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Chen Y, Anderson MT, Payne N, Santori FR, Ivanova NB. Nuclear Receptors and the Hidden Language of the Metabolome. Cells 2024; 13:1284. [PMID: 39120315 PMCID: PMC11311682 DOI: 10.3390/cells13151284] [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: 06/12/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Nuclear hormone receptors (NHRs) are a family of ligand-regulated transcription factors that control key aspects of development and physiology. The regulation of NHRs by ligands derived from metabolism or diet makes them excellent pharmacological targets, and the mechanistic understanding of how NHRs interact with their ligands to regulate downstream gene networks, along with the identification of ligands for orphan NHRs, could enable innovative approaches for cellular engineering, disease modeling and regenerative medicine. We review recent discoveries in the identification of physiologic ligands for NHRs. We propose new models of ligand-receptor co-evolution, the emergence of hormonal function and models of regulation of NHR specificity and activity via one-ligand and two-ligand models as well as feedback loops. Lastly, we discuss limitations on the processes for the identification of physiologic NHR ligands and emerging new methodologies that could be used to identify the natural ligands for the remaining 17 orphan NHRs in the human genome.
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Affiliation(s)
- Yujie Chen
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Matthew Tom Anderson
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
| | - Nathaniel Payne
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
| | - Fabio R. Santori
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
| | - Natalia B. Ivanova
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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2
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Jia L, Tian H, Sun S, Hao X, Wen Y. EID3 inhibits the osteogenic differentiation of periodontal ligament stem cells and mediates the signal transduction of TAZ-EID3-AKT/MTOR/ERK. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119662. [PMID: 38216090 DOI: 10.1016/j.bbamcr.2024.119662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/16/2023] [Accepted: 01/03/2024] [Indexed: 01/14/2024]
Abstract
Exploring the molecular mechanisms of cell behaviors is beneficial for promoting periodontal ligament stem cell (PDLSC)-mediated tissue regeneration. This study intends to explore the regulatory effects of EID3 on cell proliferation, apoptosis, and osteogenic differentiation and to preliminarily explore the regulatory mechanism of EID3. Here, EID3 was overexpressed or knocked down in PDLSCs by recombinant lentivirus. Then, cell proliferation activity was analyzed by colony-forming assay, EdU assay, and cell cycle assay. Cell apoptosis was detected by flow cytometry. The osteo-differentiation potential was analyzed using ALP activity assay, ALP staining, alizarin red staining, and mRNA and protein assay of osteo-differentiation related genes. The results showed that when EID3 was knocked down, the proliferation activity and osteogenic differentiation potential of PDLSCs decreased, while they increased when EID3 was overexpressed. The cell apoptosis rate decreased in PDLSCs with EID3 knockdown but increased in PDLSCs with EID3 overexpression. Moreover, EID3 inhibited the transduction of the AKT/MTOR and ERK signaling pathway. In addition, TAZ negatively regulated the expression of EID3, and the overexpression of EID3 partially reversed the promotive effects of TAZ on the osteogenic differentiation of PDLSCs. Taken together, EID3 inhibits the proliferation and osteogenic differentiation while promoting the apoptosis of PDLSCs. EID3 inhibits the transduction of the AKT/MTOR and ERK signaling pathways and mediates the regulatory effect of TAZ on PDLSC osteogenic differentiation.
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Affiliation(s)
- Linglu Jia
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong, China; Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration, Shandong, China; Shandong Provincial Clinical Research Center for Oral Diseases, Shandong, China
| | - Hui Tian
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong, China; Department of Stomatology, Rizhao People's Hospital, Rizhao, Shandong, China
| | - Shaoqing Sun
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong, China; Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration, Shandong, China; Shandong Provincial Clinical Research Center for Oral Diseases, Shandong, China
| | - Xingyao Hao
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong, China; Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration, Shandong, China; Shandong Provincial Clinical Research Center for Oral Diseases, Shandong, China
| | - Yong Wen
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University, Shandong, China; Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Research Center of Dental Materials and Oral Tissue Regeneration, Shandong, China; Shandong Provincial Clinical Research Center for Oral Diseases, Shandong, China.
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Nuclear receptor: Structure and function. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 196:209-227. [PMID: 36813359 DOI: 10.1016/bs.pmbts.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ligand-dependent transcription factors are nuclear receptors (NRs) that regulate various critical cellular processes such as reproduction, metabolism, development, etc. NRs are classified into (subgroup 0 to subgroup 6) seven superfamilies based on ligand-binding characteristics. All NRs share a general domain structure (A/B, C, D, and E) with distinct essential functions. NRs as monomers, homodimers, or heterodimers bind to consensus DNA sequences known as Hormone Response Elements (HREs). Furthermore, nuclear receptor-binding efficiency depends on minor differences in the sequences of HREs, spacing between the two half-sites, and the flanking sequence of the response elements. NRs can trans-activate and repress their target genes. In positively regulated genes, ligand-bound NRs recruit coactivators to activate the target gene expression, and unliganded NRs cause transcriptional repression. On the other hand, NRs repress gene expression by different mechanisms: (i) ligand-dependent transcriptional repression, (ii) ligand-independent transcriptional repression. This chapter will briefly explain NR superfamilies, their structures, molecular mechanism of action and their role in pathophysiological conditions, etc. That could enable the discovery of new receptors and their ligands and may elucidate their roles in various physiological processes. In addition, therapeutic agonists and antagonists would be developed to control the dysregulation of nuclear receptor signaling.
