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Hattori A, Fukami M. Nuclear Receptor Gene Variants Underlying Disorders/Differences of Sex Development through Abnormal Testicular Development. Biomolecules 2023; 13:691. [PMID: 37189438 PMCID: PMC10135730 DOI: 10.3390/biom13040691] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/17/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Gonadal development is the first step in human reproduction. Aberrant gonadal development during the fetal period is a major cause of disorders/differences of sex development (DSD). To date, pathogenic variants of three nuclear receptor genes (NR5A1, NR0B1, and NR2F2) have been reported to cause DSD via atypical testicular development. In this review article, we describe the clinical significance of the NR5A1 variants as the cause of DSD and introduce novel findings from recent studies. NR5A1 variants are associated with 46,XY DSD and 46,XX testicular/ovotesticular DSD. Notably, both 46,XX DSD and 46,XY DSD caused by the NR5A1 variants show remarkable phenotypic variability, to which digenic/oligogenic inheritances potentially contribute. Additionally, we discuss the roles of NR0B1 and NR2F2 in the etiology of DSD. NR0B1 acts as an anti-testicular gene. Duplications containing NR0B1 result in 46,XY DSD, whereas deletions encompassing NR0B1 can underlie 46,XX testicular/ovotesticular DSD. NR2F2 has recently been reported as a causative gene for 46,XX testicular/ovotesticular DSD and possibly for 46,XY DSD, although the role of NR2F2 in gonadal development is unclear. The knowledge about these three nuclear receptors provides novel insights into the molecular networks involved in the gonadal development in human fetuses.
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Affiliation(s)
- Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan;
- Division of Diversity Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan;
- Division of Diversity Research, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
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2
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Feng M, Gao B, Garcia LR, Sun Q. Microbiota-derived metabolites in regulating the development and physiology of Caenorhabditis elegans. Front Microbiol 2023; 14:1035582. [PMID: 36925470 PMCID: PMC10011103 DOI: 10.3389/fmicb.2023.1035582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Microbiota consist of microorganisms that provide essential health benefits and contribute to the animal's physiological homeostasis. Microbiota-derived metabolites are crucial mediators in regulating host development, system homeostasis, and overall fitness. In this review, by focusing on the animal model Caenorhabditis elegans, we summarize key microbial metabolites and their molecular mechanisms that affect animal development. We also provide, from a bacterial perspective, an overview of host-microbiota interaction networks used for maintaining host physiological homeostasis. Moreover, we discuss applicable methodologies for profiling new bacterial metabolites that modulate host developmental signaling pathways. Microbiota-derived metabolites have the potential to be diagnostic biomarkers for diseases, as well as promising targets for engineering therapeutic interventions against animal developmental or health-related defects.
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Affiliation(s)
- Min Feng
- Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Baizhen Gao
- Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - L Rene Garcia
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
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3
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Sun G, Dang Y, Lin Y, Zeng W, Wu Z, Zhang X, Dong D, Wu B. Scutellaria baicalensis Georgi regulates REV-ERBα/BMAL1 to protect against skin aging in mice. Front Pharmacol 2022; 13:991917. [PMID: 36249807 PMCID: PMC9561880 DOI: 10.3389/fphar.2022.991917] [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: 07/12/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Scutellaria baicalensis Georgi (SBG) is a traditional Chinese medicine widely used to treat disorders such as hypertension, dysentery and hemorrhaging. Here, we aimed to assess the pharmacological effects of SBG on skin aging and to investigate the underlying mechanisms. Mice with skin aging were established by treatment with D-galactose and ultraviolet-B. SBG (topical application) showed a protective effect on skin aging in mice, as evidenced by less formation of skin wrinkles, higher levels of SOD (superoxide dismutase) and HYP (hydroxyproline) as well as a lower level of MDA (malondialdehyde). In the meantime, skin MMP-1 and p53 expression were lower, epidermis was thinner and collagen amount was higher in SBG-treated mice. Anti-skin aging effects of SBG were also confirmed in NIH3T3 and HaCaT cells, as well as in mouse primary dermal fibroblasts and human primary epidermal keratinocytes. Furthermore, we found that loss of Rev-erbα (a known repressor of Bmal1) up-regulated skin BMAL1 (a clock component and a known anti-aging factor) and ameliorated skin aging in mice. Moreover, SBG dose-dependently increased the expression of BMAL1 in the skin of aged mice and in senescent NIT3H3 cells. In addition, based on a combination of Gal4 chimeric, luciferase reporter and expression assays, SBG was identified as an antagonist of REV-ERBα and thus an inducer of BMAL1 expression. In conclusion, SBG antagonizes REV-ERBα to up-regulate BMAL1 and to protect against skin aging in mice.
