vitamin A or retinol is arguably the most multifunctional vitamin in the human body, as it is essential from embryogenesis to adulthood. The pleiotropic effects of vitamin A are exerted mainly by one active metabolite, all-trans retinoic acid (atRA), which regulates the expression of a battery of target genes through several families of nuclear receptors (RARs, RXRs, and PPARβ/δ), polymorphic retinoic acid (RA) response elements, and multiple coregulators. It also involves extranuclear and nontranscriptional effects, such as the activation of kinase cascades, which are integrated in the nucleus via the phosphorylation of several actors of RA signaling. However, vitamin A itself proved recently to be active and RARs to be present in the cytosol to regulate translation and cell plasticity. These new concepts expand the scope of the biologic functions of vitamin A and RA.
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Affiliation(s)
- Ziad Al Tanoury
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM), U964, CNRS, UMR7104, Université de Strasbourg, 67404 Illkirch Cedex, France
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34
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Puzianowska-Kuznicka M, Pawlik-Pachucka E, Owczarz M, Budzińska M, Polosak J. Small-molecule hormones: molecular mechanisms of action. Int J Endocrinol 2013; 2013:601246. [PMID: 23533406 PMCID: PMC3603355 DOI: 10.1155/2013/601246] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/30/2012] [Accepted: 01/17/2013] [Indexed: 01/01/2023] Open
Abstract
Small-molecule hormones play crucial roles in the development and in the maintenance of an adult mammalian organism. On the molecular level, they regulate a plethora of biological pathways. Part of their actions depends on their transcription-regulating properties, exerted by highly specific nuclear receptors which are hormone-dependent transcription factors. Nuclear hormone receptors interact with coactivators, corepressors, basal transcription factors, and other transcription factors in order to modulate the activity of target genes in a manner that is dependent on tissue, age and developmental and pathophysiological states. The biological effect of this mechanism becomes apparent not earlier than 30-60 minutes after hormonal stimulus. In addition, small-molecule hormones modify the function of the cell by a number of nongenomic mechanisms, involving interaction with proteins localized in the plasma membrane, in the cytoplasm, as well as with proteins localized in other cellular membranes and in nonnuclear cellular compartments. The identity of such proteins is still under investigation; however, it seems that extranuclear fractions of nuclear hormone receptors commonly serve this function. A direct interaction of small-molecule hormones with membrane phospholipids and with mRNA is also postulated. In these mechanisms, the reaction to hormonal stimulus appears within seconds or minutes.
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Affiliation(s)
- Monika Puzianowska-Kuznicka
- Department of Human Epigenetics, Mossakowski Medical Research Centre, 5 Pawinskiego Street, 02-106 Warsaw, Poland
- Department of Geriatrics and Gerontology, Medical Center of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
- *Monika Puzianowska-Kuznicka:
| | - Eliza Pawlik-Pachucka
- Department of Human Epigenetics, Mossakowski Medical Research Centre, 5 Pawinskiego Street, 02-106 Warsaw, Poland
- Department of Geriatrics and Gerontology, Medical Center of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
| | - Magdalena Owczarz
- Department of Geriatrics and Gerontology, Medical Center of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
| | - Monika Budzińska
- Department of Geriatrics and Gerontology, Medical Center of Postgraduate Education, 61/63 Kleczewska Street, 01-826 Warsaw, Poland
| | - Jacek Polosak
- Department of Human Epigenetics, Mossakowski Medical Research Centre, 5 Pawinskiego Street, 02-106 Warsaw, Poland
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35
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Independent activation of hepatitis B virus biosynthesis by retinoids, peroxisome proliferators, and bile acids. J Virol 2012; 87:991-7. [PMID: 23135717 DOI: 10.1128/jvi.01562-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the human hepatoma cell line HepG2, retinoic acid, clofibric acid, and bile acid treatment can only modestly increase hepatitis B virus (HBV) biosynthesis. Utilizing the human embryonic kidney cell line 293T, it was possible to demonstrate that the retinoid X receptor α (RXRα) plus its ligand can support viral biosynthesis independently of additional nuclear receptors. In addition, RXRα/peroxisome proliferator-activated receptor α (PPARα) and RXRα/farnesoid X receptor α (FXRα) heterodimeric nuclear receptors can also mediate ligand-dependent HBV transcription and replication when activated by clofibric acid and bile acid, respectively, independently of a requirement for the ligand-dependent activation of RXRα. These observations indicate that there are at least three possible modes of ligand-mediated activation of HBV transcription and replication existing within hepatocytes, suggesting that multiple independent mechanisms control viral production in the livers of infected individuals.
