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Lockett J, Inder WJ, Clifton VL. The Glucocorticoid Receptor: Isoforms, Functions, and Contribution to Glucocorticoid Sensitivity. Endocr Rev 2024; 45:593-624. [PMID: 38551091 PMCID: PMC11244253 DOI: 10.1210/endrev/bnae008] [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] [Received: 11/15/2023] [Indexed: 07/13/2024]
Abstract
Glucocorticoids exert pleiotropic effects on all tissues to regulate cellular and metabolic homeostasis. Synthetic forms are used therapeutically in a wide range of conditions for their anti-inflammatory benefits, at the cost of dose and duration-dependent side effects. Significant variability occurs between tissues, disease states, and individuals with regard to both the beneficial and deleterious effects. The glucocorticoid receptor (GR) is the site of action for these hormones and a vast body of work has been conducted understanding its function. Traditionally, it was thought that the anti-inflammatory benefits of glucocorticoids were mediated by transrepression of pro-inflammatory transcription factors, while the adverse metabolic effects resulted from direct transactivation. This canonical understanding of the GR function has been brought into question over the past 2 decades with advances in the resolution of scientific techniques, and the discovery of multiple isoforms of the receptor present in most tissues. Here we review the structure and function of the GR, the nature of the receptor isoforms, and the contribution of the receptor to glucocorticoid sensitivity, or resistance in health and disease.
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Affiliation(s)
- Jack Lockett
- Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4101, Australia
- Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
- Department of Diabetes and Endocrinology, Princess Alexandra Hospital, Metro South Health, Woolloongabba, QLD 4102, Australia
| | - Warrick J Inder
- Faculty of Medicine, The University of Queensland, Herston, QLD 4006, Australia
- Department of Diabetes and Endocrinology, Princess Alexandra Hospital, Metro South Health, Woolloongabba, QLD 4102, Australia
| | - Vicki L Clifton
- Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4101, Australia
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2
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Kumar R. Cryo-EM technique and its application: Structure of steroid hormone receptors. VITAMINS AND HORMONES 2023; 123:385-397. [PMID: 37717991 DOI: 10.1016/bs.vh.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In recent years, cryo-electron microscopy (cryo-EM) has become one of the most powerful tools to solve the 3-D structure of macromolecules. Unlike X-ray crystallography, the cryo-EM method has advantage of providing an in-depth insight into the dynamic behavior of macromolecules, which is particularly useful to determine 3-D structural analyses of large protein complexes. Due to recent technical advancements, cryo-EM has become the method of choice for the determination of protein structures. Among other proteins, solving 3-D structure of steroid hormone receptors (SHRs) complexed with DNA and coactivators has been a challenge for decades. The limitations with X-ray crystallography and NMR to solve SHR protein structures prompted investigators to move towards cryo-EM technique. The cryo-EM structural analyses have been successful in revealing structural dynamics of several SHRs in recent years. Though, limited by low-resolution, the structural analyses of these SHRs may be useful in understanding many receptor functions as well as provide a platform to refine high-resolution structural analyses in future. This review article discusses the cryo-EM technique in general as well as structural information gained for SHRs using cryo-EM.
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Affiliation(s)
- Raj Kumar
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY, United States.
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3
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Kumar R. Structure and functions of the N-terminal domain of steroid hormone receptors. VITAMINS AND HORMONES 2023; 123:399-416. [PMID: 37717992 DOI: 10.1016/bs.vh.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The steroid hormone receptors (SHRs) belong to the large superfamily of nuclear receptors that selectively modulate gene expression in response to specific hormone ligands. The SHRs are required in a broad range of normal physiological processes as well as associated with numerous pathological conditions. Over years, the understanding of the SHR biology and mechanisms of their actions on target cells have found many clinical applications and management of various endocrine-related disorders. However, the effectiveness of SHR-based therapies in endocrine-related cancers remain a clinical challenge. This, in part, is due to the lack of in-depth understanding of structural dynamics and functions of SHRs' intrinsically disordered N-terminal domain (NTD). Recent progress in delineating SHR structural information and their correlations with receptor action in a highly dynamic environment is ultimately helping to explain how diverse SHR signaling mechanisms can elicit selective biological effects. Recent developments are providing new insights of how NTD's structural flexibility plays an important role in SHRs' allosteric regulation leading to the fine tuning of target gene expression to more precisely control SHRs' cell/tissue-specific functions. In this review article, we are discussing the up-to-date knowledge about the SHR actions with a particular emphasis on the structure and functions of the NTD.
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Affiliation(s)
- Raj Kumar
- Department of Pharmaceutical and Biomedical Sciences, Touro College of Pharmacy, New York, NY, United States.