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4
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Raimundo N. Feeding and lipophagy: it takes guts to deliver. EMBO J 2022; 41:e112180. [PMID: 35920021 PMCID: PMC9433935 DOI: 10.15252/embj.2022112180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Refeeding after a period of starvation is known to suppress autophagy in the liver. Surprising new work by Seok et al (2022) shows that refeeding activates lipophagy in the intestine, which may help fats in our diet to be efficiently processed after a meal.
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Affiliation(s)
- Nuno Raimundo
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA
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5
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Sakellakis M. Orphan receptors in prostate cancer. Prostate 2022; 82:1016-1024. [PMID: 35538397 DOI: 10.1002/pros.24370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/22/2022] [Accepted: 04/22/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND The identification of new cellular receptors has been increasing rapidly. A receptor is called "orphan" if an endogenous ligand has not been identified yet. METHODS Here we review receptors that contribute to prostate cancer and are considered orphan or partially orphan. This means that the full spectrum of their endogenous ligands remains unknown. RESULTS The orphan receptors are divided into two major families. The first group includes G protein-coupled receptors. Most are orphan olfactory receptors. OR51E1 inhibits cell proliferation and induces senescence in prostate cancer. OR51E2 inhibits prostate cancer growth, but promotes invasiveness and metastasis. GPR158, GPR110, and GPCR-X play significant roles in prostate cancer development and progression. However, GPR160 induces cell cycle arrest and apoptosis. The other major subset of orphan receptors are nuclear receptors. Receptor-related orphan receptor α (RORα) inhibits tumor growth, but RORγ stimulates androgen receptor signaling. PXR contributes to metabolic deactivation of androgens and inhibits cell proliferation. TLX has protumorigenic effects in prostate cancer, while its knockdown triggers cellular senescence and growth arrest. Estrogen-related receptor ERRγ can inhibit tumor growth but ERRα is protumorigenic. Dax1 and short heterodimeric partner are also inhibitory in prostate cancer. CONCLUSION There is a "zoo" of relatively underappreciated orphan receptors that play key roles in prostate cancer.
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Affiliation(s)
- Minas Sakellakis
- Fourth Oncology Department and Comprehensive Clinical Trials Center, Metropolitan Hospital, Athens, Greece
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Structural overview and perspectives of the nuclear receptors, a major family as the direct targets for small-molecule drugs. Acta Biochim Biophys Sin (Shanghai) 2021; 54:12-24. [PMID: 35130630 PMCID: PMC9909358 DOI: 10.3724/abbs.2021001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The nuclear receptors (NRs) are an evolutionarily related family of transcription factors, which share certain common structural characteristics and regulate the expressions of various genes by recognizing different response elements. NRs play important roles in cell differentiation, proliferation, survival and apoptosis, rendering them indispensable in many physiological activities including growth and metabolism. As a result, dysfunctions of NRs are closely related to a variety of diseases, such as diabetes, obesity, infertility, inflammation, the Alzheimer's disease, cardiovascular diseases, prostate and breast cancers. Meanwhile, small-molecule drugs directly targeting NRs have been widely used in the treatment of above diseases. Here we summarize recent progress in the structural biology studies of NR family proteins. Compared with the dozens of structures of isolated DNA-binding domains (DBDs) and the striking more than a thousand of structures of isolated ligand-binding domains (LBDs) accumulated in the Protein Data Bank (PDB) over thirty years, by now there are only a small number of multi-domain NR complex structures, which reveal the integration of different NR domains capable of the allosteric signal transduction, or the detailed interactions between NR and various coregulator proteins. On the other hand, the structural information about several orphan NRs is still totally unavailable, hindering the further understanding of their functions. The fast development of new technologies in structural biology will certainly help us gain more comprehensive information of NR structures, inspiring the discovery of novel NR-targeting drugs with a new binding site beyond the classic LBD pockets and/or a new mechanism of action.
