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Hazarika S, Yu T, Biswas A, Dube N, Villalona P, Okafor CD. Nuclear receptor interdomain communication is mediated by the hinge with ligand specificity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579785. [PMID: 38405809 PMCID: PMC10888817 DOI: 10.1101/2024.02.10.579785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Nuclear receptors are ligand-induced transcription factors that bind directly to target genes and regulate their expression. Ligand binding initiates conformational changes that propagate to other domains, allosterically regulating their activity. The nature of this interdomain communication in nuclear receptors is poorly understood, largely owing to the difficulty of experimentally characterizing full-length structures. We have applied computational modeling approaches to describe and study the structure of the full length farnesoid X receptor (FXR), approximated by the DNA binding domain (DBD) and ligand binding domain (LBD) connected by the flexible hinge region. Using extended molecular dynamics simulations (> 10 microseconds) and enhanced sampling simulations, we provide evidence that ligands selectively induce domain rearrangement, leading to interdomain contact. We use protein-protein interaction assays to provide experimental evidence of these interactions, identifying a critical role of the hinge in mediating interdomain contact. Our results illuminate previously unknown aspects of interdomain communication in FXR and provide a framework to enable characterization of other full length nuclear receptors.
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Affiliation(s)
- Saurov Hazarika
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Tracy Yu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Arumay Biswas
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Namita Dube
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Priscilla Villalona
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - C. Denise Okafor
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
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2
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Choi WJ, Haratipour Z, Blind RD. Full-length nuclear receptor allosteric regulation. J Lipid Res 2023; 64:100406. [PMID: 37356665 PMCID: PMC10388211 DOI: 10.1016/j.jlr.2023.100406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023] Open
Abstract
Nuclear receptors are a superfamily of transcription factors regulated by a wide range of lipids that include phospholipids, fatty acids, heme-based metabolites, and cholesterol-based steroids. Encoded as classic two-domain modular transcription factors, nuclear receptors possess a DNA-binding domain (DBD) and a lipid ligand-binding domain (LBD) containing a transcriptional activation function. Decades of structural studies on the isolated LBDs of nuclear receptors established that lipid-ligand binding allosterically regulates the conformation of the LBD, regulating transcriptional coregulator recruitment and thus nuclear receptor function. These structural studies have aided the development of several FDA-approved drugs, highlighting the importance of understanding the structure-function relationships between lipids and nuclear receptors. However, there are few published descriptions of full-length nuclear receptor structure and even fewer descriptions of how lipids might allosterically regulate full-length structure. Here, we examine multidomain interactions based on the published full-length nuclear receptor structures, evaluating the potential of interdomain interfaces within these nuclear receptors to act as inducible sites of allosteric regulation by lipids.
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Affiliation(s)
- Woong Jae Choi
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zeinab Haratipour
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt University Center for Structural Biology, Nashville, TN, USA; Program in Precision Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Raymond D Blind
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt University Center for Structural Biology, Nashville, TN, USA; Program in Precision Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA; Diabetes Research and Training Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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3
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Chen D, Li K, Wang B, Chen H, Jiang H, Zhao C, Yao G, Li S, Xu H. Bruceine D Acts as a Potential Insecticide by Antagonizing 20E-EcR/USP Signal Transduction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37478461 DOI: 10.1021/acs.jafc.3c02275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Bruceine D (BD) is an effective insecticidal compound found in the Chinese herb Brucea javanica (L.) Merr. BD inhibits the growth and metamorphosis of Plutella xylostella and Drosophila melanogaster; however, its target protein and the molecular mechanism of insecticidal activity remain unclear. In this study, proteins with high affinity for BD were screened using surface plasmon resonance and high-performance liquid chromatography coupled with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry, revealing the ecdysone receptor (EcR) is the main target of BD. In vivo results showed that BD inhibited insect growth and metamorphosis through inhibition of the expression of 20E response genes. In vitro dual luciferase and enhanced green fluorescent protein (EGFP) fluorescence experiments indicated that BD suppressed the transcriptional activation activity of EcR by blocking the ecdysone response element (EcRE)-triggered transcriptional cascade, suggesting that BD inhibits the formation of the 20E-EcR-USP-EcRE complex. Moreover, molecular docking demonstrated that BD bound well to EcR. Elucidating the insecticidal mechanism of BD will be helpful in the development of green pesticides to control pests.