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4
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Lee SH, Lim CL, Shen W, Tan SMX, Woo ARE, Yap YHY, Sian CAS, Goh WWB, Yu WP, Li L, Lin VCL. Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus. BMC Biol 2022; 20:222. [PMID: 36199058 PMCID: PMC9535881 DOI: 10.1186/s12915-022-01410-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Progesterone receptor (PGR) is a master regulator of uterine function through antagonistic and synergistic interplays with oestrogen receptors. PGR action is primarily mediated by activation functions AF1 and AF2, but their physiological significance is unknown. RESULTS We report the first study of AF1 function in mice. The AF1 mutant mice are infertile with impaired implantation and decidualization. This is associated with a delay in the cessation of epithelial proliferation and in the initiation of stromal proliferation at preimplantation. Despite tissue selective effect on PGR target genes, AF1 mutations caused global loss of the antioestrogenic activity of progesterone in both pregnant and ovariectomized models. Importantly, the study provides evidence that PGR can exert an antioestrogenic effect by genomic inhibition of Esr1 and Greb1 expression. ChIP-Seq data mining reveals intermingled PGR and ESR1 binding on Esr1 and Greb1 gene enhancers. Chromatin conformation analysis shows reduced interactions in these genes' loci in the mutant, coinciding with their upregulations. CONCLUSION AF1 mediates genomic inhibition of ESR1 action globally whilst it also has tissue-selective effect on PGR target genes.
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Affiliation(s)
- Shi Hao Lee
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore
| | - Chew Leng Lim
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore
| | - Wei Shen
- grid.35155.370000 0004 1790 4137College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Samuel Ming Xuan Tan
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore
| | - Amanda Rui En Woo
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore
| | - Yeannie H. Y. Yap
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore ,grid.459705.a0000 0004 0366 8575Present Address: Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, MAHSA University, Bandar Saujana Putra, 42610 Jenjarom, Selangor Malaysia
| | - Caitlyn Ang Su Sian
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore
| | - Wilson Wen Bin Goh
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore
| | - Wei-Ping Yu
- grid.185448.40000 0004 0637 0221Animal Gene Editing Laboratory (AGEL), Biological Resource Centre, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673 Singapore ,grid.418812.60000 0004 0620 9243Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673 Singapore
| | - Li Li
- College of Informatics, Huazhong Agricultural University, Wuhan, China.
| | - Valerie C. L. Lin
- grid.59025.3b0000 0001 2224 0361School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore
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5
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Lee SH, Yap YHY, Lim CL, Woo ARE, Lin VCL. Activation function 1 of progesterone receptor is required for mammary development and regulation of RANKL during pregnancy. Sci Rep 2022; 12:12286. [PMID: 35854046 PMCID: PMC9296660 DOI: 10.1038/s41598-022-16289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022] Open
Abstract
Progesterone receptor (PGR) is a member of the nuclear receptor superfamily of transcription factors. It is critical for mammary stem cells expansion, mammary ductal branching and alveologenesis. The transcriptional activity of PGR is mainly mediated by activation functions AF1 and AF2. Although the discovery of AF1 and AF2 propelled the understanding of the mechanism of gene regulation by nuclear receptors, their physiological roles are still poorly understood. This is largely due to the lack of suitable genetic models. The present study reports gain or loss of AF1 function mutant mouse models in the study of mammary development. The gain of function mutant AF1_QQQ exhibits hyperactivity while the loss of function mutant AF1_FFF shows hypoactivity on mammary development. However, the involvement of AF1 is context dependent. Whereas the AF1_FFF mutation causes significant impairment in mammary development during pregnancy or in response to estrogen and progesterone, it has no effect on mammary development in nulliparous mice. Furthermore, Rankl, but not Wnt4 and Areg is a major target gene of AF1. In conclusion, PGR AF1 is a pivotal ligand-dependent activation domain critical for mammary development during pregnancy and it exerts gene specific effect on PGR regulated genes.
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Affiliation(s)
- Shi Hao Lee
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Yeannie H Y Yap
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, MAHSA University, Bandar Saujana Putra, 42610, Jenjarom, Selangor, Malaysia
| | - Chew Leng Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Amanda Rui En Woo
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Valerie C L Lin
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
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6
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Kumar R. Role of conformational dynamics and flexibilities in the steroid receptor-coregulator protein complex formation. Gen Comp Endocrinol 2021; 309:113780. [PMID: 33882296 DOI: 10.1016/j.ygcen.2021.113780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/21/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022]
Abstract
Understanding of the mechanisms of actions of the steroid hormone receptor (SHR)-coregulator (CoR) protein complexes in the gene regulations has revolutionized the field of molecular endocrinology and endocrine-related oncology. The discovery and characterization of steroid receptor coactivators (SRCs) and their ability to bind various transcription factors including SHRs to coordinate the regulation of multiple target genes highlights their importance as key coregulators in various cellular signaling crosstalks as well as therapeutic target for various endocrine-related disorders specifically endocrine cancers. The dynamic nature of the SHR-CoR multi-protein complexes indicate the critical role of conformational flexibilities within specific protein(s). In recent years, the importance of conformational dynamics of the SHRs in the intramolecular and intermolecular allosteric regulations mediated via their intrinsically disordered (ID) surfaces has been highlighted. In this review article, we have discussed the importance of ID conformations within the SRCs that may also be playing an important role in the formation/deformation of multi protein complexes involving SHRs and CoRs and subsequent target gene regulation.