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Affiliation(s)
- Guanghui Sun
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Yongkang Dang
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yanke Lin
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wanying Zeng
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zongjian Wu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | | | - Dong Dong
- School of Medicine, Jinan University, Guangzhou, China
- *Correspondence: Dong Dong, ; Baojian Wu,
| | - Baojian Wu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Dong Dong, ; Baojian Wu,
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4
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Beachum AN, Whitehead KM, McDonald SI, Phipps DN, Berghout HE, Ables ET. Orphan nuclear receptor ftz-f1 (NR5A3) promotes egg chamber survival in the Drosophila ovary. G3-GENES GENOMES GENETICS 2021; 11:6114459. [PMID: 33693603 PMCID: PMC8022936 DOI: 10.1093/g3journal/jkab003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/30/2020] [Indexed: 11/12/2022]
Abstract
Gamete production in mammals and insects is controlled by cell signaling pathways that facilitate communication between germ cells and somatic cells. Nuclear receptor signaling is a key mediator of many aspects of reproduction, including gametogenesis. For example, the NR5A subfamily of nuclear receptors is essential for gonad development and sex steroid production in mammals. Despite the original identification of the NR5A subfamily in the model insect Drosophila melanogaster, it has been unclear whether Drosophila NR5A receptors directly control oocyte production. Ftz-f1 is expressed throughout the ovary, including in germline stem cells, germline cysts, and several populations of somatic cells. We show that ftz-f1 is required in follicle cells prior to stage 10 to promote egg chamber survival at the mid-oogenesis checkpoint. Our data suggest that egg chamber death in the absence of ftz-f1 is due, at least in part, to failure of follicle cells to exit the mitotic cell cycle or failure to accumulate oocyte-specific factors in the germline. Taken together, these results show that, as in mammals, the NR5A subfamily promotes maximal reproductive output in Drosophila. Our data underscore the importance of nuclear receptors in the control of reproduction and highlight the utility of Drosophila oogenesis as a key model for unraveling the complexity of nuclear receptor signaling in gametogenesis.
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Affiliation(s)
- Allison N Beachum
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | | | | | - Daniel N Phipps
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Hanna E Berghout
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Elizabeth T Ables
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
- Corresponding author: Department of Biology, East Carolina University, 1001 E. 10th St., Mailstop 551, 553 Science & Technology Building, Greenville, NC 27858, USA.
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5
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Finger DS, Whitehead KM, Phipps DN, Ables ET. Nuclear receptors linking physiology and germline stem cells in Drosophila. VITAMINS AND HORMONES 2021; 116:327-362. [PMID: 33752824 PMCID: PMC8063499 DOI: 10.1016/bs.vh.2020.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Maternal nutrition and physiology are intimately associated with reproductive success in diverse organisms. Despite decades of study, the molecular mechanisms linking maternal diet to the production and quality of oocytes remain poorly defined. Nuclear receptors (NRs) link nutritional signals to cellular responses and are essential for oocyte development. The fruit fly, Drosophila melanogaster, is an excellent genetically tractable model to study the relationship between NR signaling and oocyte production. In this review, we explore how NRs in Drosophila regulate the earliest stages of oocyte development. Long-recognized as an essential mediator of developmental transitions, we focus on the intrinsic roles of the Ecdysone Receptor and its ligand, ecdysone, in oogenesis. We also review recent studies suggesting broader roles for NRs as regulators of maternal physiology and their impact specifically on oocyte production. We propose that NRs form the molecular basis of a broad physiological surveillance network linking maternal diet with oocyte production. Given the functional conservation between Drosophila and humans, continued experimental investigation into the molecular mechanisms by which NRs promote oogenesis will likely aid our understanding of human fertility.
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Affiliation(s)
- Danielle S Finger
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Kaitlin M Whitehead
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Daniel N Phipps
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Elizabeth T Ables
- Department of Biology, East Carolina University, Greenville, NC, United States.
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6
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Qian H, He P, Lv F, Wu W. Genome-wide analysis of LXXLL-mediated DAX1/SHP–nuclear receptor interaction network and rational design of stapled LXXLL-based peptides to target the specific network profile. Int J Biol Macromol 2019; 129:13-22. [DOI: 10.1016/j.ijbiomac.2019.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/02/2019] [Accepted: 02/02/2019] [Indexed: 01/22/2023]
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7
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Jaiswal B, Gupta A. Modulation of Nuclear Receptor Function by Chromatin Modifying Factor TIP60. Endocrinology 2018; 159:2199-2215. [PMID: 29420715 DOI: 10.1210/en.2017-03190] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/31/2018] [Indexed: 02/07/2023]
Abstract
Nuclear receptors (NRs) are transcription factors that bind to specific DNA sequences known as hormone response elements located upstream of their target genes. Transcriptional activity of NRs can be modulated by binding of the compatible ligand and transient interaction with cellular coregulators, functioning either as coactivators or as corepressors. Many coactivator proteins possess intrinsic histone acetyltransferase (HAT) activity that catalyzes the acetylation of specific lysine residues in histone tails and loosens the histone-DNA interaction, thereby facilitating access of transcriptional factors to the regulatory sequences of the DNA. Tat interactive protein 60 (TIP60), a member of the Mof-Ybf2-Sas2-TIP60 family of HAT protein, is a multifunctional coregulator that controls a number of physiological processes including apoptosis, DNA damage repair, and transcriptional regulation. Over the last two decades or so, TIP60 has been extensively studied for its role as NR coregulator, controlling various aspect of steroid receptor functions. The aim of this review is to summarize the findings on the role of TIP60 as a coregulator for different classes of NRs and its overall functional implications. We also discuss the latest studies linking TIP60 to NR-associated metabolic disorders and cancers for its potential use as a therapeutic drug target in future.