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Affiliation(s)
- Dongping Chen
- National Key Laboratory of Green Pesticide and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Kang Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Bingfeng Wang
- National Key Laboratory of Green Pesticide and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Huimin Chen
- National Key Laboratory of Green Pesticide and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Heng Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Chen Zhao
- National Key Laboratory of Green Pesticide and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Guangkai Yao
- National Key Laboratory of Green Pesticide and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Hanhong Xu
- National Key Laboratory of Green Pesticide and the State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
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4
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Jiang L, Liu X, Liang X, Dai S, Wei H, Guo M, Chen Z, Xiao D, Chen Y. Structural basis of the farnesoid X receptor/retinoid X receptor heterodimer on inverted repeat DNA. Comput Struct Biotechnol J 2023; 21:3149-3157. [PMID: 37287811 PMCID: PMC10242635 DOI: 10.1016/j.csbj.2023.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023] Open
Abstract
Farnesoid X receptor (FXR) is a ligand-activated transcription factor known as bile acid receptor (BAR). FXR plays critical roles in various biological processes, including metabolism, immune inflammation, liver regeneration and liver carcinogenesis. FXR forms a heterodimer with the retinoid X receptor (RXR) and binds to diverse FXR response elements (FXREs) to exert its various biological functions. However, the mechanism by which the FXR/RXR heterodimer binds the DNA elements remains unclear. In this study, we aimed to use structural, biochemical and bioinformatics analyses to study the mechanism of FXR binding to the typical FXRE, such as the IR1 site, and the heterodimer interactions in the FXR-DBD/RXR-DBD complex. Further biochemical assays showed that RAR, THR and NR4A2 do not form heterodimers with RXR when bound to the IR1 sites, which indicates that IR1 may be a unique binding site for the FXR/RXR heterodimer. Our studies may provide a further understanding of the dimerization specificity of nuclear receptors.
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5
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Postel S, Wissler L, Johansson CA, Gunnarsson A, Gordon E, Collins B, Castaldo M, Köhler C, Öling D, Johansson P, Fröderberg Roth L, Beinsteiner B, Dainty I, Delaney S, Klaholz BP, Billas IML, Edman K. Quaternary glucocorticoid receptor structure highlights allosteric interdomain communication. Nat Struct Mol Biol 2023; 30:286-295. [PMID: 36747092 DOI: 10.1038/s41594-022-00914-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 12/15/2022] [Indexed: 02/08/2023]
Abstract
The glucocorticoid receptor (GR) is a ligand-activated transcription factor that binds DNA and assembles co-regulator complexes to regulate gene transcription. GR agonists are widely prescribed to people with inflammatory and autoimmune diseases. Here we present high-resolution, multidomain structures of GR in complex with ligand, DNA and co-regulator peptide. The structures reveal how the receptor forms an asymmetric dimer on the DNA and provide a detailed view of the domain interactions within and across the two monomers. Hydrogen-deuterium exchange and DNA-binding experiments demonstrate that ligand-dependent structural changes are communicated across the different domains in the full-length receptor. This study demonstrates how GR forms a distinct architecture on DNA and how signal transmission can be modulated by the ligand pharmacophore, provides a platform to build a new level of understanding of how receptor modifications can drive disease progression and offers key insight for future drug design.
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Affiliation(s)
- Sandra Postel
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Lisa Wissler
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Carina A Johansson
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Gunnarsson
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Euan Gordon
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Barry Collins
- Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Marie Castaldo
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Christian Köhler
- Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - David Öling
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Patrik Johansson
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Brice Beinsteiner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Université de Strasbourg, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Ian Dainty
- Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Stephen Delaney
- Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Université de Strasbourg, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Isabelle M L Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), Illkirch, France
- Université de Strasbourg, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Karl Edman
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden.