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Nelson AT, Wang Y, Nelson ER. TLX, an Orphan Nuclear Receptor With Emerging Roles in Physiology and Disease. Endocrinology 2021; 162:6360449. [PMID: 34463725 PMCID: PMC8462384 DOI: 10.1210/endocr/bqab184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 12/14/2022]
Abstract
TLX (NR2E1), an orphan member of the nuclear receptor superfamily, is a transcription factor that has been described to be generally repressive in nature. It has been implicated in several aspects of physiology and disease. TLX is best known for its ability to regulate the proliferation of neural stem cells and retinal progenitor cells. Dysregulation, overexpression, or loss of TLX expression has been characterized in numerous studies focused on a diverse range of pathological conditions, including abnormal brain development, psychiatric disorders, retinopathies, metabolic disease, and malignant neoplasm. Despite the lack of an identified endogenous ligand, several studies have described putative synthetic and natural TLX ligands, suggesting that this receptor may serve as a therapeutic target. Therefore, this article aims to briefly review what is known about TLX structure and function in normal physiology, and provide an overview of TLX in regard to pathological conditions. Particular emphasis is placed on TLX and cancer, and the potential utility of this receptor as a therapeutic target.
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Affiliation(s)
- Adam T Nelson
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yu Wang
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Erik R Nelson
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- University of Illinois Cancer Center, University of Illinois at Chicago, Chicago, Illinois 60612, USA
- Carl R. Woese Institute for Genomic Biology, Anticancer Discovery from Pets to People Theme, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Correspondence: Erik R. Nelson, PhD, Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 407 S Goodwin Ave (MC-114), Urbana, IL 61801, USA.
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8
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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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9
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von Hardenberg S, Gnewuch C, Schmitz G, Borlak J. ApoE is a major determinant of hepatic bile acid homeostasis in mice. J Nutr Biochem 2018; 52:82-91. [DOI: 10.1016/j.jnutbio.2017.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/13/2017] [Accepted: 09/09/2017] [Indexed: 12/27/2022]
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10
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Mackeh R, Marr AK, Dargham SR, Syed N, Fakhro KA, Kino T. Single-Nucleotide Variations of the Human Nuclear Hormone Receptor Genes in 60,000 Individuals. J Endocr Soc 2018; 2:77-90. [PMID: 29379896 PMCID: PMC5779106 DOI: 10.1210/js.2017-00406] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/28/2017] [Indexed: 01/15/2023] Open
Abstract
Nuclear hormone receptors (NRs) mediate biologic actions of lipophilic molecules to gene transcription and are phylogenetically and functionally categorized into seven subfamilies and three groups, respectively. Single-nucleotide variations (SNVs) or polymorphisms are genetic changes influencing individual response to environmental factors and susceptibility to various disorders, and are part of the genetic diversification and basis for evolution. We sorted out SNVs of the human NR genes from 60,706 individuals, calculated three parameters (percentage of all variants, percentage of loss-of-function variants, and ratio of nonsynonymous/synonymous variants in their full protein-coding or major domain-coding sequences), and compared them with several valuables. Comparison of these parameters between NRs and control groups identified that NRs form a highly conserved gene family. The three parameters for the full coding sequence are positively correlated with each other, whereas four NR genes are distinct from the others with much higher tolerance to protein sequence-changing variants. DNA-binding domain and N-terminal domain are respectively those bearing the least and the most variation. NR subfamilies based on their phylogenetic proximity or functionality as well as diversity of tissue distribution and numbers of partner molecules are all not correlated with the variation parameters, whereas their gene age demonstrates an association. Our results suggest that the natural selection driving the NR family evolution still operates in humans. Gene age and probably the potential to adapt to various new ligands, but not current functional diversity, are major determinants for SNVs of the human NR genes.
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Affiliation(s)
- Rafah Mackeh
- Department of Human Genetics, Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Alexandra K. Marr
- Department of Human Genetics, Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Soha R. Dargham
- Biostatistics, Epidemiology and Biomathematics Research Core, Weill Cornell Medicine in Qatar, Doha 24811, Qatar
| | - Najeeb Syed
- Division of Biomedical Informatics, Sidra Medical and Research Center, Doha 26999, Qatar
| | - Khalid A. Fakhro
- Department of Human Genetics, Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine in Qatar, Doha 24144, Qatar
| | - Tomoshige Kino
- Department of Human Genetics, Division of Translational Medicine, Sidra Medical and Research Center, Doha 26999, Qatar
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11
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Deciphering the Relationship between Obesity and Various Diseases from a Network Perspective. Genes (Basel) 2017; 8:genes8120392. [PMID: 29258237 PMCID: PMC5748710 DOI: 10.3390/genes8120392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/02/2017] [Accepted: 12/13/2017] [Indexed: 12/14/2022] Open
Abstract
The number of obesity cases is rapidly increasing in developed and developing countries, thereby causing significant health problems worldwide. The pathologic factors of obesity at the molecular level are not fully characterized, although the imbalance between energy intake and consumption is widely recognized as the main reason for fat accumulation. Previous studies reported that obesity can be caused by the dysfunction of genes associated with other diseases, such as myocardial infarction, hence providing new insights into dissecting the pathogenesis of obesity by investigating its associations with other diseases. In this study, we investigated the relationship between obesity and diseases from Online Mendelian Inheritance in Man (OMIM) databases on the protein–protein interaction (PPI) network. The obesity genes and genes of one OMIM disease were mapped onto the network, and the interaction scores between the two gene sets were investigated on the basis of the PPI of individual gene pairs, thereby inferring the relationship between obesity and this disease. Results suggested that diseases related to nutrition and endocrine are the top two diseases that are closely associated with obesity. This finding is consistent with our general knowledge and indicates the reliability of our obtained results. Moreover, we inferred that diseases related to psychiatric factors and bone may also be highly related to obesity because the two diseases followed the diseases related to nutrition and endocrine according to our results. Numerous obesity–disease associations were identified in the literature to confirm the relationships between obesity and the aforementioned four diseases. These new results may help understand the underlying molecular mechanisms of obesity–disease co-occurrence and provide useful insights for disease prevention and intervention.