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Affiliation(s)
- Bharti Jaiswal
- Department of Life Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
| | - Ashish Gupta
- Department of Life Sciences, Shiv Nadar University, Greater Noida, Uttar Pradesh, India
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8
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Jayakumar S, Hasan G. Neuronal Calcium Signaling in Metabolic Regulation and Adaptation to Nutrient Stress. Front Neural Circuits 2018; 12:25. [PMID: 29674958 PMCID: PMC5895653 DOI: 10.3389/fncir.2018.00025] [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] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 03/02/2018] [Indexed: 01/13/2023] Open
Abstract
All organisms can respond physiologically and behaviorally to environmental fluxes in nutrient levels. Different nutrient sensing pathways exist for specific metabolites, and their inputs ultimately define appropriate nutrient uptake and metabolic homeostasis. Nutrient sensing mechanisms at the cellular level require pathways such as insulin and target of rapamycin (TOR) signaling that integrates information from different organ systems like the fat body and the gut. Such integration is essential for coordinating growth with development. Here we review the role of a newly identified set of integrative interneurons and the role of intracellular calcium signaling within these neurons, in regulating nutrient sensing under conditions of nutrient stress. A comparison of the identified Drosophila circuit and cellular mechanisms employed in this circuit, with vertebrate systems, suggests that the identified cell signaling mechanisms may be conserved for neural circuit function related to nutrient sensing by central neurons. The ideas proposed are potentially relevant for understanding the molecular basis of metabolic disorders, because these are frequently linked to nutritional stress.
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Affiliation(s)
- Siddharth Jayakumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Gaiti Hasan
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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9
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Cunha V, Santos MM, Moradas-Ferreira P, Castro LFC, Ferreira M. Simvastatin modulates gene expression of key receptors in zebrafish embryos. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2017; 80:465-476. [PMID: 28682217 DOI: 10.1080/15287394.2017.1335258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
Nuclear receptors (NR) are involved in the regulation of several metabolic processes and it is well known that these constituents may be modulated by different chemicals classes, including pharmaceuticals that may activate or antagonize NR. In mammals, some pharmaceuticals modulate the transcription of pregnane X receptor, Pxr, peroxisome proliferator activated receptor, Ppars, and aryl hydrocarbon receptor, Ahr, affecting mRNA expression of genes belonging to various regulatory pathways, including lipid metabolism and detoxification mechanisms. The aim of this study was to determine the effects of simvastatin (SIM), an anticholesterolemic drug, on selected NR and AhR mRNA transcription levels during zebrafish early development. Embryos were collected at different development stages (0, 2, 6, 14, 24, 48, and 72 hr post fertilization (hpf)) and mRNA of all target NR was detected at all time points. Embryos (1 and 24 hpf) were exposed to different concentrations of SIM (5 or 50 μg/L) in two differing assays with varying exposure times (2 or 80 hr). The transcription levels of ahr2, raraa, rarab, rarga, pparαa, pparβ1, pparγ, pxr, rxraa, rxrab, rxrbb, rxrga, rxrgb, as well as levels of cholesterol (Chol) were measured after exposure. SIM exerted no marked effect on Chol levels, and depending upon exposure duration mRNA levels of NR and AhR either increased or decreased. After 2 hr SIM treatment in 24 hpf embryos, transcription of ppars, pxr, and ahr was up-regulated, while after 80 hr mRNA levels of pxr and ahr were decreased with no marked changes in ppars. Data demonstrate that SIM produced alterations in gene expression of NR which are involved in varying physiological functions and that may disturb regulation of different physiological processes which might impair fish survival and ecosystems regeneration.