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Liu Y, Ma L, Li M, Tian Z, Yang M, Wu X, Wang X, Shang G, Xie M, Chen Y, Liu X, Jiang L, Wu W, Xu C, Xia L, Li G, Dai S, Chen Z. Structures of human TR4LBD-JAZF1 and TR4DBD-DNA complexes reveal the molecular basis of transcriptional regulation. Nucleic Acids Res 2023; 51:1443-1457. [PMID: 36651297 PMCID: PMC9943680 DOI: 10.1093/nar/gkac1259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/30/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Testicular nuclear receptor 4 (TR4) modulates the transcriptional activation of genes and plays important roles in many diseases. The regulation of TR4 on target genes involves direct interactions with DNA molecules via the DNA-binding domain (DBD) and recruitment of coregulators by the ligand-binding domain (LBD). However, their regulatory mechanisms are unclear. Here, we report high-resolution crystal structures of TR4DBD, TR4DBD-DNA complexes and the TR4LBD-JAZF1 complex. For DNA recognition, multiple factors come into play, and a specific mutual selectivity between TR4 and target genes is found. The coactivators SRC-1 and CREBBP can bind at the interface of TR4 originally occupied by the TR4 activation function region 2 (AF-2); however, JAZF1 suppresses the binding through a novel mechanism. JAZF1 binds to an unidentified surface of TR4 and stabilizes an α13 helix never reported in the nuclear receptor family. Moreover, the cancer-associated mutations affect the interactions and the transcriptional activation of TR4 in vitro and in vivo, respectively. Overall, our results highlight the crucial role of DNA recognition and a novel mechanism of how JAZF1 reinforces the autorepressed conformation and influences the transcriptional activation of TR4, laying out important structural bases for drug design for a variety of diseases, including diabetes and cancers.
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Affiliation(s)
- Yunlong Liu
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lulu Ma
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Min Li
- National Protein Science Facility, Tsinghua University, Beijing 100084, China
| | - Zizi Tian
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Meiting Yang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xi Wu
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xue Wang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Guohui Shang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Mengjia Xie
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yiyun Chen
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Xin Liu
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lun Jiang
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wei Wu
- State Key Laboratory of Agrobiotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Chaoqun Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Liqun Xia
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Gonghui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Shaodong Dai
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Zhongzhou Chen
- To whom correspondence should be addressed. Tel: +86 10 62734078; Fax: +86 10 62734078;
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7
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Rochel N. Vitamin D and Its Receptor from a Structural Perspective. Nutrients 2022; 14:nu14142847. [PMID: 35889804 PMCID: PMC9325172 DOI: 10.3390/nu14142847] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
The activities of 1α,25-dihydroxyvitamin D3, 1,25D3, are mediated via its binding to the vitamin D receptor (VDR), a ligand-dependent transcription factor that belongs to the nuclear receptor superfamily. Numerous studies have demonstrated the important role of 1,25D3 and VDR signaling in various biological processes and associated pathologies. A wealth of information about ligand recognition and mechanism of action by structural analysis of the VDR complexes is also available. The methods used in these structural studies were mainly X-ray crystallography complemented by NMR, cryo-electron microscopy and structural mass spectrometry. This review aims to provide an overview of the current knowledge of VDR structures and also to explore the recent progress in understanding the complex mechanism of action of 1,25D3 from a structural perspective.
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Affiliation(s)
- Natacha Rochel
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
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8
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A structural signature motif enlightens the origin and diversification of nuclear receptors. PLoS Genet 2021; 17:e1009492. [PMID: 33882063 PMCID: PMC8092661 DOI: 10.1371/journal.pgen.1009492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/03/2021] [Accepted: 03/15/2021] [Indexed: 12/11/2022] Open
Abstract
Nuclear receptors are ligand-activated transcription factors that modulate gene regulatory networks from embryonic development to adult physiology and thus represent major targets for clinical interventions in many diseases. Most nuclear receptors function either as homodimers or as heterodimers. The dimerization is crucial for gene regulation by nuclear receptors, by extending the repertoire of binding sites in the promoters or the enhancers of target genes via combinatorial interactions. Here, we focused our attention on an unusual structural variation of the α-helix, called π-turn that is present in helix H7 of the ligand-binding domain of RXR and HNF4. By tracing back the complex evolutionary history of the π-turn, we demonstrate that it was present ancestrally and then independently lost in several nuclear receptor lineages. Importantly, the evolutionary history of the π-turn motif is parallel to the evolutionary diversification of the nuclear receptor dimerization ability from ancestral homodimers to derived heterodimers. We then carried out structural and biophysical analyses, in particular through point mutation studies of key RXR signature residues and showed that this motif plays a critical role in the network of interactions stabilizing homodimers. We further showed that the π-turn was instrumental in allowing a flexible heterodimeric interface of RXR in order to accommodate multiple interfaces with numerous partners and critical for the emergence of high affinity receptors. Altogether, our work allows to identify a functional role for the π-turn in oligomerization of nuclear receptors and reveals how this motif is linked to the emergence of a critical biological function. We conclude that the π-turn can be viewed as a structural exaptation that has contributed to enlarging the functional repertoire of nuclear receptors. The origin of novelties is a central topic in evolutionary biology. A fundamental question is how organisms constrained by natural selection can divert from existing schemes to set up novel structures or pathways. Among the most important strategies are exaptations, which represent pre-adaptation strategies. Many examples exist in biology, at both morphological and molecular levels, such as the one reported here that focuses on an unusual structural feature called the π-turn. It is found in the structure of the most ancestral nuclear receptors RXR and HNF4. The analyses trace back the complex evolutionary history of the π-turn to more than 500 million years ago, before the Cambrian explosion and show that this feature was essential for the heterodimerization capacity of RXR. Nuclear receptor lineages that emerged later in evolution lost the π-turn. We demonstrate here that this loss in nuclear receptors that heterodimerize with RXR was critical for the emergence of high affinity receptors, such as the vitamin D and the thyroid hormone receptors. On the other hand, the conserved π-turn in RXR allowed it to accommodate multiple heterodimer interfaces with numerous partners. This structural exaptation allowed for the remarkable diversification of nuclear receptors.