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36
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Khan AH, Lin A, Smith DJ. Discovery and characterization of human exonic transcriptional regulatory elements. PLoS One 2012; 7:e46098. [PMID: 23029400 PMCID: PMC3454335 DOI: 10.1371/journal.pone.0046098] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Accepted: 08/28/2012] [Indexed: 11/28/2022] Open
Abstract
We sought exonic transcriptional regulatory elements by shotgun cloning human cDNA fragments into luciferase reporter vectors and measuring the resulting expression levels in liver cells. We uncovered seven regulatory elements within coding regions and three within 3' untranslated regions (UTRs). Two of the putative regulatory elements were enhancers and eight were silencers. The regulatory elements were generally but not consistently evolutionarily conserved and also showed a trend toward decreased population diversity. Furthermore, the exonic regulatory elements were enriched in known transcription factor binding sites (TFBSs) and were associated with several histone modifications and transcriptionally relevant chromatin. Evidence was obtained for bidirectional cis-regulation of a coding region element within a tubulin gene, TUBA1B, by the transcription factors PPARA and RORA. We estimate that hundreds of exonic transcriptional regulatory elements exist, an unexpected finding that highlights a surprising multi-functionality of sequences in the human genome.
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Affiliation(s)
- Arshad H Khan
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, United States of America
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37
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Nagy L, Szanto A, Szatmari I, Széles L. Nuclear hormone receptors enable macrophages and dendritic cells to sense their lipid environment and shape their immune response. Physiol Rev 2012; 92:739-89. [PMID: 22535896 DOI: 10.1152/physrev.00004.2011] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A key issue in the immune system is to generate specific cell types, often with opposing activities. The mechanisms of differentiation and subtype specification of immune cells such as macrophages and dendritic cells are critical to understand the regulatory principles and logic of the immune system. In addition to cytokines and pathogens, it is increasingly appreciated that lipid signaling also has a key role in differentiation and subtype specification. In this review we explore how intracellular lipid signaling via a set of transcription factors regulates cellular differentiation, subtype specification, and immune as well as metabolic homeostasis. We introduce macrophages and dendritic cells and then we focus on a group of transcription factors, nuclear receptors, which regulate gene expression upon receiving lipid signals. The receptors we cover are the ones with a recognized physiological function in these cell types and ones which heterodimerize with the retinoid X receptor. These are as follows: the receptor for a metabolite of vitamin A, retinoic acid: retinoic acid receptor (RAR), the vitamin D receptor (VDR), the fatty acid receptor: peroxisome proliferator-activated receptor γ (PPARγ), the oxysterol receptor liver X receptor (LXR), and their obligate heterodimeric partner, the retinoid X receptor (RXR). We discuss how they can get activated and how ligand is generated and eliminated in these cell types. We also explore how activation of a particular target gene contributes to biological functions and how the regulation of individual target genes adds up to the coordination of gene networks. It appears that RXR heterodimeric nuclear receptors provide these cells with a coordinated and interrelated network of transcriptional regulators for interpreting the lipid milieu and the metabolic changes to bring about gene expression changes leading to subtype and functional specification. We also show that these networks are implicated in various immune diseases and are amenable to therapeutic exploitation.
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Affiliation(s)
- Laszlo Nagy
- Department of Biochemistry and Molecular Biology, University of Debrecen, Medical and Health Science Center, Egyetem tér 1, Debrecen, Hungary.
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38
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Moutier E, Ye T, Choukrallah MA, Urban S, Osz J, Chatagnon A, Delacroix L, Langer D, Rochel N, Moras D, Benoit G, Davidson I. Retinoic acid receptors recognize the mouse genome through binding elements with diverse spacing and topology. J Biol Chem 2012; 287:26328-41. [PMID: 22661711 DOI: 10.1074/jbc.m112.361790] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) and bind to RA response elements (RAREs) in the regulatory regions of their target genes. Although previous studies on limited sets of RA-regulated genes have defined canonical RAREs as direct repeats of the consensus RGKTCA separated by 1, 2, or 5 nucleotides (DR1, DR2, DR5), we show that in mouse embryoid bodies or F9 embryonal carcinoma cells, RARs occupy a large repertoire of sites with DR0, DR8, and IR0 (inverted repeat 0) elements. Recombinant RAR-RXR binds these non-canonical spacings in vitro with comparable affinities to DR2 and DR5. Most DR8 elements comprise three half-sites with DR2 and DR0 spacings. This specific half-site organization constitutes a previously unrecognized but frequent signature of RAR binding elements. In functional assays, DR8 and IR0 elements act as independent RAREs, whereas DR0 does not. Our results reveal an unexpected diversity in the spacing and topology of binding elements for the RAR-RXR heterodimer. The differential ability of RAR-RXR bound to DR0 compared to DR2, DR5, and DR8 to mediate RA-dependent transcriptional activation indicates that half-site spacing allosterically regulates RAR function.