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Affiliation(s)
- Raj Kumar
- Department of Biomedical Sciences, University of Houston - College of Medicine, Houston, TX, United States.
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7
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Katsu Y, Shariful IMD, Lin X, Takagi W, Urushitani H, Kohno S, Hyodo S, Baker ME. N-terminal domain regulates steroid activation of elephant shark glucocorticoid and mineralocorticoid receptors. J Steroid Biochem Mol Biol 2021; 210:105845. [PMID: 33652098 DOI: 10.1016/j.jsbmb.2021.105845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/29/2020] [Accepted: 02/04/2021] [Indexed: 12/23/2022]
Abstract
Orthologs of human glucocorticoid receptor (GR) and human mineralocorticoid receptor (MR) first appear in cartilaginous fishes. Subsequently, the MR and GR diverged to respond to different steroids: the MR to aldosterone and the GR to cortisol and corticosterone. We report that cortisol, corticosterone and aldosterone activate full-length elephant shark GR, and progesterone, which activates elephant shark MR, does not activate elephant shark GR. However, progesterone inhibits steroid binding to elephant shark GR, but not to human GR. Together, this indicates partial functional divergence of elephant shark GR from the MR. Deletion of the N-terminal domain (NTD) from elephant shark GR (truncated GR) reduced the response to corticosteroids, while truncated and full-length elephant shark MR had similar responses to corticosteroids. Swapping of NTDs of elephant shark GR and MR yielded an elephant shark MR chimera with full-length GR-like increased activation by corticosteroids and progesterone compared to full-length elephant shark MR. Elephant shark MR NTD fused to GR DBD + LBD had similar activation as full-length MR, indicating that the MR NTD lacked GR-like NTD activity. We propose that NTD activation of human GR evolved early in GR divergence from the MR.
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Affiliation(s)
- Yoshinao Katsu
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Faculty of Science, Hokkaido University, Sapporo, Japan
| | | | - Xiaozhi Lin
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Wataru Takagi
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Hiroshi Urushitani
- Department of Food and Nutrition, The University of Aizu, Junior College Division, Fukushima, Japan
| | - Satomi Kohno
- Department of Biology, St. Cloud State University, St. Cloud, MN, USA
| | - Susumu Hyodo
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Michael E Baker
- Division of Nephrology-Hypertension, Department of Medicine, University of California, San Diego, CA, USA.
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8
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Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL. An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Mol Cell 2021; 81:1484-1498.e6. [PMID: 33561389 DOI: 10.1016/j.molcel.2021.01.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific consensus motifs within the local chromatin context. The mechanisms by which TFs navigate the nuclear environment as they search for binding sites remain unclear. Here, we used single-molecule tracking and machine-learning-based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells. We revealed two distinct and dynamic low-mobility populations. One accounts for specific binding to chromatin, while the other represents a confinement state that requires an intrinsically disordered region (IDR), implicated in liquid-liquid condensate subdomains. Further analysis showed that the dwell times of both subpopulations follow a power-law distribution, consistent with a broad distribution of affinities on the GR cistrome and interactome. Together, our data link IDRs with a confinement state that is functionally distinct from specific chromatin binding and modulates the transcriptional output by increasing the local concentration of TFs at specific sites.
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Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Rikke A M Jensen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.
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9
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Guillien M, le Maire A, Mouhand A, Bernadó P, Bourguet W, Banères JL, Sibille N. IDPs and their complexes in GPCR and nuclear receptor signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:105-155. [DOI: 10.1016/bs.pmbts.2020.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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10
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Shamilov R, Aneskievich BJ. Intrinsic Disorder in Nuclear Receptor Amino Termini: From Investigational Challenge to Therapeutic Opportunity. NUCLEAR RECEPTOR RESEARCH 2019. [DOI: 10.32527/2019/101417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Rambon Shamilov
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092, USA
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11
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Woo ARE, Sze SK, Chung HH, Lin VCL. Delineation of critical amino acids in activation function 1 of progesterone receptor for recruitment of transcription coregulators. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:522-533. [DOI: 10.1016/j.bbagrm.2019.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/15/2019] [Accepted: 01/30/2019] [Indexed: 12/17/2022]
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12
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Katsu Y, Oka K, Baker ME. Evolution of human, chicken, alligator, frog, and zebrafish mineralocorticoid receptors: Allosteric influence on steroid specificity. Sci Signal 2018; 11:11/537/eaao1520. [DOI: 10.1126/scisignal.aao1520] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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13
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Chow CC, Simons SS. An Approach to Greater Specificity for Glucocorticoids. Front Endocrinol (Lausanne) 2018; 9:76. [PMID: 29593646 PMCID: PMC5859375 DOI: 10.3389/fendo.2018.00076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/19/2018] [Indexed: 11/13/2022] Open
Abstract
Glucocorticoid steroids are among the most prescribed drugs each year. Nonetheless, the many undesirable side effects, and lack of selectivity, restrict their greater usage. Research to increase glucocorticoid specificity has spanned many years. These efforts have been hampered by the ability of glucocorticoids to both induce and repress gene transcription and also by the lack of success in defining any predictable properties that control glucocorticoid specificity. Correlations of transcriptional specificity have been observed with changes in steroid structure, receptor and chromatin conformation, DNA sequence for receptor binding, and associated cofactors. However, none of these studies have progressed to the point of being able to offer guidance for increased specificity. We summarize here a mathematical theory that allows a novel and quantifiable approach to increase selectivity. The theory applies to all three major actions of glucocorticoid receptors: induction by agonists, induction by antagonists, and repression by agonists. Simple graphical analysis of competition assays involving any two factors (steroid, chemical, peptide, protein, DNA, etc.) yields information (1) about the kinetically described mechanism of action for each factor at that step where the factor acts in the overall reaction sequence and (2) about the relative position of that step where each factor acts. These two pieces of information uniquely provide direction for increasing the specificity of glucocorticoid action. Consideration of all three modes of action indicate that the most promising approach for increased specificity is to vary the concentrations of those cofactors/pharmaceuticals that act closest to the observed end point. The potential for selectivity is even greater when varying cofactors/pharmaceuticals in conjunction with a select class of antagonists.