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Affiliation(s)
- V Cunha
- a CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n , Matosinhos , Portugal
- b ICBAS/UP-Institute of Biomedical Sciences Abel Salazar, University of Porto , Porto , Portugal
| | - M M Santos
- a CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n , Matosinhos , Portugal
- c FCUP-Department of Biology , Faculty of Sciences, University of Porto, Rua do Campo Alegre , Porto , Portugal
| | - P Moradas-Ferreira
- b ICBAS/UP-Institute of Biomedical Sciences Abel Salazar, University of Porto , Porto , Portugal
- d I3S-Institute for Research and Innovation in Health, University of Porto , Porto , Portugal
| | - L F C Castro
- a CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n , Matosinhos , Portugal
- c FCUP-Department of Biology , Faculty of Sciences, University of Porto, Rua do Campo Alegre , Porto , Portugal
| | - M Ferreira
- a CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n , Matosinhos , Portugal
- e School of Marine Studies, Faculty of Science , Technology and Environment, The University of the South Pacific, Private mail box, Laucala Bay Road , Suva , Fiji Islands
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10
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Kupr B, Schnyder S, Handschin C. Role of Nuclear Receptors in Exercise-Induced Muscle Adaptations. Cold Spring Harb Perspect Med 2017; 7:a029835. [PMID: 28242783 PMCID: PMC5453380 DOI: 10.1101/cshperspect.a029835] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Skeletal muscle is not only one of the largest, but also one of the most dynamic organs. For example, plasticity elicited by endurance or resistance exercise entails complex transcriptional programs that are still poorly understood. Various signaling pathways are engaged in the contracting muscle fiber and collectively culminate in the modulation of the activity of numerous transcription factors (TFs) and coregulators. Because exercise confers many benefits for the prevention and treatment of a wide variety of pathologies, pharmacological activation of signaling pathways and TFs is an attractive avenue to elicit therapeutic effects. Members of the nuclear receptor (NR) superfamily are of particular interest owing to the presence of well-defined DNA- and ligand-binding domains. In this review, we summarize the current understanding of the involvement of NRs in muscle biology and exercise adaptation.
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Affiliation(s)
- Barbara Kupr
- Biozentrum, University of Basel, Basel 4056, Switzerland
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11
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Ables ET, Drummond-Barbosa D. Steroid Hormones and the Physiological Regulation of Tissue-Resident Stem Cells: Lessons from the Drosophila Ovary. CURRENT STEM CELL REPORTS 2017; 3:9-18. [PMID: 28458991 PMCID: PMC5407287 DOI: 10.1007/s40778-017-0070-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Stem cells respond to local paracrine signals; more recently, however, systemic hormones have also emerged as key regulators of stem cells. This review explores the role of steroid hormones in stem cells, using the Drosophila germline stem cell as a centerpiece for discussion. RECENT FINDINGS Stem cells sense and respond directly and indirectly to steroid hormones, which regulate diverse sets of target genes via interactions with nuclear hormone receptors. Hormone-regulated networks likely integrate the actions of multiple systemic signals to adjust the activity of stem cell lineages in response to changes in physiological status. SUMMARY Hormones are inextricably linked to animal physiology, and can control stem cells and their local niches. Elucidating the molecular mechanisms of hormone signaling in stem cells is essential for our understanding of the fundamental underpinnings of stem cell biology, and for informing new therapeutic interventions against cancers or for regenerative medicine.
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Affiliation(s)
- Elizabeth T. Ables
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Daniela Drummond-Barbosa
- Department of Biochemistry and Molecular Biology, Division of Reproductive Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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12
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Schmitz JF, Zimmer F, Bornberg-Bauer E. Mechanisms of transcription factor evolution in Metazoa. Nucleic Acids Res 2016; 44:6287-97. [PMID: 27288445 PMCID: PMC5291267 DOI: 10.1093/nar/gkw492] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/18/2016] [Accepted: 05/22/2016] [Indexed: 11/12/2022] Open
Abstract
Transcriptions factors (TFs) are pivotal for the regulation of virtually all cellular processes, including growth and development. Expansions of TF families are causally linked to increases in organismal complexity. Here we study the evolutionary dynamics, genetic causes and functional implications of the five largest metazoan TF families. We find that family expansions dominate across the whole metazoan tree; however, some branches experience exceptional family-specific accelerated expansions. Additionally, we find that such expansions are often predated by modular domain rearrangements, which spur the expansion of a new sub-family by separating it from the rest of the TF family in terms of protein-protein interactions. This separation allows for radical shifts in the functional spectrum of a duplicated TF. We also find functional differentiation inside TF sub-families as changes in expression specificity. Furthermore, accelerated family expansions are facilitated by repeats of sequence motifs such as C2H2 zinc fingers. We quantify whole genome duplications and single gene duplications as sources of TF family expansions, implying that some, but not all, TF duplicates are preferentially retained. We conclude that trans-regulatory changes (domain rearrangements) are instrumental for fundamental functional innovations, that cis-regulatory changes (affecting expression) accomplish wide-spread fine tuning and both jointly contribute to the functional diversification of TFs.
