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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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Jiang L, Liu X, Liang X, Dai S, Wei H, Guo M, Chen Z, Xiao D, Chen Y. Structural characterization of the DNA binding mechanism of retinoic acid-related orphan receptor gamma. Structure 2024; 32:467-475.e3. [PMID: 38309263 DOI: 10.1016/j.str.2024.01.004] [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: 09/01/2023] [Revised: 11/15/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
Retinoic acid-related orphan receptor gamma (RORγ) plays critical roles in regulating various biological processes and has been linked to immunodeficiency disorders and cancers. DNA recognition is essential for RORγ to exert its functions. However, the underlying mechanism of the DNA binding by RORγ remains unclear. In this study, we present the crystal structure of the complex of RORγ1 DNA-binding domain (RORγ1-DBD)/direct repeat DNA element DR2 at 2.3 Å resolution. We demonstrate that RORγ1-DBD binds the DR2 motif as a homodimer, with the C-terminal extension (CTE) region of RORγ1-DBD contributing to the DNA recognition and the formation of dimeric interface. Further studies reveal that REV-ERB-DBD and RXR-DBD, also bind the DR2 site as a homodimer, while NR4A2-DBD binds DR2 as a monomer. Our research uncovers a binding mechanism of RORγ1 to the DR2 site and provides insights into the biological functions of RORγ1 and the broader RORs subfamily.
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Affiliation(s)
- Longying Jiang
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xueke Liu
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xujun Liang
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuyan Dai
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hudie Wei
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ming Guo
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhuchu Chen
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Desheng Xiao
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yongheng Chen
- Department of Pathology, NHC Key Laboratory of Cancer Proteomics, State Local Joint Engineering Laboratory for Anticancer Drugs, Department of Oncology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Xu S, Kong L, Li L, Wang C, Gu J, Luo H, Meng Q. Farnesoid X receptor overexpression prevents hepatic steatosis through inhibiting AIM2 inflammasome activation in nonalcoholic fatty liver disease. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166930. [PMID: 37918680 DOI: 10.1016/j.bbadis.2023.166930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/10/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
Oxidative stress-mediated activation of inflammasome has a significant effect on the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Farnesoid X receptor (NR1H4, FXR) has been implicated in biological function and many diseases, including NAFLD. The regulatory effect of FXR on oxidative stress and whether this process is related with the activation of absent melanoma 2 (AIM2) inflammasome in NAFLD remain unclear. In the present research, we confirmed that FXR in the livers of steatosis patients is significantly reduced compared with normal liver tissue by using the Gene Expression Omnibus (GEO) database and a palmitic acid (PA) - mediated steatosis model in AML-12 cells. Under the premise of ensuring the same food intake as the control group, overexpression of FXR in mice attenuated HFD-mediated weight gain and liver steatosis, facilitated lipid metabolism, improved fatty acid β-oxidation, lipolysis, and reduced fatty acid synthesis and intake, which also inhibited the activation of AIM2 inflammasome. Overexpression of FXR alleviated PA-induced triglyceride (TG) accumulation, imbalance of lipid homeostasis, and the activation of AIM2 inflammasome in hepatic steatosis cells, while FXR knockdown appeared the opposite effects. FXR overexpression suppressed PA- and HFD-induced oxidative stress, but FXR siRNA demonstrated the opposite influence. The decreased ROS generation may be the reason why FXR weakens AIM2 activation when a fatty acid overload occurs. In conclusion, our results confirm that other than regulating lipid homeostasis and blocking NLRP3 inflammasome activation, FXR improves hepatic steatosis by a novel mechanism that inhibits oxidative stress and AIM2 inflammasome activation.
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Affiliation(s)
- Shuai Xu
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Lina Kong
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Lin Li
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Changyuan Wang
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Jiangning Gu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Haifeng Luo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China
| | - Qiang Meng
- Department of Clinical Pharmacology, College of Pharmacy, Dalian Medical University, Dalian 116044, China.
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Meadows V, Yang Z, Basaly V, Guo GL. FXR Friend-ChIPs in the Enterohepatic System. Semin Liver Dis 2023; 43:267-278. [PMID: 37442156 PMCID: PMC10620036 DOI: 10.1055/a-2128-5538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Chronic liver diseases encompass a wide spectrum of hepatic maladies that often result in cholestasis or altered bile acid secretion and regulation. Incidence and cost of care for many chronic liver diseases are rising in the United States with few Food and Drug Administration-approved drugs available for patient treatment. Farnesoid X receptor (FXR) is the master regulator of bile acid homeostasis with an important role in lipid and glucose metabolism and inflammation. FXR has served as an attractive target for management of cholestasis and fibrosis; however, global FXR agonism results in adverse effects in liver disease patients, severely affecting quality of life. In this review, we highlight seminal studies and recent updates on the FXR proteome and identify gaps in knowledge that are essential for tissue-specific FXR modulation. In conclusion, one of the greatest unmet needs in the field is understanding the underlying mechanism of intestinal versus hepatic FXR function.
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Affiliation(s)
- Vik Meadows
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, New Jersey
- Environmental and Occupational Health Science Institute, Rutgers University, Piscataway, New Jersey
| | - Zhenning Yang
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, New Jersey
- Environmental and Occupational Health Science Institute, Rutgers University, Piscataway, New Jersey
| | - Veronia Basaly
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, New Jersey
- Environmental and Occupational Health Science Institute, Rutgers University, Piscataway, New Jersey
| | - Grace L. Guo
- Department of Pharmacology and Toxicology, Rutgers University, Piscataway, New Jersey
- Environmental and Occupational Health Science Institute, Rutgers University, Piscataway, New Jersey
- Department of Veterans Affairs, New Jersey Health Care System, East Orange, New Jersey
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