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Affiliation(s)
- Carson C. Chow
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Carson C. Chow, ; S. Stoney Simons, Jr.,
| | - S. Stoney Simons
- Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Carson C. Chow, ; S. Stoney Simons, Jr.,
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14
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UTX promotes hormonally responsive breast carcinogenesis through feed-forward transcription regulation with estrogen receptor. Oncogene 2017; 36:5497-5511. [PMID: 28534508 DOI: 10.1038/onc.2017.157] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 02/07/2023]
Abstract
UTX is implicated in embryonic development and lineage specification. However, how this X-linked histone demethylase contributes to the occurrence and progression of breast cancer remains to be clarified. Here we report that UTX is physically associated with estrogen receptor (ER) and functions in ER-regulated transcription. We showed that UTX coordinates with JHDM1D and CBP to direct H3K27 methylation-acetylation transition and to create a permissive chromatin state on ER targets. Genome-wide analysis of the transcriptional targets of UTX by ChIP-seq identified a set of genes such as chemokine receptor CXCR4 that are intimately involved in breast cancer tumorigenesis and metastasis. We demonstrated that UTX promotes the proliferation and migration of ER+ breast cancer cells. Interestingly, UTX itself is transactivated by ER, forming a feed-forward loop in the regulation of hormone response. Indeed, UTX is upregulated during ER+ breast cancer progression, and the expression level of UTX is positively correlated with that of CXCR4 and negatively correlated with the overall survival of ER+ breast cancer patients. Our study identified a feed-forward loop between UTX and ER in the regulation of hormonally responsive breast carcinogenesis, supporting the pursuit of UTX as an emerging therapeutic target for the intervention of certain ER+ breast cancer with specific epigenetic vulnerability.
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15
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Abstract
Glucocorticoid hormones (GC) regulate essential physiological functions including energy homeostasis, embryonic and postembryonic development, and the stress response. From the biomedical perspective, GC have garnered a tremendous amount of attention as highly potent anti-inflammatory and immunosuppressive medications indispensable in the clinic. GC signal through the GC receptor (GR), a ligand-dependent transcription factor whose structure, DNA binding, and the molecular partners that it employs to regulate transcription have been under intense investigation for decades. In particular, next-generation sequencing-based approaches have revolutionized the field by introducing a unified platform for a simultaneous genome-wide analysis of cellular activities at the level of RNA production, binding of transcription factors to DNA and RNA, and chromatin landscape and topology. Here we describe fundamental concepts of GC/GR function as established through traditional molecular and in vivo approaches and focus on the novel insights of GC biology that have emerged over the last 10 years from the rapidly expanding arsenal of system-wide genomic methodologies.
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Affiliation(s)
- Maria A Sacta
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
| | - Yurii Chinenov
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021;
| | - Inez Rogatsky
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
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16
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Katsu Y, Kohno S, Oka K, Baker ME. Evolution of corticosteroid specificity for human, chicken, alligator and frog glucocorticoid receptors. Steroids 2016; 113:38-45. [PMID: 27317937 DOI: 10.1016/j.steroids.2016.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 05/25/2016] [Accepted: 06/12/2016] [Indexed: 12/31/2022]
Abstract
We investigated the evolution of the response of human, chicken, alligator and frog glucocorticoid receptors (GRs) to dexamethasone, cortisol, cortisone, corticosterone, 11-deoxycorticosterone, 11-deoxycortisol and aldosterone. We find significant differences among these vertebrates in the transcriptional activation of their full length GRs by these steroids, indicating that there were changes in the specificity of the GR for steroids during the evolution of terrestrial vertebrates. To begin to study the role of interactions between different domains on the GR in steroid sensitivity and specificity for terrestrial GRs, we investigated transcriptional activation of truncated GRs containing their hinge domain and ligand binding domain (LBD) fused to a GAL4 DNA binding domain (GAL4-DBD). Compared to corresponding full length GRs, transcriptional activation of GAL4-DBD_GR-hinge/LBD constructs required higher steroid concentrations and displayed altered steroid specificity, indicating that interactions between the hinge/LBD and other domains are important in glucocorticoid activation of these terrestrial GRs.