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9
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Browning C, McEwen AG, Mori K, Yokoi T, Moras D, Nakagawa Y, Billas IML. Nonsteroidal ecdysone receptor agonists use a water channel for binding to the ecdysone receptor complex EcR/USP. JOURNAL OF PESTICIDE SCIENCE 2021; 46:88-100. [PMID: 33746550 PMCID: PMC7953031 DOI: 10.1584/jpestics.d20-095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/16/2021] [Indexed: 05/27/2023]
Abstract
The ecdysone receptor (EcR) possesses the remarkable capacity to adapt structurally to different types of ligands. EcR binds ecdysteroids, including 20-hydroxyecdysone (20E), as well as nonsteroidal synthetic agonists such as insecticidal dibenzoylhydrazines (DBHs). Here, we report the crystal structures of the ligand-binding domains of Heliothis virescens EcR/USP bound to the DBH agonist BYI09181 and to the imidazole-type compound BYI08346. The region delineated by helices H7 and H10 opens up to tightly fit a phenyl ring of the ligands to an extent that depends on the bulkiness of ring substituent. In the structure of 20E-bound EcR, this part of the ligand-binding pocket (LBP) contains a channel filled by water molecules that form an intricate hydrogen bond network between 20E and LBP. The water channel present in the nuclear receptor bound to its natural hormone acts as a critical molecular adaptation spring used to accommodate synthetic agonists inside its binding cavity.
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Affiliation(s)
- Christopher Browning
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Alastair G. McEwen
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Kotaro Mori
- Graduate School of Agriculture, Kyoto University, Kyoto 606–8502, Japan
| | - Taiyo Yokoi
- Graduate School of Agriculture, Kyoto University, Kyoto 606–8502, Japan
| | - Dino Moras
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Yoshiaki Nakagawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606–8502, Japan
| | - Isabelle M. L. Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), UMR 7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
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10
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Seacrist CD, Kuenze G, Hoffmann RM, Moeller BE, Burke JE, Meiler J, Blind RD. Integrated Structural Modeling of Full-Length LRH-1 Reveals Inter-domain Interactions Contribute to Receptor Structure and Function. Structure 2020; 28:830-846.e9. [PMID: 32433991 DOI: 10.1016/j.str.2020.04.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 01/06/2023]
Abstract
Liver receptor homolog-1 (LRH-1; NR5A2) is a nuclear receptor that regulates a diverse array of biological processes. In contrast to dimeric nuclear receptors, LRH-1 is an obligate monomer and contains a subtype-specific helix at the C terminus of the DNA-binding domain (DBD), termed FTZ-F1. Although detailed structural information is available for individual domains of LRH-1, it is unknown how these domains exist in the intact nuclear receptor. Here, we developed an integrated structural model of human full-length LRH-1 using a combination of HDX-MS, XL-MS, Rosetta computational docking, and SAXS. The model predicts the DBD FTZ-F1 helix directly interacts with ligand binding domain helix 2. We confirmed several other predicted inter-domain interactions via structural and functional analyses. Comparison between the LRH-1/Dax-1 co-crystal structure and the integrated model predicted and confirmed Dax-1 co-repressor to modulate LRH-1 inter-domain dynamics. Together, these data support individual LRH-1 domains interacting to influence receptor structure and function.