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Affiliation(s)
- Jonathan F Schmitz
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hüfferstrasse 1, D-48149 Münster, Germany
| | - Fabian Zimmer
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hüfferstrasse 1, D-48149 Münster, Germany Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, Hüfferstrasse 1, D-48149 Münster, Germany
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13
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Yen CA, Curran SP. Gene-diet interactions and aging in C. elegans. Exp Gerontol 2016; 86:106-112. [PMID: 26924670 DOI: 10.1016/j.exger.2016.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/16/2016] [Accepted: 02/24/2016] [Indexed: 02/06/2023]
Abstract
Diet is the most variable aspect of life history, as most individuals have a large diversity of food choices, varying in the type and amount that they ingest. In the short-term, diet can affect metabolism and energy levels. However, in the long run, the net deficiency or excess of calories from diet can influence the progression and severity of age-related diseases. An old and yet still debated question is: how do specific dietary choices impact health- and lifespan? It is clear that genetics can play a critical role - perhaps just as important as diet choices. For example, poor diet in combination with genetic susceptibility can lead to metabolic disorders, such as obesity and type 2 diabetes. Recent work in Caenorhabditis elegans has identified the existence of diet-gene pairs, where the consequence of mutating a specific gene is only realized on specific diets. Many core metabolic pathways are conserved from worm to human. Although only a handful of these diet-gene pairs has been characterized, there are potentially hundreds, if not thousands, of such interactions, which may explain the variability in the rates of aging in humans and the incidence and severity of age-related diseases.
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Affiliation(s)
- Chia An Yen
- University of Southern California, Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, United States
| | - Sean P Curran
- University of Southern California, Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, United States; University of Southern California, Davis School of Gerontology, United States.
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14
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Wang T, Xiong JQ. The Orphan Nuclear Receptor TLX/NR2E1 in Neural Stem Cells and Diseases. Neurosci Bull 2016; 32:108-14. [PMID: 26769490 DOI: 10.1007/s12264-015-0004-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/26/2015] [Indexed: 12/24/2022] Open
Abstract
The human TLX gene encodes an orphan nuclear receptor predominantly expressed in the central nervous system. Tailess and Tlx, the TLX homologues in Drosophila and mouse, play essential roles in body-pattern formation and neurogenesis during early embryogenesis and perform crucial functions in maintaining stemness and controlling the differentiation of adult neural stem cells in the central nervous system, especially the visual system. Multiple target genes and signaling pathways are regulated by TLX and its homologues in specific tissues during various developmental stages. This review aims to summarize previous studies including many recent updates from different aspects concerning TLX and its homologues in Drosophila and mouse.
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Affiliation(s)
- Tao Wang
- Department of Intensive Care, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Jian-Qiong Xiong
- Department of Intensive Care, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China.
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15
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Mitochondrial emitted electromagnetic signals mediate retrograde signaling. Med Hypotheses 2015; 85:810-8. [DOI: 10.1016/j.mehy.2015.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 09/25/2015] [Accepted: 10/09/2015] [Indexed: 12/19/2022]
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16
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Families of nuclear receptors in vertebrate models: characteristic and comparative toxicological perspective. Sci Rep 2015; 5:8554. [PMID: 25711679 PMCID: PMC4339804 DOI: 10.1038/srep08554] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/21/2015] [Indexed: 02/07/2023] Open
Abstract
Various synthetic chemicals are ligands for nuclear receptors (NRs) and can cause adverse effects in vertebrates mediated by NRs. While several model vertebrates, such as mouse, chicken, western clawed frog and zebrafish, are widely used in toxicity testing, few NRs have been well described for most of these classes. In this report, NRs in genomes of 12 vertebrates are characterized via bioinformatics approaches. Although numbers of NRs varied among species, with 40-42 genes in birds to 66-74 genes in teleost fishes, all NRs had clear homologs in human and could be categorized into seven subfamilies defined as NR0B-NR6A. Phylogenetic analysis revealed conservative evolutionary relationships for most NRs, which were consistent with traditional morphology-based systematics, except for some exceptions in Dolphin (Tursiops truncatus). Evolution of PXR and CAR exhibited unexpected multiple patterns and the existence of CAR possibly being traced back to ancient lobe-finned fishes and tetrapods (Sarcopterygii). Compared to the more conservative DBD of NRs, sequences of LBD were less conserved: Sequences of THRs, RARs and RXRs were ≥90% similar to those of the human, ERs, AR, GR, ERRs and PPARs were more variable with similarities of 60%-100% and PXR, CAR, DAX1 and SHP were least conserved among species.
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Nitta KR, Jolma A, Yin Y, Morgunova E, Kivioja T, Akhtar J, Hens K, Toivonen J, Deplancke B, Furlong EEM, Taipale J. Conservation of transcription factor binding specificities across 600 million years of bilateria evolution. eLife 2015; 4:e04837. [PMID: 25779349 PMCID: PMC4362205 DOI: 10.7554/elife.04837] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 02/09/2015] [Indexed: 02/07/2023] Open
Abstract
Divergent morphology of species has largely been ascribed to genetic differences in the tissue-specific expression of proteins, which could be achieved by divergence in cis-regulatory elements or by altering the binding specificity of transcription factors (TFs). The relative importance of the latter has been difficult to assess, as previous systematic analyses of TF binding specificity have been performed using different methods in different species. To address this, we determined the binding specificities of 242 Drosophila TFs, and compared them to human and mouse data. This analysis revealed that TF binding specificities are highly conserved between Drosophila and mammals, and that for orthologous TFs, the similarity extends even to the level of very subtle dinucleotide binding preferences. The few human TFs with divergent specificities function in cell types not found in fruit flies, suggesting that evolution of TF specificities contributes to emergence of novel types of differentiated cells.