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Affiliation(s)
- Yoshinao Katsu
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Department of Biological Sciences, Hokkaido University, Sapporo, Japan.
| | - Satomi Kohno
- Department of Obstetrics and Gynecology, Medical University of South Carolina, and Marine Biomedicine and Environmental Science Center, Hollings Marine Laboratory, Charleston, SC, USA
| | - Kaori Oka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Michael E Baker
- Department of Medicine, University of California, San Diego, CA, USA.
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17
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Khan SH, Jasuja R, Kumar R. Trehalose induces functionally active conformation in the intrinsically disordered N-terminal domain of glucocorticoid receptor. J Biomol Struct Dyn 2016; 35:2248-2256. [DOI: 10.1080/07391102.2016.1214086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shagufta H. Khan
- Department of Basic Sciences, The Commonwealth Medical College, 525 Pine Street, Scranton, PA 18509, USA
| | - Ravi Jasuja
- Research Program in Men’s Health, Boston Claude D. Pepper Older Americans Independence Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Raj Kumar
- Department of Basic Sciences, The Commonwealth Medical College, 525 Pine Street, Scranton, PA 18509, USA
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18
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Mani O, Nashev LG, Livelo C, Baker ME, Odermatt A. Role of Pro-637 and Gln-642 in human glucocorticoid receptors and Ser-843 and Leu-848 in mineralocorticoid receptors in their differential responses to cortisol and aldosterone. J Steroid Biochem Mol Biol 2016; 159:31-40. [PMID: 26907965 DOI: 10.1016/j.jsbmb.2016.02.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 02/11/2016] [Accepted: 02/18/2016] [Indexed: 10/22/2022]
Abstract
Mineralocorticoid receptors (MR) and glucocorticoid receptors (GR) are descended from a common ancestral corticoid receptor. The basis for specificities of human MR for aldosterone and human GR for glucocorticoids, such as cortisol, bearing 17α-hydroxyl-groups, is incompletely understood. Differences in MR at S843 and L848 and GR at the corresponding P637 and Q642 have been proposed as important in their different responses to glucocorticoids with 17α-hydroxyl-groups. We investigated the impact of these residues on binding affinity (Ki) and transcriptional activation (EC50) of mutants MR-S843P, MR-L848Q and MR-S843P/L848Q and mutants GR-P637S, GR-Q642L and GR-P637S/Q642L in the presence of different corticosteroids. Aldosterone, cortisol and corticosterone had similar affinities for wild-type MR and all mutants, while dexamethasone had increased affinity for the three mutants. However, transactivation of MR-S843P and MR-S843P/L848Q by all four steroids was significantly lower than for wild-type MR. In contrast, transactivation of MR-L848Q tended to be 3-fold higher for cortisol and corticosterone and increased 7-fold for dexamethasone, indicating that MR-L848Q has an increased response to glucocorticoids, while retaining a strong response to aldosterone. Compared to wild-type GR, GR-P637S and GR-Q642L had increased affinities and significantly increased transcriptional activity with aldosterone and corticosterone, and GR-P637S had similar transcriptional activity with cortisol and dexamethasone, while GR-Q642L and GR-P637S/Q642L had a significant decrease in transcriptional activity with cortisol and dexamethasone. 3D-models of these MR and GR mutants revealed that dexamethasone and aldosterone, respectively, fit nicely into the steroid-binding pocket, consistent with the affinity of dexamethasone for MR mutants and aldosterone for GR mutants.
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Affiliation(s)
- Orlando Mani
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Lyubomir G Nashev
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Christopher Livelo
- Department of Medicine, 0693, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael E Baker
- Department of Medicine, 0693, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.