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Affiliation(s)
- Emmanuel Moutier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, 67404 Illkirch Cédex, France
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39
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Fang B, Mane-Padros D, Bolotin E, Jiang T, Sladek FM. Identification of a binding motif specific to HNF4 by comparative analysis of multiple nuclear receptors. Nucleic Acids Res 2012; 40:5343-56. [PMID: 22383578 PMCID: PMC3384313 DOI: 10.1093/nar/gks190] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nuclear receptors (NRs) regulate gene expression by binding specific DNA sequences consisting of AG[G/T]TCA or AGAACA half site motifs in a variety of configurations. However, those motifs/configurations alone do not adequately explain the diversity of NR function in vivo. Here, a systematic examination of DNA binding specificity by protein-binding microarrays (PBMs) of three closely related human NRs—HNF4α, retinoid X receptor alpha (RXRα) and COUPTF2—reveals an HNF4-specific binding motif (H4-SBM), xxxxCAAAGTCCA, as well as a previously unrecognized polarity in the classical DR1 motif (AGGTCAxAGGTCA) for HNF4α, RXRα and COUPTF2 homodimers. ChIP-seq data indicate that the H4-SBM is uniquely bound by HNF4α but not 10 other NRs in vivo, while NRs PXR, FXRα, Rev-Erbα appear to bind adjacent to H4-SBMs. HNF4-specific DNA recognition and transactivation are mediated by residues Asp69 and Arg76 in the DNA-binding domain; this combination of amino acids is unique to HNF4 among all human NRs. Expression profiling and ChIP data predict ∼100 new human HNF4α target genes with an H4-SBM site, including several Co-enzyme A-related genes and genes with links to disease. These results provide important new insights into NR DNA binding.
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Affiliation(s)
- Bin Fang
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA 92521, USA
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40
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Pawlak M, Lefebvre P, Staels B. General molecular biology and architecture of nuclear receptors. Curr Top Med Chem 2012; 12:486-504. [PMID: 22242852 PMCID: PMC3637177 DOI: 10.2174/156802612799436641] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 11/22/2011] [Indexed: 12/12/2022]
Abstract
Nuclear receptors (NRs) regulate and coordinate multiple processes by integrating internal and external signals, thereby maintaining homeostasis in front of nutritional, behavioral and environmental challenges. NRs exhibit strong similarities in their structure and mode of action: by selective transcriptional activation or repression of cognate target genes, which can either be controlled through a direct, DNA binding-dependent mechanism or through crosstalk with other transcriptional regulators, NRs modulate the expression of gene clusters thus achieving coordinated tissue responses. Additionally, non genomic effects of NR ligands appear mediated by ill-defined mechanisms at the plasma membrane. These effects mediate potential therapeutic effects as small lipophilic molecule targets, and many efforts have been put in elucidating their precise mechanism of action and pathophysiological roles. Currently, numerous nuclear receptor ligand analogs are used in therapy or are tested in clinical trials against various diseases such as hypertriglyceridemia, atherosclerosis, diabetes, allergies and cancer and others.