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Affiliation(s)
- Corey D Seacrist
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Reece M Hoffmann
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Brandon E Moeller
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Jens Meiler
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA; Institute for Drug Discovery, Leipzig University, Leipzig, Germany; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
| | - Raymond D Blind
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Department of Medicine, Division of Diabetes Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
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11
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Weikum ER, Liu X, Ortlund EA. The nuclear receptor superfamily: A structural perspective. Protein Sci 2019; 27:1876-1892. [PMID: 30109749 DOI: 10.1002/pro.3496] [Citation(s) in RCA: 252] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 12/28/2022]
Abstract
Nuclear receptors (NRs) are a family of transcription factors that regulate numerous physiological processes such as metabolism, reproduction, inflammation, as well as the circadian rhythm. NRs sense changes in lipid metabolite levels to drive differential gene expression, producing distinct physiologic effects. This is an allosteric process whereby binding a cognate ligand and specific DNA sequences drives the recruitment of diverse transcriptional co-regulators at chromatin and ultimately transactivation or transrepression of target genes. Dysregulation of NR signaling leads to various malignances, metabolic disorders, and inflammatory disease. Given their important role in physiology and ability to respond to small lipophilic ligands, NRs have emerged as valuable therapeutic targets. Here, we summarize and discuss the recent progress on understanding the complex mechanism of action of NRs, primarily from a structural perspective. Finally, we suggest future studies to improve our understanding of NR signaling and better design drugs by integrating multiple structural and biophysical approaches.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory School of Medicine, Atlanta, 30322, Georgia
| | - Xu Liu
- Department of Biochemistry, Emory School of Medicine, Atlanta, 30322, Georgia
| | - Eric A Ortlund
- Department of Biochemistry, Emory School of Medicine, Atlanta, 30322, Georgia
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12
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Ji N, Wang X, Yin C, Peng W, Liang R. CrgA Protein Represses AlkB2 Monooxygenase and Regulates the Degradation of Medium-to-Long-Chain n-Alkanes in Pseudomonas aeruginosa SJTD-1. Front Microbiol 2019; 10:400. [PMID: 30915046 PMCID: PMC6422896 DOI: 10.3389/fmicb.2019.00400] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/15/2019] [Indexed: 11/13/2022] Open
Abstract
AlkB monooxygenases in bacteria are responsible for the hydroxylation of medium- and long-chain n-alkanes. In this study, one CrgA protein of Pseudomonas aeruginosa SJTD-1, a member of LysR family, was proved to regulate AlkB2 monooxygenase and the degradation of medium-to-long-chain n-alkanes (C14-C20) by directly binding to the upstream of alkB2 gene. Two specific sites for CrgA binding were found in the promoter region of alkB2 gene, and the imperfect mirror repeat (IIR) structure was proved critical for CrgA recognition and binding. Hexadecyl CoA and octadecyl CoA could effectively release the CrgA binding and start the transcription of alkB2 gene, implying a positive regulation of metabolic intermediate. In the presence of medium-to-long-chain n-alkanes (C14-C20), deletion of crgA gene could enhance the transcription and expression of AlkB2 monooxygenase significantly; and in n-octadecane culture, strain S1ΔalkB1&crgA grew more vigorously than strain S1 ΔalkB1 &crgA . Almost no regulation of CrgA protein was observed to alkB1 gene in vitro and in vivo. Therefore, CrgA acted as a negative regulator for the medium-to-long-chain n-alkane utilization in P. aeruginosa SJTD-1. The work will promote the regulation mechanism study of n-alkane degradation in bacteria and help the bioremediation method development for petroleum pollution.