| | - Alex Odermatt
- Division of Molecular and Systems Toxicology, Department of Pharmaceutical Sciences, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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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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20
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Oka K, Hoang A, Okada D, Iguchi T, Baker ME, Katsu Y. Allosteric role of the amino-terminal A/B domain on corticosteroid transactivation of gar and human glucocorticoid receptors. J Steroid Biochem Mol Biol 2015; 154:112-9. [PMID: 26247481 DOI: 10.1016/j.jsbmb.2015.07.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 06/23/2015] [Accepted: 07/31/2015] [Indexed: 02/03/2023]
Abstract
We studied the role of the A/B domain at the amino terminus of gar (Atractosterus tropicus) and human glucocorticoid receptors (GRs) on transcriptional activation by various glucocorticoids. In transient transfection assays, dexamethasone [DEX] and cortisol had a lower half-maximal response (EC50) for transcriptional activation of full length gar GR than of human GR. Both GRs had similar responses to corticosterone, while 11-deoxycortisol had a lower EC50 for gar GR than for human GR. In contrast, constructs of gar GR and human GR consisting of their hinge (D domain), ligand binding domain (LBD) (E domain) fused to a GAL4 DNA-binding domain (DBD) had a higher EC50 (weaker response) for all glucocorticoids. To study the role of the A/B domain, which contains an intrinsically disordered region, we investigated steroid activation of chimeric gar GR and human GR, in which their A/B domains were exchanged. Replacement of human A/B domains with the gar A/B domains yielded a chimeric GR with a lower EC50 for DEX and cortisol, while the EC50 increased for these steroids for the human A/B-gar C/E chimera, indicating that gar A/B domains contributes to the lower EC50 of gar GR for glucocorticoids. Our data suggests that allosteric signaling between the A/B domains and LBD influences transcriptional activation of human and gar GR by different steroids, and this allosteric mechanism evolved over 400 million years before gar and mammals separated from a common ancestor.
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Affiliation(s)
- Kaori Oka
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Andree Hoang
- Department of Biology, University of California, San Diego, CA, USA
| | - Daijiro Okada
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | | | - Michael E Baker
- Department of Medicine, University of California, San Diego, CA, USA.
| | - Yoshinao Katsu
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Department of Biological Sciences, Hokkaido University, Sapporo, Japan.
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21
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An exposure:activity profiling method for interpreting high-throughput screening data for estrogenic activity—Proof of concept. Regul Toxicol Pharmacol 2015; 71:398-408. [DOI: 10.1016/j.yrtph.2015.01.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/13/2015] [Accepted: 01/17/2015] [Indexed: 11/17/2022]
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22
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Chow CC, Finn KK, Storchan GB, Lu X, Sheng X, Simons SS. Kinetically-defined component actions in gene repression. PLoS Comput Biol 2015; 11:e1004122. [PMID: 25816223 PMCID: PMC4376387 DOI: 10.1371/journal.pcbi.1004122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 01/11/2015] [Indexed: 11/19/2022] Open
Abstract
Gene repression by transcription factors, and glucocorticoid receptors (GR) in particular, is a critical, but poorly understood, physiological response. Among the many unresolved questions is the difference between GR regulated induction and repression, and whether transcription cofactor action is the same in both. Because activity classifications based on changes in gene product level are mechanistically uninformative, we present a theory for gene repression in which the mechanisms of factor action are defined kinetically and are consistent for both gene repression and induction. The theory is generally applicable and amenable to predictions if the dose-response curve for gene repression is non-cooperative with a unit Hill coefficient, which is observed for GR-regulated repression of AP1LUC reporter induction by phorbol myristate acetate. The theory predicts the mechanism of GR and cofactors, and where they act with respect to each other, based on how each cofactor alters the plots of various kinetic parameters vs. cofactor. We show that the kinetically-defined mechanism of action of each of four factors (reporter gene, p160 coactivator TIF2, and two pharmaceuticals [NU6027 and phenanthroline]) is the same in GR-regulated repression and induction. What differs is the position of GR action. This insight should simplify clinical efforts to differentially modulate factor actions in gene induction vs. gene repression.
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Affiliation(s)
- Carson C. Chow
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (CCC); (SSS)
| | - Kelsey K. Finn
- Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Geoffery B. Storchan
- Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xinping Lu
- Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaoyan Sheng
- Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, Maryland, United States of America
| | - S. Stoney Simons
- Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (CCC); (SSS)
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23
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Niklas KJ, Bondos SE, Dunker AK, Newman SA. Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications. Front Cell Dev Biol 2015; 3:8. [PMID: 25767796 PMCID: PMC4341551 DOI: 10.3389/fcell.2015.00008] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/26/2015] [Indexed: 11/16/2022] Open
Abstract
Models for genetic regulation and cell fate specification characteristically assume that gene regulatory networks (GRNs) are essentially deterministic and exhibit multiple stable states specifying alternative, but pre-figured cell fates. Mounting evidence shows, however, that most eukaryotic precursor RNAs undergo alternative splicing (AS) and that the majority of transcription factors contain intrinsically disordered protein (IDP) domains whose functionalities are context dependent as well as subject to post-translational modification (PTM). Consequently, many transcription factors do not have fixed cis-acting regulatory targets, and developmental determination by GRNs alone is untenable. Modeling these phenomena requires a multi-scale approach to explain how GRNs operationally interact with the intra- and intercellular environments. Evidence shows that AS, IDP, and PTM complicate gene expression and act synergistically to facilitate and promote time- and cell-specific protein modifications involved in cell signaling and cell fate specification and thereby disrupt a strict deterministic GRN-phenotype mapping. The combined effects of AS, IDP, and PTM give proteomes physiological plasticity, adaptive responsiveness, and developmental versatility without inefficiently expanding genome size. They also help us understand how protein functionalities can undergo major evolutionary changes by buffering mutational consequences.