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12
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Ma H, Sales VM, Wolf AR, Subramanian S, Matthews TJ, Chen M, Sharma A, Gall W, Kulik W, Cohen DE, Adachi Y, Griffin NW, Gordon JI, Patti ME, Isganaitis E. Attenuated Effects of Bile Acids on Glucose Metabolism and Insulin Sensitivity in a Male Mouse Model of Prenatal Undernutrition. Endocrinology 2017; 158. [PMID: 28637315 PMCID: PMC5551557 DOI: 10.1210/en.2017-00288] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Prenatal undernutrition and low birth weight are associated with risk of type 2 diabetes and obesity. Prenatal caloric restriction results in low birth weight, glucose intolerance, obesity, and reduced plasma bile acids (BAs) in offspring mice. Because BAs can regulate systemic metabolism and glucose homeostasis, we hypothesized that BA supplementation could prevent diet-induced obesity and glucose intolerance in this model of developmental programming. Pregnant dams were food restricted by 50% from gestational days 12.5 to 18.5. Offspring of both undernourished (UN) and control (C) dams given unrestricted diets were weaned to high-fat diets with or without supplementation with 0.25% w/w ursodeoxycholic acid (UDCA), yielding four experimental groups: C, UN, C + UDCA, and UN + UDCA. Glucose homeostasis, BA composition, liver and intestinal gene expression, and microbiota composition were analyzed in the four groups. Although UDCA supplementation ameliorated diet-induced obesity in C mice, there was no effect in UN mice. UDCA similarly lowered fasting insulin, and improved glucose tolerance, pyruvate tolerance, and liver steatosis in C, but not UN, animals. BA composition differed significantly, and liver and ileal expression of genes involved in BA metabolism (Cyp7b1, Shp) were differentially induced by UDCA in C vs UN animals. Bacterial taxa in fecal microbiota correlated with treatment groups and metabolic parameters. In conclusion, prenatal undernutrition alters responsiveness to the metabolic benefits of BA supplementation, with resistance to the weight-lowering and insulin-sensitizing effects of UDCA supplementation. Our findings suggest that BA metabolism may be a previously unrecognized contributor to developmentally programmed diabetes risk.
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Affiliation(s)
- Huijuan Ma
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
- Department of Endocrinology and Metabolism, Hebei General Hospital, Shijiazhuang, Hebei, 050051, China
| | - Vicencia M Sales
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Ashley R Wolf
- Center for Genome Sciences and Systems Biology, and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Sathish Subramanian
- Center for Genome Sciences and Systems Biology, and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Tucker J Matthews
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Michael Chen
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Aparna Sharma
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Walt Gall
- Metabolon, Durham, North Carolina 27713
| | - Wim Kulik
- Laboratory of Genetic Metabolic Diseases, Departments of Pediatrics and Clinical Chemistry, University of Amsterdam, 1105 AZ Amsterdam-Zuidoost, The Netherlands
| | - David E Cohen
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, New York 10021
| | - Yusuke Adachi
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Nicholas W Griffin
- Center for Genome Sciences and Systems Biology, and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, and Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Mary-Elizabeth Patti
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
| | - Elvira Isganaitis
- Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts 02115
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13
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Weikum ER, Okafor CD, D'Agostino EH, Colucci JK, Ortlund EA. Structural Analysis of the Glucocorticoid Receptor Ligand-Binding Domain in Complex with Triamcinolone Acetonide and a Fragment of the Atypical Coregulator, Small Heterodimer Partner. Mol Pharmacol 2017; 92:12-21. [PMID: 28396564 DOI: 10.1124/mol.117.108506] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/06/2017] [Indexed: 12/13/2022] Open
Abstract
The synthetic glucocorticoids (GCs) dexamethasone, mometasone furoate, and triamcinolone acetonide are pharmaceutical mainstays to treat chronic inflammatory diseases. These drugs bind to the glucocorticoid receptor (GR), a ligand-activated transcription factor and member of the nuclear receptor superfamily. The GR is widely recognized as a therapeutic target for its ability to counter proinflammatory signaling. Despite the popularity of GCs in the clinic, long-term use leads to numerous side effects, driving the need for new and improved drugs with less off-target pharmacology. X-ray crystal structures have played an important role in the drug-design process, permitting the characterization of robust structure-function relationships. However, steroid receptor ligand-binding domains (LBDs) are inherently unstable, and their crystallization requires extensive mutagenesis to enhance expression and crystallization. Here, we use an ancestral variant of GR as a tool to generate a high-resolution crystal structure of GR in complex with the potent glucocorticoid triamcinolone acetonide (TA) and a fragment of the small heterodimer partner (SHP). Using structural analysis, molecular dynamics, and biochemistry, we show that TA increases intramolecular contacts within the LBD to drive affinity and enhance stability of the receptor-ligand complex. These data support the emerging theme that ligand-induced receptor conformational dynamics at the mouth of the pocket play a major role in steroid receptor activation. This work also represents the first GR structure in complex with SHP, which has been suggested to play a role in modulating hepatic GR function.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - C Denise Okafor