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Affiliation(s)
- Michal Pawlak
- Récepteurs nucléaires, maladies cardiovasculaires et diabète
INSERM : U1011Institut Pasteur de LilleUniversité Lille II - Droit et santé1 rue du Prof Calmette 59019 Lille Cedex,FR
| | - Philippe Lefebvre
- Récepteurs nucléaires, maladies cardiovasculaires et diabète
INSERM : U1011Institut Pasteur de LilleUniversité Lille II - Droit et santé1 rue du Prof Calmette 59019 Lille Cedex,FR
| | - Bart Staels
- Récepteurs nucléaires, maladies cardiovasculaires et diabète
INSERM : U1011Institut Pasteur de LilleUniversité Lille II - Droit et santé1 rue du Prof Calmette 59019 Lille Cedex,FR
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41
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Orlov I, Rochel N, Moras D, Klaholz BP. Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA. EMBO J 2011; 31:291-300. [PMID: 22179700 DOI: 10.1038/emboj.2011.445] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 11/10/2011] [Indexed: 11/09/2022] Open
Abstract
Transcription regulation by steroid hormones and other metabolites is mediated by nuclear receptors (NRs) such as the vitamin D and retinoid X receptors (VDR and RXR). Here, we present the cryo electron microscopy (cryo-EM) structure of the heterodimeric complex of the liganded human RXR and VDR bound to a consensus DNA response element forming a direct repeat (DR3). The cryo-EM map of the 100-kDa complex allows positioning the individual crystal structures of ligand- and DNA-binding domains (LBDs and DBDs). The LBDs are arranged perpendicular to the DNA and are located asymmetrically at the DNA 5'-end of the response element. The structure reveals that the VDR N-terminal A/B domain is located close to the DNA. The hinges of both VDR and RXR are fully visible and hold the complex in an open conformation in which co-regulators can bind. The asymmetric topology of the complex provides the structural basis for RXR being an adaptive partner within NR heterodimers, while the specific helical structure of VDR's hinge connects the 3'-bound DBD with the 5'-bound LBD and thereby serves as a conserved linker of defined length sensitive to mutational deletion.
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Affiliation(s)
- Igor Orlov
- Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France
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42
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Le May M, Mach H, Lacroix N, Hou C, Chen J, Li Q. Contribution of retinoid X receptor signaling to the specification of skeletal muscle lineage. J Biol Chem 2011; 286:26806-12. [PMID: 21653693 PMCID: PMC3143641 DOI: 10.1074/jbc.m111.227058] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Pluripotent stem cells possess a tremendous potential for the treatment of many diseases because of their capacity to differentiate into a variety of cell lineages. However, they provide little promise for muscle-related diseases, mainly because of the lack of small molecule inducers to efficiently direct myogenic conversion. Retinoic acid, acting through the retinoic acid receptor (RAR) and retinoid X receptor (RXR), affects stem cell fate determination in a concentration-dependent manner, but it only has a modest efficacy on the commitment of ES cells into skeletal muscle lineage. The RXR is very important for embryonic development but is generally considered to act as a silent partner of RAR in a non-permissive mode. In this study, we have examined whether activation of the RXR by rexinoid or RXR-specific signaling play a role in the specification of stem cells into muscle lineage. Our findings demonstrate that mouse ES cells generate skeletal myocytes effectively upon treatment with rexinoid at the early stage of differentiation and that on a molecular level, rexinoid-enhanced myogenesis simulates the sequential events observed in vivo. Moreover, RXR-mediated myogenic conversion requires the function of β-catenin but not RAR. Our studies establish the feasibility of applying the RXR agonist in cell-based therapies to treat muscle-related diseases. The aptitude of mouse ES cells to generate skeletal myocytes following rexinoid induction also provides a model system to study the convergence of different signaling pathways in myogenesis.
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Affiliation(s)
- Melanie Le May
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
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43
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Kumar S, Sandell LL, Trainor PA, Koentgen F, Duester G. Alcohol and aldehyde dehydrogenases: retinoid metabolic effects in mouse knockout models. Biochim Biophys Acta Mol Cell Biol Lipids 2011; 1821:198-205. [PMID: 21515404 DOI: 10.1016/j.bbalip.2011.04.004] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/25/2011] [Accepted: 04/07/2011] [Indexed: 12/11/2022]
Abstract
Retinoic acid (RA) is the active metabolite of vitamin A (retinol) that controls growth and development. The first step of RA synthesis is controlled by enzymes of the alcohol dehydrogenase (ADH) and retinol dehydrogenase (RDH) families that catalyze oxidation of retinol to retinaldehyde. The second step of RA synthesis is controlled by members of the aldehyde dehydrogenase (ALDH) family also known as retinaldehyde dehydrogenase (RALDH) that further oxidize retinaldehyde to produce RA. RA functions as a ligand for DNA-binding RA receptors that directly regulate transcription of specific target genes. Elucidation of the vitamin A metabolic pathway and investigation of the endogenous function of vitamin A metabolites has been greatly improved by development of mouse ADH, RDH, and RALDH loss-of-function models. ADH knockouts have demonstrated a postnatal role for this enzyme family in clearance of excess retinol to prevent vitamin A toxicity and in generation of RA for postnatal survival during vitamin A deficiency. A point mutation in Rdh10 generated by ethylnitrosourea has demonstrated that RDH10 generates much of the retinaldehyde needed for RA synthesis during embryonic development. Raldh1, Raldh2, and Raldh3 knockouts have demonstrated that RALDH1, RALDH2, and RALDH3 generate most of the RA needed during embryogenesis. These mouse models serve as instrumental tools for providing new insight into retinoid function. This article is part of a Special Issue entitled: Retinoid and Lipid Metabolism.