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Affiliation(s)
- Nannan Ji
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuli Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chong Yin
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wanli Peng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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13
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Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains. Nat Commun 2018; 9:3520. [PMID: 30166540 PMCID: PMC6117352 DOI: 10.1038/s41467-018-06034-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022] Open
Abstract
Human estrogen receptor alpha (hERα) is a hormone-responsive nuclear receptor (NR) involved in cell growth and survival that contains both a DNA-binding domain (DBD) and a ligand-binding domain (LBD). Functionally relevant inter-domain interactions between the DBD and LBD have been observed in several other NRs, but for hERα, the detailed structural architecture of the complex is unknown. By utilizing integrated complementary techniques of small-angle X-ray scattering, hydroxyl radical protein footprinting and computational modeling, here we report an asymmetric L-shaped “boot” structure of the multidomain hERα and identify the specific sites on each domain at the domain interface involved in DBD–LBD interactions. We demonstrate the functional role of the proposed DBD–LBD domain interface through site-specific mutagenesis altering the hERα interfacial structure and allosteric signaling. The L-shaped structure of hERα is a distinctive DBD–LBD organization of NR complexes and more importantly, reveals a signaling mechanism mediated by inter-domain crosstalk that regulates this receptor’s allosteric function. The human estrogen receptor alpha (hERα) is a hormone-responsive transcription factor. Here the authors combine small-angle X-ray scattering, hydroxyl radical protein footprinting and computational modeling and show that multidomain hERα adopts an L-shaped boot-like architecture revealing a cross-talk between its DNA-binding domain and Ligand-binding domain.
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14
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de Vera IMS, Zheng J, Novick S, Shang J, Hughes TS, Brust R, Munoz-Tello P, Gardner WJ, Marciano DP, Kong X, Griffin PR, Kojetin DJ. Synergistic Regulation of Coregulator/Nuclear Receptor Interaction by Ligand and DNA. Structure 2017; 25:1506-1518.e4. [PMID: 28890360 DOI: 10.1016/j.str.2017.07.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/12/2017] [Accepted: 07/28/2017] [Indexed: 11/15/2022]
Abstract
Nuclear receptor (NR) transcription factors bind various coreceptors, small-molecule ligands, DNA response element sequences, and transcriptional coregulator proteins to affect gene transcription. Small-molecule ligands and DNA are known to influence receptor structure, coregulator protein interaction, and function; however, little is known on the mechanism of synergy between ligand and DNA. Using quantitative biochemical, biophysical, and solution structural methods, including 13C-detected nuclear magnetic resonance and hydrogen/deuterium exchange (HDX) mass spectrometry, we show that ligand and DNA cooperatively recruit the intrinsically disordered steroid receptor coactivator-2 (SRC-2/TIF2/GRIP1/NCoA-2) receptor interaction domain to peroxisome proliferator-activated receptor gamma-retinoid X receptor alpha (PPARγ-RXRα) heterodimer and reveal the binding determinants of the complex. Our data reveal a thermodynamic mechanism by which DNA binding propagates a conformational change in PPARγ-RXRα, stabilizes the receptor ligand binding domain dimer interface, and impacts ligand potency and cooperativity in NR coactivator recruitment.
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Affiliation(s)
- Ian Mitchelle S de Vera
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Scott Novick
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Travis S Hughes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Richard Brust
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Paola Munoz-Tello
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - William J Gardner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; TSRI High School Student Summer Internship Program, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - David P Marciano
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Xiangming Kong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA.
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15
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Orlov I, Myasnikov AG, Andronov L, Natchiar SK, Khatter H, Beinsteiner B, Ménétret JF, Hazemann I, Mohideen K, Tazibt K, Tabaroni R, Kratzat H, Djabeur N, Bruxelles T, Raivoniaina F, Pompeo LD, Torchy M, Billas I, Urzhumtsev A, Klaholz BP. The integrative role of cryo electron microscopy in molecular and cellular structural biology. Biol Cell 2016; 109:81-93. [PMID: 27730650 DOI: 10.1111/boc.201600042] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 01/10/2023]
Abstract
After gradually moving away from preparation methods prone to artefacts such as plastic embedding and negative staining for cell sections and single particles, the field of cryo electron microscopy (cryo-EM) is now heading off at unprecedented speed towards high-resolution analysis of biological objects of various sizes. This 'revolution in resolution' is happening largely thanks to new developments of new-generation cameras used for recording the images in the cryo electron microscope which have much increased sensitivity being based on complementary metal oxide semiconductor devices. Combined with advanced image processing and 3D reconstruction, the cryo-EM analysis of nucleoprotein complexes can provide unprecedented insights at molecular and atomic levels and address regulatory mechanisms in the cell. These advances reinforce the integrative role of cryo-EM in synergy with other methods such as X-ray crystallography, fluorescence imaging or focussed-ion beam milling as exemplified here by some recent studies from our laboratory on ribosomes, viruses, chromatin and nuclear receptors. Such multi-scale and multi-resolution approaches allow integrating molecular and cellular levels when applied to purified or in situ macromolecular complexes, thus illustrating the trend of the field towards cellular structural biology.