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Affiliation(s)
- Kazuhiro R Nitta
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Arttu Jolma
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden,Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Yimeng Yin
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ekaterina Morgunova
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Teemu Kivioja
- Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Junaid Akhtar
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Korneel Hens
- Institute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Jarkko Toivonen
- Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Bart Deplancke
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Eileen E M Furlong
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jussi Taipale
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden,Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland,For correspondence:
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18
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Estrogen-related receptor α is required for efficient human cytomegalovirus replication. Proc Natl Acad Sci U S A 2014; 111:E5706-15. [PMID: 25512541 DOI: 10.1073/pnas.1422361112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An shRNA-mediated screen of the 48 human nuclear receptor genes identified multiple candidates likely to influence the production of human cytomegalovirus in cultured human fibroblasts, including the estrogen-related receptor α (ERRα), an orphan nuclear receptor. The 50-kDa receptor and a 76-kDa variant were induced posttranscriptionally following infection. Genetic and pharmacological suppression of the receptor reduced viral RNA, protein, and DNA accumulation, as well as the yield of infectious progeny. In addition, RNAs encoding multiple metabolic enzymes, including enzymes sponsoring glycolysis (enolase 1, triosephosphate isomerase 1, and hexokinase 2), were reduced when the function of ERRα was inhibited in infected cells. Consistent with the effect on RNAs, a substantial number of metabolites, which are normally induced by infection, were either not increased or were increased to a reduced extent in the absence of normal ERRα activity. We conclude that ERRα is needed for the efficient production of cytomegalovirus progeny, and we propose that the nuclear receptor contributes importantly to the induction of a metabolic environment that supports optimal cytomegalovirus replication.
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Pardee K, Green AA, Ferrante T, Cameron DE, DaleyKeyser A, Yin P, Collins JJ. Paper-based synthetic gene networks. Cell 2014; 159:940-54. [PMID: 25417167 PMCID: PMC4243060 DOI: 10.1016/j.cell.2014.10.004] [Citation(s) in RCA: 446] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 09/29/2014] [Accepted: 10/03/2014] [Indexed: 01/21/2023]
Abstract
Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides an alternate, versatile venue for synthetic biologists to operate and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze dried onto paper, enabling the inexpensive, sterile, and abiotic distribution of synthetic-biology-based technologies for the clinic, global health, industry, research, and education. For field use, we create circuits with colorimetric outputs for detection by eye and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small-molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors.
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Affiliation(s)
- Keith Pardee
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA
| | - Alexander A Green
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA
| | - Tom Ferrante
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - D Ewen Cameron
- Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ajay DaleyKeyser
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Peng Yin
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - James J Collins
- Wyss Institute for Biological Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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20
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Housden BE, Perrimon N. Spatial and temporal organization of signaling pathways. Trends Biochem Sci 2014; 39:457-64. [PMID: 25155749 DOI: 10.1016/j.tibs.2014.07.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 12/14/2022]
Abstract
The development and maintenance of the many different cell types in metazoan organisms requires robust and diverse intercellular communication mechanisms. Relatively few such signaling pathways have been identified, leading to the question of how such a broad diversity of output is generated from relatively simple signals. Recent studies have revealed complex mechanisms integrating temporal and spatial information to generate diversity in signaling pathway output. We review some general principles of signaling pathways, focusing on transcriptional outputs in Drosophila. We consider the role of spatial and temporal aspects of different transduction pathways and then discuss how recently developed tools and approaches are helping to dissect the complex mechanisms linking pathway stimulation to output.
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Affiliation(s)
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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21
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Martins IJ, Creegan R. Links between Insulin Resistance, Lipoprotein Metabolism and Amyloidosis in Alzheimer’s Disease. Health (London) 2014. [DOI: 10.4236/health.2014.612190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Spatial profiling of nuclear receptor transcription patterns over the course of Drosophila development. G3-GENES GENOMES GENETICS 2013; 3:1177-89. [PMID: 23665880 PMCID: PMC3704245 DOI: 10.1534/g3.113.006023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Previous work has shown that many of the 18 family members of Drosophila nuclear receptor transcription factors function in a temporal hierarchy to coordinate developmental progression and growth with the rate limiting process of metabolism. To gain further insight into these interactions and processes, we have undertaken a whole-family analysis of nuclear receptor mRNA spatial expression patterns over the entire process of embryogenesis, as well as the 3rd instar wandering larva stage, by using high-resolution fluorescence in situ hybridization. Overall, the patterns of expression are remarkably consistent with previously mapped spatial activity profiles documented during the same time points, with similar hot spots and temporal profiles in endocrine and metabolically important tissues. Among the more remarkable of the findings is that the majority of mRNA expression patterns observed show striking subcellular distributions, indicating potentially critical roles in the control of protein synthesis and subsequent subcellular distributions. These patterns will serve as a useful reference for future studies on the tissue-specific roles and interactions of nuclear receptor proteins, partners, cofactors and ligands.