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Affiliation(s)
- Sandeep Kumar
- Sanford-Burnham Medical Research Institute, Development and Aging Program, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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Rochel N, Ciesielski F, Godet J, Moman E, Roessle M, Peluso-Iltis C, Moulin M, Haertlein M, Callow P, Mély Y, Svergun DI, Moras D. Common architecture of nuclear receptor heterodimers on DNA direct repeat elements with different spacings. Nat Struct Mol Biol 2011; 18:564-70. [DOI: 10.1038/nsmb.2054] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/27/2011] [Indexed: 11/09/2022]
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Hawk JD, Abel T. The role of NR4A transcription factors in memory formation. Brain Res Bull 2011; 85:21-9. [PMID: 21316423 DOI: 10.1016/j.brainresbull.2011.02.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 01/27/2011] [Accepted: 02/01/2011] [Indexed: 12/21/2022]
Abstract
In various physiological contexts, Nr4a genes are transcribed in response to external stimuli as part of an immediate early response that initiates a cascade of gene expression ultimately leading to distinct physiological outcomes in each of these contexts. The signaling pathway that initiates Nr4a gene expression in most of these contexts consists of elevated intracellular cAMP activating PKA, which in turn leads to phosphorylation of CREB and new gene synthesis. This cAMP-PKA-CREB pathway is a central molecular pathway in the formation of a long-term memory. Indeed, learning induces Nr4a family gene expression, and long-term memory formation requires at least two waves of transcription after learning, suggesting that NR4A nuclear receptors may contribute to the second of these waves of gene expression. In this article, we review insights gained in other physiological contexts regarding Nr4a function and regulation, and highlight how these lessons can be applied to the study of memory formation.
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Affiliation(s)
- Josh D Hawk
- University of Pennsylvania, Neuroscience Graduate Group, Philadelphia, PA, United States.
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Széles L, Póliska S, Nagy G, Szatmari I, Szanto A, Pap A, Lindstedt M, Santegoets SJAM, Rühl R, Dezsö B, Nagy L. Research resource: transcriptome profiling of genes regulated by RXR and its permissive and nonpermissive partners in differentiating monocyte-derived dendritic cells. Mol Endocrinol 2010; 24:2218-31. [PMID: 20861222 PMCID: PMC3051201 DOI: 10.1210/me.2010-0215] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Retinoid X receptors (RXRs) are heterodimerization partners for many nuclear receptors and also act as homodimers. Heterodimers formed by RXR and a nonpermissive partner, e.g. retinoic acid receptor (RAR) and vitamin D receptor (VDR), can be activated only by the agonist of the partner receptor. In contrast, heterodimers that contain permissive partners, e.g. liver X receptor (LXR) and peroxisome proliferator-activated receptor (PPAR), can be activated by agonists for either the partner receptor or RXR, raising the possibility of pleiotropic RXR signaling. However, it is not known to what extent the receptor’s activation results in triggering mechanisms dependent or independent of permissive heterodimers. In this study, we systematically and quantitatively characterized all probable RXR-signaling pathways in differentiating human monocyte-derived dendritic cells (Mo-DCs). Using pharmacological, microarray and quantitative RT-PCR techniques, we identified and characterized gene sets regulated by RXR agonists (LG100268 and 9-cis retinoic acid) and agonists for LXRs, PPARs, RARα, and VDR. Our results demonstrated that permissiveness was partially impaired in Mo-DCs, because a large number of genes regulated by PPAR or LXR agonists was not affected by RXR-specific agonists or was regulated to a lesser extent. As expected, we found that RXR agonists regulated only small portions of RARα or VDR targets. Importantly, we could identify and characterize PPAR- and LXR-independent pathways in Mo-DCs most likely mediated by RXR homodimers. These data suggested that RXR signaling in Mo-DCs was mediated via multiple permissive heterodimers and also by mechanism(s) independent of permissive heterodimers, and it was controlled in a cell-type and gene-specific manner. This works reports the mapping of RXR mediated transcription in human dendritic cells and shows that it is through multiple permissive heterodimers and also via heterodimer-independent mechanisms.