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Affiliation(s)
- Igor Orlov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexander G Myasnikov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Heena Khatter
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Brice Beinsteiner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Jean-François Ménétret
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Kareem Mohideen
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Karima Tazibt
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Rachel Tabaroni
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Hanna Kratzat
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Nadia Djabeur
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Tatiana Bruxelles
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Finaritra Raivoniaina
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Lorenza di Pompeo
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Morgan Torchy
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Isabelle Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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16
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Abstract
Nuclear receptors (NRs) are master regulators of broad genetic programs in metazoans. These programs are regulated in part by the small-molecule ligands that bind NRs and modulate their interactions with transcriptional coregulatory factors. X-ray crystallography is now delivering more complete pictures of how the multidomain architectures of NR homo- and heterodimers are physically arranged on their DNA elements and how ligands and coactivator peptides act through these complexes. Complementary studies are also pointing to a variety of novel mechanisms by which NRs access their DNA-response elements within chromatin. Here, we review the new structural advances together with proteomic discoveries that shape our understanding of how NRs form a variety of functional interactions with collaborating factors in chromatin.
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Affiliation(s)
| | - Fraydoon Rastinejad
- Integrative Metabolism Program, SBP Medical Discovery Institute, Orlando, Florida 32827
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17
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Coscia F, Estrozi LF, Hans F, Malet H, Noirclerc-Savoye M, Schoehn G, Petosa C. Fusion to a homo-oligomeric scaffold allows cryo-EM analysis of a small protein. Sci Rep 2016; 6:30909. [PMID: 27485862 PMCID: PMC4971460 DOI: 10.1038/srep30909] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/10/2016] [Indexed: 12/30/2022] Open
Abstract
Recent technical advances have revolutionized the field of cryo-electron microscopy (cryo-EM). However, most monomeric proteins remain too small (<100 kDa) for cryo-EM analysis. To overcome this limitation, we explored a strategy whereby a monomeric target protein is genetically fused to a homo-oligomeric scaffold protein and the junction optimized to allow the target to adopt the scaffold symmetry, thereby generating a chimeric particle suitable for cryo-EM. To demonstrate the concept, we fused maltose-binding protein (MBP), a 40 kDa monomer, to glutamine synthetase, a dodecamer formed by two hexameric rings. Chimeric constructs with different junction lengths were screened by biophysical analysis and negative-stain EM. The optimal construct yielded a cryo-EM reconstruction that revealed the MBP structure at sub-nanometre resolution. These findings illustrate the feasibility of using homo-oligomeric scaffolds to enable cryo-EM analysis of monomeric proteins, paving the way for applying this strategy to challenging structures resistant to crystallographic and NMR analysis.
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Affiliation(s)
- Francesca Coscia
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Leandro F Estrozi
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Fabienne Hans
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Hélène Malet
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | | | - Guy Schoehn
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Carlo Petosa
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
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18
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Belorusova A, Osz J, Petoukhov MV, Peluso-Iltis C, Kieffer B, Svergun DI, Rochel N. Solution Behavior of the Intrinsically Disordered N-Terminal Domain of Retinoid X Receptor α in the Context of the Full-Length Protein. Biochemistry 2016; 55:1741-1748. [PMID: 26937780 DOI: 10.1021/acs.biochem.5b01122] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Retinoid X receptors (RXRs) are transcription factors with important functions in embryonic development, metabolic processes, differentiation, and apoptosis. A particular feature of RXRs is their ability to act as obligatory heterodimerization partners of class II nuclear receptors. At the same time, these receptors are also able to form homodimers that bind to direct repeat separated by one nucleotide hormone response elements. Since the discovery of RXRs, most of the studies focused on its ligand binding and DNA binding domains, while its N-terminal domain (NTD) harboring a ligand-independent activation function remained poorly characterized. Here, we investigated the solution properties of the NTD of RXRα alone and in the context of the full-length receptor using small-angle X-ray scattering and nuclear magnetic resonance spectroscopy. We report the solution structure of the full-length homodimeric RXRα on DNA and show that the NTD remains highly flexible within this complex.