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Emma H D'Agostino
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Jennifer K Colucci
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia
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14
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Rudraiah S, Zhang X, Wang L. Nuclear Receptors as Therapeutic Targets in Liver Disease: Are We There Yet? Annu Rev Pharmacol Toxicol 2016; 56:605-626. [PMID: 26738480 DOI: 10.1146/annurev-pharmtox-010715-103209] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear receptors (NR) are ligand-modulated transcription factors that play diverse roles in cell differentiation, development, proliferation, and metabolism and are associated with numerous liver pathologies such as cancer, steatosis, inflammation, fibrosis, cholestasis, and xenobiotic/drug-induced liver injury. The network of target proteins associated with NRs is extremely complex, comprising coregulators, small noncoding microRNAs, and long noncoding RNAs. The importance of NRs as targets of liver disease is exemplified by the number of NR ligands that are currently used in the clinics or in clinical trials with promising results. Understanding the regulation by NR during pathophysiological conditions, and identifying ligands for orphan NR, points to a potential therapeutic approach for patients with liver diseases. An overview of complex NR metabolic networks and their pharmacological implications in liver disease is presented here.
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Affiliation(s)
- Swetha Rudraiah
- Department of Physiology and Neurobiology and The Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269
| | - Xi Zhang
- Department of Physiology and Neurobiology and The Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269
| | - Li Wang
- Department of Physiology and Neurobiology and The Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269.,Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut 06516.,Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut 06520
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15
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Tice CM, Zheng YJ. Non-canonical modulators of nuclear receptors. Bioorg Med Chem Lett 2016; 26:4157-64. [PMID: 27503683 DOI: 10.1016/j.bmcl.2016.07.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/19/2016] [Accepted: 07/27/2016] [Indexed: 12/13/2022]
Abstract
Like G protein-coupled receptors (GPCRs) and protein kinases, nuclear receptors (NRs) are a rich source of pharmaceutical targets. Over 80 NR-targeting drugs have been approved for 18 NRs. The focus of drug discovery in NRs has hitherto been on identifying ligands that bind to the canonical ligand binding pockets of the C-terminal ligand binding domains (LBDs). Due to the development of drug resistance and selectivity concerns, there has been considerable interest in exploring other, non-canonical ligand binding sites. Unfortunately, the potencies of compounds binding at other sites have generally not been sufficient for clinical development. However, the situation has changed dramatically over the last 3years, as compounds with sufficient potency have been reported for several NR targets. Here we review recent developments in this area from a medicinal chemistry point of view in the hope of stimulating further interest in this area of research.
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Affiliation(s)
- Colin M Tice
- Vitae Pharmaceuticals, Inc., 502 West Office Center Drive, Fort Washington, PA 19034, United States
| | - Ya-Jun Zheng
- Vitae Pharmaceuticals, Inc., 502 West Office Center Drive, Fort Washington, PA 19034, United States
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16
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Zhi X, Zhou XE, Melcher K, Xu HE. Structures and regulation of non-X orphan nuclear receptors: A retinoid hypothesis. J Steroid Biochem Mol Biol 2016; 157:27-40. [PMID: 26159912 DOI: 10.1016/j.jsbmb.2015.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 06/10/2015] [Accepted: 06/16/2015] [Indexed: 12/28/2022]
Abstract
Nuclear receptors are defined as a family of ligand regulated transcription factors [1-6]. While this definition reflects that ligand binding is a key property of nuclear receptors, it is still a heated subject of debate if all the nuclear receptors (48 human members) can bind ligands (ligands referred here to both physiological and synthetic ligands). Recent studies in nuclear receptor structure biology and pharmacology have undoubtedly increased our knowledge of nuclear receptor functions and their regulation. As a result, they point to new avenues for the discovery and development of nuclear receptor regulators, including nuclear receptor ligands. Here we review the recent literature on orphan nuclear receptor structural analysis and ligand identification, particularly on the orphan nuclear receptors that do not heterodimerize with retinoid X receptors, which we term as non-X orphan receptors. We also propose a speculative "retinoid hypothesis" for a subset of non-X orphan nuclear receptors, which we hope to help shed light on orphan nuclear receptor biology and drug discovery. This article is part of a Special Issue entitled 'Orphan Nuclear Receptors'.