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Affiliation(s)
- Lajos Széles
- Department of Biochemistry and Molecular Biology, Medical and Health Science Center, University of Debrecen, Egyetem Tér 1, H-4010 Debrecen, Hungary
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Huang P, Chandra V, Rastinejad F. Structural overview of the nuclear receptor superfamily: insights into physiology and therapeutics. Annu Rev Physiol 2010; 72:247-72. [PMID: 20148675 DOI: 10.1146/annurev-physiol-021909-135917] [Citation(s) in RCA: 354] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
As ligand-regulated transcription factors, the nuclear hormone receptors are nearly ideal drug targets, with internal pockets that bind to hydrophobic, drug-like molecules and well-characterized ligand-induced conformational changes that recruit transcriptional coregulators to promoter elements. Yet, due to the multitude of genes under the control of a single receptor, the major challenge has been the identification of ligands with gene-selective actions, impacting disease outcomes through a narrow subset of target genes and not across their entire gene-regulatory repertoire. Here, we summarize the concepts and work to date underlying the development of steroidal and nonsteroidal receptor ligands, including the use of crystal structures, high-throughput screens, and rational design approaches for finding useful therapeutic molecules. Difficulties in finding selective receptor modulators require a more complete understanding of receptor interdomain communications, posttranslational modifications, and receptor-protein interactions that could be exploited for target gene selectivity.
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Affiliation(s)
- Pengxiang Huang
- Department of Pharmacology, and Center for Molecular Design, University of Virginia Health System, Charlottesville, VA 22908, USA.
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Theodosiou M, Laudet V, Schubert M. From carrot to clinic: an overview of the retinoic acid signaling pathway. Cell Mol Life Sci 2010; 67:1423-45. [PMID: 20140749 PMCID: PMC11115864 DOI: 10.1007/s00018-010-0268-z] [Citation(s) in RCA: 229] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/06/2010] [Accepted: 01/11/2010] [Indexed: 01/23/2023]
Abstract
Vitamin A is essential for the formation and maintenance of many body tissues. It is also important for embryonic growth and development and can act as a teratogen at critical periods of development. Retinoic acid (RA) is the biologically active form of vitamin A and its signaling is mediated by the RA and retinoid X receptors. In addition to its role as an important molecule during development, RA has also been implicated in clinical applications, both as a potential anti-tumor agent as well as for the treatment of skin diseases. This review presents an overview of how dietary retinoids are converted to RA, hence presenting the major players in RA metabolism and signaling, and highlights examples of treatment applications of retinoids. Moreover, we discuss the origin and diversification of the retinoid pathway, which are important factors for understanding the evolution of ligand-specificity among retinoid receptors.
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Affiliation(s)
- Maria Theodosiou
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon (Université Lyon 1, CNRS, INRA, Ecole Normale Supérieure de Lyon), 46 allée d'Italie, 69364 Lyon Cedex 07, France.
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Han K, Moon I, Lim HJ. All-trans- and 9-cis-retinoic acids activate the human cyclooxynase-2 gene: a role for DR1 as RARE or RXRE. Mol Biol Rep 2010; 38:833-40. [DOI: 10.1007/s11033-010-0173-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Accepted: 03/31/2010] [Indexed: 11/28/2022]
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Stambolsky P, Tabach Y, Fontemaggi G, Weisz L, Maor-Aloni R, Siegfried Z, Shiff I, Kogan I, Shay M, Kalo E, Blandino G, Simon I, Oren M, Rotter V. Modulation of the vitamin D3 response by cancer-associated mutant p53. Cancer Cell 2010; 17:273-85. [PMID: 20227041 PMCID: PMC2882298 DOI: 10.1016/j.ccr.2009.11.025] [Citation(s) in RCA: 189] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 08/06/2009] [Accepted: 02/08/2010] [Indexed: 12/21/2022]
Abstract
The p53 gene is mutated in many human tumors. Cells of such tumors often contain abundant mutant p53 (mutp53) protein, which may contribute actively to tumor progression via a gain-of-function mechanism. We applied ChIP-on-chip analysis and identified the vitamin D receptor (VDR) response element as overrepresented in promoter sequences bound by mutp53. We report that mutp53 can interact functionally and physically with VDR. Mutp53 is recruited to VDR-regulated genes and modulates their expression, augmenting the transactivation of some genes and relieving the repression of others. Furthermore, mutp53 increases the nuclear accumulation of VDR. Importantly, mutp53 converts vitamin D into an antiapoptotic agent. Thus, p53 status can determine the biological impact of vitamin D on tumor cells.
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Affiliation(s)
- Perry Stambolsky
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel.
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