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23
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Yang CS, Yuk JM, Kim JJ, Hwang JH, Lee CH, Kim JM, Oh GT, Choi HS, Jo EK. Small heterodimer partner-targeting therapy inhibits systemic inflammatory responses through mitochondrial uncoupling protein 2. PLoS One 2013; 8:e63435. [PMID: 23704907 PMCID: PMC3660347 DOI: 10.1371/journal.pone.0063435] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 03/28/2013] [Indexed: 01/15/2023] Open
Abstract
The orphan nuclear receptor, small heterodimer partner (SHP), appears to play a negative regulatory role in innate immune signaling. Emerging evidence warrants further study on the therapeutic targeting of SHP to suppress excessive and deleterious inflammation. Here we show that fenofibrate, which targets SHP, is required for inhibiting systemic inflammation via mitochondrial uncoupling protein 2 (UCP2). In vivo administration of fenofibrate ameliorated systemic inflammatory responses and increased survival upon experimental sepsis through SHP. An abundance of SHP was observed in mice fed fenofibrate and in cultured macrophages through LKB1-dependent activation of the AMP-activated protein kinase pathway. Fenofibrate significantly blocked endotoxin-triggered inflammatory signaling responses via SHP, but not via peroxisome proliferator-activated receptor (PPAR)-α. In addition to the known mechanism by which SHP modulates innate signaling, we identify a new role of fenofibrate-induced SHP on UCP2 induction, which is required for the suppression of inflammatory responses through modulation of mitochondrial ROS production. These data strongly suggest that the SHP-inducing drug fenofibrate paves the way for novel therapies for systemic inflammation by targeting SHP.
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Affiliation(s)
- Chul-Su Yang
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, S. Korea
- Infection Signaling Network Research Center, Chungnam National University School of Medicine, Daejeon, S. Korea
| | - Jae-Min Yuk
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, S. Korea
- Infection Signaling Network Research Center, Chungnam National University School of Medicine, Daejeon, S. Korea
| | - Jwa-Jin Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, S. Korea
- Infection Signaling Network Research Center, Chungnam National University School of Medicine, Daejeon, S. Korea
| | - Jung Hwan Hwang
- Laboratory Animal Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, S. Korea
| | - Chul-Ho Lee
- Laboratory Animal Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, S. Korea
| | - Jin-Man Kim
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, S. Korea
- Infection Signaling Network Research Center, Chungnam National University School of Medicine, Daejeon, S. Korea
| | - Goo Taeg Oh
- Division of Life and Pharmaceutical Science, Ewha Womans University, Seoul, S. Korea
| | - Hueng-Sik Choi
- National Creative Research Initiatives Center for Nuclear Receptor Signals, Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju, S. Korea
| | - Eun-Kyeong Jo
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, S. Korea
- Infection Signaling Network Research Center, Chungnam National University School of Medicine, Daejeon, S. Korea
- * E-mail:
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24
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MacNeil L, Watson E, Arda HE, Zhu LJ, Walhout AJ. Diet-induced developmental acceleration independent of TOR and insulin in C. elegans. Cell 2013; 153:240-52. [PMID: 23540701 PMCID: PMC3821073 DOI: 10.1016/j.cell.2013.02.049] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 12/18/2012] [Accepted: 02/05/2013] [Indexed: 12/16/2022]
Abstract
Dietary composition has major effects on physiology. Here, we show that developmental rate, reproduction, and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard E. coli OP50 diet. We identify a set of genes that change in expression in response to this diet and use the promoter of one of these (acdh-1) as a dietary sensor. Remarkably, the effects on transcription and development occur even when Comamonas DA1877 is diluted with another diet, suggesting that Comamonas DA1877 generates a signal that is sensed by the nematode. Surprisingly, the developmental effect is independent from TOR and insulin signaling. Rather, Comamonas DA1877 affects cyclic gene expression during molting, likely through the nuclear hormone receptor NHR-23. Altogether, our findings indicate that different bacteria elicit various responses via distinct mechanisms, which has implications for diseases such as obesity and the interactions between the human microbiome and intestinal cells.
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Affiliation(s)
| | - Emma Watson
- Program in Systems Biology
- Program in Molecular Medicine
| | - H. Efsun Arda
- Program in Systems Biology
- Program in Molecular Medicine
| | - Lihua Julie Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, University of Massachusetts Medical School, Worcester, MA
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25
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Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, Kivioja T, Taipale J. DNA-binding specificities of human transcription factors. Cell 2013; 152:327-39. [PMID: 23332764 DOI: 10.1016/j.cell.2012.12.009] [Citation(s) in RCA: 870] [Impact Index Per Article: 79.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/18/2012] [Accepted: 12/03/2012] [Indexed: 12/23/2022]
Abstract
Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificities. The models represent the majority of human TFs, approximately doubling the coverage compared to existing systematic studies. Our results reveal additional specificity determinants for a large number of factors for which a partial specificity was known, including a commonly observed A- or T-rich stretch that flanks the core motifs. Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated. We further describe a binding model incorporating these features that is required to understand binding of TFs to DNA.