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Affiliation(s)
- Karl J Niklas
- Plant Biology Section, School of Integrative Plant Science, Cornell University Ithaca, NY, USA
| | - Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College Station, TX, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University Indianapolis, IN, USA
| | - Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College Valhalla, NY, USA
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24
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Abstract
The different amounts of residual partial agonist activity (PAA) of antisteroids under assorted conditions have long been useful in clinical applications but remain largely unexplained. Not only does a given antagonist often afford unequal induction for multiple genes in the same cell but also the activity of the same antisteroid with the same gene changes with variations in concentration of numerous cofactors. Using glucocorticoid receptors as a model system, we have recently succeeded in constructing from first principles a theory that accurately describes how cofactors can modulate the ability of agonist steroids to regulate both gene induction and gene repression. We now extend this framework to the actions of antisteroids in gene induction. The theory shows why changes in PAA cannot be explained simply by differences in ligand affinity for receptor and requires action at a second step or site in the overall sequence of reactions. The theory also provides a method for locating the position of this second site, relative to a concentration limited step (CLS), which is a previously identified step in glucocorticoid-regulated transactivation that always occurs at the same position in the overall sequence of events of gene induction. Finally, the theory predicts that classes of antagonist ligands may be grouped on the basis of their maximal PAA with excess added cofactor and that the members of each class differ by how they act at the same step in the overall gene induction process. Thus, this theory now makes it possible to predict how different cofactors modulate antisteroid PAA, which should be invaluable in developing more selective antagonists.
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Affiliation(s)
- Carson C Chow
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, MD 20892-5621, USA
| | - Karen M Ong
- Mathematical Biology Section, NIDDK/LBM, National Institutes of Health, Bethesda, MD 20892-5621, USA ; Computational Biology Program, New York University School of Medicine, New York, NY 10016, USA
| | - Benjamin Kagan
- Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, MD 20892-1772, USA ; Science Department, Tuscarora High School, Loudoun County Public Schools, Leesburg, VA 20176, USA
| | - S Stoney Simons
- Steroid Hormones Section, NIDDK/LERB, National Institutes of Health, Bethesda, MD 20892-1772, USA
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25
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Carruthers CW, Suh JH, Gustafsson JA, Webb P. Phosphorylation of glucocorticoid receptor tau1c transactivation domain enhances binding to CREB binding protein (CBP) TAZ2. Biochem Biophys Res Commun 2015; 457:119-23. [DOI: 10.1016/j.bbrc.2014.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 12/05/2014] [Indexed: 11/26/2022]
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26
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C. Chow C, M. Ong K, Kagan B, Stoney Simons Jr. S. Theory of partial agonist activity of steroid hormones. AIMS MOLECULAR SCIENCE 2015. [DOI: 10.3934/molsci.2015.2.101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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27
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Dunker AK, Bondos SE, Huang F, Oldfield CJ. Intrinsically disordered proteins and multicellular organisms. Semin Cell Dev Biol 2014; 37:44-55. [PMID: 25307499 DOI: 10.1016/j.semcdb.2014.09.025] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/15/2014] [Accepted: 09/30/2014] [Indexed: 12/12/2022]
Abstract
Intrinsically disordered proteins (IDPs) and IDP regions lack stable tertiary structure yet carry out numerous biological functions, especially those associated with signaling, transcription regulation, DNA condensation, cell division, and cellular differentiation. Both post-translational modifications (PTMs) and alternative splicing (AS) expand the functional repertoire of IDPs. Here we propose that an "IDP-based developmental toolkit," which is comprised of IDP regions, PTMs, especially multiple PTMs, within these IDP regions, and AS events within segments of pre-mRNA that code for these same IDP regions, allows functional diversification and environmental responsiveness for molecules that direct the development of complex metazoans.
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Affiliation(s)
- A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
| | - Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States.
| | - Fei Huang
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University Schools of Medicine and Informatics, Indianapolis, IN 46202, United States.
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28
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Blackford JA, Brimacombe KR, Dougherty EJ, Pradhan M, Shen M, Li Z, Auld DS, Chow CC, Austin CP, Simons SS. Research resource: modulators of glucocorticoid receptor activity identified by a new high-throughput screening assay. Mol Endocrinol 2014; 28:1194-206. [PMID: 24850414 DOI: 10.1210/me.2014-1069] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glucocorticoid steroids affect almost every type of tissue and thus are widely used to treat a variety of human pathological conditions. However, the severity of numerous side effects limits the frequency and duration of glucocorticoid treatments. Of the numerous approaches to control off-target responses to glucocorticoids, small molecules and pharmaceuticals offer several advantages. Here we describe a new, extended high-throughput screen in intact cells to identify small molecule modulators of dexamethasone-induced glucocorticoid receptor (GR) transcriptional activity. The novelty of this assay is that it monitors changes in both GR maximal activity (A(max)) and EC(50) (the position of the dexamethasone dose-response curve). Upon screening 1280 chemicals, 10 with the greatest changes in the absolute value of A(max) or EC(50) were selected for further examination. Qualitatively identical behaviors for 60% to 90% of the chemicals were observed in a completely different system, suggesting that other systems will be similarly affected by these chemicals. Additional analysis of the 10 chemicals in a recently described competition assay determined their kinetically defined mechanism and site of action. Some chemicals had similar mechanisms of action despite divergent effects on the level of the GR-induced product. These combined assays offer a straightforward method of identifying numerous new pharmaceuticals that can alter GR transactivation in ways that could be clinically useful.