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Affiliation(s)
- Xiaoyong Zhi
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503, USA; Autophagy Research Center, University of Texas Southwestern Medical Center, 6000Harry Hines Blvd., Dallas, TX 75390, USA.
| | - X Edward Zhou
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503, USA
| | - Karsten Melcher
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503, USA
| | - H Eric Xu
- Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Ave., N.E., Grand Rapids, MI 49503, USA; VARI-SIMM Center, Key Laboratory of Receptor Research, Shanghai Institute of MateriaMedica, Chinese Academy of Sciences, Shanghai 201203, China.
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17
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Benod C, Villagomez R, Webb P. TLX: An elusive receptor. J Steroid Biochem Mol Biol 2016; 157:41-7. [PMID: 26554934 DOI: 10.1016/j.jsbmb.2015.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 06/30/2015] [Accepted: 11/04/2015] [Indexed: 12/11/2022]
Abstract
TLX (tailless receptor) is a member of the nuclear receptor superfamily and belongs to a class of nuclear receptors for which no endogenous or synthetic ligands have yet been identified. TLX is a promising therapeutic target in neurological disorders and brain tumors. Thus, regulatory ligands for TLX need to be identified to complete the validation of TLX as a useful target and would serve as chemical probes to pursue the study of this receptor in disease models. It has recently been proved that TLX is druggable. However, to identify potent and specific TLX ligands with desirable biological activity, a deeper understanding of where ligands bind, how they alter TLX conformation and of the mechanism by which TLX mediates the transcription of its target genes is needed. While TLX is in the process of escaping from orphanhood, future ligand design needs to progress in parallel with improved understanding of (i) the binding cavity or surfaces to target with small molecules on the TLX ligand binding domain and (ii) the nature of the TLX coregulators in particular cell and disease contexts. Both of these topics are discussed in this review.
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Affiliation(s)
- Cindy Benod
- Department of Genomic Medicine, Houston Methodist Research Institute (HMRI), 6670 Bertner Avenue, Houston, TX 77030, USA.
| | - Rosa Villagomez
- Department of Genomic Medicine, Houston Methodist Research Institute (HMRI), 6670 Bertner Avenue, Houston, TX 77030, USA
| | - Paul Webb
- Department of Genomic Medicine, Houston Methodist Research Institute (HMRI), 6670 Bertner Avenue, Houston, TX 77030, USA
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18
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Waugh DS. Crystal structures of MBP fusion proteins. Protein Sci 2016; 25:559-71. [PMID: 26682969 DOI: 10.1002/pro.2863] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 12/16/2015] [Indexed: 02/06/2023]
Abstract
Although chaperone-assisted protein crystallization remains a comparatively rare undertaking, the number of crystal structures of polypeptides fused to maltose-binding protein (MBP) that have been deposited in the Protein Data Bank (PDB) has grown dramatically during the past decade. Altogether, 102 fusion protein structures were detected by Basic Local Alignment Search Tool (BLAST) analysis. Collectively, these structures comprise a range of sizes, space groups, and resolutions that are typical of the PDB as a whole. While most of these MBP fusion proteins were equipped with short inter-domain linkers to increase their rigidity, fusion proteins with long linkers have also been crystallized. In some cases, surface entropy reduction mutations in MBP appear to have facilitated the formation of crystals. A comparison of the structures of fused and unfused proteins, where both are available, reveals that MBP-mediated structural distortions are very rare.
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Affiliation(s)
- David S Waugh
- Protein Engineering Section, Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, P.O. Box B, Frederick, Maryland, 21702-1201
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19
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Zhang C, Li X, Adelmant G, Dobbins J, Geisen C, Oser MG, Wucherpfenning KW, Marto JA, Kaelin WG. Peptidic degron in EID1 is recognized by an SCF E3 ligase complex containing the orphan F-box protein FBXO21. Proc Natl Acad Sci U S A 2015; 112:15372-7. [PMID: 26631746 PMCID: PMC4687553 DOI: 10.1073/pnas.1522006112] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
EP300-interacting inhibitor of differentiation 1 (EID1) belongs to a protein family implicated in the control of transcription, differentiation, DNA repair, and chromosomal maintenance. EID1 has a very short half-life, especially in G0 cells. We discovered that EID1 contains a peptidic, modular degron that is necessary and sufficient for its polyubiquitylation and proteasomal degradation. We found that this degron is recognized by an Skp1, Cullin, and F-box (SCF)-containing ubiquitin ligase complex that uses the F-box Only Protein 21 (FBXO21) as its substrate recognition subunit. SCF(FBXO21) polyubiquitylates EID1 both in vitro and in vivo and is required for the efficient degradation of EID1 in both cycling and quiescent cells. The EID1 degron partially overlaps with its retinoblastoma tumor suppressor protein-binding domain and is congruent with a previously defined melanoma-associated antigen-binding motif shared by EID family members, suggesting that binding to retinoblastoma tumor suppressor and melanoma-associated antigen family proteins could affect the polyubiquitylation and turnover of EID family members in cells.