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Affiliation(s)
- Arttu Jolma
- Science for Life Center, Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
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Ghosh SK, Patton JR, Spanjaard RA. A small RNA derived from RNA coactivator SRA blocks steroid receptor signaling via inhibition of Pus1p-mediated pseudouridylation of SRA: evidence of a novel RNA binding domain in the N-terminus of steroid receptors. Biochemistry 2012; 51:8163-72. [PMID: 22998747 DOI: 10.1021/bi300602r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Estrogen receptors (ERs) and androgen receptors (ARs) are important targets for cancer therapy; however, the efficacy of receptor antagonists is limited, and alternative strategies are needed. Steroid receptor RNA Activator (SRA) is a long, noncoding RNA coactivator (although some protein-encoding 5' splice variants have also been reported) that requires pseudouridylation by Pus1p to stimulate steroid receptor signaling. A uridine at position 206 (U206), which is located in small hairpin structure STR5 in the conserved SRA core sequence, is a critical target for pseudouridylation. We assessed if synthetic STR5 could serve as a novel competitive inhibitor of ERα and AR signaling by disrupting the Pus1p-SRA-steroid receptor axis. STR5 specifically inhibited Pus1p-dependent pseudouridylation of SRA with higher efficiency than STR5 mutant U206A. We show that SRA binds to the N-terminal domain (NTD) of ERα and AR with high affinity despite the absence of a recognizable RNA binding motif (RBM). Finally, we show that STR5 specifically inhibits ERα- and AR-dependent transactivation of target genes in steroid-sensitive cancer cells, consistent with disruption of the targeted Pus1p-SRA pathway. Together, our results show that the NTD of ERα and AR contains a novel RBM that directly binds SRA, and that STR5 can serve as a novel class of RNA inhibitor of ERα and AR signaling by interfering with Pus1p-mediated SRA pseudouridylation. Targeting this unexplored receptor signaling pathway may pave the way for the development of new types of cancer therapeutics.
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Affiliation(s)
- Sajal K Ghosh
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA 02118, USA
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27
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Beyoğlu D, Idle JR. Metabolomics and its potential in drug development. Biochem Pharmacol 2012; 85:12-20. [PMID: 22935449 DOI: 10.1016/j.bcp.2012.08.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 01/15/2023]
Abstract
Metabolomics is the global and unbiased survey of the complement of small molecules (say, <1 kDa) in a biofluid, tissue, organ or organism and measures the end-products of the cellular metabolism of both endogenous and exogenous substrates. Many drug candidates fail during Phase II and III clinical trials at an enormous cost to the pharmaceutical industry in terms of both time lost and of financial resources. The constantly evolving model of drug development now dictates that biomarkers should be employed in preclinical development for the early detection of likely-to-fail candidates. Biomarkers may also be useful in the preselection of patients and through the subclassification of diseases in clinical drug development. Here we show with examples how metabolomics can assist in the preclinical development phases of discovery, pharmacology, toxicology, and ADME. Although not yet established as a clinical trial patient prescreening procedure, metabolomics shows considerable promise in this regard. We can be certain that metabolomics will join genomics and transcriptomics in lubricating the wheels of clinical drug development in the near future.
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Affiliation(s)
- Diren Beyoğlu
- Hepatology Research Group, Department of Clinical Research, Faculty of Medicine, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland.
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A pleiotropic role for the orphan nuclear receptor small heterodimer partner in lipid homeostasis and metabolic pathways. J Lipids 2012; 2012:304292. [PMID: 22577560 PMCID: PMC3346990 DOI: 10.1155/2012/304292] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 12/05/2011] [Indexed: 12/29/2022] Open
Abstract
Nuclear receptors (NRs) comprise one of the most abundant classes of transcriptional regulators of metabolic diseases and have emerged as promising pharmaceutical targets. Small heterodimer partner (SHP; NR0B2) is a unique orphan NR lacking a DNA-binding domain but contains a putative ligand-binding domain. SHP is a transcriptional regulator affecting multiple key biological functions and metabolic processes including cholesterol, bile acid, and fatty acid metabolism, as well as reproductive biology and glucose-energy homeostasis. About half of all mammalian NRs and several transcriptional coregulators can interact with SHP. The SHP-mediated repression of target transcription factors includes at least three mechanisms including direct interference with the C-terminal activation function 2 (AF2) coactivator domains of NRs, recruitment of corepressors, or direct interaction with the surface of NR/transcription factors. Future research must focus on synthetic ligands acting on SHP as a potential therapeutic target in a series of metabolic abnormalities. Current understanding about the pleiotropic role of SHP is examined in this paper, and principal metabolic aspects connected with SHP function will be also discussed.
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29
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