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Affiliation(s)
- John A Blackford
- Steroid Hormones Section (J.A.B., E.J.D., M.P., S.S.S.), Laboratory of Endocrinology and Receptor Biology, and Laboratory of Biological Modeling (C.C.C.), National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892; and National Center for Advancing Translational Sciences (K.R.B., M.S., Z.L., D.S.A., C.P.A.), National Institutes of Health, Rockville, Maryland 20892
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29
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Reddy KD, DeForte S, Uversky VN. Digested disorder: Quarterly intrinsic disorder digest (July-August-September, 2013). INTRINSICALLY DISORDERED PROTEINS 2014; 2:e27833. [PMID: 28232877 PMCID: PMC5314876 DOI: 10.4161/idp.27833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 01/13/2014] [Indexed: 12/26/2022]
Abstract
The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a new issue of reader's digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.
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Affiliation(s)
- Krishna D Reddy
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Shelly DeForte
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa, FL USA; USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Department of Biological Sciences; Faculty of Science; King Abdulaziz University; Jeddah, Saudi Arabia; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Moscow Region, Russia
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30
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Zhu R, Lu X, Pradhan M, Armstrong S, Storchan GB, Chow C, Simons SS. A kinase-independent activity of Cdk9 modulates glucocorticoid receptor-mediated gene induction. Biochemistry 2014; 53:1753-67. [PMID: 24559102 PMCID: PMC3985961 DOI: 10.1021/bi5000178] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/20/2014] [Indexed: 12/18/2022]
Abstract
A gene induction competition assay has recently uncovered new inhibitory activities of two transcriptional cofactors, NELF-A and NELF-B, in glucocorticoid-regulated transactivation. NELF-A and -B are also components of the NELF complex, which participates in RNA polymerase II pausing shortly after the initiation of gene transcription. We therefore asked if cofactors (Cdk9 and ELL) best known to affect paused polymerase could reverse the effects of NELF-A and -B. Unexpectedly, Cdk9 and ELL augmented, rather than prevented, the effects of NELF-A and -B. Furthermore, Cdk9 actions are not blocked either by Ckd9 inhibitors (DRB or flavopiridol) or by two Cdk9 mutants defective in kinase activity. The mode and site of action of NELF-A and -B mutants with an altered NELF domain are similarly affected by wild-type and kinase-dead Cdk9. We conclude that Cdk9 is a new modulator of GR action, that Ckd9 and ELL have novel activities in GR-regulated gene expression, that NELF-A and -B can act separately from the NELF complex, and that Cdk9 possesses activities that are independent of Cdk9 kinase activity. Finally, the competition assay has succeeded in ordering the site of action of several cofactors of GR transactivation. Extension of this methodology should be helpful in determining the site and mode of action of numerous additional cofactors and in reducing unwanted side effects.
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Affiliation(s)
- Rong Zhu
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Xinping Lu
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Madhumita Pradhan
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Stephen
P. Armstrong
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Geoffrey B. Storchan
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Carson
C. Chow
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - S. Stoney Simons
- Steroid Hormones Section, National Institute
of Diabetes and Digestive
and Kidney Diseases/Laboratory of Endocrinology and Receptor Biology, and Laboratory of
Biological Modeling, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
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31
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Riggins RB. The pERK of being a target: Kinase regulation of the orphan nuclear receptor ERRγ. RECEPTORS & CLINICAL INVESTIGATION 2014; 1:e207. [PMID: 26005698 PMCID: PMC4440692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Estrogen-related receptors (ERRs) are orphan members of the nuclear receptor superfamily that are important regulators of mitochondrial metabolism with emerging roles in cancer. In the absence of an endogenous ligand, ERRs are reliant upon other regulatory mechanisms that include protein/protein interactions and post-translational modification, though the cellular and clinical significance of this latter mechanism is unclear. We recently published a study in which we establish estrogen-related receptor gamma (ERRγ) as a target for extracellular signal-regulated kinase (ERK), and show that regulation of ERRγ by ERK has important consequences for the function of this receptor in cellular models of estrogen receptor-positive (ER+) breast cancer. In this Research Highlight, we discuss the implications of these findings from a molecular and clinical perspective.
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Affiliation(s)
- Rebecca B Riggins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057 USA
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