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Affiliation(s)
- Anna Belorusova
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Judit Osz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Carole Peluso-Iltis
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Bruno Kieffer
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Natacha Rochel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
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19
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Wu D, Kaur P, Li ZM, Bradford KC, Wang H, Erie DA. Visualizing the Path of DNA through Proteins Using DREEM Imaging. Mol Cell 2016; 61:315-23. [PMID: 26774284 DOI: 10.1016/j.molcel.2015.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 10/14/2015] [Accepted: 12/02/2015] [Indexed: 01/06/2023]
Abstract
Many cellular functions require the assembly of multiprotein-DNA complexes. A growing area of structural biology aims to characterize these dynamic structures by combining atomic-resolution crystal structures with lower-resolution data from techniques that provide distributions of species, such as small-angle X-ray scattering, electron microscopy, and atomic force microscopy (AFM). A significant limitation in these combinatorial methods is localization of the DNA within the multiprotein complex. Here, we combine AFM with an electrostatic force microscopy (EFM) method to develop an exquisitely sensitive dual-resonance-frequency-enhanced EFM (DREEM) capable of resolving DNA within protein-DNA complexes. Imaging of nucleosomes and DNA mismatch repair complexes demonstrates that DREEM can reveal both the path of the DNA wrapping around histones and the path of DNA as it passes through both single proteins and multiprotein complexes. Finally, DREEM imaging requires only minor modifications of many existing commercial AFMs, making the technique readily available.
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Affiliation(s)
- Dong Wu
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Zimeng M Li
- Department of Physics and Astronomy, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kira C Bradford
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hong Wang
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA.
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA; Curriculum in Applied Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA.
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Hoffmann JM, Partridge L. Nuclear hormone receptors: Roles of xenobiotic detoxification and sterol homeostasis in healthy aging. Crit Rev Biochem Mol Biol 2015; 50:380-92. [PMID: 26383043 DOI: 10.3109/10409238.2015.1067186] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Health during aging can be improved by genetic, dietary and pharmacological interventions. Many of these increase resistance to various stressors, including xenobiotics. Up-regulation of xenobiotic detoxification genes is a transcriptomic signature shared by long-lived nematodes, flies and mice, suggesting that protection of cells from toxicity of xenobiotics may contribute to longevity. Expression of genes involved in xenobiotic detoxification is controlled by evolutionarily conserved transcriptional regulators. Three closely related subgroups of nuclear hormone receptors (NHRs) have a major role, and these include DAF-12 and NHR-8 in C. elegans, DHR96 in Drosophila and FXR, LXRs, PXR, CAR and VDR in mammals. In the invertebrates, these NHRs have been experimentally demonstrated to play a role in extension of lifespan by genetic and environmental interventions. NHRs represent critical hubs in that they regulate detoxification enzymes with broad substrate specificities, metabolizing both endo- and xeno-biotics. They also modulate homeostasis of steroid hormones and other endogenous cholesterol derivatives and lipid metabolism, and these roles, as well as xenobiotic detoxification, may contribute to the effects of NHRs on lifespan and health during aging, an issue that is being increasingly addressed in C. elegans and Drosophila. Disentangling the contribution of these processes to longevity will require more precise understanding of the molecular mechanisms by which each is effected, including identification of ligands and co-regulators of NHRs, patterns of tissue-specificity and mechanisms of interaction between tissues. The roles of vertebrate NHRs in determination of health during aging and lifespan have yet to be investigated.
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Affiliation(s)
| | - Linda Partridge
- a Max Planck Institute for Biology of Ageing , Cologne , Germany and.,b Institute of Healthy Ageing, and GEE (Genetics, Evolution and Environment), University College , London , UK
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21
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Beinsteiner B, Michalon J, Klaholz BP. IBiSS, a versatile and interactive tool for integrated sequence and 3D structure analysis of large macromolecular complexes. Bioinformatics 2015; 31:3339-44. [DOI: 10.1093/bioinformatics/btv347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/30/2015] [Indexed: 11/13/2022] Open
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22
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Moras D, Billas IML, Rochel N, Klaholz BP. Structure-function relationships in nuclear receptors: the facts. Trends Biochem Sci 2015; 40:287-90. [PMID: 25899756 DOI: 10.1016/j.tibs.2015.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/20/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Dino Moras
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France.
| | - Isabelle M L Billas
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Natacha Rochel
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
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23
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DNA binding drives nuclear receptor architecture. Nat Rev Genet 2014. [DOI: 10.1038/nrg3789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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