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Affiliation(s)
- Cuiyan Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215
| | - Xiaotong Li
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Guillaume Adelmant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215
| | - Jessica Dobbins
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02215
| | - Christoph Geisen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215; Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215
| | - Kai W Wucherpfenning
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02215
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215; Howard Hughes Medical Institute, Chevy Chase, MD 20815
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20
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Musille PM, Kossmann BR, Kohn JA, Ivanov I, Ortlund EA. Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity. J Biol Chem 2015; 291:1411-26. [PMID: 26553876 DOI: 10.1074/jbc.m115.662874] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Indexed: 11/06/2022] Open
Abstract
Phospholipids (PLs) are unusual signaling hormones sensed by the nuclear receptor liver receptor homolog-1 (LRH-1), which has evolved a novel allosteric pathway to support appropriate interaction with co-regulators depending on ligand status. LRH-1 plays an important role in controlling lipid and cholesterol homeostasis and is a potential target for the treatment of metabolic and neoplastic diseases. Although the prospect of modulating LRH-1 via small molecules is exciting, the molecular mechanism linking PL structure to transcriptional co-regulator preference is unknown. Previous studies showed that binding to an activating PL ligand, such as dilauroylphosphatidylcholine, favors LRH-1's interaction with transcriptional co-activators to up-regulate gene expression. Both crystallographic and solution-based structural studies showed that dilauroylphosphatidylcholine binding drives unanticipated structural fluctuations outside of the canonical activation surface in an alternate activation function (AF) region, encompassing the β-sheet-H6 region of the protein. However, the mechanism by which dynamics in the alternate AF influences co-regulator selectivity remains elusive. Here, we pair x-ray crystallography with molecular modeling to identify an unexpected allosteric network that traverses the protein ligand binding pocket and links these two elements to dictate selectivity. We show that communication between the alternate AF region and classical AF2 is correlated with the strength of the co-regulator interaction. This work offers the first glimpse into the conformational dynamics that drive this unusual PL-mediated nuclear hormone receptor activation.
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Affiliation(s)
- Paul M Musille
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and
| | - Bradley R Kossmann
- the Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302
| | - Jeffrey A Kohn
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and
| | - Ivaylo Ivanov
- the Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302
| | - Eric A Ortlund
- From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and
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21
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Zou A, Lehn S, Magee N, Zhang Y. New Insights into Orphan Nuclear Receptor SHP in Liver Cancer. NUCLEAR RECEPTOR RESEARCH 2015; 2. [PMID: 26504773 PMCID: PMC4618403 DOI: 10.11131/2015/101162] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Small heterodimer partner (SHP; NR0B2) is a unique orphan nuclear receptor (NR) that contains a putative ligand-binding domain but lacks a DNA-binding domain. SHP is a transcriptional corepressor affecting diverse metabolic processes including bile acid synthesis, cholesterol and lipid metabolism, glucose and energy homeostasis, and reproductive biology via interaction with multiple NRs and transcriptional factors (TFs). Hepatocellular carcinoma (HCC) is one of the most deadly human cancers worldwide with few therapeutic options and poor prognosis. Recently, it is becoming clear that SHP plays an antitumor role in the development of liver cancer. In this review, we summarize the most recent findings regarding the new SHP interaction partners, new structural insights into SHP’s gene repressing activity, and SHP protein posttranslational modifications by bile acids. We also discuss the pleiotropic role of SHP in regulating cell proliferation, apoptosis, DNA methylation, and inflammation that are related to antitumor role of SHP in HCC. Improving our understanding of SHP’s antitumor role in the development of liver cancer will provide new insights into developing novel treatments or prevention strategies. Future research will focus on developing more efficacious and specific synthetic SHP ligands for pharmaceutical applications in liver cancer and several metabolic diseases such as hypercholesterolemia, obesity, diabetes, and fatty liver disease.
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Affiliation(s)
- An Zou
- Department of Pharmacology, Toxicology & Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sarah Lehn
- Department of Pharmacology, Toxicology & Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Nancy Magee
- Department of Pharmacology, Toxicology & Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Yuxia Zhang
- Department of Pharmacology, Toxicology & Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
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22
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Zhi X, Zhou XE, He Y, Searose-Xu K, Zhang CL, Tsai CC, Melcher K, Xu HE. Structural basis for corepressor assembly by the orphan nuclear receptor TLX. Genes Dev 2015; 29:440-50. [PMID: 25691470 PMCID: PMC4335298 DOI: 10.1101/gad.254904.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The orphan nuclear receptor TLX regulates neural stem cell self-renewal in the adult brain and functions primarily as a transcription repressor through recruitment of Atrophin corepressors, which bind to TLX via a conserved peptide motif termed the Atro box. Zhi et al. report crystal structures of the human and insect TLX ligand-binding domain in complex with Atro box peptides. Mutations that weaken the TLX–Atrophin interaction compromise the repressive activity of TLX. In addition, mutations of corresponding residues in other members of this class of receptors diminish their repressor activities. The orphan nuclear receptor TLX regulates neural stem cell self-renewal in the adult brain and functions primarily as a transcription repressor through recruitment of Atrophin corepressors, which bind to TLX via a conserved peptide motif termed the Atro box. Here we report crystal structures of the human and insect TLX ligand-binding domain in complex with Atro box peptides. In these structures, TLX adopts an autorepressed conformation in which its helix H12 occupies the coactivator-binding groove. Unexpectedly, H12 in this autorepressed conformation forms a novel binding pocket with residues from helix H3 that accommodates a short helix formed by the conserved ALXXLXXY motif of the Atro box. Mutations that weaken the TLX–Atrophin interaction compromise the repressive activity of TLX, demonstrating that this interaction is required for Atrophin to confer repressor activity to TLX. Moreover, the autorepressed conformation is conserved in the repressor class of orphan nuclear receptors, and mutations of corresponding residues in other members of this class of receptors diminish their repressor activities. Together, our results establish the functional conservation of the autorepressed conformation and define a key sequence motif in the Atro box that is essential for TLX-mediated repression.
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Affiliation(s)
- Xiaoyong Zhi
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA; Autophagy Research Center,
| | - X Edward Zhou
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Yuanzheng He
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Kelvin Searose-Xu
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - Chun-Li Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Texas 75390, USA
| | - Chih-Cheng Tsai
- Department of Cell Biology and Neuroscience, University of California at Riverside, Riverside, California 92521, USA
| | - Karsten Melcher
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
| | - H Eric Xu
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA; Van Andel Research Institute-Shanghai Institute of Materia Medica (VARI/SIMM) Center, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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23
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Gallastegui N, Mackinnon JAG, Fletterick RJ, Estébanez-Perpiñá E. Advances in our structural understanding of orphan nuclear receptors. Trends Biochem Sci 2014; 40:25-35. [PMID: 25499868 DOI: 10.1016/j.tibs.2014.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 12/24/2022]
Abstract
Nuclear receptors (NRs) are key players in the regulation of gene expression, coordinating protein assemblies upon their surfaces. NRs are regulated by ligand binding, which remodels the interaction surfaces and subsequently influences macromolecular complex formation. Structural biology has been instrumental in the discovery of some of these ligands, but there are still orphan NRs (ONRs) whose bona fide ligands have yet to be identified. Over the past decade, fundamental structural and functional breakthroughs have led to a deeper understanding of ONR actions and their multidomain organization. Here, we summarize the structural advances in ONRs with implications for the therapeutic treatment of diseases such as metabolic syndrome and cancer.
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Affiliation(s)
- Nerea Gallastegui
- The Institute of Biomedicine of the University of Barcelona (IBUB), Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Jonathan A G Mackinnon
- The Institute of Biomedicine of the University of Barcelona (IBUB), Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Baldiri Reixac 15-21, 08028 Barcelona, Spain
| | - Robert J Fletterick
- The Department of Biochemistry and Biophysics, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Eva Estébanez-Perpiñá
- The Institute of Biomedicine of the University of Barcelona (IBUB), Department of Biochemistry and Molecular Biology, University of Barcelona (UB), Baldiri Reixac 15-21, 08028 Barcelona, Spain.
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24
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The human orphan nuclear receptor tailless (TLX, NR2E1) is druggable. PLoS One 2014; 9:e99440. [PMID: 24936658 PMCID: PMC4060991 DOI: 10.1371/journal.pone.0099440] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 05/14/2014] [Indexed: 12/31/2022] Open
Abstract
Nuclear receptors (NRs) are an important group of ligand-dependent transcriptional factors. Presently, no natural or synthetic ligand has been identified for a large group of orphan NRs. Small molecules to target these orphan NRs will provide unique resources for uncovering regulatory systems that impact human health and to modulate these pathways with drugs. The orphan NR tailless (TLX, NR2E1), a transcriptional repressor, is a major player in neurogenesis and Neural Stem Cell (NSC) derived brain tumors. No chemical probes that modulate TLX activity are available, and it is not clear whether TLX is druggable. To assess TLX ligand binding capacity, we created homology models of the TLX ligand binding domain (LBD). Results suggest that TLX belongs to an emerging class of NRs that lack LBD helices α1 and α2 and that it has potential to form a large open ligand binding pocket (LBP). Using a medium throughput screening strategy, we investigated direct binding of 20,000 compounds to purified human TLX protein and verified interactions with a secondary (orthogonal) assay. We then assessed effects of verified binders on TLX activity using luciferase assays. As a result, we report identification of three compounds (ccrp1, ccrp2 and ccrp3) that bind to recombinant TLX protein with affinities in the high nanomolar to low micromolar range and enhance TLX transcriptional repressive activity. We conclude that TLX is druggable and propose that our lead compounds could serve as scaffolds to derive more potent ligands. While our ligands potentiate TLX repressive activity, the question of whether it is possible to develop ligands to de-repress TLX activity remains open.
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